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Sample records for glutamine side chains

  1. Glutamine and Asparagine Side Chain Hyperconjugation-Induced Structurally Sensitive Vibrations.

    PubMed

    Punihaole, David; Hong, Zhenmin; Jakubek, Ryan S; Dahlburg, Elizabeth M; Geib, Steven; Asher, Sanford A

    2015-10-15

    We identified vibrational spectral marker bands that sensitively report on the side chain structures of glutamine (Gln) and asparagine (Asn). Density functional theory (DFT) calculations indicate that the Amide III(P) (AmIII(P)) vibrations of Gln and Asn depend cosinusoidally on their side chain OCCC dihedral angles (the χ3 and χ2 angles of Gln and Asn, respectively). We use UV resonance Raman (UVRR) and visible Raman spectroscopy to experimentally correlate the AmIII(P) Raman band frequency to the primary amide OCCC dihedral angle. The AmIII(P) structural sensitivity derives from the Gln (Asn) Cβ-Cγ (Cα-Cβ) stretching component of the vibration. The Cβ-Cγ (Cα-Cβ) bond length inversely correlates with the AmIII(P) band frequency. As the Cβ-Cγ (Cα-Cβ) bond length decreases, its stretching force constant increases, which results in an upshift in the AmIII(P) frequency. The Cβ-Cγ (Cα-Cβ) bond length dependence on the χ3 (χ2) dihedral angle results from hyperconjugation between the Cδ═Oϵ (Cγ═Oδ) π* and Cβ-Cγ (Cα-Cβ) σ orbitals. Using a Protein Data Bank library, we show that the χ3 and χ2 dihedral angles of Gln and Asn depend on the peptide backbone Ramachandran angles. We demonstrate that the inhomogeneously broadened AmIII(P) band line shapes can be used to calculate the χ3 and χ2 angle distributions of peptides. The spectral correlations determined in this study enable important new insights into protein structure in solution, and in Gln- and Asn-rich amyloid-like fibrils and prions. PMID:26392216

  2. The Inherent Conformational Preferences of Glutamine-Containing Peptides: the Role for Side-Chain Backbone Hydrogen Bonds

    NASA Astrophysics Data System (ADS)

    Walsh, Patrick S.; McBurney, Carl; Gellman, Samuel H.; Zwier, Timothy S.

    2015-06-01

    Glutamine is widely known to be found in critical regions of peptides which readily fold into amyloid fibrils, the structures commonly associated with Alzheimer's disease and glutamine repeat diseases such as Huntington's disease. Building on previous single-conformation data on Gln-containing peptides containing an aromatic cap on the N-terminus (Z-Gln-OH and Z-Gln-NHMe), we present here single-conformation UV and IR spectra of Ac-Gln-NHBn and Ac-Ala-Gln-NHBn, with its C-terminal benzyl cap. These results point towards side-chain to backbone hydrogen bonds dominating the structures observed in the cold, isolated environment of a molecular beam. We have identified and assigned three main conformers for Ac-Gln-NHBn all involving primary side-chain to backbone interactions. Ac-Ala-Gln-NHBn extends the peptide chain by one amino acid, but affords an improvement in the conformational flexibility. Despite this increase in the flexibility, only a single conformation is observed in the gas-phase: a structure which makes use of both side-chain-to-backbone and backbone-to-backbone hydrogen bonds.

  3. On resin amino acid side chain attachment strategy for the head to tail synthesis of new glutamine containing gramicidin-S analogs and their antimicrobial activity.

    PubMed

    Derbal, Safa; Hensler, Mary; Fang, Weiqin; Nizet, Victor; Ghedira, Kamel; Nefzi, Adel

    2010-10-01

    The alarming increase in infections caused by multiple drug resistant bacteria including methicillin-resistant Staphylococcus aureus has prompted a desperate search for new antimicrobials. Augmenting the discoveries of completely new scaffolds with antimicrobial activity are efforts aimed at modifying existing molecules to optimize activity or reduce toxicity. We report herein the parallel solid-phase synthesis of analogues of the cationic antimicrobial peptide gramicidin S (GS) using amino acid side chain attachment strategy. The ornithine (Orn) residues were replaced by glutamine (Gln) and the aromatic D-phenylalanine (Phe) were replaced by different aromatic D-amino acids. Additional Gln containing GS analogues with all the possible combinations of the hydrophobic amino acids valine and leucine were also synthesized. In this work we also report the antibacterial activity of these analogs against several clinically-important drug-resistant Gram-positive and Gram-negative pathogens.

  4. Engineered Ionizable Side Chains.

    PubMed

    Cymes, Gisela D; Grosman, Claudio

    2015-01-01

    One of the great challenges of mechanistic ion-channel biology is to obtain structural information from well-defined functional states. In the case of neurotransmitter-gated ion channels, the open-channel conformation is particularly elusive owing to its transient nature and brief mean lifetime. In this Chapter, we show how the analysis of single-channel currents recorded from mutants engineered to contain single ionizable side chains in the transmembrane region can provide specific information about the open-channel conformation without any interference from the closed or desensitized conformations. The method takes advantage of the fact that the alternate binding and unbinding of protons to and from an ionizable side chain causes the charge of the protein to fluctuate by 1 unit. We show that, in mutant muscle acetylcholine nicotinic receptors (AChRs), this fluctuating charge affects the rate of ion conduction in such a way that individual proton-transfer events can be identified in a most straightforward manner. From the extent to which the single-channel current amplitude is reduced every time a proton binds, we can learn about the proximity of the engineered side chain to the lumen of the pore. And from the kinetics of proton binding and unbinding, we can calculate the side-chain's affinity for protons (pK a), and hence, we can learn about the electrostatic properties of the microenvironment around the introduced ionizable group. The application of this method to systematically mutated AChRs allowed us to identify unambiguously the stripes of the M1, M2 and M3 transmembrane α-helices that face the pore's lumen in the open-channel conformation in the context of a native membrane. PMID:26381938

  5. Peptide nanotube aligning side chains onto one side.

    PubMed

    Tabata, Yuki; Mitani, Shota; Kimura, Shunsaku

    2016-06-01

    A novel pseudo cyclic penta-β-peptide composed of a β-naphthylalanine, two β-alanines, and a sequence of ethylenediamine-succinic acid (CP5ES) is synthesized and investigated on peptide nanotube (PNT) formation. When the PNT is formed with the maximum number of intermolecular hydrogen bonds between the cyclic peptides, the sequence enables the alignment of the side chains, naphthyl groups, on one side of the PNT. Microscopic and spectroscopic observations of CP5ES crystals reveal that CP5ES forms rod- or needle-shaped molecular assemblies showing exciton coupling of the Cotton effect and predominant monomer emission, which are different from a reference cyclic tri-β-peptide composed of a β-naphthylalanine and two β-alanines. Insertion of a sequence of ethylenediamine-succinic acid into β-amino acids in the cyclic skeleton is therefore suggested to be effective to make the side chains aligning on one side of the PNT. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd. PMID:27282135

  6. Temperature dependence of amino acid side chain IR absorptions in the amide I' region.

    PubMed

    Anderson, Benjamin A; Literati, Alex; Ball, Borden; Kubelka, Jan

    2014-05-01

    Amide I' IR spectra are widely used for studies of structural changes in peptides and proteins as a function of temperature. Temperature dependent absorptions of amino acid side-chains that overlap the amide I' may significantly complicate the structural analyses. While the side-chain IR spectra have been investigated previously, thus far their dependence on temperature has not been reported. Here we present the study of the changes in the IR spectra with temperature for side-chain groups of aspartate, glutamate, asparagine, glutamine, arginine, and tyrosine in the amide I' region (in D2O). Band fitting analysis was employed to extract the temperature dependence of the individual spectral parameters, such as peak frequency, integrated intensity, band width, and shape. As expected, the side-chain IR bands exhibit significant changes with temperature. The majority of the spectral parameters, particularly the frequency and intensity, show linear dependence on temperature, but the direction and magnitude vary depending on the particular side-chain group. The exception is arginine, which exhibits a distinctly nonlinear frequency shift with temperature for its asymmetric CN3H5(+) bending signal, although a linear fit can account for this change to within ~1/3 cm(-1). The applicability of the determined spectral parameters for estimations of temperature-dependent side-chain absorptions in peptides and proteins are discussed.

  7. Microwave-assisted solid-phase synthesis of side-chain to side-chain lactam-bridge cyclic peptides.

    PubMed

    Tala, Srinivasa R; Schnell, Sathya M; Haskell-Luevano, Carrie

    2015-12-15

    Side-chain to side-chain lactam-bridged cyclic peptides have been utilized as therapeutic agents and biochemical tools. Previous synthetic methods of these peptides need special reaction conditions, form side products and take longer reaction times. Herein, an efficient microwave-assisted synthesis of side-chain to side-chain lactam-bridge cyclic peptides SHU9119 and MTII is reported. The synthesis time and efforts are significantly reduced in the present method, without side product formation. The analytical and pharmacological data of the synthesized cyclic peptides are in accordance with the commercially obtained compounds. This new method could be used to synthesize other side-chain to side-chain lactam-bridge peptides and amenable to automation and extensive SAR compound derivatization.

  8. Side-chain conformational entropy in protein unfolded states.

    PubMed

    Creamer, T P

    2000-08-15

    The largest force disfavoring the folding of a protein is the loss of conformational entropy. A large contribution to this entropy loss is due to the side-chains, which are restricted, although not immobilized, in the folded protein. In order to accurately estimate the loss of side-chain conformational entropy that occurs upon folding it is necessary to have accurate estimates of the amount of entropy possessed by side-chains in the ensemble of unfolded states. A new scale of side-chain conformational entropies is presented here. This scale was derived from Monte Carlo computer simulations of small peptide models. It is demonstrated that the entropies are independent of host peptide length. This new scale has the advantage over previous scales of being more precise with low standard errors. Better estimates are obtained for long (e.g., Arg and Lys) and rare (e.g., Trp and Met) side-chains. Excellent agreement with previous side-chain entropy scales is achieved, indicating that further advancements in accuracy are likely to be small at best. Strikingly, longer side-chains are found to possess a smaller fraction of the theoretical maximum entropy available than short side-chains. This indicates that rotations about torsions after chi(2) are significantly affected by side-chain interactions with the polypeptide backbone. This finding invalidates previous assumptions about side-chain-backbone interactions. Proteins 2000;40:443-450.

  9. Phenothiazinium photoantimicrobials with basic side chains.

    PubMed

    Wainwright, Mark; Antczak, Joanna; Baca, Martyna; Loughran, Ciara; Meegan, Katie

    2015-09-01

    Derivatives of the standard cationic photosensitiser, methylene blue, were synthesised, having extra amino (basic) functionality in the auxochromic side-chain. The resulting analogues were profiled for photodynamic activity in vitro, and screened against standard Gram-positive and Gram-negative bacteria for photobactericidal activity. The substitution pattern of the derivatives was such that ionisation of the amino groups in situ, via protonation, provided a range of charge distribution and degree of charge across the molecular framework. While most examples exhibited greater activity than the lead compound, in addition to similar activity to the known, but more powerful, phenothiazinium photoantimicrobial, dimethyl methylene blue, this was also associated with relatively high dark toxicity, inferring that these compounds were targeting crucial structures before illumination. One derivative having an asymmetrical structure, with separation between a lipophilic and a hydrophilic region exhibited a combination of very high phototoxicity coupled with very low dark effects, against both the standard screen and an additional one containing further, relevant pathogen species, including Candida albicans. It is suggested that the great activity of this analogue is due to efficient membrane targeting.

  10. Side-chain entropy and packing in proteins.

    PubMed

    Bromberg, S; Dill, K A

    1994-07-01

    What role does side-chain packing play in protein stability and structure? To address this question, we compare a lattice model with side chains (SCM) to a linear lattice model without side chains (LCM). Self-avoiding configurations are enumerated in 2 and 3 dimensions exhaustively for short chains and by Monte Carlo sampling for chains up to 50 main-chain monomers long. This comparison shows that (1) side-chain degrees of freedom increase the entropy of open conformations, but side-chain steric exclusion decreases the entropy of compact conformations, thus producing a substantial entropy that opposes folding; (2) there is side-chain "freezing" or ordering, i.e., a sharp decrease in entropy, near maximum compactness; and (3) the different types of contacts among side chains (s) and main-chain elements (m) have different frequencies, and the frequencies have different dependencies on compactness. mm contacts contribute significantly only at high densities, suggesting that main-chain hydrogen bonding in proteins may be promoted by compactness. The distributions of mm, ms, and ss contacts in compact SCM configurations are similar to the distributions in protein structures in the Brookhaven Protein Data Bank. We propose that packing in proteins is more like the packing of nuts and bolts in a jar than like the pairwise matching of jigsaw puzzle pieces. PMID:7920265

  11. 22. VIEW LOOKING FORWARD INTO CHAIN LOCKER FROM PORT SIDE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    22. VIEW LOOKING FORWARD INTO CHAIN LOCKER FROM PORT SIDE ENTRY THROUGH CHAIN LOCKER BULKHEAD. PAWL BITT SHOWN IN FOREGROUND - Pilot Schooner "Alabama", Moored in harbor at Vineyard Haven, Vineyard Haven, Dukes County, MA

  12. A Major Role for Side-Chain Polyglutamine Hydrogen Bonding in Irreversible Ataxin-3 Aggregation

    PubMed Central

    Relini, Annalisa; Apicella, Alessandra; Invernizzi, Gaetano; Casari, Carlo; Gliozzi, Alessandra; Doglia, Silvia Maria; Tortora, Paolo; Regonesi, Maria Elena

    2011-01-01

    The protein ataxin-3 consists of an N-terminal globular Josephin domain (JD) and an unstructured C-terminal region containing a stretch of consecutive glutamines that triggers the neurodegenerative disorder spinocerebellar ataxia type 3, when it is expanded beyond a critical threshold. The disease results from misfolding and aggregation, although the pathway and structure of the aggregation intermediates are not fully understood. In order to provide insight into the mechanism of the process, we monitored the aggregation of a normal (AT3Q24) ataxin-3, an expanded (AT3Q55) ataxin-3, and the JD in isolation. We observed that all of them aggregated, although the latter did so at a much slower rate. Furthermore, the expanded AT3Q55 displayed a substantially different behavior with respect to the two other variants in that at the latest stages of the process it was the only one that did the following: i) lost its reactivity towards an anti-oligomer antibody, ii) generated SDS-insoluble aggregates, iii) gave rise to bundles of elongated fibrils, and iv) displayed two additional bands at 1604 and 1656 cm−1 in FTIR spectroscopy. Although these were previously observed in other aggregated polyglutamine proteins, no one has assigned them unambiguously, yet. By H/D exchange experiments we show for the first time that they can be ascribed to glutamine side-chain hydrogen bonding, which is therefore the hallmark of irreversibly SDS-insoluble aggregated protein. FTIR spectra also showed that main-chain intermolecular hydrogen bonding preceded that of glutamine side-chains, which suggests that the former favors the latter by reorganizing backbone geometry. PMID:21533208

  13. Steric interactions determine side-chain conformations in protein cores.

    PubMed

    Caballero, D; Virrueta, A; O'Hern, C S; Regan, L

    2016-09-01

    We investigate the role of steric interactions in defining side-chain conformations in protein cores. Previously, we explored the strengths and limitations of hard-sphere dipeptide models in defining sterically allowed side-chain conformations and recapitulating key features of the side-chain dihedral angle distributions observed in high-resolution protein structures. Here, we show that modeling residues in the context of a particular protein environment, with both intra- and inter-residue steric interactions, is sufficient to specify which of the allowed side-chain conformations is adopted. This model predicts 97% of the side-chain conformations of Leu, Ile, Val, Phe, Tyr, Trp and Thr core residues to within 20°. Although the hard-sphere dipeptide model predicts the observed side-chain dihedral angle distributions for both Thr and Ser, the model including the protein environment predicts side-chain conformations to within 20° for only 60% of core Ser residues. Thus, this approach can identify the amino acids for which hard-sphere interactions alone are sufficient and those for which additional interactions are necessary to accurately predict side-chain conformations in protein cores. We also show that our approach can predict alternate side-chain conformations of core residues, which are supported by the observed electron density.

  14. Protein side chain conformation predictions with an MMGBSA energy function.

    PubMed

    Gaillard, Thomas; Panel, Nicolas; Simonson, Thomas

    2016-06-01

    The prediction of protein side chain conformations from backbone coordinates is an important task in structural biology, with applications in structure prediction and protein design. It is a difficult problem due to its combinatorial nature. We study the performance of an "MMGBSA" energy function, implemented in our protein design program Proteus, which combines molecular mechanics terms, a Generalized Born and Surface Area (GBSA) solvent model, with approximations that make the model pairwise additive. Proteus is not a competitor to specialized side chain prediction programs due to its cost, but it allows protein design applications, where side chain prediction is an important step and MMGBSA an effective energy model. We predict the side chain conformations for 18 proteins. The side chains are first predicted individually, with the rest of the protein in its crystallographic conformation. Next, all side chains are predicted together. The contributions of individual energy terms are evaluated and various parameterizations are compared. We find that the GB and SA terms, with an appropriate choice of the dielectric constant and surface energy coefficients, are beneficial for single side chain predictions. For the prediction of all side chains, however, errors due to the pairwise additive approximation overcome the improvement brought by these terms. We also show the crucial contribution of side chain minimization to alleviate the rigid rotamer approximation. Even without GB and SA terms, we obtain accuracies comparable to SCWRL4, a specialized side chain prediction program. In particular, we obtain a better RMSD than SCWRL4 for core residues (at a higher cost), despite our simpler rotamer library. Proteins 2016; 84:803-819. © 2016 Wiley Periodicals, Inc.

  15. Conservation of side-chain dynamics within a protein family.

    PubMed

    Law, Anthony B; Fuentes, Ernesto J; Lee, Andrew L

    2009-05-13

    The question of protein dynamics and its relevance to function is currently a topic of great interest. Proteins are particularly dynamic at the side-chain level on the time scale of picoseconds to nanoseconds. Here, we present a comparison of NMR-monitored side-chain motion between three PDZ domains of approximately 30% sequence identity and show that the side-chain dynamics display nontrivial conservation. Methyl (2)H relaxation was carried out to determine side-chain order parameters (S(2)), which were found to be more similar than naively expected from sequence, local packing, or a combination of the two. Thus, the dynamics of a rather distant homologue appears to be an excellent predictor of a protein's side-chain dynamics and, on average, better than current structure-based methods. Fast side-chain dynamics therefore display a high level of organization associated with global fold. Beyond simple conservation, the analysis herein suggests that the pattern of side-chain flexibility has significant contributions from nonlocal elements of the PDZ fold, such as correlated motions, and that the conserved dynamics may directly support function.

  16. Ionizable Side Chains at Catalytic Active Sites of Enzymes

    PubMed Central

    Jimenez-Morales, David; Liang, Jie

    2012-01-01

    Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1072 Å3. The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes. PMID:22484856

  17. 21. VIEW LOOKING FORWARD INTO STARBOARD SIDE OF CHAIN LOCKER ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    21. VIEW LOOKING FORWARD INTO STARBOARD SIDE OF CHAIN LOCKER FROM CHAIN LOCKER BULKHEAD; PAWL BITT SHOWN IN EXTREME LEFT FOREGROUND, WITH APRON IN BACKGROUND. BREASTHOOK, SHELF AND CLAMP SHOWN AT TOP OF IMAGE - Pilot Schooner "Alabama", Moored in harbor at Vineyard Haven, Vineyard Haven, Dukes County, MA

  18. Interstrand side chain--side chain interactions in a designed beta-hairpin: significance of both lateral and diagonal pairings.

    PubMed

    Syud, F A; Stanger, H E; Gellman, S H

    2001-09-12

    The contributions of interstrand side chain-side chain contacts to beta-sheet stability have been examined with an autonomously folding beta-hairpin model system. RYVEV(D)PGOKILQ-NH2 ((D)P = D-proline, O = ornithine) has previously been shown to adopt a beta-hairpin conformation in aqueous solution, with a two-residue loop at D-Pro-Gly. In the present study, side chains that display interstrand NOEs (Tyr-2, Lys-9, and Leu-11) are mutated to alanine or serine, and the conformational impact of the mutations is assessed. In the beta-hairpin conformation Tyr-2 and Leu-11 are directly across from one another (non-hydrogen bonded pair). This "lateral" juxtaposition of two hydrophobic side chains appears to contribute to beta-hairpin conformational stability, which is consistent with results from other beta-sheet model studies and with statistical analyses of interstrand residue contacts in protein crystal structures. Interaction between the side chains of Tyr-2 and Lys-9 also stabilizes the beta-hairpin conformation. Tyr-2/Lys-9 is a "diagonal" interstrand juxtaposition because these residues are not directly across from one another in terms of the hydrogen bonding registry between the strands. This diagonal interaction arises from the right-handed twist that is commonly observed among beta-sheets. Evidence of diagonal side chain-side chain contacts has been observed in other autonomously folding beta-sheet model systems, but we are not aware of other efforts to determine whether a diagonal interaction contributes to beta-sheet stability.

  19. Modelling protein side-chain conformations using constraint logic programming.

    PubMed

    Swain, M T; Kemp, G J

    2001-12-01

    Side-chain placement is an important sub-task in protein modelling. Selecting conformations for side-chains is a difficult problem because of the large search space to be explored. This problem can be addressed using constraint logic programming (CLP), which is an artificial intelligence technique developed to solve large combinatorial search problems. The side-chain placement problem can be expressed as a CLP program in which rotamer conformations are used as values for finite domain variables, and bad steric contacts involving rotamers are represented as constraints. This paper introduces the concept of null rotamers, and shows how these can be used in implementing a novel iterative approach. We present results that compare the accuracy of models constructed using different rotamer libraries and different domain variable enumeration heuristics. The results obtained using this CLP-based approach compare favourably with those obtained by other methods.

  20. Affinity enhancement by dendritic side chains in synthetic carbohydrate receptors.

    PubMed

    Destecroix, Harry; Renney, Charles M; Mooibroek, Tiddo J; Carter, Tom S; Stewart, Patrick F N; Crump, Matthew P; Davis, Anthony P

    2015-02-01

    Dendritic side chains have been used to modify the binding environment in anthracene-based synthetic carbohydrate receptors. Control of length, charge, and branching enabled the positioning of side-chain carboxylate groups in such a way that they assisted in binding substrates rather than blocking the cavity. Conformational degeneracy in the dendrimers resulted in effective preorganization despite the flexibility of the system. Strong binding was observed to glucosammonium ions in water, with Ka values up to 7000 M(-1) . Affinities for uncharged substrates (glucose and N-acetylglucosamine) were also enhanced, despite competition from solvent and the absence of electrostatic interactions. PMID:25645064

  1. Improved packing of protein side chains with parallel ant colonies

    PubMed Central

    2014-01-01

    Introduction The accurate packing of protein side chains is important for many computational biology problems, such as ab initio protein structure prediction, homology modelling, and protein design and ligand docking applications. Many of existing solutions are modelled as a computational optimisation problem. As well as the design of search algorithms, most solutions suffer from an inaccurate energy function for judging whether a prediction is good or bad. Even if the search has found the lowest energy, there is no certainty of obtaining the protein structures with correct side chains. Methods We present a side-chain modelling method, pacoPacker, which uses a parallel ant colony optimisation strategy based on sharing a single pheromone matrix. This parallel approach combines different sources of energy functions and generates protein side-chain conformations with the lowest energies jointly determined by the various energy functions. We further optimised the selected rotamers to construct subrotamer by rotamer minimisation, which reasonably improved the discreteness of the rotamer library. Results We focused on improving the accuracy of side-chain conformation prediction. For a testing set of 442 proteins, 87.19% of X1 and 77.11% of X12 angles were predicted correctly within 40° of the X-ray positions. We compared the accuracy of pacoPacker with state-of-the-art methods, such as CIS-RR and SCWRL4. We analysed the results from different perspectives, in terms of protein chain and individual residues. In this comprehensive benchmark testing, 51.5% of proteins within a length of 400 amino acids predicted by pacoPacker were superior to the results of CIS-RR and SCWRL4 simultaneously. Finally, we also showed the advantage of using the subrotamers strategy. All results confirmed that our parallel approach is competitive to state-of-the-art solutions for packing side chains. Conclusions This parallel approach combines various sources of searching intelligence and energy

  2. Characterization and Diagnostic Value of Amino Acid Side Chain Neutral Losses Following Electron-Transfer Dissociation

    PubMed Central

    Xia, Qiangwei; Lee, M. Violet; Rose, Christopher M.; Marsh, Alyce J.; Hubler, Shane L.; Wenger, Craig D.; Coon, Joshua J.

    2011-01-01

    Using a large set of high mass accuracy and resolution ETD tandem mass spectra, we characterized ETD-induced neutral losses. From these data we deduced the chemical formula for 20 of these losses. Many of them have been previously observed in electron-capture dissociation (ECD) spectra, such as losses of the side chains of arginine, aspartic acid, glutamic acid, glutamine, asparagine, leucine, histidine, and carbamidomethylated cysteine residues. With this information, we examined the diagnostic value of these amino acid-specific losses. Among 1285 peptide–spectrum matches, 92.5% have agreement between neutral loss-derived peptide amino acid composition and the peptide sequences. Moreover, we show that peptides can be uniquely identified by using only the accurate precursor mass and amino acid composition based on neutral losses; the median number of sequence candidates from an accurate mass query is reduced from 21 to 8 by adding side chain loss information. Besides increasing confidence in peptide identification, our findings suggest the potential use of these diagnostic losses in ETD spectra to improve false discovery rate estimation and to enhance the performance of scoring functions in database search algorithms. PMID:21472585

  3. Characterization and Diagnostic Value of Amino Acid Side Chain Neutral Losses Following Electron-Transfer Dissociation

    NASA Astrophysics Data System (ADS)

    Xia, Qiangwei; Lee, M. Violet; Rose, Christopher M.; Marsh, Alyce J.; Hubler, Shane L.; Wenger, Craig D.; Coon, Joshua J.

    2011-02-01

    Using a large set of high mass accuracy and resolution ETD tandem mass spectra, we characterized ETD-induced neutral losses. From these data we deduced the chemical formula for 20 of these losses. Many of them have been previously observed in electron-capture dissociation (ECD) spectra, such as losses of the side chains of arginine, aspartic acid, glutamic acid, glutamine, asparagine, leucine, histidine, and carbamidomethylated cysteine residues. With this information, we examined the diagnostic value of these amino acid-specific losses. Among 1285 peptide-spectrum matches, 92.5% have agreement between neutral loss-derived peptide amino acid composition and the peptide sequences. Moreover, we show that peptides can be uniquely identified by using only the accurate precursor mass and amino acid composition based on neutral losses; the median number of sequence candidates from an accurate mass query is reduced from 21 to 8 by adding side chain loss information. Besides increasing confidence in peptide identification, our findings suggest the potential use of these diagnostic losses in ETD spectra to improve false discovery rate estimation and to enhance the performance of scoring functions in database search algorithms.

  4. Melting at Alkyl Side Chain Comb Polymer Interfaces

    NASA Astrophysics Data System (ADS)

    Gautam, Keshav; Dhinojwala, Ali

    2002-03-01

    IR-visible sum-frequency generation (SFG) in combination with internal reflection geometry has been used to study structure and melting transition temperatures of alkyl side chain acrylate comb polymers at air and sapphire interfaces. At the air interface, the SFG spectra show methyl bands and two transitions are observed. The first transition from crystalline to smectic-like is near the bulk melting transition, Tm, and the second transition from smectic-like to disordered melt state is 10-20K higher than Tm. The shorter the alkyl side chain, the larger the difference between the two transition temperatures. In contrast, methylene bands are observed at sapphire interface with a single transition near Tm. These results will be discussed in context with surface freezing effects observed for n-alkanes and alcohols.

  5. Side-Chain Conformational Preferences Govern Protein-Protein Interactions.

    PubMed

    Watkins, Andrew M; Bonneau, Richard; Arora, Paramjit S

    2016-08-24

    Protein secondary structures serve as geometrically constrained scaffolds for the display of key interacting residues at protein interfaces. Given the critical role of secondary structures in protein folding and the dependence of folding propensities on backbone dihedrals, secondary structure is expected to influence the identity of residues that are important for complex formation. Counter to this expectation, we find that a narrow set of residues dominates the binding energy in protein-protein complexes independent of backbone conformation. This finding suggests that the binding epitope may instead be substantially influenced by the side-chain conformations adopted. We analyzed side-chain conformational preferences in residues that contribute significantly to binding. This analysis suggests that preferred rotamers contribute directly to specificity in protein complex formation and provides guidelines for peptidomimetic inhibitor design.

  6. Hydrogen bonding motifs of protein side chains: descriptions of binding of arginine and amide groups.

    PubMed Central

    Shimoni, L.; Glusker, J. P.

    1995-01-01

    The modes of hydrogen bonding of arginine, asparagine, and glutamine side chains and of urea have been examined in small-molecule crystal structures in the Cambridge Structural Database and in crystal structures of protein-nucleic acid and protein-protein complexes. Analysis of the hydrogen bonding patterns of each by graph-set theory shows three patterns of rings (R) with one or two hydrogen bond acceptors and two donors and with eight, nine, or six atoms in the ring, designated R2(2)(8), R2(2)(9), and R1(2)(6). These three patterns are found for arginine-like groups and for urea, whereas only the first two patterns R2(2)(8) and R2(2)(9) are found for asparagine- and glutamine-like groups. In each case, the entire system is planar within 0.7 A or less. On the other hand, in macromolecular crystal structures, the hydrogen bonding patterns in protein-nucleic acid complexes between the nucleic acid base and the protein are all R2(2)(9), whereas hydrogen bonding between Watson-Crick-like pairs of nucleic acid bases is R2(2)(8). These two hydrogen bonding arrangements [R2(2)(9)] and R2(2)(8)] are predetermined by the nature of the groups available for hydrogen bonding. The third motif identified, R1(2)(6), involves hydrogen bonds that are less linear than in the other two motifs and is found in proteins. PMID:7773178

  7. Side chain conformational averaging in human dihydrofolate reductase.

    PubMed

    Tuttle, Lisa M; Dyson, H Jane; Wright, Peter E

    2014-02-25

    The three-dimensional structures of the dihydrofolate reductase enzymes from Escherichia coli (ecDHFR or ecE) and Homo sapiens (hDHFR or hE) are very similar, despite a rather low level of sequence identity. Whereas the active site loops of ecDHFR undergo major conformational rearrangements during progression through the reaction cycle, hDHFR remains fixed in a closed loop conformation in all of its catalytic intermediates. To elucidate the structural and dynamic differences between the human and E. coli enzymes, we conducted a comprehensive analysis of side chain flexibility and dynamics in complexes of hDHFR that represent intermediates in the major catalytic cycle. Nuclear magnetic resonance relaxation dispersion experiments show that, in marked contrast to the functionally important motions that feature prominently in the catalytic intermediates of ecDHFR, millisecond time scale fluctuations cannot be detected for hDHFR side chains. Ligand flux in hDHFR is thought to be mediated by conformational changes between a hinge-open state when the substrate/product-binding pocket is vacant and a hinge-closed state when this pocket is occupied. Comparison of X-ray structures of hinge-open and hinge-closed states shows that helix αF changes position by sliding between the two states. Analysis of χ1 rotamer populations derived from measurements of (3)JCγCO and (3)JCγN couplings indicates that many of the side chains that contact helix αF exhibit rotamer averaging that may facilitate the conformational change. The χ1 rotamer adopted by the Phe31 side chain depends upon whether the active site contains the substrate or product. In the holoenzyme (the binary complex of hDHFR with reduced nicotinamide adenine dinucleotide phosphate), a combination of hinge opening and a change in the Phe31 χ1 rotamer opens the active site to facilitate entry of the substrate. Overall, the data suggest that, unlike ecDHFR, hDHFR requires minimal backbone conformational rearrangement as

  8. Bayesian statistical analysis of protein side-chain rotamer preferences.

    PubMed Central

    Dunbrack, R. L.; Cohen, F. E.

    1997-01-01

    We present a Bayesian statistical analysis of the conformations of side chains in proteins from the Protein Data Bank. This is an extension of the backbone-dependent rotamer library, and includes rotamer populations and average chi angles for a full range of phi, psi values. The Bayesian analysis used here provides a rigorous statistical method for taking account of varying amounts of data. Bayesian statistics requires the assumption of a prior distribution for parameters over their range of possible values. This prior distribution can be derived from previous data or from pooling some of the present data. The prior distribution is combined with the data to form the posterior distribution, which is a compromise between the prior distribution and the data. For the chi 2, chi 3, and chi 4 rotamer prior distributions, we assume that the probability of each rotamer type is dependent only on the previous chi rotamer in the chain. For the backbone-dependence of the chi 1 rotamers, we derive prior distributions from the product of the phi-dependent and psi-dependent probabilities. Molecular mechanics calculations with the CHARMM22 potential show a strong similarity with the experimental distributions, indicating that proteins attain their lowest energy rotamers with respect to local backbone-side-chain interactions. The new library is suitable for use in homology modeling, protein folding simulations, and the refinement of X-ray and NMR structures. PMID:9260279

  9. Rotatoelectricity in cholesteric side-chain liquid single crystal elastomers.

    PubMed

    Menzel, Andreas M; Brand, Helmut R

    2006-11-21

    We analyze the phenomenon of rotatoelectricity which is characteristic of cholesteric side-chain liquid single crystal elastomers. Using a linearized macroscopic continuum description and our previous work we show that if such a material is exposed to a static external electric field oriented parallel to the cholesteric helical axis, the director of the liquid crystalline phase will rotate around the helical axis. The material considered is assumed to be a perfect electric insulator. We propose an experiment in which the effect of rotatoelectricity should be directly observable and from which the ratio of the material parameters involved will be accessible.

  10. Purification and characterization of corticosteroid side chain isomerase

    SciTech Connect

    Marandici, A.; Monder, C. )

    1990-02-06

    Corticosteroid side chain isomerase of rat liver catalyzes the interconversion of the ketol (20-oxo-21-ol) and (20-hydroxy-21-al) forms of the corticosteroid side chain. The enzyme has now been purified to apparent homogeneity from rat liver cytosol by sequential chromatography on anionic, hydroxylapatite, and gel filtration columns. Ketol-aldol isomerization is followed by measuring the exchange of tritium from 21-tritiated steroids with water. The native enzyme is a dimer of MW 44,000. The isoelectric point is 4.8 {plus minus} 0.1 pH units. The purified enzyme is stimulated by Co{sup 3+} or Ni{sup 2+}. The enzyme utilizes 11-deoxycorticosterone, corticosterone, and 17-deoxycortisol as substrate but not cortisol, tetrahydrocortisol, and prednisolone. Tritium-water exchange of (21S)-(21-{sup 3}H)DOC is a pseudo-first-order reaction; 21-{sup 3}H exchange from the 21R isomer proceeds with first-order kinetics only after a lag associated with its epimerization to the 21S form.

  11. Stiffness parameter of brush-like polymers with rod-like side chains.

    PubMed

    Nakamura, Yo

    2016-07-01

    The stiffness parameter λ(-1) of brush-like polymers having rod-like side chains with the hard core potential was calculated. Side chains are, first, assumed to be connected with a free joint to the main chain. The free energy per molecule F was calculated invoking the single contact approximation in which only the interaction between two side chains is considered and the higher interactions are ignored. In the calculation, the contact is assumed to occur when the two side chains are in a plain and the condition for the angles between the side chain and the main chain to make a triangle by two side chains and the main chain was exactly taken into account. The change of F after bending the main chain with a certain curvature from the straight state was calculated to obtain λ(-1). The resulting λ(-1) came close to the experimental value for brush-like polymers with a poly(methacrylate) main chain and poly(hexylisocyanate) (PHIC) side chains if we add a constant as the intrinsic stiffness of the main chain, λ0 (-1), to it. By considering the potential function having a minimum when the angle between the side and main chains equals π/2, the data for brush-like polymers with a poly(styrene) main chain and PHIC side chains were also closely fitted by the theoretical values with an appropriate value of λ0 (-1) and the force constant of the angle.

  12. Glutamine supplementation.

    PubMed

    Wernerman, Jan

    2011-07-18

    Intravenous glutamine supplementation is standard care when parenteral nutrition is given for critical illness. There are data of a reduced mortality when glutamine supplementation is given. In addition, standard commercial products for parenteral nutrition do not contain any glutamine due to glutamine instability in aqueous solutions. For the majority of critical ill patients who are fed enterally, the available evidence is insufficient to recommend glutamine supplementation. Standard formulation of enteral nutrition contains some glutamine: 2-4 g/L. However, this dose is insufficient to normalize glutamine plasma concentration.Plasma concentration of glutamine is low in many patients with critical illness and a low level is an independent risk factor for mortality. A low plasma glutamine concentration is the best indicator of glutamine depletion. Data are emerging about how the endogenous production of glutamine is regulated. We know that skeletal muscle is the major producer of glutamine and that a part of the profound depletion of skeletal muscle seen in critical illness is a reflection of the need to produce glutamine.Glutamine is utilized in rapidly dividing cells in the splanchnic area. Quantitatively most glutamine is oxidized, but the availability of glutamine in surplus is important for the de novo synthesis of nucleotides and necessary for cell division and protein synthesis. More knowledge about the regulation of the endogenous production of glutamine is needed to outline better guidelines for glutamine supplementation in the future.

  13. Changes in conformational dynamics of basic side chains upon protein-DNA association.

    PubMed

    Esadze, Alexandre; Chen, Chuanying; Zandarashvili, Levani; Roy, Sourav; Pettitt, B Montgometry; Iwahara, Junji

    2016-08-19

    Basic side chains play major roles in recognition of nucleic acids by proteins. However, dynamic properties of these positively charged side chains are not well understood. In this work, we studied changes in conformational dynamics of basic side chains upon protein-DNA association for the zinc-finger protein Egr-1. By nuclear magnetic resonance (NMR) spectroscopy, we characterized the dynamics of all side-chain cationic groups in the free protein and in the complex with target DNA. Our NMR order parameters indicate that the arginine guanidino groups interacting with DNA bases are strongly immobilized, forming rigid interfaces. Despite the strong short-range electrostatic interactions, the majority of the basic side chains interacting with the DNA phosphates exhibited high mobility, forming dynamic interfaces. In particular, the lysine side-chain amino groups exhibited only small changes in the order parameters upon DNA-binding. We found a similar trend in the molecular dynamics (MD) simulations for the free Egr-1 and the Egr-1-DNA complex. Using the MD trajectories, we also analyzed side-chain conformational entropy. The interfacial arginine side chains exhibited substantial entropic loss upon binding to DNA, whereas the interfacial lysine side chains showed relatively small changes in conformational entropy. These data illustrate different dynamic characteristics of the interfacial arginine and lysine side chains. PMID:27288446

  14. Polymer side-chains as arms for molecular recognition

    NASA Astrophysics Data System (ADS)

    South, Clinton Ray

    This thesis describes research based on synthetic protocols, methodologies, and applications of polymers containing side-chain molecular recognition elements. The motivation for the thesis lies in the belief among many in the field that a strict covalent paradigm for polymer chemistry is reaching its limit. The use of molecular recognition, in lieu of covalent chemistry, potentially presents a path through the current limits of polymer science. The work described in the following chapters of this thesis is, at least in part, a testament to this proposal. The first two chapters present a basic introduction and survey of the fundamental noncovalent interactions that are ubiquitous in the research of supramolecular polymers and molecular recognition. A hierarchy of noncovalent interactions, molecular recognition, and self-assembly is outlined and discussed. Chapter 2 lays the foundation for the remaining chapters of this thesis by presenting several examples of prior work related specifically to the use of molecular recognition on the side-chains of polymers. The next two chapters present research focused on advancing the functionalization of polymers through molecular recognition. The goal of this research is primarily to develop a general polymer backbone that both site-specifically and strongly associates noncovalently with small molecular substrates. These chapters demonstrate that both architecturally controlled block copolymers and random terpolymers can accept a full load of different substrates without interference among distinct molecular recognition elements along the polymer backbone. Chapters 5 and 6 present a unique application of polymers containing molecular recognition elements, templated synthesis. Chapter 5 first discusses lessons learned from small molecule based templated synthesis in which a template and a substrate are held together by metal coordination and a subsequent bond forming reaction occurs. Ultimately, the results of this chapter

  15. Peptoid oligomers with alpha-chiral, aromatic side chains: effects of chain length on secondary structure.

    PubMed

    Wu, C W; Sanborn, T J; Zuckermann, R N; Barron, A E

    2001-04-01

    Oligomeric N-substituted glycines or "peptoids" with alpha-chiral, aromatic side chains can adopt stable helices in organic or aqueous solution, despite their lack of backbone chirality and their inability to form intrachain hydrogen bonds. Helical ordering appears to be stabilized by avoidance of steric clash as well as by electrostatic repulsion between backbone carbonyls and pi clouds of aromatic rings in the side chains. Interestingly, these peptoid helices exhibit intense circular dichroism (CD) spectra that closely resemble those of peptide alpha-helices. Here, we have utilized CD to systematically study the effects of oligomer length, concentration, and temperature on the chiral secondary structure of organosoluble peptoid homooligomers ranging from 3 to 20 (R)-N-(1-phenylethyl)glycine (Nrpe) monomers in length. We find that a striking evolution in CD spectral features occurs for Nrpe oligomers between 4 and 12 residues in length, which we attribute to a chain length-dependent population of alternate structured conformers having cis versus trans amide bonds. No significant changes are observed in CD spectra of oligomers between 13 and 20 monomers in length, suggesting a minimal chain length of about 13 residues for the formation of stable poly(Nrpe) helices. Moreover, no dependence of circular dichroism on concentration is observed for an Nrpe hexamer, providing evidence that these helices remain monomeric in solution. In light of these new data, we discuss chain length-related factors that stabilize organosoluble peptoid helices of this class, which are important for the design of helical, biomimetic peptoids sharing this structural motif.

  16. Basic amino-acid side chains regulate transmembrane integrin signalling.

    PubMed

    Kim, Chungho; Schmidt, Thomas; Cho, Eun-Gyung; Ye, Feng; Ulmer, Tobias S; Ginsberg, Mark H

    2011-12-18

    Side chains of Lys/Arg near transmembrane domain (TMD) membrane-water interfaces can 'snorkel', placing their positive charge near negatively charged phospholipid head groups; however, snorkelling's functional effects are obscure. Integrin β TMDs have such conserved basic amino acids. Here we use NMR spectroscopy to show that integrin β(3)(Lys 716) helps determine β(3) TMD topography. The α(ΙΙb)β(3) TMD structure indicates that precise β(3) TMD crossing angles enable the assembly of outer and inner membrane 'clasps' that hold the αβ TMD together to limit transmembrane signalling. Mutation of β(3)(Lys 716) caused dissociation of α(ΙΙb)β(3) TMDs and integrin activation. To confirm that altered topography of β(3)(Lys 716) mutants activated α(ΙΙb)β(3), we used directed evolution of β(3)(K716A) to identify substitutions restoring default state. Introduction of Pro(711) at the midpoint of β(3) TMD (A711P) increased α(ΙΙb)β(3) TMD association and inactivated integrin α(ΙΙb)β(3)(A711P,K716A). β(3)(Pro 711) introduced a TMD kink of 30 ± 1° precisely at the border of the outer and inner membrane clasps, thereby decoupling the tilt between these segments. Thus, widely occurring snorkelling residues in TMDs can help maintain TMD topography and membrane-embedding, thereby regulating transmembrane signalling.

  17. Effects of Alkylthio and Alkoxy Side Chains in Polymer Donor Materials for Organic Solar Cells.

    PubMed

    Cui, Chaohua; Wong, Wai-Yeung

    2016-02-01

    Side chains play a considerable role not only in improving the solubility of polymers for solution-processed device fabrication, but also in affecting the molecular packing, electron affinity and thus the device performance. In particular, electron-donating side chains show unique properties when employed to tune the electronic character of conjugated polymers in many cases. Therefore, rational electron-donating side chain engineering can improve the photovoltaic properties of the resulting polymer donors to some extent. Here, a survey of some representative examples which use electron-donating alkylthio and alkoxy side chains in conjugated organic polymers for polymer solar cell applications will be presented. It is envisioned that an analysis of the effect of such electron-donating side chains in polymer donors would contribute to a better understanding of this kind of side chain behavior in solution-processed conjugated organic polymers for polymer solar cells.

  18. Effects of Alkylthio and Alkoxy Side Chains in Polymer Donor Materials for Organic Solar Cells.

    PubMed

    Cui, Chaohua; Wong, Wai-Yeung

    2016-02-01

    Side chains play a considerable role not only in improving the solubility of polymers for solution-processed device fabrication, but also in affecting the molecular packing, electron affinity and thus the device performance. In particular, electron-donating side chains show unique properties when employed to tune the electronic character of conjugated polymers in many cases. Therefore, rational electron-donating side chain engineering can improve the photovoltaic properties of the resulting polymer donors to some extent. Here, a survey of some representative examples which use electron-donating alkylthio and alkoxy side chains in conjugated organic polymers for polymer solar cell applications will be presented. It is envisioned that an analysis of the effect of such electron-donating side chains in polymer donors would contribute to a better understanding of this kind of side chain behavior in solution-processed conjugated organic polymers for polymer solar cells. PMID:26754772

  19. Rotational Study of Natural Amino Acid Glutamine

    NASA Astrophysics Data System (ADS)

    Varela, Marcelino; Cabezas, Carlos; Alonso, José L.

    2014-06-01

    Recent improvements in laser ablation molecular beam Fourier transform microwave spectroscopy (LA-MB-FTMW) have allowed the investigation of glutamine (COOH-CH(NH2)-CH2-CH2-CONH2), a natural amino acid with a long polar side chain. One dominant structure has been detected in the rotational spectrum. The nuclear quadrupole hyperfine structure of two 14N nuclei has been totally resolved allowing the conclusive identification of the observed species.

  20. Solvation thermodynamics of amino acid side chains on a short peptide backbone

    SciTech Connect

    Hajari, Timir; Vegt, Nico F. A. van der

    2015-04-14

    The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment. A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone. To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvation free energies of nonpolar and polar side chains attached to a short peptide backbone. The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone. We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected. This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution. We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar side

  1. Macromolecular recognition: Recognition of polymer side chains by cyclodextrin

    NASA Astrophysics Data System (ADS)

    Hashidzume, Akihito; Harada, Akira

    2015-12-01

    The interaction of cyclodextrins (CD) with water soluble polymers possessing guest residues has been investigated as model systems in biological molecular recognition. The selectivity of interaction of CD with polymer-carrying guest residues is controlled by polymer chains, i.e., the steric effect of polymer main chain, the conformational effect of polymer main chain, and multi-site interaction. Macroscopic assemblies have been also realized based on molecular recognition using polyacrylamide-based gels possessing CD and guest residues.

  2. Biosynthesis of the lipophilic side chain in the cyclic hexadepsipeptide antibiotic IC101.

    PubMed

    Umezawa, Kazuo; Ikeda, Yoko; Naganawa, Hiroshi; Kondo, Shinichi

    2002-12-01

    Antibiotic IC101 is a cyclic hexadepsipeptide having a C(15) lipophilic side chain. The side chain was shown to be synthesized in Streptomyces from acetate, propionate, and 3-methylbutyrate derived from leucine. Thus, the terminal isopentyl structure came from leucine and not from the mevalonate pathway. PMID:12502350

  3. Automated side-chain model building and sequence assignment by template matching

    SciTech Connect

    Terwilliger, Thomas C.

    2003-01-01

    A method for automated macromolecular side-chain model building and for aligning the sequence to the map is described. An algorithm is described for automated building of side chains in an electron-density map once a main-chain model is built and for alignment of the protein sequence to the map. The procedure is based on a comparison of electron density at the expected side-chain positions with electron-density templates. The templates are constructed from average amino-acid side-chain densities in 574 refined protein structures. For each contiguous segment of main chain, a matrix with entries corresponding to an estimate of the probability that each of the 20 amino acids is located at each position of the main-chain model is obtained. The probability that this segment corresponds to each possible alignment with the sequence of the protein is estimated using a Bayesian approach and high-confidence matches are kept. Once side-chain identities are determined, the most probable rotamer for each side chain is built into the model. The automated procedure has been implemented in the RESOLVE software. Combined with automated main-chain model building, the procedure produces a preliminary model suitable for refinement and extension by an experienced crystallographer.

  4. Diketopyrrolopyrrole-based Conjugated Polymers Bearing Branched Oligo(Ethylene Glycol) Side Chains for Photovoltaic Devices.

    PubMed

    Chen, Xingxing; Zhang, Zijian; Ding, Zicheng; Liu, Jun; Wang, Lixiang

    2016-08-22

    Conjugated polymers are essential for solution-processable organic opto-electronic devices. In contrast to the great efforts on developing new conjugated polymer backbones, research on developing side chains is rare. Herein, we report branched oligo(ethylene glycol) (OEG) as side chains of conjugated polymers. Compared with typical alkyl side chains, branched OEG side chains endowed the resulting conjugated polymers with a smaller π-π stacking distance, higher hole mobility, smaller optical band gap, higher dielectric constant, and larger surface energy. Moreover, the conjugated polymers with branched OEG side chains exhibited outstanding photovoltaic performance in polymer solar cells. A power conversion efficiency of 5.37 % with near-infrared photoresponse was demonstrated and the device performance could be insensitive to the active layer thickness.

  5. DFT study of H-bonds in the peptide secondary structures: The backbone-side-chain and polar side-chains interactions

    NASA Astrophysics Data System (ADS)

    Vener, M. V.; Egorova, A. N.; Fomin, D. P.; Tsirelson, V. G.

    2010-05-01

    The backbone-side-chain interactions in the peptide secondary structures are studied by the density functional theory methods with/without periodic boundary conditions. The alanine-based two-stranded β-sheet structure infinite models and the cluster models of the C5 structures modified by the glutamic acid residue are considered. Several low-energy structures have been localized in the BLYP/plane-wave and the BLYP/6-311++G** approximations. Combined use of the quantum-topological analysis of the electron density and frequency shifts enables us to detect and describe quantitatively the non-covalent interactions and H-bonds. We found that the strongest backbone-side-chain interaction (˜37 kJ/mol) is due to the intra-chain H-bond formed by the C dbnd O backbone group and by the COOH side-chain group. The OH…O distance equals to 1.727 Å and the frequency shift of the OH stretching vibration is 370 cm -1. The polar side-chains interaction is studied in the infinite model of the alanine-based two-stranded β-sheet structure modified by the glutamic acid/lysine residues. Moderate inter-chain H-bond (˜40 kJ/mol) is formed by glutamic acid COOH group and lysine NH 2 group. The OH…N distance equals to 1.707 Å and the frequency shift of the OH stretching vibration is 770 cm -1.

  6. Glutamine as an immunonutrient.

    PubMed

    Kim, Hyeyoung

    2011-11-01

    Dietary supplementation with nutrients enhancing immune function is beneficial in patients with surgical and critical illness. Malnutrition and immune dysfunction are common features in hospitalized patients. Specific nutrients with immunological and pharmacological effects, when consumed in amounts above the daily requirement, are referred to as immune-enhancing nutrients or immunonutrients. Supplementation of immunonutrients is important especially for patients with immunodeficiency, virus or overwhelming infections accompanied by a state of malnutrition. Representative immunonutrients are arginine, omega-3 fatty acids, glutamine, nucleotides, beta-carotene, and/or branched-chain amino acids. Glutamine is the most abundant amino acid and performs multiple roles in human body. However, glutamine is depleted from muscle stores during severe metabolic stress including sepsis and major surgery. Therefore it is considered conditionally essential under these conditions. This review discusses the physiological role of glutamine, mode and dose for glutamine administration, as well as improvement of certain disease state after glutamine supplementation. Even though immunonutrition has not been widely assimilated by clinicians other than nutritionists, immunonutrients including glutamine may exert beneficial influence on diverse patient populations.

  7. Temperature Induced Surface Rearrangement of Alkyl Side Chain Comb Polymers at the Polymer/Air Interface

    NASA Astrophysics Data System (ADS)

    Gautam, Keshav S.; Dhinojwala, Ali

    2001-04-01

    Monitoring the structural changes of comb polymer surfaces as a function temperature is of practical importance in order to understand the molecular rearrangement and their influence on surface properties. Sum Frequency Generation (SFG) has been employed to resolve the structural changes of alkyl side chains in these comb polymers at a molecular level. The SFG response of these side chains as a function of chain length and bulk transition temperature show strong contributions from the methyl vibrations when the side chains are in the ordered crystalline state. In the melt state, the SFG spectra show peaks corresponding to methylene vibrations. The presence of methylene peaks indicate gauche defects at the surface. The range of this order-disorder transition is shown to be much broader for polymers when compared to the low molecular weight side chain alcohols.

  8. Side chain flexibility in perfluorosulfonic acid ionomers: an ab initio study.

    PubMed

    Clark, Jeffrey K; Paddison, Stephen J

    2013-10-10

    Side chain flexibility in perfluorosulfonic acid (PFSA) ionomers has been explored through ab initio electronic structure calculations. Three different PFSA side chain fragments were considered with a CF3CFCF3 backbone representation: Nafion (-OCF2CF(CF3)O(CF2)2SO3H), Aquivion or the short side chain (SSC) (-O(CF2)2SO3H), and the 3M PFSA (-O(CF2)4SO3H). Rotational potential energy surfaces for each bond along the length of the side chains were obtained using density functional theory with the B3LYP and the dispersion-corrected B97D functionals with and without the inclusion of a solvation model. Solvent effects were found to have minimal effect on bond rotations close to the tetrafluoroethylene backbone but had greater impact near the terminal sulfonic acid group. The carbon-sulfur bond was found to be the most flexible portion of the side chain in each of the fragments which was further enhanced with the inclusion of the solvent. Complete rotation about either the O-CF2 or CF-O bond in the Nafion side chain resulted in fairly high energetic barriers, but significant portions of these rotational surfaces had energetic penalties less than 1.5 kcal/mol indicating substantial conformational freedom. Fully extended and folded conformations of the Nafion side chain exhibit considerable contraction in side chain end-to-end distance and were observed to be nearly isoenergetic using B3LYP, but the folded structures with the ether oxygen atoms in gauche conformations were ~1.5 kcal/mol lower in energy using B97D. Below the second ether linkage of the Nafion side chain, the rotational potential energy profiles were identical to that determined for the SSC side chain. The 3M side chain was generally found to be the most rigid with barriers for complete rotation about the central carbon-carbon bonds of approximately 7 kcal/mol. These results indicate that minor differences in side chain length and chemistry may have a pronounced effect on the rotational potential energy

  9. Cholesterol Analogs with Degradation-resistant Alkyl Side Chains Are Effective Mycobacterium tuberculosis Growth Inhibitors.

    PubMed

    Frank, Daniel J; Zhao, Yan; Wong, Siew Hoon; Basudhar, Debashree; De Voss, James J; Ortiz de Montellano, Paul R

    2016-04-01

    Cholest-4-en-3-one, whether added exogenously or generated intracellularly from cholesterol, inhibits the growth ofMycobacterium tuberculosiswhen CYP125A1 and CYP142A1, the cytochrome P450 enzymes that initiate degradation of the sterol side chain, are disabled. Here we demonstrate that a 16-hydroxy derivative of cholesterol, which was previously reported to inhibit growth ofM. tuberculosis, acts by preventing the oxidation of the sterol side chain even in the presence of the relevant cytochrome P450 enzymes. The finding that (25R)-cholest-5-en-3β,16β,26-triol (1) (and its 3-keto metabolite) inhibit growth suggests that cholesterol analogs with non-degradable side chains represent a novel class of anti-mycobacterial agents. In accord with this, two cholesterol analogs with truncated, fluorinated side chains have been synthesized and shown to similarly block the growth in culture ofM. tuberculosis.

  10. Steric clashes determine differences in side chain dihedral angle distributions: A study of Thr versus Val

    NASA Astrophysics Data System (ADS)

    Zhou, Alice; O'Hern, Corey; Regan, Lynne

    2012-02-01

    With the long-term goal to improve the design of protein-protein interactions, we develop a simple hard sphere model for dipeptides that can predict the side-chain dihedral angle distributions of Val and Thr in both the α-helix and β-sheet backbone conformations. We find that it is essential to include the non-polar hydrogens in the model; indeed interatomic clashes involving the non-polar hydrogens largely determine the form of side-chain dihedral angle distributions. Further, we are able to explain key differences in the side-chain dihedral angle distributions for Val and Thr from intra-residue steric clashes rather than inter-residue steric clashes or hydrogen bonding. These results are the crucial first step in developing computational models that can predict the side chain conformations of residues at protein-peptide interfaces.

  11. Thermoresponsive PNIPAAM bottlebrush polymers with tailored side-chain length and end-group structure.

    PubMed

    Li, Xianyu; ShamsiJazeyi, Hadi; Pesek, Stacy L; Agrawal, Aditya; Hammouda, Boualem; Verduzco, Rafael

    2014-03-28

    We explore the phase behaviour, solution conformation, and interfacial properties of bottlebrush polymers with side-chains comprised of poly(N-isopropylacrylamide) (PNIPAAM), a thermally responsive polymer that exhibits a lower critical solution temperature (LCST) in water. PNIPAAM bottlebrush polymers with controlled side-chain length and side-chain end-group structure are prepared using a "grafting-through" technique. Due to reduced flexibility of bottlebrush polymer side-chains, side-chain end-groups have a disproportionate effect on bottlebrush polymer solubility and phase behaviour. Bottlebrush polymers with a hydrophobic end-group have poor water solubilities and depressed LCSTs, whereas bottlebrush polymers with thiol-terminated side-chains are fully water-soluble and exhibit an LCST greater than that of PNIPAAM homopolymers. The temperature-dependent solution conformation of PNIPAAM bottlebrush polymers in D2O is analyzed by small-angle neutron scattering (SANS), and data analysis using the Guinier-Porod model shows that the bottlebrush polymer radius decreases as the temperature increases towards the LCST for PNIPAAM bottlebrush polymers with relatively long 9 kg mol(-1) side-chains. Above the LCST, PNIPAAM bottlebrush polymers can form a lyotropic liquid crystal phase in water. Interfacial tension measurements show that bottlebrush polymers reduce the interfacial tension between chloroform and water to levels comparable to PNIPAAM homopolymers without the formation of microemulsions, suggesting that bottlebrush polymers are unable to stabilize highly curved interfaces. These results demonstrate that bottlebrush polymer side-chain length and flexibility impact phase behavior, solubility, and interfacial properties.

  12. Tuning the thermal conductivity of solar cell polymers through side chain engineering.

    PubMed

    Guo, Zhi; Lee, Doyun; Liu, Yi; Sun, Fangyuan; Sliwinski, Anna; Gao, Haifeng; Burns, Peter C; Huang, Libai; Luo, Tengfei

    2014-05-01

    Thermal transport is critical to the performance and reliability of polymer-based energy devices, ranging from solar cells to thermoelectrics. This work shows that the thermal conductivity of a low band gap conjugated polymer, poly(4,8-bis-alkyloxybenzo[1,2-b:4,5-b']dithiophene-2,6-diyl-alt-(alkylthieno[3,4-b]thiophene-2-carboxylate)-2,6-diyl) (PBDTTT), for photovoltaic applications can be actively tuned through side chain engineering. Compared to the original polymer modified with short branched side chains, the engineered polymer using all linear and long side chains shows a 160% increase in thermal conductivity. The thermal conductivity of the polymer exhibits a good correlation with the side chain lengths as well as the crystallinity of the polymer characterized using small-angle X-ray scattering (SAXS) experiments. Molecular dynamics simulations and atomic force microscopy are used to further probe the molecular level local order of different polymers. It is found that the linear side chain modified polymer can facilitate the formation of more ordered structures, as compared to the branched side chain modified ones. The effective medium theory modelling also reveals that the long linear side chain enables a larger heat carrier propagation length and the crystalline phase in the bulk polymer increases the overall thermal conductivity. It is concluded that both the length of the side chains and the induced polymer crystallization are important for thermal transport. These results offer important guidance for actively tuning the thermal conductivity of conjugated polymers through molecular level design.

  13. Steroids with a side chain containing a heterocyclic fragment: synthesis and transformations

    NASA Astrophysics Data System (ADS)

    Baranovskii, Aleksander V.; Litvinovskaya, Raisa P.; Khripach, Vladimir A.

    1993-07-01

    The latest data on the methods for the formation of the side chains of steroids containing a heterocyclic fragment are surveyed and described systematically. Attention is concentrated on the methods for the transformation of heterocycles in order to achieve the stereoselective formation of chiral centres in the side chain characteristic of a series of natural polyhydroxysteroids - ecdysones, brassinosteroids, vitamin D metabolites, etc. The bibliography includes 133 references.

  14. Searching for low percolation thresholds within amphiphilic polymer membranes: The effect of side chain branching

    SciTech Connect

    Dorenbos, G.

    2015-06-14

    Percolation thresholds for solvent diffusion within hydrated model polymeric membranes are derived from dissipative particle dynamics in combination with Monte Carlo (MC) tracer diffusion calculations. The polymer backbones are composed of hydrophobic A beads to which at regular intervals Y-shaped side chains are attached. Each side chain is composed of eight A beads and contains two identical branches that are each terminated with a pendant hydrophilic C bead. Four types of side chains are considered for which the two branches (each represented as [C], [AC], [AAC], or [AAAC]) are splitting off from the 8th, 6th, 4th, or 2nd A bead, respectively. Water diffusion through the phase separated water containing pore networks is deduced from MC tracer diffusion calculations. The percolation threshold for the architectures containing the [C] and [AC] branches is at a water volume fraction of ∼0.07 and 0.08, respectively. These are much lower than those derived earlier for linear architectures of various side chain length and side chain distributions. Control of side chain architecture is thus a very interesting design parameter to decrease the percolation threshold for solvent and proton transports within flexible amphiphilic polymer membranes.

  15. Searching for low percolation thresholds within amphiphilic polymer membranes: The effect of side chain branching

    NASA Astrophysics Data System (ADS)

    Dorenbos, G.

    2015-06-01

    Percolation thresholds for solvent diffusion within hydrated model polymeric membranes are derived from dissipative particle dynamics in combination with Monte Carlo (MC) tracer diffusion calculations. The polymer backbones are composed of hydrophobic A beads to which at regular intervals Y-shaped side chains are attached. Each side chain is composed of eight A beads and contains two identical branches that are each terminated with a pendant hydrophilic C bead. Four types of side chains are considered for which the two branches (each represented as [C], [AC], [AAC], or [AAAC]) are splitting off from the 8th, 6th, 4th, or 2nd A bead, respectively. Water diffusion through the phase separated water containing pore networks is deduced from MC tracer diffusion calculations. The percolation threshold for the architectures containing the [C] and [AC] branches is at a water volume fraction of ˜0.07 and 0.08, respectively. These are much lower than those derived earlier for linear architectures of various side chain length and side chain distributions. Control of side chain architecture is thus a very interesting design parameter to decrease the percolation threshold for solvent and proton transports within flexible amphiphilic polymer membranes.

  16. A Semiautomated Assignment Protocol for Methyl Group Side Chains in Large Proteins.

    PubMed

    Kim, Jonggul; Wang, Yingjie; Li, Geoffrey; Veglia, Gianluigi

    2016-01-01

    The developments of biosynthetic specific labeling strategies for side-chain methyl groups have allowed structural and dynamic characterization of very large proteins and protein complexes. However, the assignment of the methyl-group resonances remains an Achilles' heel for NMR, as the experiments designed to correlate side chains to the protein backbone become rather insensitive with the increase of the transverse relaxation rates. In this chapter, we outline a semiempirical approach to assign the resonances of methyl-group side chains in large proteins. This method requires a crystal structure or an NMR ensemble of conformers as an input, together with NMR data sets such as nuclear Overhauser effects (NOEs) and paramagnetic relaxation enhancements (PREs), to be implemented in a computational protocol that provides a probabilistic assignment of methyl-group resonances. As an example, we report the protocol used in our laboratory to assign the side chains of the 42-kDa catalytic subunit of the cAMP-dependent protein kinase A. Although we emphasize the labeling of isoleucine, leucine, and valine residues, this method is applicable to other methyl group side chains such as those of alanine, methionine, and threonine, as well as reductively methylated cysteine side chains.

  17. Side chain chemistry mediates backbone fragmentation in hydrogen deficient peptide radicals.

    PubMed

    Sun, Qingyu; Nelson, Hosea; Ly, Tony; Stoltz, Brian M; Julian, Ryan R

    2009-02-01

    A crown ether based, photolabile radical precursor which forms noncovalent complexes with peptides has been prepared. The peptide/precursor complexes can be electrosprayed, isolated in an ion trap, and then subjected to laser photolysis and collision induced dissociation to generate hydrogen deficient peptide radicals. It is demonstrated that these peptide radicals behave very differently from the hydrogen rich peptide radicals generated by electron capture methods. In fact, it is shown that side chain chemistry dictates both the occurrence and relative abundance of backbone fragments that are observed. Fragmentation at aromatic residues occurs preferentially over most other amino acids. The origin of this selectivity relates to the mechanism by which backbone dissociation is initiated. The first step is abstraction of a beta-hydrogen from the side chain, followed by beta-elimination to yield primarily a-type fragment ions. Calculations reveal that those side chains which can easily lose a beta-hydrogen correlate well with experimentally favored sites for backbone fragmentation. In addition, radical mediated side chain losses from the parent peptide are frequently observed. Eleven amino acids exhibit unique mass losses from side chains which positively identify that particular amino acid as part of the parent peptide. Therefore, side chain losses allow one to unambiguously narrow the possible sequences for a parent peptide, which when combined with predictable backbone fragmentation should lead to greatly increased confidence in peptide identification.

  18. A Markov Random Field Framework for Protein Side-Chain Resonance Assignment

    NASA Astrophysics Data System (ADS)

    Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

    Nuclear magnetic resonance (NMR) spectroscopy plays a critical role in structural genomics, and serves as a primary tool for determining protein structures, dynamics and interactions in physiologically-relevant solution conditions. The current speed of protein structure determination via NMR is limited by the lengthy time required in resonance assignment, which maps spectral peaks to specific atoms and residues in the primary sequence. Although numerous algorithms have been developed to address the backbone resonance assignment problem [68,2,10,37,14,64,1,31,60], little work has been done to automate side-chain resonance assignment [43, 48, 5]. Most previous attempts in assigning side-chain resonances depend on a set of NMR experiments that record through-bond interactions with side-chain protons for each residue. Unfortunately, these NMR experiments have low sensitivity and limited performance on large proteins, which makes it difficult to obtain enough side-chain resonance assignments. On the other hand, it is essential to obtain almost all of the side-chain resonance assignments as a prerequisite for high-resolution structure determination. To overcome this deficiency, we present a novel side-chain resonance assignment algorithm based on alternative NMR experiments measuring through-space interactions between protons in the protein, which also provide crucial distance restraints and are normally required in high-resolution structure determination. We cast the side-chain resonance assignment problem into a Markov Random Field (MRF) framework, and extend and apply combinatorial protein design algorithms to compute the optimal solution that best interprets the NMR data. Our MRF framework captures the contact map information of the protein derived from NMR spectra, and exploits the structural information available from the backbone conformations determined by orientational restraints and a set of discretized side-chain conformations (i.e., rotamers). A Hausdorff

  19. Influence of side chain configuration on anti-inflammatory analgesic and anti-pyretic properties of 4-biphenylyl alkanoic acids.

    PubMed

    Tenconi, F; Barzaghi, F; Riva, M; Meli, A

    1976-04-01

    A study on the influence of the number of carbon atoms in the side chain as well as side chain configuration on some pharmacologic properties of 4-biphenylyl alkanoic acids is presented. Unlike the chemical structure dependent anti-inflammatory properties, mild analgesic and anti-pyretic properties were neither dependent upon number of carbon atoms nor side chain configuration. PMID:939325

  20. Side-chain modification and "grafting onto" via olefin cross-metathesis.

    PubMed

    de Espinosa, Lucas Montero; Kempe, Kristian; Schubert, Ulrich S; Hoogenboom, Richard; Meier, Michael A R

    2012-12-13

    Olefin cross-metathesis is introduced as a versatile polymer side-chain modification technique. The reaction of a poly(2-oxazoline) featuring terminal double bonds in the side chains with a variety of functional acrylates has been successfully performed in the presence of Hoveyda-Grubbs second-generation catalyst. Self-metathesis, which would lead to polymer-polymer coupling, can be avoided by using an excess of the cross-metathesis partner and a catalyst loading of 5 mol%. The results suggest that bulky acrylates reduce chain-chain coupling due to self-metathesis. Moreover, different functional groups such as alkyl chains, hydroxyl, and allyl acetate groups, as well as an oligomeric poly(ethylene glycol) and a perfluorinated alkyl chain have been grafted with quantitative conversions.

  1. Linear rheology and structure of molecular bottlebrushes with short side chains

    SciTech Connect

    López-Barrón, Carlos R. Brant, Patrick; Crowther, Donna J.; Eberle, Aaron P. R.

    2015-05-15

    We investigate the microstructure and linear viscoelasticity of model molecular bottlebrushes (BBs) using rheological and small-angle X-ray and neutron scattering measurements. Our polymers have short atactic polypropylene (aPP) side chains of molecular weight ranging from 119 g/mol to 259 g/mol and narrow molecular weight distribution (M{sub w}/M{sub n} 1.02–1.05). The side chain molecular weights are a small fraction of the entanglement molecular weight of the corresponding linear polymer (M{sub e,aPP}= 7.05 kg/mol), and as such, they are unentangled. The morphology of the aPP BBs is characterized as semiflexible thick chains with small side chain interdigitation. Their dynamic master curves, obtained by time-temperature superposition, reveal two sequential relaxation processes corresponding to the segmental relaxation and the relaxation of the BB backbone. Due to the short length of the side chains, their fast relaxation could not be distinguished from the glassy relaxation. The fractional free volume is an increasing function of the side chain length (N{sub SC}). Therefore, the glassy behavior of these polymers as well as their molecular friction and dynamic properties are influenced by their N{sub SC} values. The apparent flow activation energies are a decreasing function of N{sub SC}, and their values explain the differences in zero-shear viscosity measured at different temperatures.

  2. Sparse networks of directly coupled, polymorphic, and functional side chains in allosteric proteins.

    PubMed

    Soltan Ghoraie, Laleh; Burkowski, Forbes; Zhu, Mu

    2015-03-01

    Recent studies have highlighted the role of coupled side-chain fluctuations alone in the allosteric behavior of proteins. Moreover, examination of X-ray crystallography data has recently revealed new information about the prevalence of alternate side-chain conformations (conformational polymorphism), and attempts have been made to uncover the hidden alternate conformations from X-ray data. Hence, new computational approaches are required that consider the polymorphic nature of the side chains, and incorporate the effects of this phenomenon in the study of information transmission and functional interactions of residues in a molecule. These studies can provide a more accurate understanding of the allosteric behavior. In this article, we first present a novel approach to generate an ensemble of conformations and an efficient computational method to extract direct couplings of side chains in allosteric proteins, and provide sparse network representations of the couplings. We take the side-chain conformational polymorphism into account, and show that by studying the intrinsic dynamics of an inactive structure, we are able to construct a network of functionally crucial residues. Second, we show that the proposed method is capable of providing a magnified view of the coupled and conformationally polymorphic residues. This model reveals couplings between the alternate conformations of a coupled residue pair. To the best of our knowledge, this is the first computational method for extracting networks of side chains' alternate conformations. Such networks help in providing a detailed image of side-chain dynamics in functionally important and conformationally polymorphic sites, such as binding and/or allosteric sites.

  3. SDRL: a sequence-dependent protein side-chain rotamer library.

    PubMed

    Taghizadeh, Mohammad; Goliaei, Bahram; Madadkar-Sobhani, Armin

    2015-07-01

    Since the introduction of the first protein side-chain rotamer library (RL) almost half a century ago, RLs have been components of many programs and algorithms in structural bioinformatics. Based on the dependence of side-chain dihedral angles on the local backbone, three types of RLs have been identified: backbone-independent, secondary-structure-dependent and backbone-dependent. In all previous studies, the effect of sequence specificity on side-chain conformational preferences was neglected. In the effort to develop a new class of RLs, we considered that the side-chain conformation of the central residue in each triplet on a protein backbone depends on the sequence of the triplet; therefore, we developed a sequence-dependent rotamer library (SDRL). To accomplish this, 400 possible triplet sequences for 18 natural amino acids as the central residue, which corresponds to 7200 triplet sequences in total, were considered. Searching the set of 11 546 selected PDB entries for the 7200 triplet sequences resulted in 2 364 541 instances occurring for 18 amino acids. Our results show that Leu and Val experience minimal impact from the adjacent residues in adopting side-chain conformations. Cys, Ile, Trp, His, Asp, Met, Glu, Gln, Arg and Lys, on the other hand, adopt their side-chain conformations mostly based on the adjacent residues on the backbone. The remaining residue types were moderately dependent on the adjacent residues. Using the new library, side-chain repacking algorithms can find preferred conformations of each residue more easily than with other backbone-independent RLs.

  4. From Isotropic to Anisotropic Side Chain Representations: Comparison of Three Models for Residue Contact Estimation

    PubMed Central

    Sun, Weitao; He, Jing

    2011-01-01

    The criterion to determine residue contact is a fundamental problem in deriving knowledge-based mean-force potential energy calculations for protein structures. A frequently used criterion is to require the side chain center-to-center distance or the -to- atom distance to be within a pre-determined cutoff distance. However, the spatially anisotropic nature of the side chain determines that it is challenging to identify the contact pairs. This study compares three side chain contact models: the Atom Distance criteria (ADC) model, the Isotropic Sphere Side chain (ISS) model and the Anisotropic Ellipsoid Side chain (AES) model using 424 high resolution protein structures in the Protein Data Bank. The results indicate that the ADC model is the most accurate and ISS is the worst. The AES model eliminates about 95% of the incorrectly counted contact-pairs in the ISS model. Algorithm analysis shows that AES model is the most computational intensive while ADC model has moderate computational cost. We derived a dataset of the mis-estimated contact pairs by AES model. The most misjudged pairs are Arg-Glu, Arg-Asp and Arg-Tyr. Such a dataset can be useful for developing the improved AES model by incorporating the pair-specific information for the cutoff distance. PMID:21552527

  5. Dynamical view of the positions of key side chains in protein-protein recognition.

    PubMed Central

    Kimura, S R; Brower, R C; Vajda, S; Camacho, C J

    2001-01-01

    When a complex is constructed from the separately determined rigid structures of a receptor and its ligand, some key side chains are usually in wrong positions. These distortions of the interface yield an apparent loss in affinity and would unfavorably affect the kinetics of association. It is generally assumed that the interacting proteins should drive the appropriate conformational changes, leading to their complementarity, but this hypothesis does not explain their fast association rates. However, nanosecond explicit solvent molecular dynamics simulations of misfolded surface side chains from the independently solved structures of barstar, bovine pancreatic trypsin inhibitor, and lysozyme show that even before any receptor-ligand interaction, key side chains frequently visit the rotamer conformations seen in the complex. We show that these simple structural motifs can reconcile most of the binding affinity required for a rapid and highly specific association process. Side chains amenable to induced fit are also identified. These results corroborate that solvent-side chain interactions play a critical role in the recognition process. Our findings are also supported by crystallographic data. PMID:11159432

  6. From isotropic to anisotropic side chain representations: comparison of three models for residue contact estimation.

    PubMed

    Sun, Weitao; He, Jing

    2011-01-01

    The criterion to determine residue contact is a fundamental problem in deriving knowledge-based mean-force potential energy calculations for protein structures. A frequently used criterion is to require the side chain center-to-center distance or the -to- atom distance to be within a pre-determined cutoff distance. However, the spatially anisotropic nature of the side chain determines that it is challenging to identify the contact pairs. This study compares three side chain contact models: the Atom Distance criteria (ADC) model, the Isotropic Sphere Side chain (ISS) model and the Anisotropic Ellipsoid Side chain (AES) model using 424 high resolution protein structures in the Protein Data Bank. The results indicate that the ADC model is the most accurate and ISS is the worst. The AES model eliminates about 95% of the incorrectly counted contact-pairs in the ISS model. Algorithm analysis shows that AES model is the most computational intensive while ADC model has moderate computational cost. We derived a dataset of the mis-estimated contact pairs by AES model. The most misjudged pairs are Arg-Glu, Arg-Asp and Arg-Tyr. Such a dataset can be useful for developing the improved AES model by incorporating the pair-specific information for the cutoff distance. PMID:21552527

  7. Side chains control dynamics and self-sorting in fluorescent organic nanoparticles.

    PubMed

    Kaeser, Adrien; Fischer, Irén; Abbel, Robert; Besenius, Pol; Dasgupta, Debarshi; Gillisen, Martijn A J; Portale, Giuseppe; Stevens, Amy L; Herz, Laura M; Schenning, Albertus P H J

    2013-01-22

    To develop fluorescent organic nanoparticles with tailored properties for imaging and sensing, full control over the size, fluorescence, stability, dynamics, and supramolecular organization of these particles is crucial. We have designed, synthesized, and fully characterized 12 nonionic fluorene co-oligomers that formed self-assembled fluorescent nanoparticles in water. In these series of molecules, the ratio of hydrophilic ethylene glycol and hydrophobic alkyl side chains was systematically altered to investigate its role on the above-mentioned properties. The nanoparticles consisting of π-conjugated oligomers containing polar ethylene glycol side chains were less stable and larger in size, while nanoparticles self-assembled from oligomers containing nonpolar pendant chains were more stable, smaller, and generally had a higher fluorescence quantum yield. Furthermore, the dynamics of the molecules between the nanoparticles was enhanced if the number of hydrophilic side chains increased. Energy transfer studies between naphthalene and benzothiadiazole fluorene co-oligomers with the same side chains showed no exchange of molecules between the particles for the apolar molecules. For the more polar systems, the exchange of molecules between nanoparticles took place at room temperature or after annealing. Self-assembled nanoparticles consisting of π-conjugated oligomers having different side chains caused self-sorting, resulting either in the formation of domains within particles or the formation of separate nanoparticles. Our results show that we can control the stability, fluorescence, dynamics, and self-sorting properties of the nanoparticles by simply changing the nature of the side chains of the π-conjugated oligomers. These findings are not only important for the field of self-assembled nanoparticles but also for the construction of well-defined multicomponent supramolecular materials in general.

  8. Influence of the sterol aliphatic side chain on membrane properties: a molecular dynamics study.

    PubMed

    Robalo, João R; Ramalho, J P Prates; Huster, Daniel; Loura, Luís M S

    2015-09-21

    Following a recent experimental investigation of the effect of the length of the alkyl side chain in a series of cholesterol analogues (Angew. Chem., Int. Ed., 2013, 52, 12848-12851), we report here an atomistic molecular dynamics characterization of the behaviour of methyl-branched side chain sterols (iso series) in POPC bilayers. The studied sterols included androstenol (i-C0-sterol) and cholesterol (i-C8-sterol), as well as four other derivatives (i-C5, i-C10, i-C12 and i-C14-sterol). For each sterol, both subtle local effects and more substantial differential alterations of membrane properties along the iso series were investigated. The location and orientation of the tetracyclic ring system is almost identical in all compounds. Among all the studied sterols, cholesterol is the sterol that presents the best matching with the hydrophobic length of POPC acyl chains, whereas longer-chained sterols interdigitate into the opposing membrane leaflet. In accordance with the experimental observations, a maximal ordering effect is observed for intermediate sterol chain length (i-C5, cholesterol, i-C10). Only for these sterols a preferential interaction with the saturated sn-1 chain of POPC (compared to the unsaturated sn-2 chain) was observed, but not for either shorter or longer-chained derivatives. This work highlights the importance of the sterol alkyl chain in the modulation of membrane properties and lateral organization in biological membranes.

  9. Molecular dynamics simulations of end-grafted centipede-like polymers with stiff charged side chains.

    PubMed

    Cao, Q Q; Zuo, C C; Li, L J

    2010-05-01

    We use molecular dynamics simulations to investigate centipede-like polymers with stiff charged side chains, end-grafted to a planar wall. The effect of the grafting density and the Bjerrum length on the conformational behaviour of the brush is examined in detail. In addition, we make a comparison of centipede-like polyelectrolyte (CPE) brushes with neutral centipede-like polymer (NCP) and linear polyelectrolyte (LPE) brushes. At weak electrostatic interaction, the main chains of the CPE chains adopt a strongly stretched conformation, and the monomer density profiles of side chains exhibit a clear oscillatory behaviour. With increasing Bjerrum length, the CPE brush undergoes a collapse transition. Compared to the CPE brushes, the counterion condensation effect is stronger for the LPE brushes, regardless of whether the electrostatic interaction is weak or strong and of whether the grafting density is low or high. Additionally, it is shown that the architecture of the grafted chains makes a weak contribution to the counterion condensation at strong electrostatic interaction. We also find that the electrostatic repulsion between charged side chains can enhance the stiffness of the main chains and thus limit the range of movement of the free-end monomers.

  10. Synthesis of cyclic polyesters: effects of alkoxy side chains in salicylaldiminato tin(II) complexes.

    PubMed

    Wongmahasirikun, Phonpimon; Prom-on, Paweenuch; Sangtrirutnugul, Preeyanuch; Kongsaeree, Palangpon; Phomphrai, Khamphee

    2015-07-21

    A new class of salicylaldiminato tin(II) catalysts having different alkoxy side chains has been developed. The ligands were modified to have different lengths and flexibilities such as –(CH2)2– (2a), –(CH2)3– (2b), –(ortho-C6H4)CH2– (2c) and –(CH2)2–O–(CH2)2– (2d). Complexes 2a, b were characterized crystallographically revealing a more constrained environment around the metal in complex 2a. These catalysts are active for the solvent-free polymerization of L-lactide and ε-caprolactone. Complex 2a having a shorter side chain was shown to better promote intramolecular transesterification affording cyclic polylactides and cyclic poly(ε-caprolactone). Complexes 2b and 2d having longer side chains produced cyclic poly(ε-caprolactone) as a major product but failed to give cyclic polylactides.

  11. Keto-Functionalized Polymer Scaffolds As Versatile Precursors to Polymer Side Chain Conjugates

    PubMed Central

    Liu, Jingquan; Li, Ronald C.; Sand, Gregory J.; Bulmus, Volga; Davis, Thomas P.; Maynard, Heather D.

    2014-01-01

    A new methacrylate monomer with a reactive ketone side-chain, 2-(4-oxo-pentanoate) ethyl methacrylate (PAEMA), was synthesized and subsequently polymerized by reversible addition-fragmentation chain transfer (RAFT) polymerization to give a polymer with a narrow molecular weight distribution (PDI = 1.25). The polymer was chain extended with poly(ethylene glycol methyl ether acrylate) (PEGMA) to yield a block copolymer. Aminooxy containing small molecules and oligoethylene glycol were conjugated to the ketone functionality of the side chain in high yields. Cytotoxicity of the oxime-linked tetra(ethylene glycol) polymer to mouse fibroblast cells was investigated; the polymer was found to be non-cytotoxic up to 1 mg/mL. The ease with which this polymer is functionalized, suggests that it may be useful in forming tailored polymeric medicines. PMID:24761032

  12. BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization

    PubMed Central

    Ryu, Joonghyun; Lee, Mokwon; Cha, Jehyun; Laskowski, Roman A.; Ryu, Seong Eon; Kim, Deok-Soo

    2016-01-01

    Many applications, such as protein design, homology modeling, flexible docking, etc. require the prediction of a protein's optimal side-chain conformations from just its amino acid sequence and backbone structure. Side-chain prediction (SCP) is an NP-hard energy minimization problem. Here, we present BetaSCPWeb which efficiently computes a conformation close to optimal using a geometry-prioritization method based on the Voronoi diagram of spherical atoms. Its outputs are visual, textual and PDB file format. The web server is free and open to all users at http://voronoi.hanyang.ac.kr/betascpweb with no login requirement. PMID:27151195

  13. Porous organic material from discotic tricarboxyamide: side chain-core interactions.

    PubMed

    Jana, Poulami; Paikar, Arpita; Bera, Santu; Maity, Suman Kumar; Haldar, Debasish

    2014-01-01

    The benzene-1,3,5-tricarboxyamide containing three l-methionine (1) self-assemble through 3-fold amide-amide hydrogen bonds and π-π stacking to fabricate one-dimensional nanorod like structure. However, the tyrosine analogue (2) carrying multiple H-bonding side chains lost the C3 symmetry and 3-fold amide-amide hydrogen bonds and developed a porous structure. The porous material exhibits ten times more N2 sorption (155 cc/g) than the columnar one, indicating that side chain-core interactions have a drastic effect on structure and function.

  14. SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures.

    PubMed

    Nadzirin, Nurul; Gardiner, Eleanor J; Willett, Peter; Artymiuk, Peter J; Firdaus-Raih, Mohd

    2012-07-01

    Similarities in the 3D patterns of amino acid side chains can provide insights into their function despite the absence of any detectable sequence or fold similarities. Search for protein sites (SPRITE) and amino acid pattern search for substructures and motifs (ASSAM) are graph theoretical programs that can search for 3D amino side chain matches in protein structures, by representing the amino acid side chains as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. Both programs require the input file to be in the PDB format. The objective of using SPRITE is to identify matches of side chains in a query structure to patterns with characterized function. In contrast, a 3D pattern of interest can be searched for existing occurrences in available PDB structures using ASSAM. Both programs are freely accessible without any login requirement. SPRITE is available at http://mfrlab.org/grafss/sprite/ while ASSAM can be accessed at http://mfrlab.org/grafss/assam/. PMID:22573174

  15. Arabidopsis GUX Proteins Are Glucuronyltransferases Responsible for the Addition of Glucuronic Acid Side Chains onto Xylan

    EPA Science Inventory

    Xylan, the second most abundant cell wall polysaccharide, is composed of a linear backbone of β-(1,4)-linked xylosyl residues that are often substituted with sugar side chains, such as glucuronic acid (GlcA) and methylglucuronic acid (MeGlcA). It has recently been shown that muta...

  16. Structure and dynamics of an imidazoline nitroxide side chain with strongly hindered internal motion in proteins

    NASA Astrophysics Data System (ADS)

    Toledo Warshaviak, Dora; Khramtsov, Valery V.; Cascio, Duilio; Altenbach, Christian; Hubbell, Wayne L.

    2013-07-01

    A disulfide-linked imidazoline nitroxide side chain (V1) has a similar and highly constrained internal motion at diverse topological sites in a protein, unlike that for the disulfide-linked pyrroline nitroxide side chain (R1) widely used in site directed spin labeling EPR. Crystal structures of V1 at two positions in a helix of T4 Lysozyme and quantum mechanical calculations suggest the source of the constraints as intra-side chain interactions of the disulfide sulfur atoms with both the protein backbone and the 3-nitrogen in the imidazoline ring. These interactions apparently limit the conformation of the side chain to one of only three possible rotamers, two of which are observed in the crystal structure. An inter-spin distance measurement in frozen solution using double electron-electron resonance (DEER) gives a value essentially identical to that determined from the crystal structure of the protein containing two copies of V1, indicating that lattice forces do not dictate the rotamers observed. Collectively, the results suggest the possibility of predetermining a unique rotamer of V1 in helical structures. In general, the reduced rotameric space of V1 compared to R1 should simplify interpretation of inter-spin distance information in terms of protein structure, while the highly constrained internal motion is expected to extend the dynamic range for characterizing large amplitude nanosecond backbone fluctuations.

  17. Exploring the Effects of Glycosylation and Etherification of the Side Chains of the Anticancer Drug Mitoxantrone.

    PubMed

    Shaul, Pazit; Steinbuch, Kfir B; Blacher, Eran; Stein, Reuven; Fridman, Micha

    2015-09-01

    Herein we report the synthesis and biological evaluation of symmetric and asymmetric analogues of the DNA intercalating drug mitoxantrone (MTX) in which the side chains of the parent drug were modified through glycosylation or methyl etherification. Several analogues with glycosylated side chains exhibited higher DNA affinity than the parent MTX. The most potent in vitro cytotoxicity was observed for MTX analogue 8 (1,4-dimethoxy-5,8-bis[2-(2-methoxyethylamino)ethylamino]anthracene-9,10-dione) with methoxy ether containing side chains. Treatment of melanoma-bearing mice with MTX or analogue 8 decreased the intraperitoneal tumor burden relative to untreated mice; the effect of 8 was less pronounced than that of MTX. In vitro metabolism assays of MTX with rabbit liver S9 fraction gave rise to several metabolites; almost no metabolites were detected for MTX analogue 8. The results presented indicate that derivatization of the MTX side chain primary hydroxy groups may result in a significant improvement in DNA affinity and lower susceptibility to the formation of potentially toxic metabolites.

  18. Supramolecular control of self-assembling terthiophene-peptide conjugates through the amino acid side chain

    SciTech Connect

    Lehrman, Jessica A.; Cui, Honggang; Tsai, Wei-Wen; Moyer, Tyson J.; Stupp, Samuel I.

    2013-07-30

    The self-assembly of oligothiophene–peptide conjugates can be directed through the systematic variation of the peptide sequence into different nanostructures, including flat spicules, nanotubes, spiral sheets, and giant, flat sheets. Furthermore, the assembly of these molecules is not controlled by steric interactions between the amino acid side chains.

  19. Energetic, Structural, and Antimicrobial Analyses of [beta]-Lactam Side Chain Recognition by [beta]-Lactamases

    SciTech Connect

    Caselli, E.; Powers, R.A.; Blaszczak, L.C.; Wu, C.Y.E.; Prati, F.; Shoichet, B.K.

    2010-03-05

    Penicillins and cephalosporins are among the most widely used and successful antibiotics. The emergence of resistance to these {beta}-lactams, most often through bacterial expression of {beta}-lactamases, threatens public health. To understand how {beta}-lactamases recognize their substrates, it would be helpful to know their binding energies. Unfortunately, these have been difficult to measure because {beta}-lactams form covalent adducts with {beta}-lactamases. This has complicated functional analyses and inhibitor design. To investigate the contribution to interaction energy of the key amide (R1) side chain of {beta}-lactam antibiotics, eight acylglycineboronic acids that bear the side chains of characteristic penicillins and cephalosporins, as well as four other analogs, were synthesized. These transition-state analogs form reversible adducts with serine {beta}-lactamases. Therefore, binding energies can be calculated directly from K{sub i} values. The K{sub i} values measured span four orders of magnitude against the Group I {beta}-lactamase AmpC and three orders of magnitude against the Group II {beta}-lactamase TEM-1. The acylglycineboronic acids have K{sub i} values as low as 20 nM against AmpC and as low as 390 nM against TEM-1. The inhibitors showed little activity against serine proteases, such as chymotrypsin. R1 side chains characteristic of {beta}-lactam inhibitors did not have better affinity for AmpC than did side chains characteristic of {beta}-lactam substrates. Two of the inhibitors reversed the resistance of pathogenic bacteria to {beta}-lactams in cell culture. Structures of two inhibitors in their complexes with AmpC were determined by X-ray crystallography to 1.90 {angstrom} and 1.75 {angstrom} resolution; these structures suggest interactions that are important to the affinity of the inhibitors. Acylglycineboronic acids allow us to begin to dissect interaction energies between {beta}-lactam side chains and {beta}-lactamases. Surprisingly

  20. Effect of side-chain substituents on self-assembly of perylene diimide molecules: morphology control.

    PubMed

    Balakrishnan, Kaushik; Datar, Aniket; Naddo, Tammene; Huang, Jialing; Oitker, Randy; Yen, Max; Zhao, Jincai; Zang, Ling

    2006-06-01

    Effect of side-chain substitutions on the morphology of self-assembly of perylene diimide molecules has been studied with two derivatives modified with distinctly different side-chains, N,N'-di(dodecyl)-perylene-3,4,9,10-tetracarboxylic diimide (DD-PTCDI) and N,N'-di(nonyldecyl)-perylene-3,4,9,10-tetracarboxylic diimide (ND-PTCDI). Due to the different side-chain interference, the self-assembly of the two molecules results in totally different morphologies in aggregate: one-dimensional (1D) nanobelt vs zero-dimensional (0D) nanoparticle. The size, shape, and topography of the self-assemblies were extensively characterized by a variety of microscopies including SEM, TEM, AFM, and fluorescence microscopy. The distinct morphologies of self-assembly have been obtained from both the solution-based processing and surface-supported solvent-vapor annealing. The nanobelts of DD-PTCDI fabricated in solution can feasibly be transferred to both polar (e.g., glass) and nonpolar (e.g., carbon) surfaces, implying the high stability of the molecular assembly (due to the strong pi-pi stacking). The side-chain-dependent molecular interaction was comparatively investigated using various spectrometries including UV-vis absorption, fluorescence, X-ray diffraction, and differential scanning calorimetry. Compared to the emission of ND-PTCDI aggregate, the emission of DD-PTCDI aggregate was significantly red-shifted (ca. 30 nm) and the emission quantum yield decreased about three times, primarily due to the more favorable molecular stacking for DD-PTCID. Moreover, the aggregate of DD-PTCDI shows a pronounced absorption band at the longer wavelength, whereas the absorption of ND-PTCDI aggregate is not significant in the same wavelength region. These optical spectral observations are reminiscent of the previous theoretical investigation on the side-chain-modulated electronic properties of PTCDI assembly.

  1. Arginine side chain interactions and the role of arginine as a gating charge carrier in voltage sensitive ion channels

    NASA Astrophysics Data System (ADS)

    Armstrong, Craig T.; Mason, Philip E.; Anderson, J. L. Ross; Dempsey, Christopher E.

    2016-02-01

    Gating charges in voltage-sensing domains (VSD) of voltage-sensitive ion channels and enzymes are carried on arginine side chains rather than lysine. This arginine preference may result from the unique hydration properties of the side chain guanidinium group which facilitates its movement through a hydrophobic plug that seals the center of the VSD, as suggested by molecular dynamics simulations. To test for side chain interactions implicit in this model we inspected interactions of the side chains of arginine and lysine with each of the 19 non-glycine amino acids in proteins in the protein data bank. The arginine guanidinium interacts with non-polar aromatic and aliphatic side chains above and below the guanidinium plane while hydrogen bonding with polar side chains is restricted to in-plane positions. In contrast, non-polar side chains interact largely with the aliphatic part of the lysine side chain. The hydration properties of arginine and lysine are strongly reflected in their respective interactions with non-polar and polar side chains as observed in protein structures and in molecular dynamics simulations, and likely underlie the preference for arginine as a mobile charge carrier in VSD.

  2. Backbone dependency further improves side chain prediction efficiency in the Energy-based Conformer Library (bEBL).

    PubMed

    Subramaniam, Sabareesh; Senes, Alessandro

    2014-11-01

    Side chain optimization is an integral component of many protein modeling applications. In these applications, the conformational freedom of the side chains is often explored using libraries of discrete, frequently occurring conformations. Because side chain optimization can pose a computationally intensive combinatorial problem, the nature of these conformer libraries is important for ensuring efficiency and accuracy in side chain prediction. We have previously developed an innovative method to create a conformer library with enhanced performance. The Energy-based Library (EBL) was obtained by analyzing the energetic interactions between conformers and a large number of natural protein environments from crystal structures. This process guided the selection of conformers with the highest propensity to fit into spaces that should accommodate a side chain. Because the method requires a large crystallographic data-set, the EBL was created in a backbone-independent fashion. However, it is well established that side chain conformation is strongly dependent on the local backbone geometry, and that backbone-dependent libraries are more efficient in side chain optimization. Here we present the backbone-dependent EBL (bEBL), whose conformers are independently sorted for each populated region of Ramachandran space. The resulting library closely mirrors the local backbone-dependent distribution of side chain conformation. Compared to the EBL, we demonstrate that the bEBL uses fewer conformers to produce similar side chain prediction outcomes, thus further improving performance with respect to the already efficient backbone-independent version of the library.

  3. Arginine side chain interactions and the role of arginine as a gating charge carrier in voltage sensitive ion channels.

    PubMed

    Armstrong, Craig T; Mason, Philip E; Anderson, J L Ross; Dempsey, Christopher E

    2016-01-01

    Gating charges in voltage-sensing domains (VSD) of voltage-sensitive ion channels and enzymes are carried on arginine side chains rather than lysine. This arginine preference may result from the unique hydration properties of the side chain guanidinium group which facilitates its movement through a hydrophobic plug that seals the center of the VSD, as suggested by molecular dynamics simulations. To test for side chain interactions implicit in this model we inspected interactions of the side chains of arginine and lysine with each of the 19 non-glycine amino acids in proteins in the protein data bank. The arginine guanidinium interacts with non-polar aromatic and aliphatic side chains above and below the guanidinium plane while hydrogen bonding with polar side chains is restricted to in-plane positions. In contrast, non-polar side chains interact largely with the aliphatic part of the lysine side chain. The hydration properties of arginine and lysine are strongly reflected in their respective interactions with non-polar and polar side chains as observed in protein structures and in molecular dynamics simulations, and likely underlie the preference for arginine as a mobile charge carrier in VSD. PMID:26899474

  4. Arginine side chain interactions and the role of arginine as a gating charge carrier in voltage sensitive ion channels

    PubMed Central

    Armstrong, Craig T.; Mason, Philip E.; Anderson, J. L. Ross; Dempsey, Christopher E.

    2016-01-01

    Gating charges in voltage-sensing domains (VSD) of voltage-sensitive ion channels and enzymes are carried on arginine side chains rather than lysine. This arginine preference may result from the unique hydration properties of the side chain guanidinium group which facilitates its movement through a hydrophobic plug that seals the center of the VSD, as suggested by molecular dynamics simulations. To test for side chain interactions implicit in this model we inspected interactions of the side chains of arginine and lysine with each of the 19 non-glycine amino acids in proteins in the protein data bank. The arginine guanidinium interacts with non-polar aromatic and aliphatic side chains above and below the guanidinium plane while hydrogen bonding with polar side chains is restricted to in-plane positions. In contrast, non-polar side chains interact largely with the aliphatic part of the lysine side chain. The hydration properties of arginine and lysine are strongly reflected in their respective interactions with non-polar and polar side chains as observed in protein structures and in molecular dynamics simulations, and likely underlie the preference for arginine as a mobile charge carrier in VSD. PMID:26899474

  5. Preparation of quinolinium salts differing in the length of the alkyl side chain.

    PubMed

    Marek, Jan; Buchta, Vladimir; Soukup, Ondrej; Stodulka, Petr; Cabal, Jiri; Ghosh, Kallol K; Musilek, Kamil; Kuca, Kamil

    2012-05-25

    Quaternary quinolinium salts differing in alkyl chain length are members of a widespread group of cationic surfactants. These compounds have numerous applications in various branches of industry and research. In this work, the preparation of quinoline-derived cationic surface active agents differing in the length of the side alkyl chains (from C₈ to C₂₀) is described. An HPLC method was successfully developed for distinction of all members of the series of prepared long-chain quinolinium derivatives. In conclusion, some possibilities of intended tests or usage have been summarized. In vitro testing using a microdilution broth method showed good activity of a substance with a C12 chain length against Gram-positive cocci and Candida species.

  6. Sub-cellular internalization and organ specific oral elivery of PABA nanoparticles by side chain variation

    PubMed Central

    2011-01-01

    Background Organic nanomaterials having specific biological properties play important roles in in vivo delivery and clearance from the live cells. To develop orally deliverable nanomaterials for different biological applications, we have synthesized several fluorescently labelled, self-assembled PABA nanoparticles using possible acid side chain combinations and tested against insect and human cell lines and in vivo animal model. Flurophores attached to nanostructures help in rapid in vivo screening and tracking through complex tissues. The sub-cellular internalization mechanism of the conjugates was determined. A set of physio-chemical parameters of engineered nanoskeletons were also defined that is critical for preferred uptake in multiple organs of live Drosophila. Results The variability of side chains alter size, shape and surface texture of each nanomaterial that lead to differential uptake in human and insect cells and to different internal organs in live Drosophila via energy dependent endocytosis. Our results showed that physical and chemical properties of C-11 and C-16 acid chain are best fitted for delivery to complex organs in Drosophila. However a distinct difference in uptake of same nanoparticle in human and insect cells postulated that different host cell physiology plays a critical role in the uptake mechanism. Conclusions The physical and chemical properties of the nanoparticle produced by variation in the acid side chains that modify size and shape of engineered nanostructure and their interplay with host cell physiology might be the major criteria for their differential uptake to different internal organs. PMID:21443763

  7. Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains

    PubMed Central

    Mann, Martin; Saunders, Rhodri; Smith, Cameron; Backofen, Rolf; Deane, Charlotte M.

    2012-01-01

    Lattice models are a common abstraction used in the study of protein structure, folding, and refinement. They are advantageous because the discretisation of space can make extensive protein evaluations computationally feasible. Various approaches to the protein chain lattice fitting problem have been suggested but only a single backbone-only tool is available currently. We introduce LatFit, a new tool to produce high-accuracy lattice protein models. It generates both backbone-only and backbone-side-chain models in any user defined lattice. LatFit implements a new distance RMSD-optimisation fitting procedure in addition to the known coordinate RMSD method. We tested LatFit's accuracy and speed using a large nonredundant set of high resolution proteins (SCOP database) on three commonly used lattices: 3D cubic, face-centred cubic, and knight's walk. Fitting speed compared favourably to other methods and both backbone-only and backbone-side-chain models show low deviation from the original data (~1.5 Å RMSD in the FCC lattice). To our knowledge this represents the first comprehensive study of lattice quality for on-lattice protein models including side chains while LatFit is the only available tool for such models. PMID:22934109

  8. Producing high-accuracy lattice models from protein atomic coordinates including side chains.

    PubMed

    Mann, Martin; Saunders, Rhodri; Smith, Cameron; Backofen, Rolf; Deane, Charlotte M

    2012-01-01

    Lattice models are a common abstraction used in the study of protein structure, folding, and refinement. They are advantageous because the discretisation of space can make extensive protein evaluations computationally feasible. Various approaches to the protein chain lattice fitting problem have been suggested but only a single backbone-only tool is available currently. We introduce LatFit, a new tool to produce high-accuracy lattice protein models. It generates both backbone-only and backbone-side-chain models in any user defined lattice. LatFit implements a new distance RMSD-optimisation fitting procedure in addition to the known coordinate RMSD method. We tested LatFit's accuracy and speed using a large nonredundant set of high resolution proteins (SCOP database) on three commonly used lattices: 3D cubic, face-centred cubic, and knight's walk. Fitting speed compared favourably to other methods and both backbone-only and backbone-side-chain models show low deviation from the original data (~1.5 Å RMSD in the FCC lattice). To our knowledge this represents the first comprehensive study of lattice quality for on-lattice protein models including side chains while LatFit is the only available tool for such models. PMID:22934109

  9. Producing high-accuracy lattice models from protein atomic coordinates including side chains.

    PubMed

    Mann, Martin; Saunders, Rhodri; Smith, Cameron; Backofen, Rolf; Deane, Charlotte M

    2012-01-01

    Lattice models are a common abstraction used in the study of protein structure, folding, and refinement. They are advantageous because the discretisation of space can make extensive protein evaluations computationally feasible. Various approaches to the protein chain lattice fitting problem have been suggested but only a single backbone-only tool is available currently. We introduce LatFit, a new tool to produce high-accuracy lattice protein models. It generates both backbone-only and backbone-side-chain models in any user defined lattice. LatFit implements a new distance RMSD-optimisation fitting procedure in addition to the known coordinate RMSD method. We tested LatFit's accuracy and speed using a large nonredundant set of high resolution proteins (SCOP database) on three commonly used lattices: 3D cubic, face-centred cubic, and knight's walk. Fitting speed compared favourably to other methods and both backbone-only and backbone-side-chain models show low deviation from the original data (~1.5 Å RMSD in the FCC lattice). To our knowledge this represents the first comprehensive study of lattice quality for on-lattice protein models including side chains while LatFit is the only available tool for such models.

  10. Novel Fluorinated Polymers Containing Short Perfluorobutyl Side Chains and Their Super Wetting Performance on Diverse Substrates.

    PubMed

    Jiang, Jingxian; Zhang, Guangfa; Wang, Qiongyan; Zhang, Qinghua; Zhan, Xiaoli; Chen, Fengqiu

    2016-04-27

    Because the emission of perfluorooctanoic acid (PFOA) was completely prohibited in 2015, the widely used poly- and perfluoroalkyl substances with long perfluoroalkyl groups must be substituted by environmentally friendly alternatives. In this study, one kind of potential alternative (i.e., fluorinated polymers with short perfluorobutyl side chains) has been synthesized from the prepared monomers {i.e., (perfluorobutyl)ethyl acrylate (C4A), (perfluorobutyl)ethyl methacrylate (C4MA), 2-[[[[2-(perfluorobutyl)]sulfonyl]methyl]amino]ethyl acrylate (C4SA), and methacrylate (C4SMA)}, and the microstructure, super wetting performance, and applications of the synthesized fluorinated polymers were systematically investigated. The thermal and crystallization behaviors of the fluoropolymer films were characterized by differential scanning calorimetry and wide-angle X-ray diffraction analysis, respectively. Dynamic water-repellent models were constructed. The stable low surface energy and dynamic water- and oil-repellent properties of these synthesized fluorinated polymers with short perfluorobutyl side chains were attributed to the synergetic effect of amorphous fluorinated side chains in perfluoroalkyl acrylate and crystalline hydrocarbon pendant groups in stearyl acrylate. Outstanding water- and oil-repellent properties of fabrics and any other substrates could be achieved by a facile dip-coating treatment using a fluorinated copolymer dispersion. As a result, we believe that our prepared fluorinated copolymers are potential candidates to replace the fluoroalkylated polymers with long perfluorinated chains in nonstick and self-cleaning applications in our daily life. PMID:27052113

  11. Too packed to change: side-chain packing and site-specific substitution rates in protein evolution.

    PubMed

    Marcos, María Laura; Echave, Julian

    2015-01-01

    In protein evolution, due to functional and biophysical constraints, the rates of amino acid substitution differ from site to site. Among the best predictors of site-specific rates are solvent accessibility and packing density. The packing density measure that best correlates with rates is the weighted contact number (WCN), the sum of inverse square distances between a site's C α and the C α of the other sites. According to a mechanistic stress model proposed recently, rates are determined by packing because mutating packed sites stresses and destabilizes the protein's active conformation. While WCN is a measure of C α packing, mutations replace side chains. Here, we consider whether a site's evolutionary divergence is constrained by main-chain packing or side-chain packing. To address this issue, we extended the stress theory to model side chains explicitly. The theory predicts that rates should depend solely on side-chain contact density. We tested this prediction on a data set of structurally and functionally diverse monomeric enzymes. We compared side-chain contact density with main-chain contact density measures and with relative solvent accessibility (RSA). We found that side-chain contact density is the best predictor of rate variation among sites (it explains 39.2% of the variation). Moreover, the independent contribution of main-chain contact density measures and RSA are negligible. Thus, as predicted by the stress theory, site-specific evolutionary rates are determined by side-chain packing.

  12. Contribution of active-site glutamine to rate enhancement in ubiquitin carboxy terminal hydrolases

    PubMed Central

    Boudreaux, David; Chaney, Joseph; Maiti, Tushar K.; Das, Chittaranjan

    2012-01-01

    Ubiquitin carboxy terminal hydrolases (UCHs) are cysteine proteases featuring a classical cysteine-histidine-aspartate catalytic triad, also a highly conserved glutamine thought to be a part of the oxyanion hole. However, the contribution of this side chain to the catalysis by UCH enzymes is not known. Herein, we demonstrate that the glutamine side chain contributes to rate enhancement in UCHL1, UCHL3 and UCHL5. Mutation of the glutamine to alanine in these enzymes impairs the catalytic efficiency mainly due to a 16 to 30-fold reduction in kcat, which is consistent with a loss of approximately 2 kcal/mol in transition-state stabilization. However, the contribution to transition-state stabilization observed here is rather modest for the side chain’s role in oxyanion stabilization. Interestingly, we discovered that the carbonyl oxygen of this side chain is engaged in a C—H•••O hydrogen-bonding contact with the CεH group of the catalytic histidine. Upon further analysis, we found that this interaction is a common active-site structural feature in most cysteine proteases, including papain, belonging to families with the QCH(N/D) type of active-site configuration. It is possible that removal of the glutamine side chain might have abolished the C—H•••O interaction, which typically accounts for 2 kcal/mol of stabilization, leading to the effect on catalysis observed here. Additional studies performed on UCHL3 by mutating the glutamine to glutamate (strong C—H•••O acceptor but oxyanion destabilizer) and to lysine (strong oxyanion stabilizer but lacking C—H•••O hydrogen-bonding property) suggest that the C—H•••O hydrogen bond could contribute to catalysis. PMID:22284438

  13. Synthetic studies on maitotoxin. 1. Stereoselective synthesis of the C'D'E'F'-ring system having a side chain.

    PubMed

    Morita, Masayuki; Ishiyama, Seishi; Koshino, Hiroyuki; Nakata, Tadashi

    2008-05-01

    The stereoselective synthesis of the maitotoxin C'D'E'F'-ring system having a side chain has been accomplished through a convergent strategy. The key reactions include Horner-Wadsworth-Emmons coupling of the C'D'E'-ring and the side chain and subsequent construction of the F'-ring by silane reduction of dihydropyran.

  14. MgO encapsulated mesoporous zeolite for the side chain alkylation of toluene with methanol.

    PubMed

    Jiang, Nanzhe; Jin, Hailian; Jeong, Eun-Young; Park, Sang-Eon

    2010-01-01

    Side chain alkylation of toluene with methanol was studied over mesoporous zeolite supported MgO catalysts. MgO were supported onto the carbon templated mesoporous silicalite-1 by direct synthesis route under microwave conditions. This direct synthesis route yields the majority of MgO highly dispersed into the mesopores of the silicalite-1 crystals. The vapor phase alkylation of toluene with methanol was performed over these catalysts under vapor phase conditions at atmospheric pressure. Mesoporous silicalite-1 supported MgO catalysts gave improved yields towards side chain alkylated products compared to the bulk MgO. The higher activity exhibited by 5% MgO supported on mesoporous silicalite compared to the one with 1% MgO can be attributed to the large number of weak basic sites observed from the CO2 TPD.

  15. Optical probe for the cytochrome P-450 cholesterol side chain cleavage enzyme

    DOEpatents

    Marrone, Babetta L.; Simpson, Daniel J.; Unkefer, Clifford J.; Whaley, Thomas W.

    1992-01-01

    An optical probe enables the study of enzyme activity by absorbance spectroscopy or by sensitive fluorescence methods. In particular, the probe provides the ability to monitor the activity of cytochrome P-450.sub.scc enzyme, the rate limiting enzyme for steroid biosynthesis. Located on the inner mitochondrial membrane, P-450.sub.scc catalyzes the conversion of cholesterol to pregnenolone and isocapraldehyde by sequential oxidations of the cholesterol side chain. The fluorogenic probe includes a cholesterol-like steroid linked to a chromophore through a linking group. The chromophore is selected to have little optical response when linked to the steroid substrate and an enhanced optical response when cleaved from the substrate and linking group. Thus, a fluorescent anion that can be optically detected is generated by the side-chain cleavage reaction during steroidogenesis.

  16. Optical probe for the cytochrome P-450 cholesterol side chain cleavage enzyme

    DOEpatents

    Marrone, Babetta L.; Simpson, Daniel J.; Unkefer, Clifford J.; Whaley, Thomas W.

    1993-01-01

    An optical probe enables the study of enzyme activity by absorbance spectroscopy or by sensitive fluorescence methods. In particular, the probe provides the ability to monitor the activity of cytochrome P-450.sub.scc enzyme, the rate limiting enzyme for steroid biosynthesis. Located on the inner mitochondrial membrane, P-450.sub.scc catalyzes the conversion of cholesterol to pregnenolone and isocapraldehyde by sequential oxidations of the cholesterol side chain. The fluorogenic probe includes a cholesterol-like steroid linked to a chromophore through a linking group. The chromophore is selected to have little optical response when linked to the steroid substrate and an enhanced optical response when cleaved from the substrate and linking group. Thus, a fluorescent anion that can be optically detected is generated by the side-chain cleavage reaction during steroidogenesis.

  17. Multichromophoric electrochromic polymers: colour tuning of conjugated polymers through the side chain functionalization approach.

    PubMed

    Beverina, L; Pagani, G A; Sassi, M

    2014-05-28

    Organic electrochromic materials have gained constantly increasing interest over the years with respect to their inorganic counterpart due to essentially two distinctive characteristics: their processability through solution based low cost processes and their wide colour palette. Such characteristic features enabled their application in displays, smart windows, electronic paper and ophthalmic lenses. Alongside the established concept of donor-acceptor polymers, side chain functionalized multichromophoric polymers are gaining attention as a highly performing and synthetically feasible alternative, particularly relevant to applications requiring a complete colourlessness in one of the accessible redox states of the material. The primary aim of the present article is to review all the results involving the tuning of the native electrochromic properties of simple conjugated polymers through the introduction of a discrete electrochromic molecule as a side chain substituent. PMID:24647618

  18. Structure–Activity Relationships for Side Chain Oxysterol Agonists of the Hedgehog Signaling Pathway

    PubMed Central

    2012-01-01

    Oxysterols (OHCs) are byproducts of cholesterol oxidation that are known to activate the Hedeghog (Hh) signaling pathway. While OHCs that incorporate hydroxyl groups throughout the scaffold are known, those that act as agonists of Hh signaling primarily contain a single hydroxyl on the alkyl side chain. We sought to further explore how side chain hydroxylation patterns affect oxysterol-mediated Hh activation, by performing a structure–activity relationship study on a series of synthetic OHCs. The most active analogue, 23(R)-OHC (35), demonstrated potent activation of Hh signaling in two Hh-dependent cell lines (EC50 values 0.54–0.65 μM). In addition, OHC 35 was approximately 3-fold selective for the Hh pathway as compared to the liver X receptor, a nuclear receptor that is also activated by endogenous OHCs. Finally, 35 induced osteogenic differentiation and osteoblast formation in cultured cells, indicating functional agonism of the Hh pathway. PMID:24900386

  19. IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank.

    PubMed

    Nadzirin, Nurul; Willett, Peter; Artymiuk, Peter J; Firdaus-Raih, Mohd

    2013-07-01

    We describe a server that allows the interrogation of the Protein Data Bank for hypothetical 3D side chain patterns that are not limited to known patterns from existing 3D structures. A minimal side chain description allows a variety of side chain orientations to exist within the pattern, and generic side chain types such as acid, base and hydroxyl-containing can be additionally deployed in the search query. Moreover, only a subset of distances between the side chains need be specified. We illustrate these capabilities in case studies involving arginine stacks, serine-acid group arrangements and multiple catalytic triad-like configurations. The IMAAAGINE server can be accessed at http://mfrlab.org/grafss/imaaagine/. PMID:23716645

  20. Quantitative Profiling of Feruloylated Arabinoxylan Side-Chains from Graminaceous Cell Walls

    PubMed Central

    Schendel, Rachel R.; Meyer, Marleen R.; Bunzel, Mirko

    2016-01-01

    Graminaceous arabinoxylans are distinguished by decoration with feruloylated monosaccharidic and oligosaccharidic side-chains. Although it is hypothesized that structural complexity and abundance of these feruloylated arabinoxylan side-chains may contribute, among other factors, to resistance of plant cell walls to enzymatic degradation, quantitative profiling approaches for these structural units in plant cell wall materials have not been described yet. Here we report the development and application of a rapid and robust method enabling the quantitative comparison of feruloylated side-chain profiles in cell wall materials following mildly acidic hydrolysis, C18-solid phase extraction (SPE), reduction under aprotic conditions, and liquid chromatography with diode-array detection/mass spectrometry (LC-DAD/MS) separation and detection. The method was applied to the insoluble fiber/cell wall materials isolated from 12 whole grains: wild rice (Zizania aquatica L.), long-grain brown rice (Oryza sativa L.), rye (Secale cereale L.), kamut (Triticum turanicum Jakubz.), wheat (Triticum aestivum L.), spelt (Triticum spelta L.), intermediate wheatgrass (Thinopyrum intermedium), maize (Zea mays L.), popcorn (Zea mays L. var. everta), oat (Avena sativa L.) (dehulled), barley (Hordeum vulgare L.) (dehulled), and proso millet (Panicum miliaceum L.). Between 51 and 96% of the total esterified monomeric ferulates were represented in the quantified compounds captured in the feruloylated side-chain profiles, which confirms the significance of these structures to the global arabinoxylan structure in terms of quantity. The method provided new structural insights into cereal grain arabinoxylans, in particular, that the structural moiety α-l-galactopyranosyl-(1→2)-β-d-xylopyranosyl-(1→2)-5-O-trans-feruloyl-l-arabinofuranose (FAXG), which had previously only been described in maize, is ubiquitous to cereal grains. PMID:26834763

  1. Communication: Accurate determination of side-chain torsion angle χ1 in proteins: Phenylalanine residues

    NASA Astrophysics Data System (ADS)

    Suardíaz, R.; Crespo-Otero, R.; Pérez, C.; Fabián, J. San; de la Vega, J. M. García

    2011-02-01

    Quantitative side-chain torsion angle χ1 determinations of phenylalanine residues in Desulfovibrio vulgaris flavodoxin are carried out using exclusively the correlation between the experimental vicinal coupling constants and theoretically determined Karplus equations. Karplus coefficients for nine vicinal coupling related with the torsion angle χ1 were calculated using the B3LYP functional and basis sets of different size. Optimized χ1 angles are in outstanding agreement with those previously reported by employing x ray and NMR measurements.

  2. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

    PubMed

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-02-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/.

  3. Improved prediction of protein side-chain conformations with SCWRL4

    PubMed Central

    Krivov, Georgii G.; Shapovalov, Maxim V.; Dunbrack, Roland L.

    2010-01-01

    Determination of side-chain conformations is an important step in protein structure prediction and protein design. Many such methods have been presented, although only a small number are in widespread use. SCWRL is one such method, and the SCWRL3 program (2003) has remained popular due to its speed, accuracy, and ease-of-use for the purpose of homology modeling. However, higher accuracy at comparable speed is desirable. This has been achieved through: 1) a new backbone-dependent rotamer library based on kernel density estimates; 2) averaging over samples of conformations about the positions in the rotamer library; 3) a fast anisotropic hydrogen bonding function; 4) a short-range, soft van der Waals atom-atom interaction potential; 5) fast collision detection using k-discrete oriented polytopes; 6) a tree decomposition algorithm to solve the combinatorial problem; and 7) optimization of all parameters by determining the interaction graph within the crystal environment using symmetry operators of the crystallographic space group. Accuracies as a function of electron density of the side chains demonstrate that side chains with higher electron density are easier to predict than those with low electron density and presumed conformational disorder. For a testing set of 379 proteins, 86% of χ1 angles and 75% of χ1+2 are predicted correctly within 40° of the X-ray positions. Among side chains with higher electron density (25th–100th percentile), these numbers rise to 89% and 80%. The new program maintains its simple command-line interface, designed for homology modeling, and is now available as a dynamic-linked library for incorporation into other software programs. PMID:19603484

  4. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations

    PubMed Central

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-01-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-‘one-click’ experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/. PMID:26894674

  5. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

    PubMed

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-02-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/. PMID:26894674

  6. Dimerization of Amino Acid Side Chains: Lessons from the Comparison of Different Force Fields.

    PubMed

    de Jong, Djurre H; Periole, Xavier; Marrink, Siewert J

    2012-03-13

    The interactions between amino acid side chains govern protein secondary, tertiary, and quaternary structure formation. For molecular modeling approaches to be able to realistically describe these phenomena, the underlying force fields have to represent these interactions as accurately as possible. Here, we compare the side chain-side chain interactions for a number of commonly used force fields, namely the all-atom OPLS, the united-atom GROMOS, and the coarse-grain MARTINI force field. We do so by calculating the dimerization free energies between selected pairs of side chains and structural characterization of their binding modes. To mimic both polar and nonpolar environments, the simulations are performed in water, n-octanol, and decane. In general, reasonable correlations are found between all three force fields, with deviations on the order of 1 kT in aqueous solvent. In apolar solvent, however, significantly larger differences are found, especially for charged amino acid pairs between the OPLS and GROMOS force fields, and for polar interactions in the MARTINI force field in comparison to the higher resolution models. Interestingly, even in cases where the dimerization free energies are similar, the binding mode may differ substantially between the force fields. This was found to be especially the case for aromatic residues. In addition to the inter-force-field comparison, we compared the various force fields to a knowledge-based potential. The two independent approaches show good correlation in aqueous solvent with an exception of aromatic residues for which the interaction strength is lower in the knowledge-based potentials.

  7. Improved prediction of protein side-chain conformations with SCWRL4.

    PubMed

    Krivov, Georgii G; Shapovalov, Maxim V; Dunbrack, Roland L

    2009-12-01

    Determination of side-chain conformations is an important step in protein structure prediction and protein design. Many such methods have been presented, although only a small number are in widespread use. SCWRL is one such method, and the SCWRL3 program (2003) has remained popular because of its speed, accuracy, and ease-of-use for the purpose of homology modeling. However, higher accuracy at comparable speed is desirable. This has been achieved in a new program SCWRL4 through: (1) a new backbone-dependent rotamer library based on kernel density estimates; (2) averaging over samples of conformations about the positions in the rotamer library; (3) a fast anisotropic hydrogen bonding function; (4) a short-range, soft van der Waals atom-atom interaction potential; (5) fast collision detection using k-discrete oriented polytopes; (6) a tree decomposition algorithm to solve the combinatorial problem; and (7) optimization of all parameters by determining the interaction graph within the crystal environment using symmetry operators of the crystallographic space group. Accuracies as a function of electron density of the side chains demonstrate that side chains with higher electron density are easier to predict than those with low-electron density and presumed conformational disorder. For a testing set of 379 proteins, 86% of chi(1) angles and 75% of chi(1+2) angles are predicted correctly within 40 degrees of the X-ray positions. Among side chains with higher electron density (25-100th percentile), these numbers rise to 89 and 80%. The new program maintains its simple command-line interface, designed for homology modeling, and is now available as a dynamic-linked library for incorporation into other software programs.

  8. Quantitative Profiling of Feruloylated Arabinoxylan Side-Chains from Graminaceous Cell Walls.

    PubMed

    Schendel, Rachel R; Meyer, Marleen R; Bunzel, Mirko

    2015-01-01

    Graminaceous arabinoxylans are distinguished by decoration with feruloylated monosaccharidic and oligosaccharidic side-chains. Although it is hypothesized that structural complexity and abundance of these feruloylated arabinoxylan side-chains may contribute, among other factors, to resistance of plant cell walls to enzymatic degradation, quantitative profiling approaches for these structural units in plant cell wall materials have not been described yet. Here we report the development and application of a rapid and robust method enabling the quantitative comparison of feruloylated side-chain profiles in cell wall materials following mildly acidic hydrolysis, C18-solid phase extraction (SPE), reduction under aprotic conditions, and liquid chromatography with diode-array detection/mass spectrometry (LC-DAD/MS) separation and detection. The method was applied to the insoluble fiber/cell wall materials isolated from 12 whole grains: wild rice (Zizania aquatica L.), long-grain brown rice (Oryza sativa L.), rye (Secale cereale L.), kamut (Triticum turanicum Jakubz.), wheat (Triticum aestivum L.), spelt (Triticum spelta L.), intermediate wheatgrass (Thinopyrum intermedium), maize (Zea mays L.), popcorn (Zea mays L. var. everta), oat (Avena sativa L.) (dehulled), barley (Hordeum vulgare L.) (dehulled), and proso millet (Panicum miliaceum L.). Between 51 and 96% of the total esterified monomeric ferulates were represented in the quantified compounds captured in the feruloylated side-chain profiles, which confirms the significance of these structures to the global arabinoxylan structure in terms of quantity. The method provided new structural insights into cereal grain arabinoxylans, in particular, that the structural moiety α-l-galactopyranosyl-(1→2)-β-d-xylopyranosyl-(1→2)-5-O-trans-feruloyl-l-arabinofuranose (FAXG), which had previously only been described in maize, is ubiquitous to cereal grains. PMID:26834763

  9. Preliminary assessment of the C13-side chain 2'-hydroxylase involved in Taxol biosynthesis

    SciTech Connect

    Long, Robert M.; Croteau, Rodney . E-mail: croteau@wsu.edu

    2005-12-09

    The biosynthesis of the anticancer drug Taxol in yew (Taxus) species is thought to involve the preliminary formation of the advanced taxane diterpenoid intermediate baccatin III upon which the functionally important N-benzoyl phenylisoserinoyl side chain is subsequently assembled at the C13-O-position. In vivo feeding studies with Taxus tissues and characterization of the two transferases responsible for C13-side chain construction have suggested a sequential process in which an aminomutase converts {alpha}-phenylalanine to {beta}-phenylalanine which is then activated to the corresponding CoA ester and transferred to baccatin III to yield {beta}-phenylalanoyl baccatin III (i.e., N-debenzoyl-2'-deoxytaxol) that undergoes subsequent 2'-hydroxylation and N-benzoylation to afford Taxol. However, because the side chain transferase can utilize both {beta}-phenylalanoyl CoA and phenylisoserinoyl CoA in the C13-O-esterification of baccatin III, ambiguity remained as to whether the 2'-hydroxylation step occurs before or after transfer of the amino phenylpropanoyl moiety. Using cell-free enzyme systems from Taxus suspension cells, no evidence was found for the direct hydroxylation of {beta}-phenylalanine to phenylisoserine; however, microsomal preparations from this tissue appeared capable of the cytochrome P450-mediated hydroxylation of {beta}-phenylalanoyl baccatin III to phenylisoserinoyl baccatin III (i.e., N-debenzoyltaxol) as the penultimate step in the formation of Taxol and related N-substituted taxoids. These preliminary results, which are consistent with the proposed side chain assembly process, have clarified an important step of Taxol biosynthesis and set the foundation for cloning the responsible cytochrome P450 hydroxylase gene.

  10. Using Surface Scans for the Evaluation of Halogen Bonds toward the Side Chains of Aspartate, Asparagine, Glutamate, and Glutamine.

    PubMed

    Zimmermann, Markus O; Lange, Andreas; Zahn, Stefan; Exner, Thomas E; Boeckler, Frank M

    2016-07-25

    Using halogen-specific Connolly type molecular surfaces, we herein invented a new type of surface-based interaction analysis employed for the study of halogen bonding toward model systems of biologically relevant carboxylates (ASP/GLU) and carboxamides (ASN/GLN). Database mining and statistical assessment of the PDB revealed that such interactions are widely underrepresented at the moment. We observed important distance-dependent adaptions of the binding modes of halobenzenes from a preferential oxygen-directed to a bifurcated interaction geometry of the carboxylate. In addition, halogen···π contacts perpendicular to the nitrogen atom of the carboxamide become increasingly important for the lighter halogens. Our analysis on a MP2/TZVPP level of theory is backed by CCSD(T)/CBS reference calculations. To put the vast interaction energies into perspective, we also performed COSMO-RS calculations of the solvation free energy. Facilitating the visualization of our results mapped onto any binding site of choice, we aim to inspire more design studies showcasing these underrepresented interactions. PMID:27380316

  11. Cation alkyl side chain length and symmetry effects on the surface tension of ionic liquids.

    PubMed

    Almeida, Hugo F D; Freire, Mara G; Fernandes, Ana M; Lopes-da-Silva, José A; Morgado, Pedro; Shimizu, Karina; Filipe, Eduardo J M; Lopes, José N Canongia; Santos, Luís M N B F; Coutinho, João A P

    2014-06-10

    Aiming at providing a comprehensive study of the influence of the cation symmetry and alkyl side chain length on the surface tension and surface organization of ionic liquids (ILs), this work addresses the experimental measurements of the surface tension of two extended series of ILs, namely R,R'-dialkylimidazolium bis[(trifluoromethyl)sulfonyl]imide ([C(n)C(n)im][NTf2]) and R-alkyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide ([C(n)C(1)im][NTf2]), and their dependence with temperature (from 298 to 343 K). For both series of ILs the surface tension decreases with an increase in the cation side alkyl chain length up to aliphatic chains no longer than hexyl, here labeled as critical alkyl chain length (CACL). For ILs with aliphatic moieties longer than CACL the surface tension displays an almost constant value up to [C12C12im][NTf2] or [C16C1im][NTf2]. These constant values further converge to the surface tension of long chain n-alkanes, indicating that, for sufficiently long alkyl side chains, the surface ordering is strongly dominated by the aliphatic tails present in the IL. The enthalpies and entropies of surface were also derived and the critical temperatures were estimated from the experimental data. The trend of the derived thermodynamic properties highlights the effect of the structural organization of the IL at the surface with visible trend shifts occurring at a well-defined CACL in both symmetric and asymmetric series of ILs. Finally, the structure of a long-alkyl side chain IL at the vacuum-liquid interface was also explored using Molecular Dynamics simulations. In general, it was found that for the symmetric series of ILs, at the outermost polar layers, more cations point one of their aliphatic tails outward and the other inward, relative to the surface, than cations pointing both tails outward. The number of the former, while being the preferred conformation, exceeds the latter by around 75%.

  12. Contribution of cutinase serine 42 side chain to the stabilization of the oxyanion transition state.

    PubMed

    Nicolas, A; Egmond, M; Verrips, C T; de Vlieg, J; Longhi, S; Cambillau, C; Martinez, C

    1996-01-16

    Cutinase from the fungus Fusarium solani pisi is a lipolytic enzyme able to hydrolyze both aggregated and soluble substrates. It therefore provides a powerful tool for probing the mechanisms underlying lipid hydrolysis. Lipolytic enzymes have a catalytic machinery similar to those present in serine proteinases. It is characterized by the triad Ser, His, and Asp (Glu) residues, by an oxyanion binding site that stabilizes the transition state via hydrogen bonds with two main chain amide groups, and possibly by other determinants. It has been suggested on the basis of a covalently bond inhibitor that the cutinase oxyanion hole may consist not only of two main chain amide groups but also of the Ser42 O gamma side chain. Among the esterases and the serine and the cysteine proteases, only Streptomyces scabies esterase, subtilisin, and papain, respectively, have a side chain residue which is involved in the oxyanion hole formation. The position of the cutinase Ser42 side chain is structurally conserved in Rhizomucor miehei lipase with Ser82 O gamma, in Rhizopus delemar lipase with Thr83 O gamma 1, and in Candida antartica B lipase with Thr40 O gamma 1. To evaluate the increase in the tetrahedral intermediate stability provided by Ser42 O gamma, we mutated Ser42 into Ala. Furthermore, since the proper orientation of Ser42 O gamma is directed by Asn84, we mutated Asn84 into Ala, Leu, Asp, and Trp, respectively, to investigate the contribution of this indirect interaction to the stabilization of the oxyanion hole. The S42A mutation resulted in a drastic decrease in the activity (450-fold) without significantly perturbing the three-dimensional structure. The N84A and N84L mutations had milder kinetic effects and did not disrupt the structure of the active site, whereas the N84W and N84D mutations abolished the enzymatic activity due to drastic steric and electrostatic effects, respectively. PMID:8555209

  13. Contribution of cutinase serine 42 side chain to the stabilization of the oxyanion transition state.

    PubMed

    Nicolas, A; Egmond, M; Verrips, C T; de Vlieg, J; Longhi, S; Cambillau, C; Martinez, C

    1996-01-16

    Cutinase from the fungus Fusarium solani pisi is a lipolytic enzyme able to hydrolyze both aggregated and soluble substrates. It therefore provides a powerful tool for probing the mechanisms underlying lipid hydrolysis. Lipolytic enzymes have a catalytic machinery similar to those present in serine proteinases. It is characterized by the triad Ser, His, and Asp (Glu) residues, by an oxyanion binding site that stabilizes the transition state via hydrogen bonds with two main chain amide groups, and possibly by other determinants. It has been suggested on the basis of a covalently bond inhibitor that the cutinase oxyanion hole may consist not only of two main chain amide groups but also of the Ser42 O gamma side chain. Among the esterases and the serine and the cysteine proteases, only Streptomyces scabies esterase, subtilisin, and papain, respectively, have a side chain residue which is involved in the oxyanion hole formation. The position of the cutinase Ser42 side chain is structurally conserved in Rhizomucor miehei lipase with Ser82 O gamma, in Rhizopus delemar lipase with Thr83 O gamma 1, and in Candida antartica B lipase with Thr40 O gamma 1. To evaluate the increase in the tetrahedral intermediate stability provided by Ser42 O gamma, we mutated Ser42 into Ala. Furthermore, since the proper orientation of Ser42 O gamma is directed by Asn84, we mutated Asn84 into Ala, Leu, Asp, and Trp, respectively, to investigate the contribution of this indirect interaction to the stabilization of the oxyanion hole. The S42A mutation resulted in a drastic decrease in the activity (450-fold) without significantly perturbing the three-dimensional structure. The N84A and N84L mutations had milder kinetic effects and did not disrupt the structure of the active site, whereas the N84W and N84D mutations abolished the enzymatic activity due to drastic steric and electrostatic effects, respectively.

  14. High-Performance Electron Acceptor with Thienyl Side Chains for Organic Photovoltaics.

    PubMed

    Lin, Yuze; Zhao, Fuwen; He, Qiao; Huo, Lijun; Wu, Yang; Parker, Timothy C; Ma, Wei; Sun, Yanming; Wang, Chunru; Zhu, Daoben; Heeger, Alan J; Marder, Seth R; Zhan, Xiaowei

    2016-04-13

    We develop an efficient fused-ring electron acceptor (ITIC-Th) based on indacenodithieno[3,2-b]thiophene core and thienyl side-chains for organic solar cells (OSCs). Relative to its counterpart with phenyl side-chains (ITIC), ITIC-Th shows lower energy levels (ITIC-Th: HOMO = -5.66 eV, LUMO = -3.93 eV; ITIC: HOMO = -5.48 eV, LUMO = -3.83 eV) due to the σ-inductive effect of thienyl side-chains, which can match with high-performance narrow-band-gap polymer donors and wide-band-gap polymer donors. ITIC-Th has higher electron mobility (6.1 × 10(-4) cm(2) V(-1) s(-1)) than ITIC (2.6 × 10(-4) cm(2) V(-1) s(-1)) due to enhanced intermolecular interaction induced by sulfur-sulfur interaction. We fabricate OSCs by blending ITIC-Th acceptor with two different low-band-gap and wide-band-gap polymer donors. In one case, a power conversion efficiency of 9.6% was observed, which rivals some of the highest efficiencies for single junction OSCs based on fullerene acceptors.

  15. Entropy and enthalpy of interaction between amino acid side chains in nanopores.

    PubMed

    Vaitheeswaran, S; Thirumalai, D

    2014-12-14

    Understanding the stabilities of proteins in nanopores requires a quantitative description of confinement induced interactions between amino acid side chains. We use molecular dynamics simulations to study the nature of interactions between the side chain pairs ALA-PHE, SER-ASN, and LYS-GLU in bulk water and in water-filled nanopores. The temperature dependence of the bulk solvent potentials of mean force and the interaction free energies in cylindrical and spherical nanopores is used to identify the corresponding entropic and enthalpic components. The entropically stabilized hydrophobic interaction between ALA and PHE in bulk water is enthalpically dominated upon confinement depending on the relative orientations between the side chains. In the case of SER-ASN, hydrogen bonded configurations that are similar in bulk water are thermodynamically distinct in a cylindrical pore, thus making rotamer distributions different from those in the bulk. Remarkably, salt bridge formation between LYS-GLU is stabilized by entropy in contrast to the bulk. Implications of our findings for confinement-induced alterations in protein stability are briefly outlined.

  16. Controlling the mode of operation of organic transistors through side-chain engineering

    PubMed Central

    Giovannitti, Alexander; Sbircea, Dan-Tiberiu; Inal, Sahika; Nielsen, Christian B.; Bandiello, Enrico; Hanifi, David A.; Sessolo, Michele; Malliaras, George G.; McCulloch, Iain; Rivnay, Jonathan

    2016-01-01

    Electrolyte-gated organic transistors offer low bias operation facilitated by direct contact of the transistor channel with an electrolyte. Their operation mode is generally defined by the dimensionality of charge transport, where a field-effect transistor allows for electrostatic charge accumulation at the electrolyte/semiconductor interface, whereas an organic electrochemical transistor (OECT) facilitates penetration of ions into the bulk of the channel, considered a slow process, leading to volumetric doping and electronic transport. Conducting polymer OECTs allow for fast switching and high currents through incorporation of excess, hygroscopic ionic phases, but operate in depletion mode. Here, we show that the use of glycolated side chains on a thiophene backbone can result in accumulation mode OECTs with high currents, transconductance, and sharp subthreshold switching, while maintaining fast switching speeds. Compared with alkylated analogs of the same backbone, the triethylene glycol side chains shift the mode of operation of aqueous electrolyte-gated transistors from interfacial to bulk doping/transport and show complete and reversible electrochromism and high volumetric capacitance at low operating biases. We propose that the glycol side chains facilitate hydration and ion penetration, without compromising electronic mobility, and suggest that this synthetic approach can be used to guide the design of organic mixed conductors. PMID:27790983

  17. The dead-end elimination theorem and its use in protein side-chain positioning

    NASA Astrophysics Data System (ADS)

    Desmet, Johan; Maeyer, Marc De; Hazes, Bart; Lasters, Ignace

    1992-04-01

    THE prediction of a protein's tertiary structure is still a considerable problem because the huge amount of possible conformational space1 makes it computationally difficult. With regard to side-chain modelling, a solution has been attempted by the grouping of side-chain conformations into representative sets of rotamers2-5. Nonetheless, an exhaustive combinatorial search is still limited to carefully identified packing units5,6containing a limited number of residues. For larger systems other strategies had to be develop-ped, such as the Monte Carlo Procedure6,7 and the genetic algorithm and clustering approach8. Here we present a theorem, referred to as the 'dead-end elimination' theorem, which imposes a suitable condition to identify rotamers that cannot be members of the global minimum energy conformation. Application of this theorem effectively controls the computational explosion of the rotamer combinatorial problem, thereby allowing the determination of the global minimum energy conformation of a large collection of side chains.

  18. Pectic arabinan side chains are essential for pollen cell wall integrity during pollen development.

    PubMed

    Cankar, Katarina; Kortstee, Anne; Toonen, Marcel A J; Wolters-Arts, Mieke; Houbein, Rudolf; Mariani, Celestina; Ulvskov, Peter; Jorgensen, Bodil; Schols, Henk A; Visser, Richard G F; Trindade, Luisa M

    2014-05-01

    Pectin is a complex polysaccharide and an integral part of the primary plant cell wall and middle lamella, contributing to cell wall mechanical strength and cell adhesion. To understand the structure-function relationships of pectin in the cell wall, a set of transgenic potato lines with altered pectin composition was analysed. The expression of genes encoding enzymes involved in pectin acetylation, degradation of the rhamnogalacturonan backbone and type and length of neutral side chains, arabinan and galactan in particular, has been altered. Upon crossing of different transgenic lines, some transgenes were not transmitted to the next generation when these lines were used as a pollen donor, suggesting male sterility. Viability of mature pollen was severely decreased in potato lines with reduced pectic arabinan, but not in lines with altered galactan side chains. Anthers and pollen of different developmental stages were microscopically examined to study the phenotype in more detail. Scanning electron microscopy of flowers showed collapsed pollen grains in mature anthers and in earlier stages cytoplasmic protrusions at the site of the of kin pore, eventually leading to bursting of the pollen grain and leaking of the cytoplasm. This phenomenon is only observed after the microspores are released and the tapetum starts to degenerate. Timing of the phenotype indicates a role for pectic arabinan side chains during remodelling of the cell wall when the pollen grain is maturing and dehydrating.

  19. Rhamnoarabinosyl and rhamnoarabinoarabinosyl side chains as structural features of coffee arabinogalactans.

    PubMed

    Nunes, Fernando M; Reis, Ana; Silva, Artur M S; Domingues, M Rosário M; Coimbra, Manuel A

    2008-05-01

    The hot water soluble green coffee arabinogalactans, representing nearly 7% of total coffee bean arabinogalactans, were characterized by (1)H and (13)C NMR and, after partial acid hydrolysis, by ESI-MS/MS. Data obtained showed that these are highly branched type II arabinogalactans covalently linked to proteins (AGP), with a protein moiety containing 10% of 4-hydroxyproline residues. They possess a beta-(1-->3)-Galp/beta-(1-->3,6)-Galp ratio of 0.80, with a sugars composition of Rha:Ara:Gal of 0.25:1.0:1.5, and containing 2mol% of glucuronic acid residues. Beyond the occurrence of single alpha-L-Araf residues and [alpha-L-Araf-(1-->5)-alpha-L-Araf-(1-->] disaccharide residues as side chains, these AGPs contain unusual side chains at O-3 position of the beta-(1-->6)-linked galactopyranosyl residues composed by [alpha-L-Rhap-(1-->5)-alpha-L-Araf-(1-->] and [alpha-L-Rhap-(1-->5)-alpha-L-Araf-(1-->5)-alpha-L-Araf-(1-->] oligosaccharides. Rhamnoarabinosyl and rhamnoarabinoarabinosyl side chains are reported for the first time as structural features of plant arabinogalactan-proteins.

  20. Predicting side-chain conformations of methionine using a hard-sphere model with stereochemical constraints

    NASA Astrophysics Data System (ADS)

    Virrueta, A.; Gaines, J.; O'Hern, C. S.; Regan, L.

    2015-03-01

    Current research in the O'Hern and Regan laboratories focuses on the development of hard-sphere models with stereochemical constraints for protein structure prediction as an alternative to molecular dynamics methods that utilize knowledge-based corrections in their force-fields. Beginning with simple hydrophobic dipeptides like valine, leucine, and isoleucine, we have shown that our model is able to reproduce the side-chain dihedral angle distributions derived from sets of high-resolution protein crystal structures. However, methionine remains an exception - our model yields a chi-3 side-chain dihedral angle distribution that is relatively uniform from 60 to 300 degrees, while the observed distribution displays peaks at 60, 180, and 300 degrees. Our goal is to resolve this discrepancy by considering clashes with neighboring residues, and averaging the reduced distribution of allowable methionine structures taken from a set of crystallized proteins. We will also re-evaluate the electron density maps from which these protein structures are derived to ensure that the methionines and their local environments are correctly modeled. This work will ultimately serve as a tool for computing side-chain entropy and protein stability. A. V. is supported by an NSF Graduate Research Fellowship and a Ford Foundation Fellowship. J. G. is supported by NIH training Grant NIH-5T15LM007056-28.

  1. Entropy and enthalpy of interaction between amino acid side chains in nanopores

    SciTech Connect

    Vaitheeswaran, S.; Thirumalai, D.

    2014-12-14

    Understanding the stabilities of proteins in nanopores requires a quantitative description of confinement induced interactions between amino acid side chains. We use molecular dynamics simulations to study the nature of interactions between the side chain pairs ALA-PHE, SER-ASN, and LYS-GLU in bulk water and in water-filled nanopores. The temperature dependence of the bulk solvent potentials of mean force and the interaction free energies in cylindrical and spherical nanopores is used to identify the corresponding entropic and enthalpic components. The entropically stabilized hydrophobic interaction between ALA and PHE in bulk water is enthalpically dominated upon confinement depending on the relative orientations between the side chains. In the case of SER-ASN, hydrogen bonded configurations that are similar in bulk water are thermodynamically distinct in a cylindrical pore, thus making rotamer distributions different from those in the bulk. Remarkably, salt bridge formation between LYS-GLU is stabilized by entropy in contrast to the bulk. Implications of our findings for confinement-induced alterations in protein stability are briefly outlined.

  2. Improved side-chain torsion potentials for the Amber ff99SB protein force field.

    PubMed

    Lindorff-Larsen, Kresten; Piana, Stefano; Palmo, Kim; Maragakis, Paul; Klepeis, John L; Dror, Ron O; Shaw, David E

    2010-06-01

    Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these force fields. Recent modifications to the Amber and CHARMM protein force fields, for example, have improved the backbone torsion potentials, remedying deficiencies in earlier versions. Here, we further advance simulation accuracy by improving the amino acid side-chain torsion potentials of the Amber ff99SB force field. First, we used simulations of model alpha-helical systems to identify the four residue types whose rotamer distribution differed the most from expectations based on Protein Data Bank statistics. Second, we optimized the side-chain torsion potentials of these residues to match new, high-level quantum-mechanical calculations. Finally, we used microsecond-timescale MD simulations in explicit solvent to validate the resulting force field against a large set of experimental NMR measurements that directly probe side-chain conformations. The new force field, which we have termed Amber ff99SB-ILDN, exhibits considerably better agreement with the NMR data.

  3. A new model for ligand release. Role of side chain in gating the enediyne antibiotic.

    PubMed

    Hariharan, Parameswaran; Liang, Wenchuan; Chou, Shan-Ho; Chin, Der-Hang

    2006-06-01

    Antitumor antibiotic chromoproteins such as neocarzinostatin involve a labile toxin that is tightly bound by a protective protein with very high affinity but must also be freed to exert its function. Contrary to the prevalent concept of ligand release, we established that toxin release from neocarzinostatin requires no major backbone conformational changes. We report, herein, that subtle changes in the side chains of specific amino acid residues are adequate to gate the release of chromophore. A recombinant wild type aponeocarzinostatin and its variants mutated around the opening of the chromophore binding cleft are employed to identify specific side chains likely to affect chromophore release. Preliminary, biophysical characterization of mutant apoproteins by circular dichroism and thermal denaturation indicate that the fundamental structural characteristics of wild type protein are conserved in these mutants. The chromophore reconstitution studies further show that all mutants are able to bind chromophore efficiently with similar complex structures. NMR studies on 15N-labeled mutants also suggest the intactness of binding pocket structure. Kinetic studies of chromophore release monitored by time course fluorescence and quantitative high pressure liquid chromatography analyses show that the ligand release rate is significantly enhanced only in Phe78 mutants. The extent of DNA cleavage in vitro corresponds well to the rate of chromophore release. The results provide the first clear-cut indication of how toxin release can be controlled by a specific side chain of a carrier protein.

  4. Nascent Peptide Side-chains Induce Rearrangements in Distinct Locations of the Ribosomal Tunnel

    PubMed Central

    Lu, Jianli; Hua, Zhengmao; Kobertz, William R.; Deutsch, Carol

    2011-01-01

    Although we have numerous structures of ribosomes, none disclose side-chain rearrangements of the nascent peptide during chain elongation. This study reports for the first time that rearrangement of the peptide and/or tunnel occurs in distinct regions of the tunnel and is directed by the unique primary sequence of each nascent peptide. In the tunnel mid-region, the accessibility of an introduced cysteine to a series of novel hydrophilic maleimide reagents increases with increasing volume of the adjacent chain residue, a sensitivity not manifest at the constriction and exit port. This surprising result reveals molecular movements not yet resolvable from structural studies. These findings map solvent accessible volumes along the tunnel and provide novel insights critical to our understanding of allosteric communication within the ribosomal tunnel, translational arrest, chaperone interaction, folding, and rates of elongation. PMID:21663746

  5. Self-assembly of a series of random copolymers bearing amphiphilic side chains.

    PubMed

    Wu, Xu; Qiao, Yingjie; Yang, Hui; Wang, Jinben

    2010-09-15

    A novel series of comb-like random copolymers were prepared by polymerization of amphiphilic macromonomers, 2-(acrylamido)-octane sulfonic acid (AMC(8)S), 2-(acrylamido)-dodecane sulfonic acid (AMC(12)S), and 2-(acrylamido)-hexadecane sulfonic acid (AMC(16)S), with 2-(acrylamido)-2-methylpropanesulfonic acid (AMPS) respectively. The synthesis of the polymers with the same contents of amphiphilic units as side chains, but different chain length, enabled us to study the chain length dependence of their association in salt solution. Steady-state fluorescence measurements with pyrene as a polarity probe, quasielastic light scattering techniques (QELS) and transmission electron micrograph (TEM) were employed to investigate the associative properties of the system. The above investigations showed that all kinds of side chains begin to assemble at certain polymer concentrations and the critical aggregation concentration (CAC) decrease dramatically with the increase in the length and content of alkyl. An interesting phenomenon is that the assembly tends more favorably to occur among different molecules rather than within single molecule when the number of carbon atoms in the alkyl groups or the polymer concentration increases, leading to the formation of larger multimolecular micelle-like aggregate. The aim of the present work is to establish the fundamental preconditions of intramolecular and intermolecular association fashions for the polymers, which is useful for the exploitation of functional groups and contributes to the development of amphiphilic random polymers. PMID:20576273

  6. Molecular structure and rheological properties of short-side-chain heavily glycosylated porcine stomach mucin.

    PubMed

    Yakubov, Gleb E; Papagiannopoulos, Aristeidis; Rat, Elodie; Easton, Richard L; Waigh, Thomas A

    2007-11-01

    The current accepted model for high-molecular-weight gastric mucins of the MUC family is that they adopt a polydisperse coil conformation in bulk solutions. We develop this model using well-characterized highly purified porcine gastric mucin Orthana that is genetically close to the human MUC6 type. It has short side chains and low levels of sialic acid residues and includes minute amounts of cysteine residues that, if abundant, can be responsible for the self-polymerization of mucin. We have established that the mucin structure in bulk solutions corresponds to a daisy-chain random coil. Dynamic light scattering experiments probe the internal dynamics of globular subunits (individual daisies) at the approximately 9 nm length scale, whereas viscosity and light scattering measurements indicate that the size of the whole mucin chains is much larger, approximately 50 nm. The bulk viscosity (eta) scales with mucin concentration (c) in a manner similar to that found for short-side-chain synthetic comb polyelectrolytes and is characterized by a transition between semidilute (eta approximately c1/2) and entangled (eta approximately c3/2) regimes. PMID:17910495

  7. Actinobacterial Acyl Coenzyme A Synthetases Involved in Steroid Side-Chain Catabolism

    PubMed Central

    Casabon, Israël; Swain, Kendra; Crowe, Adam M.

    2014-01-01

    Bacterial steroid catabolism is an important component of the global carbon cycle and has applications in drug synthesis. Pathways for this catabolism involve multiple acyl coenzyme A (CoA) synthetases, which activate alkanoate substituents for β-oxidation. The functions of these synthetases are poorly understood. We enzymatically characterized four distinct acyl-CoA synthetases from the cholate catabolic pathway of Rhodococcus jostii RHA1 and the cholesterol catabolic pathway of Mycobacterium tuberculosis. Phylogenetic analysis of 70 acyl-CoA synthetases predicted to be involved in steroid metabolism revealed that the characterized synthetases each represent an orthologous class with a distinct function in steroid side-chain degradation. The synthetases were specific for the length of alkanoate substituent. FadD19 from M. tuberculosis H37Rv (FadD19Mtb) transformed 3-oxo-4-cholesten-26-oate (kcat/Km = 0.33 × 105 ± 0.03 × 105 M−1 s−1) and represents orthologs that activate the C8 side chain of cholesterol. Both CasGRHA1 and FadD17Mtb are steroid-24-oyl-CoA synthetases. CasG and its orthologs activate the C5 side chain of cholate, while FadD17 and its orthologs appear to activate the C5 side chain of one or more cholesterol metabolites. CasIRHA1 is a steroid-22-oyl-CoA synthetase, representing orthologs that activate metabolites with a C3 side chain, which accumulate during cholate catabolism. CasI had similar apparent specificities for substrates with intact or extensively degraded steroid nuclei, exemplified by 3-oxo-23,24-bisnorchol-4-en-22-oate and 1β(2′-propanoate)-3aα-H-4α(3″-propanoate)-7aβ-methylhexahydro-5-indanone (kcat/Km = 2.4 × 105 ± 0.1 × 105 M−1 s−1 and 3.2 × 105 ± 0.3 × 105 M−1 s−1, respectively). Acyl-CoA synthetase classes involved in cholate catabolism were found in both Actinobacteria and Proteobacteria. Overall, this study provides insight into the physiological roles of acyl-CoA synthetases in steroid catabolism and

  8. Contribution of a tyrosine side chain to ribonuclease A catalysis and stability.

    PubMed Central

    Eberhardt, E. S.; Wittmayer, P. K.; Templer, B. M.; Raines, R. T.

    1996-01-01

    An intricate architecture of covalent bonds and noncovalent interactions appear to position the side chain of Lys 41 properly within the active site of bovine pancreatic ribonuclease A (RNase A). One of these interactions arises from Tyr 97, which is conserved in all 41 RNase A homologues of known sequence. Tyr 97 has a solvent-inaccessible side chain that donates a hydrogen bond to the main-chain oxygen of Lys 41. Here, the role of Tyr 97 was examined by replacing Tyr 97 with a phenylalanine, alanine, or glycine residue. All three mutant proteins have diminished catalytic activity, with the value of Kcat being perturbed more significantly than that of Km. The free energies with which Y97F, Y97A, and Y97G RNase A bind to the rate-limiting transition state during the cleavage of poly(cytidylic acid) are diminished by 0.74, 3.3, and 3.8 kcal/mol, respectively. These results show that even though Tyr 97 is remote from the active site, its side chain contributes to catalysis. The role of Tyr 97 in the thermal stability of RNase A is large. The conformational free energies of native Y97F, Y97A, and Y97G RNase A are decreased by 3.54, 12.0, and 11.7 kcal/mol, respectively. The unusually large decrease in stability caused by the Tyr-->Phe mutation could result from a decrease in the barrier to isomerization of the Lys 41-Pro 42 peptide bond. PMID:8844858

  9. Effect of side-chain asymmetry on the intermolecular structure and order-disorder transition in alkyl-substituted polyfluorenes

    NASA Astrophysics Data System (ADS)

    Knaapila, M.; Stepanyan, R.; Torkkeli, M.; Haase, D.; Fröhlich, N.; Helfer, A.; Forster, M.; Scherf, U.

    2016-04-01

    We study relations among the side-chain asymmetry, structure, and order-disorder transition (ODT) in hairy-rod-type poly(9,9-dihexylfluorene) (PF6) with two identical side chains and atactic poly(9-octyl-9-methyl-fluorene) (PF1-8) with two different side chains per repeat. PF6 and PF1-8 organize into alternating side-chain and backbone layers that transform into an isotropic phase at TODT(PF 6 ) and TbiODT(PF 1 -8 ) . We interpret polymers in terms of monodisperse and bidisperse brushes and predict scenarios TODTside-chain length above or below the average grafting distance). Calorimetry and x-ray scattering indicate the condition TODT(PF 6 ) ˜TbiODT(PF 1 -8 ) following the low grafting prediction. PF6 side chains coming from the alternating backbone layers appear as two separate layers with thickness H (PF 6 ) , whereas PF1-8 side chains appear as an indistinguishable bilayer with a half thickness Hbilayer(PF 1 -8 ) /2 ≈H (PF 6 ) . The low grafting density region is structurally possible but not certain for PF6 and confirmed for PF1-8.

  10. Dependence of crystallite formation and preferential backbone orientations on the side chain pattern in PBDTTPD polymers.

    PubMed

    El Labban, Abdulrahman; Warnan, Julien; Cabanetos, Clément; Ratel, Olivier; Tassone, Christopher; Toney, Michael F; Beaujuge, Pierre M

    2014-11-26

    Alkyl substituents appended to the π-conjugated main chain account for the solution-processability and film-forming properties of most π-conjugated polymers for organic electronic device applications, including field-effect transistors (FETs) and bulk-heterojunction (BHJ) solar cells. Beyond film-forming properties, recent work has emphasized the determining role that side-chain substituents play on polymer self-assembly and thin-film nanostructural order, and, in turn, on device performance. However, the factors that determine polymer crystallite orientation in thin-films, implying preferential backbone orientation relative to the device substrate, are a matter of some debate, and these structural changes remain difficult to anticipate. In this report, we show how systematic changes in the side-chain pattern of poly(benzo[1,2-b:4,5-b']dithiophene-alt-thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymers can (i) influence the propensity of the polymer to order in the π-stacking direction, and (ii) direct the preferential orientation of the polymer crystallites in thin films (e.g., "face-on" vs "edge-on"). Oriented crystallites, specifically crystallites that are well-ordered in the π-stacking direction, are believed to be a key contributor to improved thin-film device performance in both FETs and BHJ solar cells. PMID:25347287

  11. Nanophase separation and hindered glass transition in side-chain polymers.

    PubMed

    Beiner, Mario; Huth, Heiko

    2003-09-01

    Nanophase separation on length scales of 1-5 nanometres has been reported previously for small-molecule liquids, metallic glasses and also for several semicrystalline, liquid-crystalline and amorphous polymers. Here we show that nanophase separation of incompatible main and side-chain parts is a general phenomenon in amorphous side-chain polymers with long alkyl groups. We conclude from X-ray scattering and relaxation spectroscopy data for higher poly(n-alkyl acrylates) (PnAA) and poly(n-alkyl methacrylates) (PnAMA) that alkyl groups of different monomeric units aggregate in the melt and form self-assembled alkyl nanodomains with a typical size of 0.5-2 nm. A comparison with data for other polymer series having alkyl groups reveals that important structural and dynamic aspects are main-chain independent. A polyethylene-like glass transition within the alkyl nanodomains is observed and discussed in the context of a hindered glass transition in self-assembled confinements. This is an interesting link between central questions in glass-transition research and structural aspects in nanophase-separated materials.

  12. Microscopic theory of light-induced deformation in amorphous side-chain azobenzene polymers.

    PubMed

    Toshchevikov, V; Saphiannikova, M; Heinrich, G

    2009-04-16

    We propose a microscopic theory of light-induced deformation of side-chain azobenzene polymers taking into account the internal structure of polymer chains. Our theory is based on the fact that interaction of chromophores with the polarized light leads to the orientation anisotropy of azobenzene macromolecules which is accompanied by the appearance of mechanical stress. It is the first microscopic theory which provides the value of the light-induced stress larger than the yield stress. This result explains a possibility for the inscription of surface relief gratings in glassy side-chain azobenzene polymers. For some chemical architectures, elongation of a sample demonstrates a nonmonotonic behavior with the light intensity and can change its sign (a stretched sample starts to be uniaxially compressed), in agreement with experiments. Using a viscoplastic approach, we show that the irreversible strain of a sample, which remains after the light is switched off, decreases with increasing temperature and can disappear at certain temperature below the glass transition temperature. This theoretical prediction is also confirmed by recent experiments.

  13. Effect of side chain length on intrahelical interactions between carboxylate- and guanidinium-containing amino acids.

    PubMed

    Kuo, Hsiou-Ting; Yang, Po-An; Wang, Wei-Ren; Hsu, Hao-Chun; Wu, Cheng-Hsun; Ting, Yu-Te; Weng, Ming-Huei; Kuo, Li-Hung; Cheng, Richard P

    2014-08-01

    The charge-containing hydrophilic functionalities of encoded charged amino acids are linked to the backbone via different numbers of hydrophobic methylenes, despite the apparent electrostatic nature of protein ion pairing interactions. To investigate the effect of side chain length of guanidinium- and carboxylate-containing residues on ion pairing interactions, α-helical peptides containing Zbb-Xaa (i, i + 3), (i, i + 4) and (i, i + 5) (Zbb = carboxylate-containing residues Aad, Glu, Asp in decreasing length; Xaa = guanidinium residues Agh, Arg, Agb, Agp in decreasing length) sequence patterns were studied by circular dichroism spectroscopy (CD). The helicity of Aad- and Glu-containing peptides was similar and mostly pH independent, whereas the helicity of Asp-containing peptides was mostly pH dependent. Furthermore, the Arg-containing peptides consistently exhibited higher helicity compared to the corresponding Agp-, Agb-, and Agh-containing peptides. Side chain conformational analysis by molecular mechanics calculations showed that the Zbb-Xaa (i, i + 3) and (i, i + 4) interactions mainly involved the χ 1 dihedral combinations (g+, g+) and (g-, g+), respectively. These low energy conformations were also observed in intrahelical Asp-Arg and Glu-Arg salt bridges of natural proteins. Accordingly, Asp and Glu provides variation in helix characteristics associated with Arg, but Aad does not provide features beyond those already delivered by Glu. Importantly, nature may have chosen the side chain length of Arg to support helical conformations through inherent high helix propensity coupled with stabilizing intrahelical ion pairing interactions with the carboxylate-containing residues.

  14. Side Chain Degradable Cationic-Amphiphilic Polymers with Tunable Hydrophobicity Show in Vivo Activity.

    PubMed

    Uppu, Divakara S S M; Samaddar, Sandip; Hoque, Jiaul; Konai, Mohini M; Krishnamoorthy, Paramanandham; Shome, Bibek R; Haldar, Jayanta

    2016-09-12

    Cationic-amphiphilic antibacterial polymers with optimal amphiphilicity generally target the bacterial membranes instead of mammalian membranes. To date, this balance has been achieved by varying the cationic charge or side chain hydrophobicity in a variety of cationic-amphiphilic polymers. Optimal hydrophobicity of cationic-amphiphilic polymers has been considered as the governing factor for potent antibacterial activity yet minimal mammalian cell toxicity. However, the concomitant role of hydrogen bonding and hydrophobicity with constant cationic charge in the interactions of antibacterial polymers with bacterial membranes is not understood. Also, degradable polymers that result in nontoxic degradation byproducts offer promise as safe antibacterial agents. Here we show that amide- and ester (degradable)-bearing cationic-amphiphilic polymers with tunable side chain hydrophobicity can modulate antibacterial activity and cytotoxicity. Our results suggest that an amide polymer can be a potent antibacterial agent with lower hydrophobicity whereas the corresponding ester polymer needs a relatively higher hydrophobicity to be as effective as its amide counterpart. Our studies reveal that at higher hydrophobicities both amide and ester polymers have similar profiles of membrane-active antibacterial activity and mammalian cell toxicity. On the contrary, at lower hydrophobicities, amide and ester polymers are less cytotoxic, but the former have potent antibacterial and membrane activity compared to the latter. Incorporation of amide and ester moieties made these polymers side chain degradable, with amide polymers being more stable than the ester polymers. Further, the polymers are less toxic, and their degradation byproducts are nontoxic to mice. More importantly, the optimized amide polymer reduces the bacterial burden of burn wound infections in mice models. Our design introduces a new strategy of interplay between the hydrophobic and hydrogen bonding interactions

  15. Revealing the Supramolecular Nature of Side-Chain Terpyridine-Functionalized Polymer Networks

    PubMed Central

    Brassinne, Jérémy; Jochum, Florian D.; Fustin, Charles-André; Gohy, Jean-François

    2015-01-01

    Nowadays, finely controlling the mechanical properties of polymeric materials is possible by incorporating supramolecular motifs into their architecture. In this context, the synthesis of a side-chain terpyridine-functionalized poly(2-(dimethylamino)ethyl methacrylate) is reported via reversible addition-fragmentation chain transfer polymerization. By addition of transition metal ions, concentrated aqueous solutions of this polymer turn into metallo-supramolecular hydrogels whose dynamic mechanical properties are investigated by rotational rheometry. Hence, the possibility for the material to relax mechanical constrains via dissociation of transient cross-links is brought into light. In addition, the complex phenomena occurring under large oscillatory shear are interpreted in the context of transient networks. PMID:25569082

  16. Theoretical Studies of Interactions between O-Phosphorylated and Standard Amino-Acid Side-Chain Models in Water

    PubMed Central

    Wiśniewska, Marta; Sobolewski, Emil; Ołdziej, Stanisław; Liwo, Adam; Scheraga, Harold A.; Makowski, Mariusz

    2015-01-01

    Phosphorylation is a common post-translational modification of the amino-acid side chains (serine, tyrosine, and threonine) that contain hydroxyl groups. The transfer of the negatively charged phosphate group from an ATP molecule to such amino-acid side chains leads to changes in the local conformations of proteins and the pattern of interactions with other amino-acid side-chains. A convenient characteristic of the side chain–side chain interactions in the context of an aqueous environment is the potential of mean force (PMF) in water. A series of umbrella-sampling molecular dynamic (MD) simulations with the AMBER force field were carried out for pairs of O-phosphorylated serine (pSer), threonine (pThr), and tyrosine, (pTyr) with natural amino acids in a TIP3P water model as a solvent at 298 K. The weighted-histogram analysis method was used to calculate the four-dimensional potentials of mean force. The results demonstrate that the positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the relative orientation depend on the character of the interacting pairs. More distinct minima are observed for oppositely charged pairs such as, e.g., O-phosphorylated side-chains and positively charged ones, such as the side-chains of lysine and arginine. PMID:26100791

  17. Observation of shear-induced nematic-isotropic transition in side-chain liquid crystal polymers

    NASA Astrophysics Data System (ADS)

    Pujolle-Robic, Caroline; Noirez, Laurence

    2001-01-01

    Flow-induced phase transitions are a fundamental (but poorly understood) property of non-equilibrium systems, and are also of practical importance for tuning the processing conditions for plastics, petroleum products, and other related materials. Recognition that polymers may exhibit liquid crystal properties has led to the discovery of the first tailored side-chain liquid crystal polymers (SCLCPs), which are formed by inserting a spacer between the main polymer chain and the lateral mesogen liquid-crystalline graftings. Subsequent research has sought to understand the nature of the coupling between the main polymer chain and the mesogens, with a view to obtaining better control of the properties of these tailored structures. We show here that the parallel or perpendicular orientation of the mesogens with respect to the main chain can be reversed by the application of an external field produced by a shear flow, demonstrating the existence of an isotropic nematic phase transition in SCLCPs. Such a transition, which was theoretically predicted for low-molecular-weight liquid crystals but never observed, is shown to be a general property of SCLCPs too. We expect that these SCLCPs will prove to be good candidate systems for the experimental study of these non-equilibrium phenomena.

  18. Backbone and side-chain resonance assignments of the membrane localization domain from Pasteurella multocida toxin.

    PubMed

    Brothers, Michael C; Geissler, Brett; Hisao, Grant S; Satchell, Karla J F; Wilson, Brenda A; Rienstra, Chad M

    2014-04-01

    (1)H, (13)C, and (15)N chemical shift assignments are presented for the isolated four-helical bundle membrane localization domain (MLD) from Pasteurella multocida toxin (PMT) in its solution state. We have assigned 99% of all backbone and side-chain carbon atoms, including 99% of all backbone residues excluding proline amide nitrogens. Secondary chemical shift analysis using TALOS+ demonstrates four helices, which align with those observed within the MLD in the crystal structure of the C-terminus of PMT (PDB 2EBF) and confirm the use of the available crystal structures as templates for the isolated MLDs.

  19. Side chain packing below the fusion peptide strongly modulates triggering of the Hendra virus F protein.

    PubMed

    Smith, Everett Clinton; Dutch, Rebecca Ellis

    2010-10-01

    Triggering of the Hendra virus fusion (F) protein is required to initiate the conformational changes which drive membrane fusion, but the factors which control triggering remain poorly understood. Mutation of a histidine predicted to lie near the fusion peptide to alanine greatly reduced fusion despite wild-type cell surface expression levels, while asparagine substitution resulted in a moderate restoration in fusion levels. Slowed kinetics of six-helix bundle formation, as judged by sensitivity to heptad repeat B-derived peptides, was observed for all H372 mutants. These data suggest that side chain packing beneath the fusion peptide is an important regulator of Hendra virus F triggering.

  20. Third-order nonlinear optical characterization of side-chain copolymers

    NASA Astrophysics Data System (ADS)

    Norwood, Robert A.; Sounik, James R.; Popolo, J.; Holcomb, Douglas P.

    1991-12-01

    Third order nonlinear optical properties of side-chain methacrylate copolymers incorporating 4-amino-4'-nitrostilbene, 4-oxy-4'nitrostilbene, and functionalized silicon phthalocyanine chromophores are measured by picosecond degenerate four wave mixing at 598 nm. The nonresonant stilbene system exhibits a pulse limited ultrafast response, while the resonant phthalocyanine system has a large excited state nonlinearity. Comparison of silicon phthalocyanine copolymers with solubilized guest/host systems dispersed in polymethylmethacrylate illustrate the importance of aggregation and phthalocyanine ring interaction in determining the linear optical properties and the magnitude and speed of the nonlinear optical response.

  1. Cyclic side-chain phenylazo naphthalene polymers: enhanced fluorescence emission and surface relief grating formation.

    PubMed

    Zhang, Hao; Zhou, Nianchen; Zhu, Xing; Chen, Xinrong; Zhang, Zhengbiao; Zhang, Wei; Zhu, Jian; Hu, Zhijun; Zhu, Xiulin

    2012-11-14

    Well-defined cyclic-polymers (cyclic-PAzoMMAs), bearing side-chain phenylazo naphthalene chromophore, were successfully synthesized by the combination of atom transfer radical polymerization (ATRP) and copper(I)-catalyzed azide/alkyne cycloaddition "click" reaction, as verified by GPC, (1) H NMR, FTIR, and MALDI-TOF mass spectrometry. The cyclic-PAzoMMA showed higher glass transition temperatures than the linear-PAzoMMA with the same molecular weight. Interestingly, the cyclic-PAzoMMA exhibited deeper modulation depth (M.D.) induced by SRG, larger value of the photoinduced birefringence, increased fluorescence emission, and longer fluorescence lifetime in comparison with its linear counterpart. PMID:22965741

  2. Recent advances in metathesis-derived polymers containing transition metals in the side chain

    PubMed Central

    Demonceau, Albert; Fischer, Helmut

    2015-01-01

    Summary This account critically surveys the field of side-chain transition metal-containing polymers as prepared by controlled living ring-opening metathesis polymerization (ROMP) of the respective metal-incorporating monomers. Ferrocene- and other metallocene-modified polymers, macromolecules including metal-carbonyl complexes, polymers tethering early or late transition metal complexes, etc. are herein discussed. Recent advances in the design and syntheses reported mainly during the last three years are highlighted, with special emphasis on new trends for superior applications of these hybrid materials. PMID:26877797

  3. Side chain engineering of poly-thiophene and its impact on crystalline silicon based hybrid solar cells

    SciTech Connect

    Zellmeier, M.; Rappich, J.; Nickel, N. H.; Klaus, M.; Genzel, Ch.; Janietz, S.; Frisch, J.; Koch, N.

    2015-11-16

    The influence of ether groups in the side chain of spin coated regioregular polythiophene derivatives on the polymer layer formation and the hybrid solar cell properties was investigated using electrical, optical, and X-ray diffraction experiments. The polymer layers are of high crystallinity but the polymer with 3 ether groups in the side chain (P3TOT) did not show any vibrational fine structure in the UV-Vis spectrum. The presence of ether groups in the side chains leads to better adhesion resulting in thinner and more homogeneous polymer layers. This, in turn, enhances the electronic properties of the planar c-Si/poly-thiophene hybrid solar cell. We find that the power conversion efficiency increases with the number of ether groups in the side chains, and a maximum power conversion efficiency of η = 9.6% is achieved even in simple planar structures.

  4. Side chain engineering of poly-thiophene and its impact on crystalline silicon based hybrid solar cells

    NASA Astrophysics Data System (ADS)

    Zellmeier, M.; Rappich, J.; Klaus, M.; Genzel, Ch.; Janietz, S.; Frisch, J.; Koch, N.; Nickel, N. H.

    2015-11-01

    The influence of ether groups in the side chain of spin coated regioregular polythiophene derivatives on the polymer layer formation and the hybrid solar cell properties was investigated using electrical, optical, and X-ray diffraction experiments. The polymer layers are of high crystallinity but the polymer with 3 ether groups in the side chain (P3TOT) did not show any vibrational fine structure in the UV-Vis spectrum. The presence of ether groups in the side chains leads to better adhesion resulting in thinner and more homogeneous polymer layers. This, in turn, enhances the electronic properties of the planar c-Si/poly-thiophene hybrid solar cell. We find that the power conversion efficiency increases with the number of ether groups in the side chains, and a maximum power conversion efficiency of η = 9.6% is achieved even in simple planar structures.

  5. Evidence for in vitro binding of pectin side chains to cellulose.

    PubMed

    Zykwinska, Agata W; Ralet, Marie-Christine J; Garnier, Catherine D; Thibault, Jean-François J

    2005-09-01

    Pectins of varying structures were tested for their ability to interact with cellulose in comparison to the well-known adsorption of xyloglucan. Our results reveal that sugar beet (Beta vulgaris) and potato (Solanum tuberosum) pectins, which are rich in neutral sugar side chains, can bind in vitro to cellulose. The extent of binding varies with respect to the nature and structure of the side chains. Additionally, branched arabinans (Br-Arabinans) or debranched arabinans (Deb-Arabinans; isolated from sugar beet) and galactans (isolated from potato) were shown bind to cellulose microfibrils. The adsorption of Br-Arabinan and galactan was lower than that of Deb-Arabinan. The maximum adsorption affinity of Deb-Arabinan to cellulose was comparable to that of xyloglucan. The study of sugar beet and potato alkali-treated cell walls supports the hypothesis of pectin-cellulose interaction. Natural composites enriched in arabinans or galactans and cellulose were recovered. The binding of pectins to cellulose microfibrils may be of considerable significance in the modeling of primary cell walls of plants as well as in the process of cell wall assembly.

  6. Cyclic side-chain-linked opioid analogs utilizing cis- and trans-4-aminocyclohexyl-D-alanine.

    PubMed

    Piekielna, Justyna; Gentilucci, Luca; De Marco, Rossella; Perlikowska, Renata; Adamska, Anna; Olczak, Jacek; Mazur, Marzena; Artali, Roberto; Modranka, Jakub; Janecki, Tomasz; Tömböly, Csaba; Janecka, Anna

    2014-12-01

    Cyclization of linear sequences is a well recognized tool in opioid peptide chemistry for generating analogs with improved bioactivities. Cyclization can be achieved through various bridging bonds between peptide ends or side-chains. In our earlier paper we have reported the synthesis and biological activity of a cyclic peptide, Tyr-c[D-Lys-Phe-Phe-Asp]NH2 (1), which can be viewed as an analog of endomorphin-2 (EM-2, Tyr-Pro-Phe-Phe-NH2). Cyclization was achieved through an amide bond between side-chains of D-Lys and Asp residues. Here, to increase rigidity of the cyclic structure, we replaced d-Lys with cis- or trans-4-aminocyclohexyl-D-alanine (D-ACAla). Two sets of analogs incorporating either Tyr or Dmt (2',6'-dimethyltyrosine) residues in position 1 were synthesized. In the binding studies the analog incorporating Dmt and trans-D-ACAla showed high affinity for both, μ- and δ-opioid receptors (MOR and DOR, respectively) and moderate affinity for the κ-opioid receptor (KOR), while analog with Dmt and cis-D-ACAla was exceptionally MOR-selective. Conformational analyses by NMR and molecular docking studies have been performed to investigate the molecular structural features responsible for the noteworthy MOR selectivity.

  7. Side chain flexibility and the pore dimensions in the GABAA receptor.

    PubMed

    Rossokhin, Alexey V; Zhorov, Boris S

    2016-07-01

    Permeation of ions through open channels and their accessibility to pore-targeting drugs depend on the pore cross-sectional dimensions, which are known only for static X-ray and cryo-EM structures. Here, we have built homology models of the closed, open and desensitized α1β2γ2 GABAA receptor (GABAAR). The models are based, respectively, on the X-ray structure of α3 glycine receptor (α3 GlyR), cryo-EM structure of α1 GlyR and X-ray structure of β3 GABAAR. We employed Monte Carlo energy minimizations to explore how the pore lumen may increase due to repulsions of flexible side chains from a variable-diameter electroneutral atom (an expanding sphere) pulled through the pore. The expanding sphere computations predicted that the pore diameter averaged along the permeation pathway is larger by approximately 3 Å than that computed for the models with fixed sidechains. Our models predict three major pore constrictions located at the levels of -2', 9' and 20' residues. Residues around the -2' and 9' rings are known to form the desensitization and activation gates of GABAAR. Our computations predict that the 20' ring may also serve as GABAAR gate whose physiological role is unclear. The side chain flexibility of residues -2', 9' and 20' and hence the dimensions of the constrictions depend on the GABAAR functional state. PMID:27460059

  8. Enzyme directed formation of un-natural side-chains for covalent surface attachment of proteins.

    PubMed

    Cho, Hwayoung; Jaworski, Justyn

    2014-10-01

    The covalent immobilization of proteins onto surfaces is an essential aspect of several fields of research, including proteomics, sensing, heterogeneous biocatalysis, and more broadly biotechnology. Site-specific, covalent attachment of proteins has been achieved in recent years by the use of expanded genetic codes to produce proteins with controlled placement of un-natural amino acids bearing bio-orthogonal functional groups. Unfortunately, the complexity of developing such systems is impractical for most laboratories; hence, a less complicated approach to generating un-natural amino acid side-chains has been employed. Utilizing a straightforward reaction with formylglycine generating enzyme, we use the site-specific modification of engineered proteins to yield un-natural amino acid side-chains for protein immobilization. Using this approach, we demonstrate the controlled immobilization of various enzymes onto a variety of amine coated surfaces. Our results reveal reusability of the immobilized enzymes via this strategy, and furthermore, we find the activity of the immobilized enzymes to remain even after a month of use indicating significant stability of the linkage.

  9. Steric selectivity in Na channels arising from protein polarization and mobile side chains.

    PubMed

    Boda, Dezso; Nonner, Wolfgang; Valiskó, Mónika; Henderson, Douglas; Eisenberg, Bob; Gillespie, Dirk

    2007-09-15

    Monte Carlo simulations of equilibrium selectivity of Na channels with a DEKA locus are performed over a range of radius R and protein dielectric coefficient epsilon(p). Selectivity arises from the balance of electrostatic forces and steric repulsion by excluded volume of ions and side chains of the channel protein in the highly concentrated and charged (approximately 30 M) selectivity filter resembling an ionic liquid. Ions and structural side chains are described as mobile charged hard spheres that assume positions of minimal free energy. Water is a dielectric continuum. Size selectivity (ratio of Na+ occupancy to K+ occupancy) and charge selectivity (Na+ to Ca2+) are computed in concentrations as low as 10(-5) M Ca2+. In general, small R reduces ion occupancy and favors Na+ over K+ because of steric repulsion. Small epsilon(p) increases occupancy and favors Na+ over Ca2+ because protein polarization amplifies the pore's net charge. Size selectivity depends on R and is independent of epsilon(p); charge selectivity depends on both R and epsilon(p). Thus, small R and epsilon(p) make an efficient Na channel that excludes K+ and Ca2+ while maximizing Na+ occupancy. Selectivity properties depend on interactions that cannot be described by qualitative or verbal models or by quantitative models with a fixed free energy landscape. PMID:17526571

  10. Predictions of the physicochemical properties of amino acid side chain analogs using molecular simulation.

    PubMed

    Ahmed, Alauddin; Sandler, Stanley I

    2016-03-01

    A candidate drug compound is released for clinical trails (in vivo activity) only if its physicochemical properties meet desirable bioavailability and partitioning criteria. Amino acid side chain analogs play vital role in the functionalities of protein and peptides and as such are important in drug discovery. We demonstrate here that the predictions of solvation free energies in water, in 1-octanol, and self-solvation free energies computed using force field-based expanded ensemble molecular dynamics simulation provide good accuracy compared to existing empirical and semi-empirical methods. These solvation free energies are then, as shown here, used for the prediction of a wide range of physicochemical properties important in the assessment of bioavailability and partitioning of compounds. In particular, we consider here the vapor pressure, the solubility in both water and 1-octanol, and the air-water, air-octanol, and octanol-water partition coefficients of amino acid side chain analogs computed from the solvation free energies. The calculated solvation free energies using different force fields are compared against each other and with available experimental data. The protocol here can also be used for a newly designed drug and other molecules where force field parameters and charges are obtained from density functional theory. PMID:26864716

  11. A new classification of the amino acid side chains based on doublet acceptor energy levels.

    PubMed Central

    Sneddon, S F; Morgan, R S; Brooks, C L

    1988-01-01

    We describe a new classification of the amino acid side chains based on the potential energy level at which each will accept an extra (doublet) electron. The doublet acceptor energy level, and the doublet acceptor orbital were calculated using semiempirical INDO/2-UHF molecular orbital theory. The results of these calculations show that the side chains fall into four groups. We have termed these groups repulsive, insulating, semiconducting, and attractive in accordance with where each lies on the relative energy scale. We use this classification to examine the role of residues between the donor and acceptor in modulating the rate and mechanism of electron transfer in proteins. With the calculated acceptor levels, we construct a potential barrier for those residues between the donor and acceptor. It is the area beneath this barrier that determines the decay of electronic coupling between donor and acceptor, and thus the transfer rate. We have used this schematic approach to characterize the four electron transfer pathways in myoglobin recently studied by Mayo et al. (Mayo, S.L., W.R. Ellis, R.J. Crutchley, and H.B. Gray. 1986. Science [Wash. DC]. 233:948-952). PMID:3342271

  12. Side chain flexibility and the pore dimensions in the GABAA receptor.

    PubMed

    Rossokhin, Alexey V; Zhorov, Boris S

    2016-07-01

    Permeation of ions through open channels and their accessibility to pore-targeting drugs depend on the pore cross-sectional dimensions, which are known only for static X-ray and cryo-EM structures. Here, we have built homology models of the closed, open and desensitized α1β2γ2 GABAA receptor (GABAAR). The models are based, respectively, on the X-ray structure of α3 glycine receptor (α3 GlyR), cryo-EM structure of α1 GlyR and X-ray structure of β3 GABAAR. We employed Monte Carlo energy minimizations to explore how the pore lumen may increase due to repulsions of flexible side chains from a variable-diameter electroneutral atom (an expanding sphere) pulled through the pore. The expanding sphere computations predicted that the pore diameter averaged along the permeation pathway is larger by approximately 3 Å than that computed for the models with fixed sidechains. Our models predict three major pore constrictions located at the levels of -2', 9' and 20' residues. Residues around the -2' and 9' rings are known to form the desensitization and activation gates of GABAAR. Our computations predict that the 20' ring may also serve as GABAAR gate whose physiological role is unclear. The side chain flexibility of residues -2', 9' and 20' and hence the dimensions of the constrictions depend on the GABAAR functional state.

  13. Side chain effects in reactions of the potassium-tyrosine charge transfer complex

    NASA Astrophysics Data System (ADS)

    da Silva, F. Ferreira; Meneses, G.; Ingólfsson, O.; Limão-Vieira, P.

    2016-10-01

    Fragmentation of transient negative ions of tyrosine formed through electron transfer in collisions with neutral potassium atoms is presented in the collision energy range from 30 to 75 eV. At low collision energies the dominating side chain channel observed corresponds to the cleavage of the bond from the para-position of the phenyl ring to the β-C of the remaining moiety, but cleavage of the Cαsbnd Cβ bond is also observed. Further fragments are formed through cleavage of the Cα bond to the carbonyl group, through decomposition of the carboxyl group or through significant decomposition of the backbone. The dehydrogenated molecular anion is also observed with appreciable intensity. These results are discussed in the context of earlier studies on dissociative electron attachment to tyrosine and other amino acids, as well as within the role of the side chain in electron induced decomposition of this aromatic amino acid. Stabilization of the temporary molecular anion in the transient collision complex is discussed and we argue that this may have significant influence on the branching ratios observed.

  14. SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling.

    PubMed

    Wang, Qiang; Canutescu, Adrian A; Dunbrack, Roland L

    2008-01-01

    SCWRL and MolIDE are software applications for prediction of protein structures. SCWRL is designed specifically for the task of prediction of side-chain conformations given a fixed backbone usually obtained from an experimental structure determined by X-ray crystallography or NMR. SCWRL is a command-line program that typically runs in a few seconds. MolIDE provides a graphical interface for basic comparative (homology) modeling using SCWRL and other programs. MolIDE takes an input target sequence and uses PSI-BLAST to identify and align templates for comparative modeling of the target. The sequence alignment to any template can be manually modified within a graphical window of the target-template alignment and visualization of the alignment on the template structure. MolIDE builds the model of the target structure on the basis of the template backbone, predicted side-chain conformations with SCWRL and a loop-modeling program for insertion-deletion regions with user-selected sequence segments. SCWRL and MolIDE can be obtained at (http://dunbrack.fccc.edu/Software.php).

  15. An experimental and theoretical study of the amino acid side chain Raman bands in proteins

    NASA Astrophysics Data System (ADS)

    Sjöberg, Béatrice; Foley, Sarah; Cardey, Bruno; Enescu, Mironel

    2014-07-01

    The Raman spectra of a series of tripeptides with the basic formula GlyAAGly where the central amino acid (AA) was tryptophan, tyrosine, phenylalanine, glycine, methionine, histidine, lysine and leucine were measured in H2O. The theoretical Raman spectra obtained using density functional theory (DFT) calculations at the B3LYP/6-311+G(2df,2pd) level of theory allows a precise attribution of the vibrational bands. The experimental results show that there is a blue shift in the frequencies of several bands of the amino acid side chains in tripeptides compared to free amino acids, especially in the case of AAs containing aromatic rings. On the other hand, a very good agreement was found between the Raman bands of AA residues in tripeptides and those measured on three model proteins: bovine serum albumin, β-lactoglobulin and lysozyme. The present analysis contributes to an unambiguous interpretation of the protein Raman spectra that is useful in monitoring the biological reactions involving AA side chains alteration.

  16. A New Distributed Algorithm for Side-Chain Positioning in the Process of Protein Docking*

    PubMed Central

    Moghadasi, Mohammad; Kozakov, Dima; Vakili, Pirooz; Vajda, Sandor; Paschalidis, Ioannis Ch.

    2014-01-01

    Side-chain positioning (SCP) is an important component of computational protein docking methods. Existing SCP methods and available software have been designed for protein folding applications where side-chain positioning is also important. As a result they do not take into account significant special structure that SCP for docking exhibits. We propose a new algorithm which poses SCP as a Maximum Weighted Independent Set (MWIS) problem on an appropriately constructed graph. We develop an approximate algorithm which solves a relaxation of the MWIS and then rounds the solution to obtain a high-quality feasible solution to the problem. The algorithm is fully distributed and can be executed on a large network of processing nodes requiring only local information and message-passing between neighboring nodes. Motivated by the special structure in docking, we establish optimality guarantees for a certain class of graphs. Our results on a benchmark set of enzyme-inhibitor protein complexes show that our predictions are close to the native structure and are comparable to the ones obtained by a state-of-the-art method. The results are substantially improved if rotamers from unbound protein structures are included in the search. We also establish that the use of our SCP algorithm substantially improves docking results. PMID:24844567

  17. Differential scanning calorimetric study of the effect of sterol side chain length and structure on dipalmitoylphosphatidylcholine thermotropic phase behavior.

    PubMed Central

    McMullen, T. P.; Vilchèze, C.; McElhaney, R. N.; Bittman, R.

    1995-01-01

    We have investigated the thermotropic phase behavior of dipalmitoylphosphatidylcholine (DPPC) bilayers containing a series of cholesterol analogues varying in the length and structure of their alkyl side chains. We find that upon the incorporation of up to approximately 25 mol % of any of the side chain analogues, the DPPC main transition endotherm consists of superimposed sharp and broad components representing the hydrocarbon chain melting of sterol-poor and sterol-rich phospholipid domains, respectively. Moreover, the behavior of these components is dependent on sterol side chain length. Specifically, for all sterol/DPPC mixtures, the sharp component enthalpy decreases linearly to zero by 25 mol % sterol while the cooperativity is only moderately reduced from that observed in the pure phospholipid. In addition, the sharp component transition temperature decreases for all sterol/DPPC mixtures; however, the magnitude of the decrease is dependent on the sterol side chain length. With respect to the broad component, the enthalpy initially increases to a maximum around 25 mol % sterol, thereafter decreasing toward zero by 50 mol % sterol with the exception of the sterols with very short alkyl side chains. Both the transition temperature and cooperativity of the broad component clearly exhibit alkyl chain length-dependent effects, with both the transition temperature and cooperativity decreasing more dramatically for sterols with progressively shorter side chains. We ascribe the chain length-dependent effects on transition temperature and cooperativity to the hydrophobic mismatch between the sterol and the host DPPC bilayer (see McMullen, T. P. W., Lewis, R. N. A. H., and McElhaney, R. N. (1993) Biochemistry 32:516-522). Moreover, the effective stoichiometry of sterol/DPPC interactions is altered by a significantly large degree of hydrophobic mismatch between the sterol and the DPPC bilayer. Thus the short chain sterols appear to exhibit considerable immiscibility in

  18. Dual mesomorphic assemblage of chitin normal acylates and rapid enthalpy relaxation of their side chains.

    PubMed

    Teramoto, Yoshikuni; Miyata, Tomoya; Nishio, Yoshiyuki

    2006-01-01

    Chitin derivatives having normalacyl groups (C(n)H(2n-1)O-; n = 4-20) were synthesized with pyridine, p-toluenesulfonyl chloride, and normal alkanoic acid in an N,N-dimethylacetamide-lithium chloride homogeneous system. The products (C(n)-ACs; degree of acyl substitution, DS = 1.7-1.9) showed an n-dependent thermal transition behavior: no evident transition (n = 4-10), a glass transition (n = 12 and 14), and a pseudo-first-order phase transition (n = 16-20), the latter two occurring usually below room temperature when examined by differential scanning calorimetry. Wide-angle X-ray diffractometry (WAXD) at 20 degrees C displayed a sharp diffraction peak (2theta = 2 degrees -7 degrees ) and a diffuse halo (2theta approximately 20 degrees ) for the respective C(n)-ACs. The former d-spacing (1.5-3.6 nm) increased with an increase in n to yield two stages of mutually different increasing rates, which reflects a systematic n-dependence of the period of a layered structure of the main chains. The molecular assembly of C(n)-ACs exhibited "dual mesomorphy"; nematic ordering for the semirigid carbohydrate trunk and smectic one for the flexible side chains. On the other hand, WAXD profiles of C(n)-ACs (n = 14-18) indicated almost no temperature dependence from -150 to +220 degrees C. Therefore, it was reasonably assumed that the pseudo-first-order transition observed in thermograms of C(n)-ACs (n = 16-20) was due to the enthalpy relaxation of the side-chain assemblage. An insight was provided into the kinetics of the characteristic aging behavior as a liquid-crystalline glass, in comparison with the corresponding data for other noncrystalline macromolecules.

  19. Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state

    PubMed Central

    Cote, Yoann; Senet, Patrick; Delarue, Patrice; Maisuradze, Gia G.; Scheraga, Harold A.

    2012-01-01

    Structural fluctuations of a protein are essential for a protein to function and fold. By using molecular dynamics (MD) simulations of the model α/β protein VA3 in its native state, the coupling between the main-chain (MC) motions [represented by coarse-grained dihedral angles (CGDAs) γn based on four successive Cα atoms (n - 1, n, n + 1, n + 2) along the amino acid sequence] and its side-chain (SC) motions [represented by CGDAs δn formed by the virtual bond joining two consecutive Cα atoms (n, n + 1) and the bonds joining these Cα atoms to their respective Cβ atoms] was analyzed. The motions of SCs (δn) and MC (γn) over time occur on similar free-energy profiles and were found to be subdiffusive. The fluctuations of the SCs (δn) and those of the MC (γn) are generally poorly correlated on a ps time-scale with a correlation increasing with time to reach a maximum value at about 10 ns. This maximum value is close to the correlation between the δn(t) and γn(t) time-series extracted from the entire duration of the MD runs (400 ns) and varies significantly along the amino acid sequence. High correlations between the SC and MC motions [δ(t) and γ(t) time-series] were found only in flexible regions of the protein for a few residues which contribute the most to the slowest collective modes of the molecule. These results are a possible indication of the role of the flexible regions of proteins for the biological function and folding. PMID:22689963

  20. Physics-based side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials for coarse-grained UNRES force field. 2. Comparison with statistical potentials and implementation

    PubMed Central

    Kozłowska, Urszula; Maisuradze, Gia G.; Liwo, Adam; Scheraga, Harold A.

    2009-01-01

    Using the harmonic-approximation approach of the accompanying paper and AM1 energy surfaces of terminally-blocked amino-acid residues, we determined physics-based side-chain-rotamer potentials and the side-chain virtual-bond-deformation potentials of 19 natural amino-acid residues with side chains. The potentials were approximated by analytical formulas and implemented in the UNRES mesoscopic dynamics program. For comparison, the corresponding statistical potentials were determined from 19,682 high-resolution protein structures. The low-free-energy region of both the AM1-derived and the statistical potentials is determined by the valence geometry and the L-chirality, and its size increases with side-chain flexibility and decreases with increasing virtual-bond-angle θ. The differences between the free energies of rotamers are greater for the AM1-derived potentials compared to the statistical potentials and, for alanine and other residues with small side chains, a region corresponding to the Cax7 conformation has remarkably low free energy for the AM1-derived potentials, as opposed to the statistical potentials. These differences probably result from the interactions between neighboring residues and indicate the need for introduction of cooperative terms accounting for the coupling between side-chain-rotamer and backbone interactions. Both AM1-derived and statistical virtual-bond-deformation potentials are multimodal for flexible side chains and are topologically similar; however, the regions of minima of the statistical potentials are much narrower, which probably results from imposing restraints in structure determination. The force field with the new potentials was preliminarily optimized using the FBP WW domain (1E0L) and the engrailed homeodomain (1ENH) as training proteins and assessed to be reasonably transferable. PMID:20017135

  1. Lattice and off-lattice side chain models of protein folding: Linear time structure prediction better than 86% of optimal

    SciTech Connect

    Hart, W.E.; Istrail, S.

    1996-08-09

    This paper considers the protein structure prediction problem for lattice and off-lattice protein folding models that explicitly represent side chains. Lattice models of proteins have proven extremely useful tools for reasoning about protein folding in unrestricted continuous space through analogy. This paper provides the first illustration of how rigorous algorithmic analyses of lattice models can lead to rigorous algorithmic analyses of off-lattice models. The authors consider two side chain models: a lattice model that generalizes the HP model (Dill 85) to explicitly represent side chains on the cubic lattice, and a new off-lattice model, the HP Tangent Spheres Side Chain model (HP-TSSC), that generalizes this model further by representing the backbone and side chains of proteins with tangent spheres. They describe algorithms for both of these models with mathematically guaranteed error bounds. In particular, the authors describe a linear time performance guaranteed approximation algorithm for the HP side chain model that constructs conformations whose energy is better than 865 of optimal in a face centered cubic lattice, and they demonstrate how this provides a 70% performance guarantee for the HP-TSSC model. This is the first algorithm in the literature for off-lattice protein structure prediction that has a rigorous performance guarantee. The analysis of the HP-TSSC model builds off of the work of Dancik and Hannenhalli who have developed a 16/30 approximation algorithm for the HP model on the hexagonal close packed lattice. Further, the analysis provides a mathematical methodology for transferring performance guarantees on lattices to off-lattice models. These results partially answer the open question of Karplus et al. concerning the complexity of protein folding models that include side chains.

  2. Influence of O Side Chains on the Attachment of the Felix O-1 Bacteriophage to Salmonella Bacteria

    PubMed Central

    Lindberg, A. A.; Holme, T.

    1969-01-01

    The adsorption rate constant (ARC) of the Felix O-1 (FO) bacteriophage to sensitive Salmonella strains was used to determine the effect of variations in surface antigens on phage attachment. The N-acetylglucosamine of the common-core polysaccharide of the Salmonella lipopolysaccharide (LPS) was found to be an essential part of the receptor for the FO phage in conformation with earlier reports. It was found that (i) the ARC was low for strains having O side chains containing two or three non core monosaccharides, (ii) the ARC varied when the O side chain contained no, or only one, noncore monosaccharide, (iii) the ARC was high when the O side chain contained only one repeating unit, and (iv) the ARC was high to mutants of chemotype Ra in which the N-acetylglucosamine was the terminal sugar of the LPS. Since a good correlation was found between the ARC of the FO phage and the phage-inactivating capacity of phenol water-extracted LPS, the results suggest that only the structure and composition of the LPS determines the adsorption rate of the FO phage. The phage-inactivating capacity of LPS from the Ra mutants increased in parallel with higher glucosamine contents in the core polysaccharide. In smooth strains having long and numerous O side chains, the access of the FO phage to its receptor is probably blocked by the presence of the side chains, whereas short and numerous side chains or T1 side chains do not interfere with the FO attachment. PMID:4897114

  3. Vacuum-Ultraviolet Circular Dichroism Spectra of Escherichia coli Dihydrofolate Reductase and Its Mutants: Contributions of Phenylalanine and Tyrosine Side Chains and Exciton Coupling of Two Tryptophan Side Chains.

    PubMed

    Ohmae, Eiji; Tanaka, Suguru; Miyashita, Yurina; Katayanagi, Katsuo; Matsuo, Koichi

    2015-10-15

    Vacuum-ultraviolet (VUV) circular dichroism (CD) spectroscopy has recently been used for secondary structure analysis of proteins; however, the contribution of aromatic side chains to protein VUV CD spectra is unresolved. In this report, VUV CD spectra of 10 Escherichia coli dihydrofolate reductase (DHFR) mutants, in which each phenylalanine or tyrosine residue was mutated to leucine, were measured down to 175 nm at 25 °C and pH 8.0 to elucidate the contributions of these aromatic side chains to the high-energy transitions of peptide bonds. The VUV CD spectra of these mutants were different from the spectrum of the wild-type protein, indicating that the contribution of the phenylalanine and tyrosine side chains of DHFR extends to the VUV region. Furthermore, the VUV CD spectrum and the folate- or NADP(+)-induced spectral change of F103L mutant DHFR indicated a modification and regeneration of exciton coupling between the Trp47 and Trp74 side chains, respectively, suggesting that exciton coupling may also contribute to the CD spectrum of DHFR in the VUV region. These results should be useful for theoretically characterizing the contribution of aromatic side chains to protein CD spectra, leading to the improvement of protein secondary-structure analysis by VUV CD spectroscopy.

  4. Excited-state dynamics of water-soluble polythiophene derivatives: temperature and side-chain length effects.

    PubMed

    Ma, Ying-Zhong; Shaw, Robert W; Yu, Xiang; O'Neill, Hugh M; Hong, Kunlun

    2012-12-13

    We report synthesis and detailed spectroscopic study of three water-soluble polythiophene derivatives with distinct homologous oligo(ethylene oxide) side-chain lengths and lower critical solution temperatures (LCSTs). The linear absorption spectra exhibit reversible shifts and broadening with the variation of their aqueous solution temperature, whereas the corresponding steady-state fluorescence emission spectra were found to show negligible shifts and only minor changes in their line shape. Measurements of picosecond time-resolved fluorescence at chosen emission wavelengths reveal a strong dependence of the isotropic decays on both side-chain length and aqueous solution temperature. With lengthening of the side chain, the isotropic decays become not only remarkably slow but also increasingly complex. Except for the polymer with the shortest side chain, significant acceleration of the isotropic decays was found when the solution temperature was raised to the corresponding LCSTs and beyond, which further causes formation of large aggregates as evident by the physical appearance change from clear solutions to turbid suspensions. Direct evidence for a temperature-induced change of polymer chain conformation was obtained through measurements of time-resolved fluorescence anisotropies, which are characterized by a substantial increase of the initial values from ~0.2 to 0.4 and the appearance of a pronounced fast decay component with an estimated lifetime of 36 ps. The high initial anisotropy of ~0.4 observed for the two polymers with longer side-chains above their LCSTs suggests that the polymer chains are highly ordered in the aggregates. The observed effects of side-chain length and solution temperature are discussed by considering the conformational relaxation of the polymer backbones and occurrence of interchain energy transfer.

  5. High electro-optic side-chain polymer by vapor deposition polymerization

    NASA Astrophysics Data System (ADS)

    Roberts, C. C.; Yang, G.-R.; Cocoziello, A.; Zhao, Y.-P.; Wnek, G.; Lu, T.-M.

    1996-04-01

    In this letter, we report high electro-optic methylene di(phenylene isocyanate) (MDI)/DR19 side-chain polymer film polymerization by vapor deposition polymerization. For samples deposited at substrate temperatures from 10 to 30 °C, the electro-optic (EO) coefficient, r33, was measured to be 5 pm/V after poling. A lifetime of about one week was obtained. The highest EO effect observed were films deposited at -40 °C and polymerized after poling. The EO coefficient of these samples is about 24 pm/V while the lifetime is only about 30 min. The effect of substrate temperature, the ratio of monomers, and the poling temperature on the nonlinearity of the films are studied.

  6. Discovery of thiochroman derivatives bearing a carboxy-containing side chain as orally active pure antiestrogens.

    PubMed

    Kanbe, Yoshitake; Kim, Myung-Hwa; Nishimoto, Masahiro; Ohtake, Yoshihito; Tsunenari, Toshiaki; Taniguchi, Kenji; Ohizumi, Iwao; Kaiho, Shin-ichi; Nabuchi, Yoshiaki; Kawata, Setsu; Morikawa, Kazumi; Jo, Jae-Chon; Kwon, Hee-An; Lim, Hyun-Suk; Kim, Hak-Yeop

    2006-08-01

    In order to search for alternatives to the sulfoxide moiety in the long side chain of pure antiestrogens, several molecules that may interact with water in a fashion similar to ICI164,384 were designed and it was found that compounds with the carboxy, the sulfamide, or the sulfonamide instead of the sulfoxide moiety also functioned as pure antiestrogens. Interestingly, the compound possessing the carboxy moiety showed superior antiestrogen activity compared to ICI182,780 when dosed orally. Results of the pharmacokinetic evaluation indicated that the potent antiestrogen activity at oral dosing attributed to both the improved absorption from the intestinal wall and the metabolic stability of the compound in liver. PMID:16709454

  7. Molecular modelling studies of side-chain rotation in substituted triazine rings

    NASA Astrophysics Data System (ADS)

    Birkett, Helen E.; Cherryman, Julian C.; Margaret Chippendale, A.; Hazendonk, Paul; Harris, Robin K.

    2002-01-01

    Molecular modelling computation using the GAUSSIAN 94 package of programs was carried out to estimate four different barriers to internal rotation about amine nitrogen to sp 2 carbon bonds for two compounds with triazine rings. Whereas two of the processes appear to retain a planar side-chain nitrogen environment throughout the internal rotation, the other two involve pyramidalisation. In the latter two cases, after the barrier is passed, the process may or may not include a transient inversion at nitrogen. The internal rotation for cyclotriazine systems is discussed in relation to those for aniline and formamide. The four barrier magnitudes calculated for the triazines are in the same order as (though somewhat larger than) those measured by variable-temperature NMR bandshape analysis for a relevant compound.

  8. Side chain and backbone contributions of Phe508 to CFTR folding

    SciTech Connect

    Thibodeau, Patrick H.; Brautigam, Chad A.; Machius, Mischa; Thomas, Philip J.

    2010-12-07

    Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an integral membrane protein, cause cystic fibrosis (CF). The most common CF-causing mutant, deletion of Phe508, fails to properly fold. To elucidate the role Phe508 plays in the folding of CFTR, missense mutations at this position were generated. Only one missense mutation had a pronounced effect on the stability and folding of the isolated domain in vitro. In contrast, many substitutions, including those of charged and bulky residues, disrupted folding of full-length CFTR in cells. Structures of two mutant nucleotide-binding domains (NBDs) reveal only local alterations of the surface near position 508. These results suggest that the peptide backbone plays a role in the proper folding of the domain, whereas the side chain plays a role in defining a surface of NBD1 that potentially interacts with other domains during the maturation of intact CFTR.

  9. The phase dependent photophysics and photochemistry of side-chain substituted liquid crystalline polyaryl cinnamates

    SciTech Connect

    Singh, S.; Creed, D.; Hoyle, C.E.

    1993-12-31

    The photochemical behavior of a polymethacrylate polymer with a side-chain cinnamate ester mesogen has been investigated. Photolysis at 313 nm of the polymer film in the smectic A or smectic B phase results in only a 2+2 cycloaddition reaction at low photolysis times. In contrast, photolysis (313 nm) of the polymer film in the nematic phase yields both 2+2 cycloaddition and photo-Fries products at short photolysis times. The preference for 2+2 cyloaddition product formation in the smectic phases is attributed to preferential reaction of cinnamate ester aggregates. Accordingly, photolysis at 366 nm where only aggregates absorb yields exclusively cycloadducts even after exhaustive photolysis for long time periods.

  10. Poly-dimethylsiloxane derivates side chains effect on syntan functionalized Polyamide fabric

    NASA Astrophysics Data System (ADS)

    Migani, V.; Weiss, H.; Massafra, M. R.; Merlo, A.; Colleoni, C.; Rosace, G.

    2011-02-01

    Poly-dimethylsiloxane (PDMS) polymers finishing of Polyamide-6,6 (PA66) fabrics involves ionic interactions between reactive groups on the PDMS polymers and the ones of the textile fabric. Such interactions could be strengthened by a pretreatment with a fixing agent to promote either ion-ion and H-bonding and ion-dipole forces. These forces could contribute towards the building of substantial PDMS-PA66 systems and the achieving of better adhesion properties to fabrics. Four different silicone polymers based on PDMS were applied on a synthetic tanning agent (syntan) finished Polyamide-6,6 fabric under acid conditions. Soxhlet extraction method and ATR FT-IR technique were used to investigate the application conditions. The finishing parameters such as pH and temperature together with fastness, mechanical and performance properties of the treated samples were studied and related to PDMS side chains effect on syntan functionalized Polyamide fabric.

  11. Backbone and side chain chemical shift assignments of apolipophorin III from Galleria mellonella.

    PubMed

    Crowhurst, Karin A; Horn, James V C; Weers, Paul M M

    2016-04-01

    Apolipophorin III, a 163 residue monomeric protein from the greater wax moth Galleria mellonella (abbreviated as apoLp-IIIGM), has roles in upregulating expression of antimicrobial proteins as well as binding and deforming bacterial membranes. Due to its similarity to vertebrate apolipoproteins there is interest in performing atomic resolution analysis of apoLp-IIIGM as part of an effort to better understand its mechanism of action in innate immunity. In the first step towards structural characterization of apoLp-IIIGM, 99 % of backbone and 88 % of side chain (1)H, (13)C and (15)N chemical shifts were assigned. TALOS+ analysis of the backbone resonances has predicted that the protein is composed of five long helices, which is consistent with the reported structures of apolipophorins from other insect species. The next stage in the characterization of apoLp-III from G. mellonella will be to utilize these resonance assignments in solving the solution structure of this protein.

  12. Non-innocent side-chains with dipole moments in organic solar cells improve charge separation.

    PubMed

    de Gier, Hilde D; Broer, Ria; Havenith, Remco W A

    2014-06-28

    Providing sustainable energy is one of the biggest challenges nowadays. An attractive answer is the use of organic solar cells to capture solar energy. Recently a promising route to increase their efficiency has been suggested: developing new organic materials with a high dielectric constant. This solution focuses on lowering the coulomb attraction between electrons and holes, thereby increasing the yield of free charges. In here, we demonstrate from a theoretical point of view that incorporation of dipole moments in organic materials indeed lowers the coulomb attraction. A combination of molecular dynamics simulations for modelling the blend and ab initio quantum chemical calculations to study specific regions was performed. This approach gives predictive insight in the suitability of new materials for application in organic solar cells. In addition to all requirements that make conjugated polymers suitable for application in organic solar cells, this study demonstrates the importance of large dipole moments in polymer side-chains.

  13. Calcium ions induce collapse of charged O-side chains of lipopolysaccharides from Pseudomonas aeruginosa

    PubMed Central

    Schneck, Emanuel; Papp-Szabo, Erzsebet; Quinn, Bonnie E.; Konovalov, Oleg V.; Beveridge, Terry J.; Pink, David A.; Tanaka, Motomu

    2009-01-01

    Lipopolysaccharide (LPS) monolayers deposited on planar, hydrophobic substrates were used as a defined model of outer membranes of Pseudomonas aeruginosa strain dps 89. To investigate the influence of ions on the (out-of-plane) monolayer structure, we measured specular X-ray reflectivity at high energy (22 keV) to ensure transmission through water. Electron density profiles were reconstructed from the reflectivity curves, and they indicate that the presence of Ca2+ ions induces a significant change in the conformation of the charged polysaccharide head groups (O-side chains). Monte Carlo simulations based on a minimal computer model of LPS molecules allow for the modelling of 100 or more molecules over 10−3 s and theoretically explained the tendency found by experiments. PMID:19605401

  14. Shape-Selectivity with Liquid Crystal and Side-Chain Liquid Crystalline Polymer SAW Sensor Interfaces

    SciTech Connect

    FRYE-MASON,GREGORY CHARLES; OBORNY,MICHAEL C.; PUGH,COLEEN; RICCO,ANTONIO; THOMAS,ROSS C.; ZELLERS,EDWARD T.; ZHANG,GUO-ZHENG

    1999-09-23

    A liquid crystal (LC) and a side-chain liquid crystalline polymer (SCLCP) were tested as surface acoustic wave (SAW) vapor sensor coatings for discriminating between pairs of isomeric organic vapors. Both exhibit room temperature smectic mesophases. Temperature, electric-field, and pretreatment with self-assembled monolayers comprising either a methyl-terminated or carboxylic acid-terminated alkane thiol anchored to a gold layer in the delay path of the sensor were explored as means of affecting the alignment and selectivity of the LC and SCLCP films. Results for the LC were mixed, while those for the SCLCP showed a consistent preference for the more rod-like isomer of each isomer pair examined.

  15. Synthesis of brassinosteroids with a keto group in the side chain.

    PubMed

    Baradzenka, Aliona G; Barysau, Barys M; Hurski, Alaksiej L; Zhabinskii, Vladimir N; Khripach, Vladimir A

    2015-09-01

    The aim of this work was to prepare 24-epicryptolide and 22-dehydro-24-epibrassinolide as possible metabolites of 24-epibrassinolide. The main synthetic problem to be solved was the differentiation of functional groups in brassinosteroids. Distinguishing 2α,3α-diol function from another diol group in 24-epibrassinolide was achieved via selective hydrolysis of 2α,3α-cyclic carbonate or via regioselective reaction of boric acid with the functional groups in the side chain. The hydroxyl at C-23 was more reactive than the 22-OH in the oxidation with bromine in the presence of bis(tributyltin) oxide and in the benzylation reaction that resulted in the predominant formation of the corresponding α-hydroxy ketone derivatives with the ratio ranging from 4:1 to 1.5:1.

  16. Ozonolysis of surface adsorbed methoxyphenols: kinetics of aromatic ring cleavage vs. alkene side-chain oxidation

    NASA Astrophysics Data System (ADS)

    O'Neill, E. M.; Kawam, A. Z.; Van Ry, D. A.; Hinrichs, R. Z.

    2013-07-01

    Lignin pyrolysis products, which include a variety of substituted methoxyphenols, constitute a major component of organics released by biomass combustion and may play a central role in the formation of atmospheric brown carbon. Understanding the atmospheric fate of these compounds upon exposure to trace gases is therefore critical to predicting the chemical and physical properties of biomass burning aerosol. We used diffuse reflectance infrared spectroscopy to monitor the heterogeneous ozonolysis of 4-propylguaiacol, eugenol, and isoeugenol adsorbed on NaCl and α-Al2O3 substrates. Adsorption of gaseous methoxyphenols onto these substrates produced near monolayer surface concentrations of 3 × 1018 molecules m-2. The subsequent dark heterogeneous ozonolysis of adsorbed 4-propylguaiacol cleaved the aromatic ring between the methoxy and phenol groups with the product conclusively identified by GC-MS and 1H-NMR. Kinetic analysis of eugenol and isoeugenol dark ozonolysis also suggested the formation of ring-cleaved products, although ozonolysis of the unsaturated substituent groups forming carboxylic acids and aldehydes was an order of magnitude faster. Average uptake coefficients for NaCl-adsorbed methoxyphenols were γ = 2.3 (±0.8) × 10-7 and 2 (±1) × 10-6 for ozonolysis of the aromatic ring and the unsaturated side chain, respectively, and reactions on α-Al2O3 were approximately two times slower. UV-visible radiation (λ>300 nm) enhanced eugenol ozonolysis of the aromatic ring by a factor of 4(±1) but had no effect on ozonolysis of the alkene side-chain.

  17. Molecular modeling of proton transport in the short-side-chain perfluorosulfonic acid ionomer.

    PubMed

    Hristov, Iordan H; Paddison, Stephen J; Paul, Reginald

    2008-03-13

    An explanation for the superior proton conductivity of low equivalent weight (EW) short-side-chain (SSC) perfluorosulfonic acid membranes is pursued through the determination of hydrated morphology and hydronium ion diffusion coefficients using classical molecular dynamics (MD) simulations. A unique force field set for the SSC ionomer was derived from torsion profiles determined from ab initio electronic structure calculations of an oligomeric fragment consisting of two side chains. MD simulations were performed on a system consisting of a single macromolecule of the polymer (EW of 580) with the general formula F3C-[CF(OCF2CF2SO3H)-(CF2)7]40-CF3 at hydration levels corresponding to 3, 6, and 13 water molecules per sulfonic acid group. Examination of the hydrated morphology indicates the formation of hydrogen bond "bridges" between distant sulfonate groups without significant bending of the polytetrafluoroethylene backbone. Pair correlation functions of the system identify the presence of ion cages consisting of hydronium ions hydrogen-bonded to three sulfonate groups at the lowest water content. Such structures exhibit very low S-OH3+ separations, well below 4 A and severely inhibit vehicular diffusion of the protons. The number of sulfonate groups in the first solvation shell of a given hydronium ion correlates well with the differences between Nafion and the SSC polymer (Hyflon). The calculated hydronium ion diffusion coefficients of 2.84 x 10-7, 1.36 x 10-6, and 3.47 x 10-6 cm2/s for water contents of 3, 6, and 13, respectively, show only good agreement to experimentally measured values at the lowest water content, underscoring the increasing contribution of proton shuttling or hopping at the higher hydration levels. At the highest water content, the vehicular diffusion accounts for only about 1/5 of the total proton transport similar to that observed in Nafion. PMID:18281980

  18. Glutamine and cancer.

    PubMed Central

    Souba, W W

    1993-01-01

    OBJECTIVE: This overview on glutamine and cancer discusses the importance of glutamine for tumor growth, summarizes the alterations in interorgan glutamine metabolism that develop in the tumor-bearing host, and reviews the potential benefits of glutamine nutrition in the patient with cancer. SUMMARY BACKGROUND DATA: Glutamine is the most abundant amino acid in the blood and tissues. It is essential for tumor growth and marked changes in organ glutamine metabolism are characteristic of the host with cancer. Because host glutamine depletion has adverse effects, it is important to study the regulation of glutamine metabolism in cancer and to evaluate the impact of glutamine nutrition in the tumor-bearing state. METHODS: Data from a variety of investigations on glutamine metabolism and nutrition related to the host with cancer were compiled and summarized. RESULTS: Numerous studies on glutamine metabolism in cancer indicate that many tumors are avid glutamine consumers in vivo and in vitro. As a consequence of progressive tumor growth, host glutamine depletion develops and becomes a hallmark. This glutamine depletion occurs in part because the tumor behaves as a "glutamine trap" but also because of cytokine-mediated alterations in glutamine metabolism in host tissues. Animal and human studies that have investigated the use of glutamine-supplemented nutrition in the host with cancer suggest that pharmacologic doses of dietary glutamine may be beneficial. CONCLUSIONS: Understanding the control of glutamine metabolism in the tumor-bearing host not only improves the knowledge of metabolic regulation in the patient with cancer but also will lead to improved nutritional support regimens targeted to benefit the host. PMID:8257221

  19. Multi-functionalized side-chain supramolecular polymers: A methodology towards tunable functional materials

    NASA Astrophysics Data System (ADS)

    Nair, Kamlesh Prabhakaran

    Even as we see a significant growth in the field of supramolecular polymers in the last ten years, multi-functionalized systems have been scarcely studied. Noncovalent multi-functionalization provides unique advantages such as rapid materials optimization via reversible functionalization as well as for the tuning of materials properties by exploiting the differences in the nature of these reversible interactions. This thesis involves the design principles, synthesis & methodology of supramolecular side-chain multi-functionalized polymers. The combination of a functionally tolerant & controlled polymerization technique such as ROMP with multiple noncovalent interactions such as hydrogen bonding, metal coordination and ionic interactions has been successfully used to synthesize these polymers. Furthermore, the orthogonality between the above interactions in block/random copolymers has been studied in detail. It has been found that the studied interactions were orthogonal to each other. To validate the viability of this methodology using multiple orthogonal interactions towards materials design noncovalent crosslinking of polymers has been used as a potential application. Three classes of networks have been studied: complementary multiple hydrogen bonded networks, metal crosslinked networks, & multi-functionalized hydrogen bonded and metal coordinated networks. The first room temperature decrosslinking by exclusive complementary hydrogen bonded interactions has been successfully achieved. Furthermore network properties have been successfully tuned by varying the network micro-structure which in turn was tuned by the hydrogen bonding motifs used for inter-chain crosslinking. By combining two different noncovalent interactions used for inter-chain crosslinking, it was possible to make multi-functionalized materials whose properties could be controlled by varying the crosslinking strategy. Hence by employing multi-functionalization methodology, important materials

  20. Conformation-Specific IR and UV Spectroscopy of the Amino Acid Glutamine: Amide-Stacking and Hydrogen Bonding in AN Important Residue in Neurodegenerative Diseases

    NASA Astrophysics Data System (ADS)

    Walsh, Patrick S.; Dean, Jacob C.; Zwier, Timothy S.

    2014-06-01

    Glutamine plays an important role in several neurodegenerative diseases including Huntington's disease (HD) and Alzheimer's disease (AD). An intriguing aspect of the structure of glutamine is its incorporation of an amide group in its side chain, thereby opening up the possibility of forming amide-amide H-bonds between the peptide backbone and side chain. In this study the conformational preferences of two capped gluatamines Z(carboxybenzyl)-Glutamine-X (X=OH, NHMe) are studied under jet-cooled conditions in the gas phase in order to unlock the intrinsic structural motifs that are favored by this flexible sidechain. Conformational assignments are made by comparing the hydride stretch ( 3100-3700 cm-1) and amide I and II ( 1400-1800 cm-1) resonant ion-dip infrared spectra with predictions from harmonic frequency calculations. Assigned structures will be compared to previously published results on both natural and unnatural residues. Particular emphasis will be placed on the comparison between glutamine and unconstrained γ-peptides due to the similar three-carbon spacing between backbone and side chain in glutamine to the backbone spacing in γ-peptides. The ability of the glutamine side-chain to form amide stacked conformations will be a main focus, along with the prevalence of extended backbone type structures. W. H. James, III, C W. Müller, E. G. Buchanan, M. G. D. Nix, L. Guo, L. Roskop, M. S. Gordon, L. V. Slipchenko, S. H. Gellman, and T. S. Zwier, J. Am. Chem. Soc., 2009, 131(40), 14243-14245.

  1. Synthesis and biological activities of new side chain and backbone cyclic bradykinin analogues.

    PubMed

    Schumann, C; Seyfarth, L; Greiner, G; Paegelow, I; Reissmann, S

    2002-08-01

    A series of conformationally constrained cyclic analogues of the peptide hormone bradykinin (BK, Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg) was synthesized to check different turned structures proposed for the bioactive conformation of BK agonists and antagonists. Cycles differing in the size and direction of the lactam bridge were performed at the C- and N-terminal sequences of the molecule. Glutamic acid and lysine were introduced into the native BK sequence at different positions for cyclization through their side chains. Backbone cyclic analogues were synthesized by incorporation of N-carboxy alkylated and N-amino alkylated amino acids into the peptide chain. Although the coupling of Fmoc-glycine to the N-alkylated phenylalanine derivatives was effected with DIC/HOAt in SPPS, the dipeptide building units with more bulky amino acids were pre-built in solution. For backbone cyclization at the C-terminus an alternative building unit with an acylated reduced peptide bond was preformed in solution. Both types of building units were handled in the SPPS in the same manner as amino acids. The agonistic and antagonistic activities of the cyclic BK analogues were determined in rat uterus (RUT) and guinea-pig ileum (GPI) assays. Additionally, the potentiation of the BK-induced effects was examined. Among the series of cyclic BK agonists only compound 3 with backbone cyclization between positions 2 and 5 shows a significant agonistic activity on RUT. To study the influence of intramolecular ring closure we used an antagonistic analogue with weak activity, [D-Phe7]-BK. Side chain as well as backbone cyclization in the N-terminus of [D-Phe7]-BK resulted in analogues with moderate antagonistic activity on RUT. Also, compound 18 in which a lactam bridge between positions 6 and 9 was achieved via an acylated reduced peptide bond has moderate antagonistic activity on RUT. These results support the hypothesis of turn structures in both parts of the molecule as a requirement for BK

  2. Probing the Role of Side-Chain Interconnecting Groups in the Structural Hydrophobicity of Comblike Fluorinated Polystyrene by Solid-State NMR Spectroscopy.

    PubMed

    Ryu, Su-Yeol; Chung, Jae Woo; Kwak, Seung-Yeop

    2015-09-01

    In order to probe the role of side-chain interconnecting groups (-O-, -S-, and -SO2- linkages between the polystyrene (PST) main chain and fluorooctyl side chain) in the hydrophobicity of the comblike fluorinated polystyrenes, the molecular motion and structure of polymers are explored using the spin-lattice relaxation times (T1 and T1ρ) by solid-state (1)H and (19)F nuclear magnetic resonance spectroscopy. The chain-end motions of the polystyrene main chain and the fluorooctyl side chain are homogeneous, regardless of the interconnecting groups, which means that the chain-end motions of the main chain and the side chain maintain consistency, and these are irrelevant to each other. However, the local dynamic of the main chain shows the structural heterogeneity composed of the mobile and rigid regions, attributed to the rigidity of the side chain. The mobile dynamic portions of the main chain for PST-O and PST-S increase, and their rigid dynamic portions decrease as the temperature increases, whereas the ratio of structural heterogeneity for PST-SO2 is maintained despite increasing temperature. The activation energies (Ea) corresponding to the local motion of fluorooctyl side chains for PST-O and PST-S are drastically increased on the fast motion side compared to the slow motion side, suggesting the motional transformation of side chains for PST-O and PST-S from the small local motion into the large-scale movements related to a cooperative segmental motion when heated. Also, the local motion of the fluorooctyl side chain for PST-SO2 has similar Ea values on both sides, indicating that the relaxation time of PST-SO2 does not change with temperature. Therefore, PST-SO2 is structurally more stable than PST-O or PST-S, which can be attributed to the densely packed fluorooctyl side chain structure caused by the large dipole moment of the sulfone interconnecting group.

  3. Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures.

    PubMed

    Yesselman, Joseph D; Horowitz, Scott; Brooks, Charles L; Trievel, Raymond C

    2015-03-01

    The propensity of backbone Cα atoms to engage in carbon-oxygen (CH · · · O) hydrogen bonding is well-appreciated in protein structure, but side chain CH · · · O hydrogen bonding remains largely uncharacterized. The extent to which side chain methyl groups in proteins participate in CH · · · O hydrogen bonding is examined through a survey of neutron crystal structures, quantum chemistry calculations, and molecular dynamics simulations. Using these approaches, methyl groups were observed to form stabilizing CH · · · O hydrogen bonds within protein structure that are maintained through protein dynamics and participate in correlated motion. Collectively, these findings illustrate that side chain methyl CH · · · O hydrogen bonding contributes to the energetics of protein structure and folding.

  4. Tuning the electronic coupling in a low-bandgap donor-acceptor copolymer via the placement of side-chains

    SciTech Connect

    Oberhumer, Philipp M.; Huang, Ya-Shih; Massip, Sylvain; Albert-Seifried, Sebastian; Greenham, Neil C.; Hodgkiss, Justin M.; Friend, Richard H.; James, David T.; Kim, Ji-Seon; Tu Guoli; Huck, Wilhelm T. S.; Beljonne, David; Cornil, Jerome

    2011-03-21

    We present a spectroscopic and theoretical investigation of the effect of the presence and position of hexyl side-chains in the novel low-bandgap alternating donor-acceptor copolymer poly[bis-N,N-(4-octylphenyl)-bis-N,N-phenyl-1, 4-phenylenediamine-alt-5,5'-4',7',-di-2-thienyl-2',1',3'-benzothiadiazole] (T8TBT). We use electronic absorption and Raman spectroscopic measurements supported by calculations of chain conformation, electronic transitions, and Raman modes. Using these tools, we find that sterically demanding side-chain configurations induce twisting in the electronic acceptor unit and reduce the electronic interaction with the donor. This leads to a blue-shifted and weakened (partial) charge-transfer absorption band together with a higher photoluminescence efficiency. On the other hand, sterically relaxed side-chain configurations promote coupling between donor and acceptor units and exhibit enhanced absorption at the expense of luminescence efficiency. The possibility of tuning the donor-acceptor character of conjugated polymers by varying the placement of side-chains has very important ramifications for light emitting diode, Laser, display, and photovoltaic device optimization.

  5. Structural Origins of Nitroxide Side Chain Dynamics on Membrane Protein [alpha]-Helical Sites

    SciTech Connect

    Kroncke, Brett M.; Horanyi, Peter S.; Columbus, Linda

    2010-12-07

    Understanding the structure and dynamics of membrane proteins in their native, hydrophobic environment is important to understanding how these proteins function. EPR spectroscopy in combination with site-directed spin labeling (SDSL) can measure dynamics and structure of membrane proteins in their native lipid environment; however, until now the dynamics measured have been qualitative due to limited knowledge of the nitroxide spin label's intramolecular motion in the hydrophobic environment. Although several studies have elucidated the structural origins of EPR line shapes of water-soluble proteins, EPR spectra of nitroxide spin-labeled proteins in detergents or lipids have characteristic differences from their water-soluble counterparts, suggesting significant differences in the underlying molecular motion of the spin label between the two environments. To elucidate these differences, membrane-exposed {alpha}-helical sites of the leucine transporter, LeuT, from Aquifex aeolicus, were investigated using X-ray crystallography, mutational analysis, nitroxide side chain derivatives, and spectral simulations in order to obtain a motional model of the nitroxide. For each crystal structure, the nitroxide ring of a disulfide-linked spin label side chain (R1) is resolved and makes contacts with hydrophobic residues on the protein surface. The spin label at site I204 on LeuT makes a nontraditional hydrogen bond with the ortho-hydrogen on its nearest neighbor F208, whereas the spin label at site F177 makes multiple van der Waals contacts with a hydrophobic pocket formed with an adjacent helix. These results coupled with the spectral effect of mutating the i {+-} 3, 4 residues suggest that the spin label has a greater affinity for its local protein environment in the low dielectric than on a water-soluble protein surface. The simulations of the EPR spectra presented here suggest the spin label oscillates about the terminal bond nearest the ring while maintaining weak contact

  6. XANES measurements of the rate of radiation damage to selenomethionine side chains

    PubMed Central

    Holton, James M.

    2009-01-01

    The radiation-induced disordering of selenomethionine (SeMet) side chains represents a significant impediment to protein structure solution. Not only does the increased B-factor of these sites result in a serious drop in phasing power, but some sites decay much faster than others in the same unit cell. These radiolabile SeMet side chains decay faster than high-order diffraction spots with dose, making it difficult to detect this kind of damage by inspection of the diffraction pattern. The selenium X-ray absorbance near-edge spectrum (XANES) from samples containing SeMet was found to change significantly after application of X-ray doses of 10–100 MGy. Most notably, the sharp ‘white line’ feature near the canonical Se edge disappears. The change was attributed to breakage of the Cγ—Se bond in SeMet. This spectral change was used as a probe to measure the decay rate of SeMet with X-ray dose in cryo-cooled samples. Two protein crystal types and 15 solutions containing free SeMet amino acid were examined. The damage rate was influenced by the chemical and physical condition of the sample, and the half-decaying dose for the selenium XANES signal ranged from 5 to 43 MGy. These decay rates were 34- to 3.8-fold higher than the rate at which the Se atoms interacted directly with X-ray photons, so the damage mechanism must be a secondary effect. Samples that cooled to a more crystalline state generally decayed faster than samples that cooled to an amorphous solid. The single exception was a protein crystal where a nanocrystalline cryoprotectant had a protective effect. Lowering the pH, especially with ascorbic or nitric acids, had a protective effect, and SeMet lifetime increased monotonically with decreasing sample temperature (down to 93 K). The SeMet lifetime in one protein crystal was the same as that of the free amino acid, and the longest SeMet lifetime measured was found in the other protein crystal type. This protection was found to arise from the folded

  7. Influence of LC Content on the Phase Structures of Side-Chain Liquid

    SciTech Connect

    Tenneti, K.; Chen, X; Li, C; Shen, Z; Wan, X; Fan, X; Zhou, Q; Rong, L; Hsiao, B

    2009-01-01

    We report the phase structures of a series of poly(styrene-block-{l_brace}3'-[4-(4-n-dodecyloxybenzoyloxy)benzoyloxy]-4-(12-methacryloyloxydodecyloxy)benzoyloxybiphenyl{r_brace}) (PS-b-PMAC) side-chain liquid crystalline block copolymers (SC LCBCP). The SC liquid crystalline polymer was formed by side attaching a bent-core mesogen to the polymer backbone using a 12-carbon spacer. The phase structure of the high and low fPMAC samples were investigated using differential scanning calorimetry, small-angle and wide-angle X-ray scattering, and transmission electron microscopy techniques. The PS coil block and PMAC LC block phase separate into a lamellar morphology in all of the samples investigated (volume fraction of PMAC fPMAC 0.31-0.65). However, both the LC phase and the orientation of the hierarchical structure under mechanical shear showed strong dependence on the LC content. Samples having a high fPMAC (0.5-0.65) showed a SmC2 LC phase (Smectic C denotes the LC molecules are tilted with respect to the layer normal, and 2 represents a bilayered structure), similar to that observed in PMAC homopolymers. Upon mechanical shear, these smectic layers oriented parallel to the shear plane and the BCP lamellae oriented perpendicular to the shear plane with the layer normal parallel to the vorticity direction. In samples having a lower fPMAC, the BCP lamellae laid parallel to the shear plane and the LC phase structure in these samples was columnar rectangular. A detailed structural and morphological study will be reported.

  8. Binding of tetramethylammonium to polyether side-chained aromatic hosts. Evaluation of the binding contribution from ether oxygen donors.

    PubMed

    Bartoli, Sandra; De Nicola, Gina; Roelens, Stefano

    2003-10-17

    A set of macrocyclic and open-chain aromatic ligands endowed with polyether side chains has been prepared to assess the contribution of ether oxygen donors to the binding of tetramethylammonium (TMA), a cation believed incapable of interacting with oxygen donors. The open-chain hosts consisted of an aromatic binding site and side chains possessing a variable number of ether oxygen donors; the macrocyclic ligands were based on the structure of a previously investigated host, the dimeric cyclophane 1,4-xylylene-1,4-phenylene diacetate (DXPDA), implemented with polyether-type side chains in the backbone. Association to tetramethylammonium picrate (TMAP) was measured in CDCl(3) at T = 296 K by (1)H NMR titrations. Results confirm that the main contribution to the binding of TMA comes from the cation-pi interaction established with the aromatic binding sites, but they unequivocally show that polyether chains participate with cooperative contributions, although of markedly smaller entity. Water is also bound, but the two guests interact with aromatic rings and oxygen donors in an essentially noncompetitive way. An improved procedure for the preparation of cyclophanic tetraester derivatives has been developed that conveniently recycles the oligomeric ester byproducts formed in the one-pot cyclization reaction. An alternative entry to benzylic diketones has also been provided that makes use of a low-order cyanocuprate reagent to prepare in fair yields a class of compounds otherwise uneasily accessible.

  9. Hydrogen-bonded side chain liquid crystalline block copolymer: Molecular design, synthesis, characterization and applications

    NASA Astrophysics Data System (ADS)

    Chao, Chi-Yang

    Block copolymers can self-assemble into highly regular, microphase-separated morphologies with dimensions at nanometer length scales. Potential applications such as optical wavelength photonic crystals, templates for nanolithographic patterning, or nanochannels for biomacromolecular separation take advantage of the well-ordered, controlled size microdomains of block copolymers. Side-chain liquid crystalline block copolymers (SCLCBCPs) are drawing increasing attention since the incorporation of liquid crystallinity turns their well-organized microstructures into dynamic functional materials. As a special type of block copolymer, hydrogen-bonded SCLCBCPs are unique, compositionally tunable materials with multiple dynamic functionalities that can readily respond to thermal, electrical and mechanical fields. Hydrogen-bonded SCLCBCPs were synthesized and assembled from host poly(styrene- b-acrylic acid) diblock copolymers with narrow molecular weight distributions as proton donors and guest imidazole functionalized mesogenic moieties as proton acceptors. In these studies non-covalent hydrogen bonding is employed to connect mesogenic side groups to a block copolymer backbone, both for its dynamic character as well as for facile materials preparation. The homogeneity and configuration of the hydrogen-bonded complexes were determined by both the molecular architecture of imidazolyl side groups and the process conditions. A one-dimensional photonic crystal composed of high molecular weight hydrogen-bonded SCLCBCP, with temperature dependent optical wavelength stop bands was successfully produced. The microstructures of hydrogen-bonded complexes could be rapidly aligned in an AC electric field at temperatures below the order-disorder transition but above their glass transitions. Remarkable dipolar properties of the mesogenic groups and thermal dissociation of hydrogen bonds are key elements to fast orientation switching. Studies of a wide range of mesogen and polymer

  10. Shear Flow Induced Transition from Liquid-Crystalline to Polymer Behavior in Side-Chain Liquid Crystal Polymers

    SciTech Connect

    Noirez, L.; Lapp, A.

    1997-01-01

    We determine the structure and conformation of side-chain liquid-crystalline polymers subjected to shear flow in the vicinity of the smectic phase by neutron scattering on the velocity gradient plane. Below the nematic-smectic transition we observe a typical liquid-crystal behavior; the smectic layers slide, leading to a main-chain elongation parallel to the velocity direction. In contrast,a shear applied above the transition induces a tilted main-chain conformation which is typical for polymer behavior. {copyright} {ital 1996} {ital The American Physical Society}

  11. Nucleic acid chemistry in the organic phase: from functionalized oligonucleotides to DNA side chain polymers.

    PubMed

    Liu, Kai; Zheng, Lifei; Liu, Qing; de Vries, Jan Willem; Gerasimov, Jennifer Y; Herrmann, Andreas

    2014-10-01

    DNA-incorporating hydrophobic moieties can be synthesized by either solid-phase or solution-phase coupling. On a solid support the DNA is protected, and hydrophobic units are usually attached employing phosphoramidite chemistry involving a DNA synthesizer. On the other hand, solution coupling in aqueous medium results in low yields due to the solvent incompatibility of DNA and hydrophobic compounds. Hence, the development of a general coupling method for producing amphiphilic DNA conjugates with high yield in solution remains a major challenge. Here, we report an organic-phase coupling strategy for nucleic acid modification and polymerization by introducing a hydrophobic DNA-surfactant complex as a reactive scaffold. A remarkable range of amphiphile-DNA structures (DNA-pyrene, DNA-triphenylphosphine, DNA-hydrocarbon, and DNA block copolymers) and a series of new brush-type DNA side-chain homopolymers with high DNA grafting density are produced efficiently. We believe that this method is an important breakthrough in developing a generalized approach to synthesizing functional DNA molecules for self-assembly and related technological applications.

  12. Differentiating amino acid residues and side chain orientations in peptides using scanning tunneling microscopy.

    PubMed

    Claridge, Shelley A; Thomas, John C; Silverman, Miles A; Schwartz, Jeffrey J; Yang, Yanlian; Wang, Chen; Weiss, Paul S

    2013-12-11

    Single-molecule measurements of complex biological structures such as proteins are an attractive route for determining structures of the large number of important biomolecules that have proved refractory to analysis through standard techniques such as X-ray crystallography and nuclear magnetic resonance. We use a custom-built low-current scanning tunneling microscope to image peptide structures at the single-molecule scale in a model peptide that forms β sheets, a structural motif common in protein misfolding diseases. We successfully differentiate between histidine and alanine amino acid residues, and further differentiate side chain orientations in individual histidine residues, by correlating features in scanning tunneling microscope images with those in energy-optimized models. Beta sheets containing histidine residues are used as a model system due to the role histidine plays in transition metal binding associated with amyloid oligomerization in Alzheimer's and other diseases. Such measurements are a first step toward analyzing peptide and protein structures at the single-molecule level.

  13. In Vitro Cytotoxicity of Benzopyranone Derivatives with Basic Side Chain Against Human Lung Cell Lines

    PubMed Central

    Musa, Musiliyu A.; Badisa, Veera L.D.; Latinwo, Lekan M.; Waryoba, Caroline; Ugochukwu, Ngozi

    2013-01-01

    Background Coumarins belong to an important group of useful drugs with diverse pharmacological properties. In the present study, the in vitro cytotoxicity of new coumarin-based benzopyranone derivatives containing diethylaminoethoxy (5), dimethylaminoethoxy (6), morpholinoethoxy (7), piperidinylethoxy (8) and pyrrolidinylethoxyl (9) amino side chain against human carcinoma (A549) and normal (LL47) lung cell lines was evaluated. Materials and Methods The cytotoxicity was evaluated by crystal violet dye binding assay. The effect of compound 9 on different phases of the cell cycle was determined using flow cytometry. Results In A549 cells, the 50% lethal dose (LD50) for compounds 5–9 were found to be 7.08, 5.0, 34.2, 8.33 and 5.83 µM, respectively, while in LL47 cells, the LD50 values were found to be 16.7, 20.4, 34.6, 15.4 and 8.75 µM, respectively after 48 h treatment. Cell cycle data indicated that A549 cells were arrested at different phases depending on the concentration. Conclusion Compounds 5–9 showed anticancer activity against lung cancer cell lines, while compound 6 showed highly selective anticancer activity. PMID:21115914

  14. Changes in cytochrome P450 side chain cleavage expression in the rat hippocampus after kainate injury.

    PubMed

    Chia, Wan-Jie; Jenner, Andrew M; Farooqui, Akhlaq A; Ong, Wei-Yi

    2008-03-01

    Our previous study showed an increase in total cholesterol level of the hippocampus after kainate-induced injury, but whether this is further metabolized to neurosteroids is not known. The first step in neurosteroid biosynthesis is the conversion of cholesterol to pregnenolone by the enzyme cytochrome P450 side chain cleavage (P450scc). This study was carried out to elucidate the expression of this enzyme in the kainate-lesioned rat hippocampus. A net decrease in P450scc protein was detected in hippocampal homogenates by Western blots at 2 weeks post-kainate injection (time of peak cholesterol concentration after kainate injury). Immunohistochemistry showed decreased labeling of the enzyme in neurons, but increased expression in a small number of astrocytes. The level of pregnenolone was also analyzed using a newly developed gas chromatography-mass spectrometry (GC-MS) method, optimized for the rat hippocampus. A non-significant tendency to a decrease in pregnenolone level was detected 2 weeks post-lesion. This is in contrast to a large increase in oxysterols in the lesioned hippocampus at this time (He et al. 2006). Together, they indicate that increased cholesterol in the kainate lesioned hippocampus is mostly metabolized to oxysterols, and not neurosteroids. PMID:18040670

  15. Improving ranking of models for protein complexes with side chain modeling and atomic potentials.

    PubMed

    Viswanath, Shruthi; Ravikant, D V S; Elber, Ron

    2013-04-01

    An atomically detailed potential for docking pairs of proteins is derived using mathematical programming. A refinement algorithm that builds atomically detailed models of the complex and combines coarse grained and atomic scoring is introduced. The refinement step consists of remodeling the interface side chains of the top scoring decoys from rigid docking followed by a short energy minimization. The refined models are then re-ranked using a combination of coarse grained and atomic potentials. The docking algorithm including the refinement and re-ranking, is compared favorably to other leading docking packages like ZDOCK, Cluspro, and PATCHDOCK, on the ZLAB 3.0 Benchmark and a test set of 30 novel complexes. A detailed analysis shows that coarse grained potentials perform better than atomic potentials for realistic unbound docking (where the exact structures of the individual bound proteins are unknown), probably because atomic potentials are more sensitive to local errors. Nevertheless, the atomic potential captures a different signal from the residue potential and as a result a combination of the two scores provides a significantly better prediction than each of the approaches alone.

  16. Anti-Biofouling Properties of Comblike Block Copolymers with Amphiphilic Side Chains

    SciTech Connect

    Krishnan,S.; Ayothi, R.; Hexemer, A.; Finlay, J.; Sohn, K.; Perry, R.; Ober, C.; Kramer, E.; Callow, M.; et al.

    2006-01-01

    Surfaces of novel block copolymers with amphiphilic side chains were studied for their ability to influence the adhesion of marine organisms. The surface-active polymer, obtained by grafting fluorinated molecules with hydrophobic and hydrophilic blocks to a block copolymer precursor, showed interesting bioadhesion properties. Two different algal species, one of which adhered strongly to hydrophobic surfaces, and the other, to hydrophilic surfaces, showed notably weak adhesion to the amphiphilic surfaces. Both organisms are known to secrete adhesive macromolecules, with apparently different wetting characteristics, to attach to underwater surfaces. The ability of the amphiphilic surface to undergo an environment-dependent transformation in surface chemistry when in contact with the extracellular polymeric substances is a possible reason for its antifouling nature. Near-edge X-ray absorption fine structure spectroscopy (NEXAFS) was used, in a new approach based on angle-resolved X-ray photoelectron spectroscopy (XPS), to determine the variation in chemical composition within the top few nanometers of the surface and also to study the surface segregation of the amphiphilic block. A mathematical model to extract depth-profile information from the normalized NEXAFS partial electron yield is developed.

  17. Synthesis, characterisation and drug release properties of microspheres of polystyrene with aliphatic polyester side-chains.

    PubMed

    Kukut, Manolya; Karal-Yilmaz, Oksan; Yagci, Yusuf

    2014-01-01

    A series of graft copolymers consisting of polystyrene backbone with biocompatible side chains based on (co)polymers of l-lactic acid and glycolic acid were synthesised by combination two controlled polymerisations, namely, nitroxide mediated radical polymerisation (NMRP) and ring opening polymerisation (ROP) with "Click" chemistry. The main goal of this work was to design new biodegradable microspheres using obtained graft copolymers for long-term sustained release of imatinib mesylate (IMM) as a model drug. The IMM loaded microspheres of the graft copolymers, polystyrene-g-poly(lactide-co-glycolide) (PS-g-PLLGA), polystyrene-g-poly(lactic acid) (PS-g-PLLA) and poly(lactic-coglycolic acid) (PLLGA) were then prepared by a modified water-in-oil-in-water (w1/o/w2) double emulsion/solvent evaporation technique. The optimised microspheres were characterised by particle size, encapsulation efficiency, and surface morphology also; their degradation and release properties were studied in vitro. The degradation studies of three different types of microspheres showed that the PS backbone of the graft copolymers slows down the degradation rate compared to PLLGA.

  18. Tunable transport through a quantum dot chain with side-coupled Majorana bound states

    SciTech Connect

    Jiang, Cui; Lu, Gang; Gong, Wei-Jiang

    2014-09-14

    We investigate the transport properties of a quantum dot (QD) chain side-coupled to a pair of Majorana bound states (MBSs). It is found that the zero-bias conductance is tightly dependent on the parity of QD number. First, if a Majorana zero mode is introduced to couple to one QD of the odd-numbered QD structure, the zero-bias conductance is equal to (e{sup 2})/(2h) , but the zero-bias conductance will experience a valley-to-peak transition if the Majorana zero mode couples to the different QDs of the even-numbered QD structure. On the other hand, when the inter-MBS coupling is nonzero, the zero-bias conductance spectrum shows a peak in the odd-numbered QD structure, and in the even-numbered QD structure one conductance valley appears at the zero-bias limit. These results show the feasibility to manipulate the current in a multi-QD structure based on the QD-MBS coupling. Also, such a system can be a candidate for detecting the MBSs.

  19. The identification of two arabinosyltransferases from tomato reveals functional equivalency of xyloglucan side chain substituents.

    PubMed

    Schultink, Alex; Cheng, Kun; Park, Yong Bum; Cosgrove, Daniel J; Pauly, Markus

    2013-09-01

    Xyloglucan (XyG) is the dominant hemicellulose present in the primary cell walls of dicotyledonous plants. Unlike Arabidopsis (Arabidopsis thaliana) XyG, which contains galactosyl and fucosyl substituents, tomato (Solanum lycopersicum) XyG contains arabinofuranosyl residues. To investigate the biological function of these differing substituents, we used a functional complementation approach. Candidate glycosyltransferases were identified from tomato by using comparative genomics with known XyG galactosyltransferase genes from Arabidopsis. These candidate genes were expressed in an Arabidopsis mutant lacking XyG galactosylation, and two of them resulted in the production of arabinosylated XyG, a structure not previously found in this plant species. These genes may therefore encode XyG arabinofuranosyltransferases. Moreover, the addition of arabinofuranosyl residues to the XyG of this Arabidopsis mutant rescued a growth and cell wall biomechanics phenotype, demonstrating that the function of XyG in plant growth, development, and mechanics has considerable flexibility in terms of the specific residues in the side chains. These experiments also highlight the potential of reengineering the sugar substituents on plant wall polysaccharides without compromising growth or viability. PMID:23893172

  20. Side-Chain Liquid Crystalline Poly(meth)acrylates with Bent-Core Mesogens

    SciTech Connect

    Chen,X.; Tenneti, K.; Li, C.; Bai, Y.; Wan, X.; Fan, X.; Zhou, Q.; Rong, L.; Hsiao, B.

    2007-01-01

    We report the design, synthesis, and characterization of side-chain liquid crystalline (LC) poly(meth)acrylates with end-on bent-core liquid crystalline (BCLC) mesogens. Both conventional free radical polymerization and atom transfer radical polymerization have been used to synthesize these liquid crystalline polymers (LCP). The resulting polymers exhibit thermotropic LC behavior. Differential scanning calorimetry, thermopolarized light microscopy, wide-angle X-ray diffraction, and small-angle X-ray scattering were used to characterize the LC structure of both monomers and polymers. The electro-optic (EO) measurement was carried out by applying a triangular wave and measuring the LC EO response. SmCP (Smectic C indicates the LC molecules are tilted with respect to the layer normal; P denotes polar ordering) phases were observed for both monomers and polymers. In LC monomers, typical antiferroelectric switching was observed. In the ground state, SmCP{sub A} (A denotes antiferroelectric) was observed which switched to SmCP{sub F} (F denotes ferroelectric) upon applying an electric field. In the corresponding LCP, a unique bilayer structure was observed, which is different from the reported BCLC bilayer SmCG (G denotes generated) phase. Most of the LCPs did not switch upon applying electric field while weak AF switching was observed in a low molecular weight poly{l_brace}3'-[4-(4-n-dodecyloxybenzoyloxy)benzoyloxy]-4-(12-acryloyloxydodecyloxy)benzoyloxybiphenyl{r_brace} sample.

  1. Characterization of novel perylene diimides containing aromatic amino acid side chains

    NASA Astrophysics Data System (ADS)

    Farooqi, Mohammed J.; Penick, Mark A.; Burch, Jessica; Negrete, George R.; Brancaleon, Lorenzo

    2016-01-01

    Perylene diimide derivatives have attracted initial interest as industrial dyes. Recently, much attention has been focused on their strong π- π stacks resulting from the large PDI aromatic core. These PDI stacks have distinct optical properties, and provide informative models that could mimic light-harvesting systems and initial charge transfer typical of photosynthetic systems. The absorption property of PDI derivatives may be tuned from visible to near-infrared region by peripheral substitution. We have studied a new class of PDI derivatives with aryl substituents derived from the side chains of aromatic aminoacids (Tyrosine, Tryptophan and Phenylalanine). We have investigated their absorption and the fluorescence properties in a set of organic solvents and established their different tendencies to aggregate in solution despite their solubility. Most aggregation appears to be unordered. One PDI analogue (the one formed from Tyr) in Methanol, however, appears to form J-type aggregates. Based on our results the compounds appear to be promising for future investigations regarding the interaction of these dyes with biomolecules.

  2. Evaluations of Mesogen Orientation in Thin Films of Polyacrylate with Cyanobiphenyl Side Chain.

    PubMed

    Tanaka, Daisuke; Mizuno, Tasuku; Hara, Mitsuo; Nagano, Shusaku; Saito, Itsuki; Yamamoto, Katsuhiro; Seki, Takahiro

    2016-04-19

    The orientation behavior of mesogens in a polyacrylate with cyanobiphenyl (CB) side chain in thin films was investigated in detail by UV-vis absorption spectroscopy and grazing incidence small-angle X-ray scattering (GI-SAXS) measurements using both high-energy X-rays of Cu Kα line (λ = 0.154 nm) and low-energy synchrotron X-rays (λ = 0.539 nm). By changing the film thickness ranging 7-200 nm, it is concluded that the planar orientation is predominant for thin films with thickness below 10-15 nm. This planar mesogen orientation near the substrate surface coexists with the homeotropically aligned CB mesogens in films thicker than 30 nm. For the thinnest 7 nm film, the planar orientation is unexpectedly lost, which is in consort with a disordering of smectic layer structure. Peculiar orienting characteristics of CB mesogen are suggested, which probably stem from the tendency to form an antiparallel arrangement of mesogens due to the strong dipole moment of the terminal cyano group. PMID:27031094

  3. Characterization of novel perylene diimides containing aromatic amino acid side chains

    PubMed Central

    Farooqi, Mohammed J.; Penick, Mark A.; Burch, Jessica; Negrete, George R.; Brancaleon, Lorenzo

    2015-01-01

    Perylene diimide derivatives have attracted initial interest as industrial dyes. Recently, much attention has been focused on their strong π–π stacks resulting from the large PDI aromatic core. These PDI stacks have distinct optical properties, and provide informative models that could mimic light-harvesting systems and initial charge transfer typical of photosynthetic systems. The absorption property of PDI derivatives may be tuned from visible to near-infrared region by peripheral substitution. We have studied a new class of PDI derivatives with aryl substituents derived from the side chains of aromatic aminoacids (Tyrosine, Tryptophan and Phenylalanine). We have investigated their absorption and the fluorescence properties in a set of organic solvents and established their different tendencies to aggregate in solution despite their solubility. Most aggregation appears to be unordered. One PDI analogue (the one formed from Tyr) in Methanol, however, appears to form J-type aggregates. Based on our results the compounds appear to be promising for future investigations regarding the interaction of these dyes with biomolecules. PMID:26298679

  4. Side-chain engineering of benzodithiophene-fluorinated quinoxaline low-band-gap co-polymers for high-performance polymer solar cells.

    PubMed

    Xu, Xiaopeng; Wu, Yulei; Fang, Junfeng; Li, Zuojia; Wang, Zhenguo; Li, Ying; Peng, Qiang

    2014-10-01

    A new series of donor-acceptor co-polymers based on benzodithiophene and quinoxaline with various side chains have been developed for polymer solar cells. The effect of the degree of branching and dimensionality of the side chains were systematically investigated on the thermal stability, optical absorption, energy levels, molecular packing, and photovoltaic performance of the resulting co-polymers. The results indicated that the linear and 2D conjugated side chains improved the thermal stabilities and optical absorptions. The introduction of alkylthienyl side chains could efficiently lower the energy levels compared with the alkoxyl-substituted analogues, and the branched alkoxyl side chains could deepen the HOMO levels relative to the linear alkoxyl chains. The branched alkoxyl groups induced better lamellar-like ordering, but poorer face-to-face packing behavior. The 2D conjugated side chains had a negative influence on the crystalline properties of the co-polymers. The performance of the devices indicated that the branched alkoxyl side chains improved the Voc, but decreased the Jsc and fill factor (FF). However, the 2D conjugated side chains would increase the Voc, Jsc, and FF simultaneously. For the first time, our work provides insight into molecular design strategies through side-chain engineering to achieve efficient polymer solar cells by considering both the degree of branching and dimensionality.

  5. The Relationship of Pretilt Angle and Chemical Structure of Rubbed Organo-Soluble Side-Chain Polyimides

    NASA Astrophysics Data System (ADS)

    Mann, Ian K.; Bai, F.; Bai, Z.; Ge, J.; Sun, L.; Wang, H.; Zhang, Z.; Harris, Frank W.; Cheng, Stephen Z. D.

    2000-03-01

    This work is concerned with the relationship between the properties of the pretilt angles and chemical structure of the alignment layer for a series of novel organo-soluble side-chain polyimides developed at The University of Akron. The polyimides were spin cast on ITO glass substrates and mechanically rubbed with a velvet cloth. Liquid crystal display cells were constructed with an anti-parallel geometry using 10μm glass spacers and filled with the nematic liquid crystal mixture E7. The pretilt angle, which is defined as the angle between the liquid crystal director and the substrate, was measured using the magnetic null method. Various side-chain polyimide films were prepared and pretilt angles were determined employing identical processing conditions. In general, polyimides containing long flexible aliphatic side-chains (no. carbons >12) resulted in high pretilt angles (>20^o) however over time the pretilt shifted to a homeotropic alignment (i.e. 90^o to the substrate). The stability of the pretilt angles was improved when polyimide copolymers were used. Further enhancement of the stability was achieved by crosslinking the system prior to rubbing. Liquid crystal like side-chains (cyanobiphenol and biphenol based) resulted in stable pretilt angles ranging from 20 to 40^o for a spacer length of six carbons. Several surface techniques were used to study the effect of rubbing, including; atomic force microscopy, surfaced enhanced Raman scattering, and contact angle.

  6. Attenuating HIV Tat/TAR-mediated protein expression by exploring the side chain length of positively charged residues.

    PubMed

    Wu, Cheng-Hsun; Chen, Yi-Ping; Liu, Shing-Lung; Chien, Fan-Ching; Mou, Chung-Yuan; Cheng, Richard P

    2015-12-01

    RNA is a drug target involved in diverse cellular functions and viral processes. Molecules that inhibit the HIV TAR RNA-Tat protein interaction may attenuate Tat/TAR-dependent protein expression and potentially serve as anti-HIV therapeutics. By incorporating positively charged residues with mixed side chain lengths, we designed peptides that bind TAR RNA with enhanced intracellular activity. Tat-derived peptides that were individually substituted with positively charged residues with varying side chain lengths were evaluated for TAR RNA binding. Positively charged residues with different side chain lengths were incorporated at each Arg and Lys position in the Tat-derived peptide to enhance TAR RNA binding. The resulting peptides showed enhanced TAR RNA binding affinity, cellular uptake, nuclear localization, proteolytic resistance, and inhibition of intracellular Tat/TAR-dependent protein expression compared to the parent Tat-derived peptide with no cytotoxicity. Apparently, the enhanced inhibition of protein expression by these peptides was not determined by RNA binding affinity, but by proteolytic resistance. Despite the high TAR binding affinity, a higher binding specificity would be necessary for practical purposes. Importantly, altering the positively charged residue side chain length should be a viable strategy to generate potentially useful RNA-targeting bioactive molecules.

  7. Cyclization and unsaturation rather than isomerisation of side chains govern the selective antibacterial activity of cationic-amphiphilic polymers.

    PubMed

    Uppu, D S S M; Bhowmik, M; Samaddar, S; Haldar, J

    2016-03-28

    Membrane-active agents represent a promising alternative to overcome antibiotic resistance. Here, we report cationic-amphiphilic polymers with variations in the side chain architecture such as cyclization, isomerization and unsaturation that resulted in potent antibacterial activity and low mammalian cell toxicity with a membrane-active mode of action.

  8. Thiophene-thiazolothiazole copolymers: significant impact of side chain composition on backbone orientation and solar cell performances.

    PubMed

    Osaka, Itaru; Saito, Masahiko; Koganezawa, Tomoyuki; Takimiya, Kazuo

    2014-01-15

    The backbone orientation in the thiophene-thiazolothiazole (TzTz) copolymer system can be altered by tuning of the alky side chain composition. We highlight that the orientation significantly impact their solar cell efficiency in particular when using thicker active layers.

  9. Synthesis and the third-order non-linear optical properties of new azobenzene-containing side-chain polymers

    NASA Astrophysics Data System (ADS)

    Li, Najun; Lu, Jianmei; Xu, Qingfeng; Wang, Lihua

    2006-09-01

    A new series of aromatic azobenzol compounds containing vinyl have been designed as monomers. The azobenzene-containing side-chain polymers containing azo NLO chromophore in each side chain have been synthesized via free radical polymerization. FT-IR, elemental analysis and 1H NMR were performed to characterize the azo monomers. The molecular weight of the polymers and their distribution were determined by gel permeation chromatography (GPC). The third-order NLO coefficient of azo monomers and their polymers were measured by degenerated four wave mixing (DFWM) technique. As a result, the enhancement of the molecular conjugation and the increase of the NLO chromophore concentration in the molecular chain contribute much to heightening the third-order NLO effect. The electronic effect of substituent on the azobenzol group and the push-pull electronic structure contributes much to enhancing the NLO property.

  10. Amphiphilic Surface Active Triblock Copolymers with Mixed Hydrophobic and Hydrophilic Side Chains for Tuned Marine Fouling-Release Properties

    SciTech Connect

    Park, D.; Weinman, C; Finlay, J; Fletcher, B; Paik, M; Sundaram, H; Dimitriou, M; Sohn, K; Callow, M; et al.

    2010-01-01

    Two series of amphiphilic triblock surface active block copolymers (SABCs) were prepared through chemical modification of two polystyrene-block-poly(ethylene-ran-butylene)-block-polyisoprene ABC triblock copolymer precursors. The methyl ether of poly(ethylene glycol) [M{sub n} {approx} 550 g/mol (PEG550)] and a semifluorinated alcohol (CF{sub 3}(CF{sub 2}){sub 9}(CH{sub 2}){sub 10}OH) [F10H10] were attached at different molar ratios to impart both hydrophobic and hydrophilic groups to the isoprene segment. Coatings on glass slides consisting of a thin layer of the amphiphilic SABC deposited on a thicker layer of an ABA polystyrene-block-poly(ethylene-ran-butylene)-block-polystyrene thermoplastic elastomer were prepared for biofouling assays with algae. Dynamic water contact angle analysis, X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) measurements were utilized to characterize the surfaces. Clear differences in surface structure were realized as the composition of attached side chains was varied. In biofouling assays, the settlement (attachment) of zoospores of the green alga Ulva was higher for surfaces incorporating a large proportion of the hydrophobic F10H10 side chains, while surfaces with a large proportion of the PEG550 side chains inhibited settlement. The trend in attachment strength of sporelings (young plants) of Ulva did not show such an obvious pattern. However, amphiphilic SABCs incorporating a mixture of PEG550 and F10H10 side chains performed the best. The number of cells of the diatom Navicula attached after exposure to flow decreased as the content of PEG550 to F10H10 side chains increased.

  11. Microbial biodegradation of aromatic alkanoic naphthenic acids is affected by the degree of alkyl side chain branching

    PubMed Central

    Johnson, Richard J; Smith, Ben E; Sutton, Paul A; McGenity, Terry J; Rowland, Steven J; Whitby, Corinne

    2011-01-01

    Naphthenic acids (NAs) occur naturally in oil sands and enter the environment through natural and anthropogenic processes. NAs comprise toxic carboxylic acids that are difficult to degrade. Information on NA biodegradation mechanisms is limited, and there are no studies on alkyl branched aromatic alkanoic acid biodegradation, despite their contribution to NA toxicity and recalcitrance. Increased alkyl side chain branching has been proposed to explain NA recalcitrance. Using soil enrichments, we examined the biodegradation of four aromatic alkanoic acid isomers that differed in alkyl side chain branching: (4′-n-butylphenyl)-4-butanoic acid (n-BPBA, least branched); (4′-iso-butylphenyl)-4-butanoic acid (iso-BPBA); (4′-sec-butylphenyl)-4-butanoic acid (sec-BPBA) and (4′-tert-butylphenyl)-4-butanoic acid (tert-BPBA, most branched). n-BPBA was completely metabolized within 49 days. Mass spectral analysis confirmed that the more branched isomers iso-, sec- and tert-BPBA were transformed to their butylphenylethanoic acid (BPEA) counterparts at 14 days. The BPEA metabolites were generally less toxic than BPBAs as determined by Microtox assay. n-BPEA was further transformed to a diacid, showing that carboxylation of the alkyl side chain occurred. In each case, biodegradation of the carboxyl side chain proceeded through beta-oxidation, which depended on the degree of alkyl side chain branching, and a BPBA degradation pathway is proposed. Comparison of 16S rRNA gene sequences at days 0 and 49 showed an increase and high abundance at day 49 of Pseudomonas (sec-BPBA), Burkholderia (n-, iso-, tert-BPBA) and Sphingomonas (n-, sec-BPBA). PMID:20962873

  12. Oligosaccharide Side Chains of Glycoproteins that Remain in the High-Mannose Form Are Not Accessible to Glycosidases 1

    PubMed Central

    Faye, Loïc; Johnson, Kenneth D.; Chrispeels, Maarten J.

    1986-01-01

    Glycoproteins present in the soluble and organelle fractions of developing bean (Phaseolus vulgaris) cotyledons were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, affinoblotting, fractionation on immobilized concanavalin A (ConA), and digestion of the oligosaccharide side chains with specific glycosidases before and after protein denaturation. These studies led to the following observations. (a) Bean cotyledons contain a large variety of glycoproteins that bind to ConA. Binding to ConA can be eliminated by prior digestion of denatured proteins with α-mannosidase or endoglycosidase H, indicating that binding to ConA is mediated by high-mannose oligosaccharide side chains. (b) Bean cotyledons contain a large variety of fucosylated glycoproteins which bind to ConA. Because fucose-containing oligosaccharide side chains do not bind to ConA, such proteins must have both high-mannose and modified oligosaccharides. (c) For all the glycoproteins examined except one, the high-mannose oligosaccharides on the undenatured proteins are accessible to ConA and partially accessible to jack bean α-mannosidase. (d) Treatment of the native proteins with α-mannosidase removes only 1 or 2 mannose residues from the high-mannose oligosaccharides. Similar treatments of sodium dodecyl sulfate-denatured or pronase-digested glycoproteins removes all α-mannose residues. The results support the following conclusions: certain side chains remain unmodified as high-mannose oligosaccharides even though the proteins to which they are attached pass through the Golgi apparatus, where other oligosaccharide chains are modified. The chains remain unmodified because they are not accessible to processing enzymes such as the Golgilocalized α-mannosidase. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:16664775

  13. Polymer gels with associating side chains and their interaction with surfactants

    NASA Astrophysics Data System (ADS)

    Gordievskaya, Yulia D.; Rumyantsev, Artem M.; Kramarenko, Elena Yu.

    2016-05-01

    Conformational behaviour of hydrophobically modified (HM) polymer gels in solutions of nonionic surfactants is studied theoretically. A HM gel contains hydrophobic side chains (stickers) grafted to its subchains. Hydrophobic stickers are capable to aggregate into joint micelles with surfactant molecules. Micelles containing more than one sticker serve as additional physical cross-links of the network, and their formation causes gel shrinking. In the proposed theoretical model, the interior of the gel/surfactant complex is treated as an array of densely packed spherical polymer brushes consisting of gel subchains tethered to the surface of the spherical sticker/surfactant micelles. Effect of stickers length and grafting density, surfactant concentration and hydrophobicity on gel swelling as well as on hydrophobic association inside it is analyzed. It is shown that increasing surfactant concentration can result in a gel collapse, which is caused by surfactant-induced hydrophobic aggregation of stickers, and a successive gel reswelling. The latter should be attributed to a growing fraction of surfactants in joint aggregates and, hence, increasing number of micelles containing only one sticker and not participating in gel physical cross-linking. In polyelectrolyte (PE) gels hydrophobic aggregation is opposed by osmotic pressure of mobile counterions, so that at some critical ionization degree hydrophobic association is completely suppressed. Hydrophobic modification of polymers is shown to open new ways for controlling gel responsiveness. In particular, it is discussed that incorporation of photosensitive groups into gel subchains and/or surfactant tail could give a possibility to vary the gel volume by light. Since hydrophobic aggregation regularities in gels and solutions are common, we hope our findings will be useful for design of polymer based self-healing materials as well.

  14. Studies on Deprotection of Cysteine and Selenocysteine Side-Chain Protecting Groups†

    PubMed Central

    Harris, Katharine M.; Flemer, Stevenson; Hondal, Robert J.

    2013-01-01

    We present here a simple method for deprotecting p-methoxybenzyl groups and acetamidomethyl groups from the side-chains of cysteine and selenocysteine. This method uses the highly elecrophilic, aromatic disulfides 2,2′-dithiobis(5-nitropyridine) (DTNP) and 2,2′-dithiodipyridine (DTP) dissolved in TFA to effect removal of these heretofore difficult to remove protecting groups. The dissolution of these reagents in TFA in fact serves to “activate” them for the deprotection reaction because protonation of the nitrogen atom of the pyridine ring makes the disulfide bond more electrophilic. Thus these reagents can be added to any standard cleavage cocktail used in peptide synthesis. The p-methoxybenzyl group of selenocysteine is easily removed by DTNP. Only sub-stoichiometric amounts of DTNP are required to cause full removal of the p-methoxybenzyl group, with as little as 0.2 equivalents necessary to effect 70% removal of the protecting group. The ability to remove the p-methoxybenzyl group from cysteine using DTNP required 2 equivalents of DTNP and the addition of thioanisole for complete deprotection. Thioanisole was absolutely required for the reaction in the case of the sulfur-containing amino acids, while it was not required for selenocysteine. The results are consistent with thioanisole acting as a catalyst. The acetamidomethyl group of cysteine can also be removed using DTNP, but required the addition of > 15 equivalents to be effective. DTP was less robust as a deprotection reagent. We also demonstrate that this chemistry can be used in a simultaneous cyclization/deprotection reaction between selenocysteine and cysteine residues protected by p-methoxybenzyl groups to form a selenylsulfide bond, demonstrating future high utility of the deprotection method. PMID:17031870

  15. One-sided polymerase chain reaction: the amplification of cDNA.

    PubMed Central

    Ohara, O; Dorit, R L; Gilbert, W

    1989-01-01

    We report a rapid technique, based on the polymerase chain reaction (PCR), for the direct targeting, enhancement, and sequencing of previously uncharacterized cDNAs. This method is not limited to previously sequenced transcripts, since it requires only two adjacent or partially overlapping specific primers from only one side of the region to be amplified. These primers can be located anywhere within the message. The specific primers are used in conjunction with nonspecific primers targeted either to the poly(A)+ region of the message or to an enzymatically synthesized d(A) tail. Pairwise combinations of specific and general primers allow for the amplification of regions both 3' and 5' to the point of entry into the message. The amplified PCR products can be cloned, sequenced directly by genomic sequencing, or labeled for sequencing by amplifying with a radioactive primer. We illustrate the power of this approach by deriving the cDNA sequences for the skeletal muscle alpha-tropomyosins of European common frog (Rana temporaria) and zebrafish (Brachydanio rerio) using only 300 ng of a total poly(A)+ preparation. In these examples, we gained initial entry into the tropomyosin messages by using heterologous primers (to conserved regions) derived from the rat skeletal muscle alpha-tropomyosin sequence. The frog and zebrafish sequences are used in an analysis of tropomyosin evolution across the vertebrate phylogenetic spectrum. The results underscore the conservative nature of the tropomyosin molecule and support the notion of a constrained heptapeptide unit as the fundamental structural motif of tropomyosin. Images PMID:2788276

  16. Structure-Function Studies of Hydrophobic Residues That Clamp a Basic Glutamate Side Chain during Catalysis by Triosephosphate Isomerase.

    PubMed

    Richard, John P; Amyes, Tina L; Malabanan, M Merced; Zhai, Xiang; Kim, Kalvin J; Reinhardt, Christopher J; Wierenga, Rik K; Drake, Eric J; Gulick, Andrew M

    2016-05-31

    Kinetic parameters are reported for the reactions of whole substrates (kcat/Km, M(-1) s(-1)) (R)-glyceraldehyde 3-phosphate (GAP) and dihydroxyacetone phosphate (DHAP) and for the substrate pieces [(kcat/Km)E·HPi/Kd, M(-2) s(-1)] glycolaldehyde (GA) and phosphite dianion (HPi) catalyzed by the I172A/L232A mutant of triosephosphate isomerase from Trypanosoma brucei brucei (TbbTIM). A comparison with the corresponding parameters for wild-type, I172A, and L232A TbbTIM-catalyzed reactions shows that the effect of I172A and L232A mutations on ΔG(⧧) for the wild-type TbbTIM-catalyzed reactions of the substrate pieces is nearly the same as the effect of the same mutations on TbbTIM previously mutated at the second side chain. This provides strong evidence that mutation of the first hydrophobic side chain does not affect the functioning of the second side chain in catalysis of the reactions of the substrate pieces. By contrast, the effects of I172A and L232A mutations on ΔG(⧧) for wild-type TbbTIM-catalyzed reactions of the whole substrate are different from the effect of the same mutations on TbbTIM previously mutated at the second side chain. This is due to the change in the rate-determining step that determines the barrier to the isomerization reaction. X-ray crystal structures are reported for I172A, L232A, and I172A/L232A TIMs and for the complexes of these mutants to the intermediate analogue phosphoglycolate (PGA). The structures of the PGA complexes with wild-type and mutant enzymes are nearly superimposable, except that the space opened by replacement of the hydrophobic side chain is occupied by a water molecule that lies ∼3.5 Å from the basic side chain of Glu167. The new water at I172A mutant TbbTIM provides a simple rationalization for the increase in the activation barrier ΔG(⧧) observed for mutant enzyme-catalyzed reactions of the whole substrate and substrate pieces. By contrast, the new water at the L232A mutant does not predict the decrease in

  17. Structure-Function Studies of Hydrophobic Residues That Clamp a Basic Glutamate Side Chain during Catalysis by Triosephosphate Isomerase.

    PubMed

    Richard, John P; Amyes, Tina L; Malabanan, M Merced; Zhai, Xiang; Kim, Kalvin J; Reinhardt, Christopher J; Wierenga, Rik K; Drake, Eric J; Gulick, Andrew M

    2016-05-31

    Kinetic parameters are reported for the reactions of whole substrates (kcat/Km, M(-1) s(-1)) (R)-glyceraldehyde 3-phosphate (GAP) and dihydroxyacetone phosphate (DHAP) and for the substrate pieces [(kcat/Km)E·HPi/Kd, M(-2) s(-1)] glycolaldehyde (GA) and phosphite dianion (HPi) catalyzed by the I172A/L232A mutant of triosephosphate isomerase from Trypanosoma brucei brucei (TbbTIM). A comparison with the corresponding parameters for wild-type, I172A, and L232A TbbTIM-catalyzed reactions shows that the effect of I172A and L232A mutations on ΔG(⧧) for the wild-type TbbTIM-catalyzed reactions of the substrate pieces is nearly the same as the effect of the same mutations on TbbTIM previously mutated at the second side chain. This provides strong evidence that mutation of the first hydrophobic side chain does not affect the functioning of the second side chain in catalysis of the reactions of the substrate pieces. By contrast, the effects of I172A and L232A mutations on ΔG(⧧) for wild-type TbbTIM-catalyzed reactions of the whole substrate are different from the effect of the same mutations on TbbTIM previously mutated at the second side chain. This is due to the change in the rate-determining step that determines the barrier to the isomerization reaction. X-ray crystal structures are reported for I172A, L232A, and I172A/L232A TIMs and for the complexes of these mutants to the intermediate analogue phosphoglycolate (PGA). The structures of the PGA complexes with wild-type and mutant enzymes are nearly superimposable, except that the space opened by replacement of the hydrophobic side chain is occupied by a water molecule that lies ∼3.5 Å from the basic side chain of Glu167. The new water at I172A mutant TbbTIM provides a simple rationalization for the increase in the activation barrier ΔG(⧧) observed for mutant enzyme-catalyzed reactions of the whole substrate and substrate pieces. By contrast, the new water at the L232A mutant does not predict the decrease in

  18. Calculation of electron paramagnetic resonance spectra from Brownian dynamics trajectories: application to nitroxide side chains in proteins.

    PubMed Central

    Steinhoff, H J; Hubbell, W L

    1996-01-01

    We present a method to simulate electron paramagnetic resonance spectra of spin-labeled proteins that explicitly includes the protein structure in the vicinity of the attached spin label. The method is applied to a spin-labeled polyleucine alpha-helix trimer. From short (6 ns) stochastic dynamics simulations of this trimer, an effective potential energy function is calculated. Interaction with secondary and tertiary structures determine the reorientational motion of the spin label side chains. After reduction to a single particle problem, long stochastic dynamic trajectories (700 ns) of the spin label side-chain reorientation are calculated from which the Lamor frequency trajectory and subsequently the electron paramagnetic resonance spectrum is determined. The simulated spectra agree well with experimental electron paramagnetic resonance spectra of bacteriorhodopsin mutants with spin labels in similar secondary and tertiary environments as in the polyleucine. Images FIGURE 1 PMID:8889196

  19. Tuning Structural and Mechanical Properties of Two-Dimensional Molecular Crystals: The Roles of Carbon Side Chains

    SciTech Connect

    Cun, Huanyao; Wang, Yeliang; Du, S X; Zhang, Lei; Zhang, Lizhi; Yang, Bing; He, Xiaobo; Wang, Yue; Zhu, Xueyan; Yuan, Quanzi; Zhao, Ya-Pu; Ouyang, Min; Hofer, Werner A.; Pennycook, Stephen J; Gao, Hong-jun

    2012-01-01

    A key requirement for the future applicability of molecular electronics devices is a resilience of their properties to mechanical deformation. At present, however, there is no fundamental understanding of the origins of mechanical properties of molecular films. Here we use quinacridone, which possesses flexible carbon side chains, as a model molecular system to address this issue. Eight molecular configurations with different molecular coverage are identified by scanning tunneling microscopy. Theoretical calculations reveal quantitatively the roles of different molecule-molecule and molecule-substrate interactions and predict the observed sequence of configurations. Remarkably, we find that a single Young's modulus applies for all configurations, the magnitude of which is controlled by side chain length, suggesting a versatile avenue for tuning not only the physical and chemical properties of molecular films but also their elastic properties.

  20. Fourier transform microwave spectroscopy of Ac-Ser-NH2: the role of side chain interactions in peptide folding.

    PubMed

    Cabezas, Carlos; Robben, Martinus A T; Rijs, Anouk M; Peña, Isabel; Alonso, J L

    2015-08-21

    Serine capped dipeptide N-acetyl-l-serinamide (Ac-Ser-NH2) has been investigated using Fourier transform microwave spectroscopic techniques combined with laser ablation sources. Spectral signatures originating from one dominant species have been detected in the supersonic expansion. Rotational and nuclear quadrupole coupling constants of the two (14)N nuclei have been used in the characterization of a C/γ-turn structure, which is stabilized by a CO∙∙∙HN intramolecular hydrogen bond closing a seven-membered ring. Two extra hydrogen bonds involving the polar side chain (-CH2OH) further stabilize the structure. The non-observation of C5 species, attributed to the presence of the polar side chain, is in contrast with the previous gas phase observation of the related dipeptides containing glycine or alanine residues. The A-E splitting pattern arising from the internal rotation of the methyl group has been analyzed and the internal rotation barrier has been determined.

  1. Tuning structural and mechanical properties of two-dimensional molecular crystals: the roles of carbon side chains.

    PubMed

    Cun, Huanyao; Wang, Yeliang; Du, Shixuan; Zhang, Lei; Zhang, Lizhi; Yang, Bing; He, Xiaobo; Wang, Yue; Zhu, Xueyan; Yuan, Quanzi; Zhao, Ya-Pu; Ouyang, Min; Hofer, Werner A; Pennycook, Stephen J; Gao, Hong-jun

    2012-03-14

    A key requirement for the future applicability of molecular electronics devices is a resilience of their properties to mechanical deformation. At present, however, there is no fundamental understanding of the origins of mechanical properties of molecular films. Here we use quinacridone, which possesses flexible carbon side chains, as a model molecular system to address this issue. Eight molecular configurations with different molecular coverage are identified by scanning tunneling microscopy. Theoretical calculations reveal quantitatively the roles of different molecule-molecule and molecule-substrate interactions and predict the observed sequence of configurations. Remarkably, we find that a single Young's modulus applies for all configurations, the magnitude of which is controlled by side chain length, suggesting a versatile avenue for tuning not only the physical and chemical properties of molecular films but also their elastic properties.

  2. Triazine-Based Sequence-Defined Polymers with Side-Chain Diversity and Backbone-Backbone Interaction Motifs.

    PubMed

    Grate, Jay W; Mo, Kai-For; Daily, Michael D

    2016-03-14

    Sequence control in polymers, well-known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence-defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone-backbone interactions, including H-bonding motifs and pi-pi interactions. This architecture is arguably biomimetic while differing from sequence-defined polymers having peptide bonds. The synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone-backbone hydrogen-bonding motifs, and will thus enable new macromolecules and materials with useful functions. PMID:26865312

  3. Specific Interactions of Neutral Side Chains of an Adsorbed Protein with the Surface of α-Quartz and Silica Gel.

    PubMed

    Odinokov, Alexey V; Bagaturyants, Alexander A

    2015-07-16

    Many key features of the protein adsorption on the silica surfaces still remain unraveled. One of the open questions is the interaction of nonpolar side chains with siloxane cavities. Here, we use nonequilibrium molecular dynamics simulations for the detailed investigation of the binding of several hydrophobic and amphiphilic protein side chains with silica surface. These interactions were found to be a possible driving force for protein adsorption. The free energy gain was larger for the disordered surface of amorphous silica gel as compared to α-quartz, but the impact depended on the type of amino acid. The dependence was analyzed from the structural point of view. For every amino acid an enthalpy-entropy compensation behavior was observed. These results confirm a hypothesis of an essential role of hydrophobic interactions in protein unfolding and irreversible adsorption on the silica surface.

  4. Phenylalanyl-Glycyl-Phenylalanine Tripeptide: A Model System for Aromatic-Aromatic Side Chain Interactions in Proteins

    SciTech Connect

    Valdes, Haydee; Pluhackova, Kristyna; Hobza, Pavel

    2009-09-08

    The performance of a wide range of quantum chemical calculations for the ab initio study of realistic model systems of aromatic-aromatic side chain interactions in proteins (in particular those π-π interactions occurring between adjacent residues along the protein sequence) is here assessed on the phenylalanyl-glycyl-phenylalanine (FGF) tripeptide. Energies and geometries obtained at different levels of theory are compared with CCSD(T)/CBS benchmark energies and RI-MP2/cc-pVTZ benchmark geometries, respectively. Consequently, a protocol of calculation alternative to the very expensive CCSD(T)/CBS is proposed. In addition to this, the preferred orientation of the Phe aromatic side chains is discussed and compared with previous results on the topic.

  5. Study of Class I and Class III Polyhydroxyalkanoate (PHA) Synthases with Substrates Containing a Modified Side Chain.

    PubMed

    Jia, Kaimin; Cao, Ruikai; Hua, Duy H; Li, Ping

    2016-04-11

    Polyhydroxyalkanoates (PHAs) are carbon and energy storage polymers produced by a variety of microbial organisms under nutrient-limited conditions. They have been considered as an environmentally friendly alternative to oil-based plastics due to their renewability, versatility, and biodegradability. PHA synthase (PhaC) plays a central role in PHA biosynthesis, in which its activity and substrate specificity are major factors in determining the productivity and properties of the produced polymers. However, the effects of modifying the substrate side chain are not well understood because of the difficulty to accessing the desired analogues. In this report, a series of 3-(R)-hydroxyacyl coenzyme A (HACoA) analogues were synthesized and tested with class I synthases from Chromobacterium sp. USM2 (PhaCCs and A479S-PhaCCs) and Caulobacter crescentus (PhaCCc) as well as class III synthase from Allochromatium vinosum (PhaECAv). It was found that, while different PHA synthases displayed distinct preference with regard to the length of the alkyl side chains, they could withstand moderate side chain modifications such as terminal unsaturated bonds and the azide group. Specifically, the specific activity of PhaCCs toward propynyl analogue (HHxyCoA) was only 5-fold less than that toward the classical substrate HBCoA. The catalytic efficiency (kcat/Km) of PhaECAv toward azide analogue (HABCoA) was determined to be 2.86 × 10(5) M(-1) s(-1), which was 6.2% of the value of HBCoA (4.62 × 10(6) M(-1) s(-1)) measured in the presence of bovine serum albumin (BSA). These side chain modifications may be employed to introduce new material functions to PHAs as well as to study PHA biogenesis via click-chemistry, in which the latter remains unknown and is important for metabolic engineering to produce PHAs economically. PMID:26974339

  6. Independent Metrics for Protein Backbone and Side-Chain Flexibility: Time Scales and Effects of Ligand Binding.

    PubMed

    Fuchs, Julian E; Waldner, Birgit J; Huber, Roland G; von Grafenstein, Susanne; Kramer, Christian; Liedl, Klaus R

    2015-03-10

    Conformational dynamics are central for understanding biomolecular structure and function, since biological macromolecules are inherently flexible at room temperature and in solution. Computational methods are nowadays capable of providing valuable information on the conformational ensembles of biomolecules. However, analysis tools and intuitive metrics that capture dynamic information from in silico generated structural ensembles are limited. In standard work-flows, flexibility in a conformational ensemble is represented through residue-wise root-mean-square fluctuations or B-factors following a global alignment. Consequently, these approaches relying on global alignments discard valuable information on local dynamics. Results inherently depend on global flexibility, residue size, and connectivity. In this study we present a novel approach for capturing positional fluctuations based on multiple local alignments instead of one single global alignment. The method captures local dynamics within a structural ensemble independent of residue type by splitting individual local and global degrees of freedom of protein backbone and side-chains. Dependence on residue type and size in the side-chains is removed via normalization with the B-factors of the isolated residue. As a test case, we demonstrate its application to a molecular dynamics simulation of bovine pancreatic trypsin inhibitor (BPTI) on the millisecond time scale. This allows for illustrating different time scales of backbone and side-chain flexibility. Additionally, we demonstrate the effects of ligand binding on side-chain flexibility of three serine proteases. We expect our new methodology for quantifying local flexibility to be helpful in unraveling local changes in biomolecular dynamics.

  7. A simple strategy to the side chain functionalization on the quinoxaline unit for efficient polymer solar cells.

    PubMed

    Yuan, Jun; Qiu, Lixia; Zhang, Zhiguo; Li, Yongfang; He, Yuehui; Jiang, Lihui; Zou, Yingping

    2016-05-25

    A new tetrafluoridequinoxaline electron accepting block from a quinoxaline core, which is substituted with a fluorine atom onto its backbone and side chains, was designed. A new copolymer (PBDTT-ffQx) was synthesized from tetrafluoridequinoxaline and benzodithiophene. The copolymer was characterized in detail. The photovoltaic properties were well investigated. A high PCE of 8.6% based on the single junction device was obtained.

  8. Asymmetric synthesis of N-protected chiral 1-aminoalkylphosphonic acids and synthesis of side chain-functionalized depsiphosphonopeptides.

    PubMed

    Liu, Han; Cai, Shuzong; Xu, Jiaxi

    2006-05-01

    Optically active 1-aminoalkylphosphonic acid derivatives were synthesized in moderate yields and optical purities via Mannich-type reactions of benzyl carbamate, aldehydes, and optically pure chlorophosphites. Side chain-functionalized depsiphosphonopeptides were also prepared in satisfactory yields directly from one-pot reactions of benzyl carbamate, aldehydes, and diethyl (R,R)-2-chloro-1,3,2-dioxaphospholane-4,5-dicarboxylate. PMID:16285019

  9. Addition of ‘Charge-Shifting’ Side Chains to Linear Poly(ethyleneimine) Enhances Cell Transfection Efficiency

    PubMed Central

    Liu, Xianghui; Yang, Jennifer W.

    2008-01-01

    We reported recently that the addition of ester-functionalized, ‘charge-shifting’ side chains to linear poly(ethyleneimine) (LPEI) can be used to design polyamines that promote both self-assembly and self-disassembly with DNA in aqueous environments. This investigation sought to characterize the influence of charge-shifting side chains on the ability of LPEI to mediate cell transfection and understand the extent to which increases (or decreases) in levels of transfection could be understood in terms of time-dependent changes in the net charges of these polymers. We report that the addition of ‘charge-shifting’ side chains to LPEI leads to significant increases in levels of LPEI-mediated transfection. In particular, polymer 1e, functionalized with 20 mol% ester-functionalized side chains, mediates levels of transgene expression in vitro up to eight-fold higher than LPEI. Experiments using an amide-functionalized analog of polymer 1e demonstrated that the esters in polymer 1e play an important role in promoting increased levels of transfection. These results, in combination with the results of additional gel electrophoresis experiments, provide support for the view that increases in transfection result from time-dependent changes in the net charge of polymer 1e and the disruption of ionic interactions in polyplexes. Additional support for this view is provided by the results of confocal microscopy experiments and measurements of fluorescence resonance energy transfer, which suggest that polymer 1e promotes the disruption of polyplexes in intracellular environments effectively. The approach reported here provides a means of addressing one important ‘late-stage’ obstacle to polyplex-mediated transfection (polyplex unpackaging). If integrated successfully with methods that have been developed to address other important barriers to transfection, this general approach could lead to the development of multifunctional polyplexes that mimic more effectively the

  10. ω-Turn: a novel β-turn mimic in globular proteins stabilized by main-chain to side-chain C−H···O interaction.

    PubMed

    Dhar, Jesmita; Chakrabarti, Pinak; Saini, Harpreet; Raghava, Gajendra Pal Singh; Kishore, Raghuvansh

    2015-02-01

    Mimicry of structural motifs is a common feature in proteins. The 10-membered hydrogen-bonded ring involving the main-chain C − O in a β-turn can be formed using a side-chain carbonyl group leading to Asx-turn. We show that the N − H component of hydrogen bond can be replaced by a C(γ) -H group in the side chain, culminating in a nonconventional C − H···O interaction. Because of its shape this β-turn mimic is designated as ω-turn, which is found to occur ∼ three times per 100 residues. Three residues (i to i + 2) constitute the turn with the C − H···O interaction occurring between the terminal residues, constraining the torsion angles ϕi + 1, ψi + 1, ϕi + 2 and χ'1(i + 2) (using the interacting C(γ) atom). Based on these angles there are two types of ω-turns, each of which can be further divided into two groups. C(β) -branched side-chains, and Met and Gln have high propensities to occur at i + 2; for the last two residues the carbonyl oxygen may participate in an additional interaction involving the S and amino group, respectively. With Cys occupying the i + 1 position, such turns are found in the metal-binding sites. N-linked glycosylation occurs at the consensus pattern Asn-Xaa-Ser/Thr; with Thr at i + 2, the sequence can adopt the secondary structure of a ω-turn, which may be the recognition site for protein modification. Location between two β-strands is the most common occurrence in protein tertiary structure, and being generally exposed ω-turn may constitute the antigenic determinant site. It is a stable scaffold and may be used in protein engineering and peptide design.

  11. 5-N-Substituted-2-(substituted benzenesulphonyl) glutamines as antitumor agents. Part II: synthesis, biological activity and QSAR study.

    PubMed

    Samanta, Soma; Srikanth, K; Banerjee, Suchandra; Debnath, Bikash; Gayen, Shovanlal; Jha, Tarun

    2004-03-15

    Cancer is a major killer disease throughout human history. Thus, cancer becomes a major point of interest in life science. It was proved that cancer is a nitrogen trap and tumor cells are avid glutamine consumers. The non-essential amino acid glutamine, which is a glutamic acid derivative, supplies its amide nitrogen to tumor cells in the biosynthesis of purine and pyrimidine bases of nucleic acids as well as takes part in protein synthesis. Based on these and in continuation of our composite programme of development of new potential anticancer agents through rational drug design, 17 new 5-N-Substituted-2-(substituted benzenesulphonyl) glutamines were selected for synthesis. These compounds as well as 36 earlier synthesized glutamine analogues were screened for antitumor activity using percentage inhibition of tumor cell count as the activity parameter. QSAR study was performed with 53 compounds in order to design leads with increased effectiveness for antitumor activity using both physicochemical and topological parameters. QSAR study showed that steric effect on the aromatic ring is conducive to the activity. n-butyl substitution on aliphatic side chain and atom no 12 is important for antitumor activity of glutamine analogues.

  12. Nature versus design: the conformational propensities of D-amino acids and the importance of side chain chirality.

    PubMed

    Towse, Clare-Louise; Hopping, Gene; Vulovic, Ivan; Daggett, Valerie

    2014-11-01

    D-amino acids are useful building blocks for de novo peptide design and they play a role in aging-related diseases associated with gradual protein racemization. For amino acids with achiral side chains, one should be able to presume that the conformational propensities of L- and D-amino acids are a reflection of one another due to the straightforward geometric inversion at the Cα atom. However, this presumption does not account for the directionality of the backbone dipole and the inverted propensities have never been definitively confirmed in this context. Furthermore, there is little known of how alternative side chain chirality affects the backbone conformations of isoleucine and threonine. Using a GGXGG host-guest pentapeptide system, we have completed exhaustive sampling of the conformational propensities of the D-amino acids, including D-allo-isoleucine and D-allo-threonine, using atomistic molecular dynamics simulations. Comparison of these simulations with the same systems hosting the cognate L-amino acids verifies that the intrinsic backbone conformational propensities of the D-amino acids are the inverse of their cognate L-enantiomers. Where amino acids have a chiral center in their side chain (Thr, Ile) the β-configuration affects the backbone sampling, which in turn can confer different biological properties.

  13. Water, proton, and oxygen transport in high IEC, short side chain PFSA ionomer membranes: consequences of a frustrated network.

    PubMed

    Luo, Xiaoyan; Holdcroft, Steven; Mani, Ana; Zhang, Yongming; Shi, Zhiqing

    2011-10-28

    The effect of ion exchange capacity (IEC) on the water sorption properties of high IEC, short side chain (SSC) PFSA ionomer membranes, and the relationships between water content, proton conductivity, proton mobility, water permeation, oxygen diffusion, and oxygen permeation are investigated. SSC PFSA ionomer membranes possessing 1.3, 1.4, and 1.5 mmol g(-1) IEC are compared to a series of long side chain (LSC) PFSA ionomer membranes ranging in IEC from 0.9 to 1.13 mmol g(-1). At 25 °C, fully-hydrated SSC ionomer membranes are characterized as possessing higher water contents (56-75 vol%), moderate λ values (15-18), high analytical acid concentrations (2-2.8 M), and moderate conductivity (88-115 mS/cm); but lower than anticipated effective proton mobility. Complementary measurements of water permeability, oxygen diffusion, and oxygen permeability also yield lower than expected values given their much higher water contents. Potential benefits afforded by reducing the side chain length of PFSA ionomer membranes, such as increased crystallinity, higher IEC, and high hydrated acid concentration are offset by a less-developed, frustrated hydrophilic percolation network, which provides a motivation for future improvements of transport properties for this class of material.

  14. Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.

    PubMed

    Zhu, Tong; Zhang, John Z H; He, Xiao

    2014-09-14

    In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method for ab initio calculation of chemical shifts, incorrect side chain packing was detected in the NMR structures of the Pin1 WW domain. The NMR structure is then refined by using molecular dynamics simulation and the polarized protein-specific charge (PPC) model. The computationally refined structure of the Pin1 WW domain is in excellent agreement with the corresponding X-ray structure. In particular, the use of the PPC model yields a more accurate structure than that using the standard (nonpolarizable) force field. For comparison, some of the widely used empirical models for chemical shift calculations are unable to correctly describe the relationship between the particular proton chemical shift and protein structures. The AF-QM/MM method can be used as a powerful tool for protein NMR structure validation and structural flaw detection.

  15. Effect of O side-chain length and composition on the virulence of Shigella flexneri 2a.

    PubMed

    Sandlin, R C; Goldberg, M B; Maurelli, A T

    1996-10-01

    IcsA of Shigella flexneri is required for intercellular spread and is located in the outer membrane at one pole of the bacterium, where it catalyses the polymerization of host-cell actin. The formation of the a tin tail provides the force to move the bacterium in a unidirectional manner through the host-cell cytoplasm. We have previously demonstrated that rough lipopolysaccharide (LPS) mutants of S. flexneri 2a are avirulent and cannot form plaques in tissue-culture monolayers. This inability to form plaques is associated with non-polar localization of IcsA and loss of host-cell membrane-protrusion formation ("fireworks'). To define the minimal LPS structure required for fireworks formation, we constructed a strain of S. flexneri (BS497) that contains a mutation in rfc, encoding the O side-chain polymerase, and a strain, BS520, that possesses a defective O side-chain ligase due to a mutation in rfaL. BS497 produces a LPS that consists of a core with one repeat unit of the O side-chain, while BS520 produces a LPS consisting of a complete core with no O side-chain. BS497 remained invasive but did not form fireworks or plaques in tissue-culture monolayers and was negative in the Serény test. BS520 was invasive, generated reduced numbers of short fireworks, and made tiny plaques, but it was negative in the Serény test. Analysis of BS497 with anti-IcsA antibody demonstrated that IcsA was distributed over the entire cell surface. The distribution of IcsA on the surface of BS520 was predominantly unipolar, with some trail-back of IcsA label along the sides of the bacterium. A similar pattern was seen when infected monolayers were stained for polymerized actin. These results suggest that both the presence and the length of the O side-chain are important in the proper localization or maintenance of IcsA at the pole which subsequently affects the ability to form actin tails and produce fireworks. This reduced ability to form actin tails and fireworks results in a decreased

  16. δ-Methyl Branching in the Side Chain Makes the Difference: Access to Room-Temperature Discotics.

    PubMed

    Kirres, Jochen; Knecht, Friederike; Seubert, Philipp; Baro, Angelika; Laschat, Sabine

    2016-04-18

    Although discotic liquid crystals are attractive functional materials, their use in electronic devices is often restricted by high melting and clearing points. Among the promising candidates for applications are [15]crown-5 ether-based liquid crystals with peripheral n-alkoxy side chains, which, however, still have melting points above room temperature. To overcome this problem, a series of o-terphenyl and triphenylene [15]crown-5 ether derivatives was prepared in which δ-methyl-branched alkoxy side chains of varying lengths substitute the peripheral linear alkoxy chains. The mesomorphic properties of the novel crown ethers were studied by differential scanning calorimetry, polarizing optical microscopy, and X-ray diffraction. δ-Methyl branching indeed lowers melting points resulting in room-temperature hexagonal columnar mesophases. The mesophase widths, which ranged from 87 to 30 K for o-terphenyls, significantly increased to 106-147 K for the triphenylenes depending on the chain lengths, revealing the beneficial effect of a flat mesogen, due to improved π-π interactions.

  17. δ-Methyl Branching in the Side Chain Makes the Difference: Access to Room-Temperature Discotics.

    PubMed

    Kirres, Jochen; Knecht, Friederike; Seubert, Philipp; Baro, Angelika; Laschat, Sabine

    2016-04-18

    Although discotic liquid crystals are attractive functional materials, their use in electronic devices is often restricted by high melting and clearing points. Among the promising candidates for applications are [15]crown-5 ether-based liquid crystals with peripheral n-alkoxy side chains, which, however, still have melting points above room temperature. To overcome this problem, a series of o-terphenyl and triphenylene [15]crown-5 ether derivatives was prepared in which δ-methyl-branched alkoxy side chains of varying lengths substitute the peripheral linear alkoxy chains. The mesomorphic properties of the novel crown ethers were studied by differential scanning calorimetry, polarizing optical microscopy, and X-ray diffraction. δ-Methyl branching indeed lowers melting points resulting in room-temperature hexagonal columnar mesophases. The mesophase widths, which ranged from 87 to 30 K for o-terphenyls, significantly increased to 106-147 K for the triphenylenes depending on the chain lengths, revealing the beneficial effect of a flat mesogen, due to improved π-π interactions. PMID:26853226

  18. Influence of the side chain and substrate on polythiophene thin film surface, bulk, and buried interfacial structures.

    PubMed

    Xiao, Minyu; Jasensky, Joshua; Zhang, Xiaoxian; Li, Yaoxin; Pichan, Cayla; Lu, Xiaolin; Chen, Zhan

    2016-08-10

    The molecular structures of organic semiconducting thin films mediate the performance of various devices composed of such materials. To fully understand how the structures of organic semiconductors alter on substrates due to different polymer side chains and different interfacial interactions, thin films of two kinds of polythiophene derivatives with different side-chains, poly(3-hexylthiophene) (P3HT) and poly(3-potassium-6-hexanoate thiophene) (P3KHT), were deposited and compared on various surfaces. A combination of analytical tools was applied in this research: contact angle goniometry and X-ray photoelectron spectroscopy (XPS) were used to characterize substrate dielectric surfaces with varied hydrophobicity for polymer film deposition; X-ray diffraction and UV-vis spectroscopy were used to examine the polythiophene film bulk structure; sum frequency generation (SFG) vibrational spectroscopy was utilized to probe the molecular structures of polymer film surfaces in air and buried solid/solid interfaces. Both side-chain hydrophobicity and substrate hydrophobicity were found to mediate the crystallinity of the polythiophene film, as well as the orientation of the thiophene ring within the polymer backbone at the buried polymer/substrate interface and the polymer thin film surface in air. For the same type of polythiophene film deposited on different substrates, a more hydrophobic substrate surface induced thiophene ring alignment with the surface normal at both the buried interface and on the surface in air. For different films (P3HT vs. P3KHT) deposited on the same dielectric substrate, a more hydrophobic polythiophene side chain caused the thiophene ring to align more towards the surface at the buried polymer/substrate interface and on the surface in air. We believe that the polythiophene surface, bulk, and buried interfacial molecular structures all influence the hole mobility within the polythiophene film. Successful characterization of an organic conducting

  19. Extent of salmeterol-mediated reassertion of relaxation in guinea-pig trachea pretreated with aliphatic side chain structural analogues.

    PubMed Central

    Bergendal, A.; Lindén, A.; Skoogh, B. E.; Gerspacher, M.; Anderson, G. P.; Löfdahl, C. G.

    1996-01-01

    1. Salmeterol is a potent, selective and long acting beta 2-adrenoceptor agonist. In vitro, salmeterol exerts 'reassertion' relaxation of airways smooth muscle. Reassertion relaxation refers to the capacity of salmeterol to cause repeated functional antagonism of induced contraction when airway smooth muscle is intermittently exposed to, then washed free from, beta-adrenoceptor antagonists such as sotalol. The mechanism(s) underlying reassertion relaxation are unknown but may relate to high affinity binding of the long aliphatic side chain of salmeterol to an accessory site, distinct from the agonist recognition site, in or near the beta 2-adrenoceptor (exosite binding hypothesis). 2. In order to test the exosite hypothesis, three pure analogues of salmeterol, each exactly preserving the molecular structure of the aliphatic side chain but with zero or low efficacy at the beta 2-adrenoceptor were synthesized. The effect of pre-incubating guinea-pig tracheal smooth muscle with these analogues on salmeterol-induced reassertion relaxation was determined. 3. Computer Assisted Molecular Modelling of these molecules revealed that each of them exactly preserved the low energy linear conformation of the aliphatic side chain of salmeterol. Measurement of lipophilicity (octanol:water partition coefficient; log P) and direct partition into synthetic membranes (membrane partition coefficient; Kpmem) showed that all compounds had high affinity for lipids and membranes. In particular the biophysical properties of CGP 59162 (log P 1.89, Kpmem 16500) were very similar to salmeterol (log P 1.73, Kpmem 16800). 4. Two of the analogues, CGP 54103 and D 2543 (1 microM), which are structural mimics of the side chain of salmeterol, differing slightly in their length, did not prevent either the initial relaxation induced by salmeterol (0.1 microM) or the reassertion relaxation; however, it was not possible to determine whether either of these molecules occupied the beta 2-adrenoceptor. 5

  20. Influence of the side chain and substrate on polythiophene thin film surface, bulk, and buried interfacial structures.

    PubMed

    Xiao, Minyu; Jasensky, Joshua; Zhang, Xiaoxian; Li, Yaoxin; Pichan, Cayla; Lu, Xiaolin; Chen, Zhan

    2016-08-10

    The molecular structures of organic semiconducting thin films mediate the performance of various devices composed of such materials. To fully understand how the structures of organic semiconductors alter on substrates due to different polymer side chains and different interfacial interactions, thin films of two kinds of polythiophene derivatives with different side-chains, poly(3-hexylthiophene) (P3HT) and poly(3-potassium-6-hexanoate thiophene) (P3KHT), were deposited and compared on various surfaces. A combination of analytical tools was applied in this research: contact angle goniometry and X-ray photoelectron spectroscopy (XPS) were used to characterize substrate dielectric surfaces with varied hydrophobicity for polymer film deposition; X-ray diffraction and UV-vis spectroscopy were used to examine the polythiophene film bulk structure; sum frequency generation (SFG) vibrational spectroscopy was utilized to probe the molecular structures of polymer film surfaces in air and buried solid/solid interfaces. Both side-chain hydrophobicity and substrate hydrophobicity were found to mediate the crystallinity of the polythiophene film, as well as the orientation of the thiophene ring within the polymer backbone at the buried polymer/substrate interface and the polymer thin film surface in air. For the same type of polythiophene film deposited on different substrates, a more hydrophobic substrate surface induced thiophene ring alignment with the surface normal at both the buried interface and on the surface in air. For different films (P3HT vs. P3KHT) deposited on the same dielectric substrate, a more hydrophobic polythiophene side chain caused the thiophene ring to align more towards the surface at the buried polymer/substrate interface and on the surface in air. We believe that the polythiophene surface, bulk, and buried interfacial molecular structures all influence the hole mobility within the polythiophene film. Successful characterization of an organic conducting

  1. Gel-like elasticity in glass-forming side-chain liquid-crystal polymers

    NASA Astrophysics Data System (ADS)

    Pozo, O.; Collin, D.; Finkelmann, H.; Rogez, D.; Martinoty, P.

    2009-09-01

    We study the complex shear modulus G of two side-chain liquid-crystal polymers (SCLCPs), a methoxy-phenylbenzoate substituted polyacrylate (thereafter called PAOCH3 ), and a cyanobiphenyl substituted polyacrylate supplied by Merck (thereafter called LCP105) using a piezoelectric rheometer. Two methods of filling the cell are used: (a) a capillary method, which can be used only at high temperature because of the low value of the viscosity, and (b) the classical one, thereafter called compression method, which consists in placing the sample between the two slides of the cell and to bring them closer. By filling the cell at high temperature either with the compression or the capillary method, we show that the response of both compounds is liquidlike ( G'˜f2 and G″˜f , where f is the frequency) for temperatures higher than a certain temperature T0 and gel-like (G'˜const,G″˜f) below T0 . This change in behavior from the conventional flow response to a gel-like response, when approaching the glass transition, is observed for nonsliding conditions and for very weak-imposed shear strains. It can be explained by a percolation-type mechanism of preglassy elastic clusters, which correspond to long-range and long-lived density fluctuations that are frozen at the time scale of the experiment. The sample response is therefore the sum of two contributions: one is due to the flow response of the polymer melt and the other to the elastic response of the network formed by the preglassy elastic clusters. By filling the cell below T0 with the compression method, both compounds exhibit a gel-type behavior by gently bringing closer the slides of the cell and an anomalous low-frequency behavior characterized by G'=const and G″=const by increasing the pressure used to bring closer the slides of the cell. A compression-assisted aggregation of the preglassy elastic clusters can explain both the increase in the low-frequency elastic plateau when the sample thickness is decreased

  2. All-acrylic multigraft copolymers: Effect of side chain molecular weight and volume fraction on mechanical behavior

    SciTech Connect

    Goodwin, Andrew; Wang, Weiyu; Kang, Nam -Goo; Wang, Yangyang; Hong, Kunlun; Mays, Jimmy

    2015-08-21

    We present in this paper the synthesis of poly(n-butyl acrylate)-g-poly(methyl methacrylate) (PnBA-g-PMMA) multigraft copolymers via a grafting-through (macromonomer) approach. The synthesis was performed using two controlled polymerization techniques. The PMMA macromonomer was obtained by high-vacuum anionic polymerization followed by the copolymerization of n-butyl acrylate and PMMA macromonomer using reversible addition–fragmentation chain transfer (RAFT) polymerization to yield the desired all-acrylic multigraft structures. The PnBA-g-PMMA multigraft structures exhibit randomly spaced branch points with various PMMA contents, ranging from 15 to 40 vol %, allowing an investigation into how physical properties vary with differences in the number of branch points and molecular weight of grafted side chains. The determination of molecular weight and polydispersity indices of both the PMMA macromonomer and the graft copolymers was carried out using size exclusion chromatography with triple detection, and the structural characteristics of both the macromonomer and PnBA-g-PMMA graft materials were characterized by 1H and 13C NMR. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was employed for monitoring the macromonomer synthesis. Thermal characteristics of the materials were analyzed using differential scanning calorimetry and thermogravimetric analysis. The mechanical performance of the graft materials was characterized by rheology and dynamic mechanical analysis, revealing that samples with PMMA content of 25–40 vol % exhibit superior elastomeric properties as compared to materials containing short PMMA side chains or <25 vol % PMMA. In conclusion, atomic force microscopy showed a varying degree of microphase separation between the glassy and rubbery components that is strongly dependent on PMMA side chain molecular weight.

  3. All-acrylic multigraft copolymers: Effect of side chain molecular weight and volume fraction on mechanical behavior

    DOE PAGES

    Goodwin, Andrew; Wang, Weiyu; Kang, Nam -Goo; Wang, Yangyang; Hong, Kunlun; Mays, Jimmy

    2015-08-21

    We present in this paper the synthesis of poly(n-butyl acrylate)-g-poly(methyl methacrylate) (PnBA-g-PMMA) multigraft copolymers via a grafting-through (macromonomer) approach. The synthesis was performed using two controlled polymerization techniques. The PMMA macromonomer was obtained by high-vacuum anionic polymerization followed by the copolymerization of n-butyl acrylate and PMMA macromonomer using reversible addition–fragmentation chain transfer (RAFT) polymerization to yield the desired all-acrylic multigraft structures. The PnBA-g-PMMA multigraft structures exhibit randomly spaced branch points with various PMMA contents, ranging from 15 to 40 vol %, allowing an investigation into how physical properties vary with differences in the number of branch points and molecular weightmore » of grafted side chains. The determination of molecular weight and polydispersity indices of both the PMMA macromonomer and the graft copolymers was carried out using size exclusion chromatography with triple detection, and the structural characteristics of both the macromonomer and PnBA-g-PMMA graft materials were characterized by 1H and 13C NMR. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was employed for monitoring the macromonomer synthesis. Thermal characteristics of the materials were analyzed using differential scanning calorimetry and thermogravimetric analysis. The mechanical performance of the graft materials was characterized by rheology and dynamic mechanical analysis, revealing that samples with PMMA content of 25–40 vol % exhibit superior elastomeric properties as compared to materials containing short PMMA side chains or <25 vol % PMMA. In conclusion, atomic force microscopy showed a varying degree of microphase separation between the glassy and rubbery components that is strongly dependent on PMMA side chain molecular weight.« less

  4. Side-chain-bulk effects on the molecular packing and photovoltaic performance of benzotrithiophene-benzooxadiazole conjugated copolymers.

    PubMed

    Lan, Shang-Che; Chang, Chiao-Kai; Wang, Yi-Chien; Wei, Kung-Hwa

    2015-04-27

    Two alternating donor-acceptor conjugated polymers, PBTTBO-C13 C11 and PBTTBO-C13 C8 , comprising 5-alkylbenzo[1,2-b:3,4-b':5,6-d'']trithiophene (BTT) as the donor and 4,7-bis(4-dodecylthien-2-yl)benzo[1,2,5]oxadiazole (BO) as the acceptor, with different alkyl side-chain architectures on their BTT units are synthesized, and their bulk heterojunction photovoltaic properties when blended with the fullerene PC71 BM are characterized. Even a slight change in the length of the alkyl chain of the BTT units influences the steric bulk to such a degree that it substantially affects the molecular packing of the polymers and the performance of their photovoltaic devices. The bulkier side chains of the polymer PBTTBO-C13 C11 not only prevent its crystallization, but also suppress its light-absorption coefficient relative to that of PBTTBO-C13 C8 , as evidenced by X-ray diffraction and UV/Vis absorption studies, presumably because of weakened intermolecular interactions. Moreover, the polymer bearing bulkier side chains, PBTTBO-C13 C11 , is less miscible with PC71 BM than PBTTBO-C13 C8 , and this characteristic determines the morphology of their annealed blended films, as shown by TEM studies. The best efficiency is obtained with a device containing an annealed PBTTBO-C13 C8 /PC71 BM (1/2 w/w) active layer that was maintained at 120 °C for 10 min, which shows a power conversion efficiency of 6.2 %, an open-circuit voltage of 0.75 V, a short-circuit current density of 12.6 mA cm(-2) , and a fill factor of 66 %.

  5. Inversion of the stereochemistry around the sulfur atom of the axial methionine side chain through alteration of amino acid side chain packing in Hydrogenobacter thermophilus cytochrome C552 and its functional consequences.

    PubMed

    Tai, Hulin; Tonegawa, Ken; Shibata, Tomokazu; Hemmi, Hikaru; Kobayashi, Nagao; Yamamoto, Yasuhiko

    2013-07-16

    In cytochrome c, the coordination of the axial Met Sδ atom to the heme Fe atom occurs in one of two distinctly different stereochemical manners, i.e., R and S configurations, depending upon which of the two lone pairs of the Sδ atom is involved in the bond; hence, the Fe-coordinated Sδ atom becomes a chiral center. In this study, we demonstrated that an alteration of amino acid side chain packing induced by the mutation of a single amino acid residue, i.e., the A73V mutation, in Hydrogenobacter thermophilus cytochrome c552 (HT) forces the inversion of the stereochemistry around the Sδ atom from the R configuration [Travaglini-Allocatelli, C., et al. (2005) J. Biol. Chem. 280, 25729-25734] to the S configuration. Functional comparison between the wild-type HT and the A73V mutant possessing the R and S configurations as to the stereochemistry around the Sδ atom, respectively, demonstrated that the redox potential (Em) of the mutant at pH 6.00 and 25 °C exhibited a positive shift of ∼20 mV relative to that of the wild-type HT, i.e., 245 mV, in an entropic manner. Because these two proteins have similar enthalpically stabilizing interactions, the difference in the entropic contribution to the Em value between them is likely to be due to the effect of the conformational alteration of the axial Met side chain associated with the inversion of the stereochemistry around the Sδ atom due to the effect of mutation on the internal mobility of the loop bearing the axial Met. Thus, the present study demonstrated that the internal mobility of the loop bearing the axial Met, relevant to entropic control of the redox function of the protein, is affected quite sensitively by the contextual stereochemical packing of amino acid side chains in the proximity of the axial Met.

  6. Low resistance, large dimension entrance to the inner cavity of BK channels determined by changing side-chain volume.

    PubMed

    Geng, Yanyan; Niu, Xiaowei; Magleby, Karl L

    2011-06-01

    Large-conductance Ca(2+)- and voltage-activated K(+) (BK) channels have the largest conductance (250-300 pS) of all K(+)-selective channels. Yet, the contributions of the various parts of the ion conduction pathway to the conductance are not known. Here, we examine the contribution of the entrance to the inner cavity to the large conductance. Residues at E321/E324 on each of the four α subunits encircle the entrance to the inner cavity. To determine if 321/324 is accessible from the inner conduction pathway, we measured single-channel current amplitudes before and after exposure and wash of thiol reagents to the intracellular side of E321C and E324C channels. MPA(-) increased currents and MTSET(+) decreased currents, with no difference between positions 321 and 324, indicating that side chains at 321/324 are accessible from the inner conduction pathway and have equivalent effects on conductance. For neutral amino acids, decreasing the size of the entrance to the inner cavity by substituting large side-chain amino acids at 321/324 decreased outward single-channel conductance, whereas increasing the size of the entrance with smaller side-chain substitutions had little effect. Reductions in outward conductance were negated by high [K(+)](i). Substitutions had little effect on inward conductance. Fitting plots of conductance versus side-chain volume with a model consisting of one variable and one fixed resistor in series indicated an effective diameter and length of the entrance to the inner cavity for wild-type channels of 17.7 and 5.6 Å, respectively, with the resistance of the entrance ∼7% of the total resistance of the conduction pathway. The estimated dimensions are consistent with the structure of MthK, an archaeal homologue to BK channels. Our observations suggest that BK channels have a low resistance, large entrance to the inner cavity, with the entrance being as large as necessary to not limit current, but not much larger. PMID:21576375

  7. On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain order parameters.

    PubMed

    O'Brien, Evan S; Wand, A Joshua; Sharp, Kim A

    2016-06-01

    Molecular dynamics (MD) simulations have become a central tool for investigating various biophysical questions with atomistic detail. While many different proxies are used to qualify MD force fields, most are based on largely structural parameters such as the root mean square deviation from experimental coordinates or nuclear magnetic resonance (NMR) chemical shifts and residual dipolar couplings. NMR derived Lipari-Szabo squared generalized order parameter (O(2) ) values of amide NH bond vectors of the polypeptide chain were also often employed for refinement and validation. However, with a few exceptions, side chain methyl symmetry axis order parameters have not been incorporated into experimental reference sets. Using a test set of five diverse proteins, the performance of several force fields implemented in the NAMDD simulation package was examined. It was found that simulations employing explicit water implemented using the TIP3 model generally performed significantly better than those using implicit water in reproducing experimental methyl symmetry axis O(2) values. Overall the CHARMM27 force field performs nominally better than two implementations of the Amber force field. It appeared that recent quantum mechanics modifications to side chain torsional angles of leucine and isoleucine in the Amber force field have significantly hindered proper motional modeling for these residues. There remained significant room for improvement as even the best correlations of experimental and simulated methyl group Lipari-Szabo generalized order parameters fall below an R(2) of 0.8.

  8. Polypropylene non-woven meshes with conformal glycosylated layer for lectin affinity adsorption: the effect of side chain length.

    PubMed

    Ye, Xiang-Yu; Huang, Xiao-Jun; Xu, Zhi-Kang

    2014-03-01

    The unique characteristics of polypropylene non-woven meshes (PPNWMs), like random network of overlapped fibers, multiple connected pores and overall high porosity, make them high potentials for use as separation or adsorption media. Meanwhile, carbohydrates can specifically recognize certain lectin through multivalent interactions. Therefore glycosylated PPNWMs, combing the merits of both, can be regarded as superior affinity membranes for lectin adsorption and purification. Here, we describe a versatile strategy for the glycosylation of PPNWMs. Two hydrophilic polymers with different side chain length, poly(2-hydroxyethyl methacrylate) (PHEMA) and poly(oligo(ethylene glycol) methacrylate) (POEGMA), were first conformally tethered on the polypropylene fiber surface by a modified plasma pretreatment and benzophenone (BP) entrapment UV irradiation process. Then glucose ligands were bound through the reaction between the hydroxyl group and acetyl glucose. Chemical changes of the PPNWMs surface were monitored by FT-IR/ATR. SEM pictures show that conformal glucose ligands can be achieved through the modified process. After deprotection, the glycosylated PPNWMs became superhydrophilic and had high specific recognition capability toward Concanavalin A (Con A). Static Con A adsorption experiments were further performed and the results indicate that fast adsorption kinetics and high binding capacity can be accomplished at the same time. We also found that increasing the side chain length of polymer brushes had positive effect on protein binding capacity due to improved chain mobility. Model studies suggest a multilayer adsorption behavior of Con A. PMID:24398082

  9. Design and synthesis of novel opioid ligands with an azabicyclo[2.2.2]octane skeleton having a 7-amide side chain and their pharmacologies.

    PubMed

    Watanabe, Yoshikazu; Kitazawa, Shota; Nemoto, Toru; Hirayama, Shigeto; Iwai, Takashi; Fujii, Hideaki; Nagase, Hiroshi

    2013-06-01

    Several derivatives with an azabicyclo[2.2.2]octane skeleton having a 7-amide side chain were synthesized. Compounds that had an electron-donating group exhibited high affinity for the μ opioid receptor while those with a bulky substituent at the 8-nitrogen atom had low affinities for all receptor types. High affinities and selectivities for the κ receptor resulted from the introduction of the longer amide side chain at the 7α-position. Our studies indicate that the orientation of the amide side chain at the 7-position within the azabicyclo[2.2.2]octane skeleton is related to selectivity for the κ receptor.

  10. Syntheses of protoporphyrin-IX derivatives bearing extended propionate side-chains.

    PubMed

    Holmes, Robert T; Lu, Jianming; Mwakwari, Celinah; Smith, Kevin M

    2009-05-29

    In order to investigate the relationship between depth within membranes of singlet oxygen generation and effectiveness of photodynamic therapy of tumors, analogs of protoporphyrin-IX 1 bearing five 4 and seven 5 carbon atoms (in place of the 3-carbon atom chain in 1) were synthesized from monopyrrole precursors.

  11. Modification of eucalyptus pulp fiber using silane coupling agents with aliphatic side chains of different length

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this work was to evaluate the effect of three silane coupling agents with different aliphatic chain lengths on the hydrophobicity of eucalyptus pulp fiber. The three silanes coupling agents used (isobutyltrimethoxysilane, methyltrimethoxysilane, and n-octyltriethoxysilane [OTES]) we...

  12. Syntheses of protoporphyrin-IX derivatives bearing extended propionate side-chains.

    PubMed

    Holmes, Robert T; Lu, Jianming; Mwakwari, Celinah; Smith, Kevin M

    2009-05-29

    In order to investigate the relationship between depth within membranes of singlet oxygen generation and effectiveness of photodynamic therapy of tumors, analogs of protoporphyrin-IX 1 bearing five 4 and seven 5 carbon atoms (in place of the 3-carbon atom chain in 1) were synthesized from monopyrrole precursors. PMID:20161404

  13. Characterization of the orientational behavior of liquid-crystalline side-chain polymers for reversible optical data storage by Fourier transform IR spectroscopy

    NASA Astrophysics Data System (ADS)

    Kulinna, Ch.; Zebger, I.; Siesler, Heinz W.; Hvilsted, Soeren; Ramanujam, P. S.

    1994-01-01

    It has been demonstrated that the photo-induced orientation or reorientation of dye-containing liquid-crystalline side-chain (LCSC) polymers can be used for reversible optical data storage. A method which enables the determination of this orientational behavior in addition to the order parameter is infrared dichroism. The present experimental approach uses Fourier- Transform infrared (FTIR) spectroscopy with polarized radiation to determine the orientation of the main chain and side chains in a LCSC polyester with a dodecamethylene spacing of the ester groups in the main chain and six methylene groups in the spacer, after irradiation with an Argon ion laser beam.

  14. Evaluating the Effect of Ionic Strength on Duplex Stability for PNA Having Negatively or Positively Charged Side Chains

    PubMed Central

    De Costa, N. Tilani S.; Heemstra, Jennifer M.

    2013-01-01

    The enhanced thermodynamic stability of PNA:DNA and PNA:RNA duplexes compared with DNA:DNA and DNA:RNA duplexes has been attributed in part to the lack of electrostatic repulsion between the uncharged PNA backbone and negatively charged DNA or RNA backbone. However, there are no previously reported studies that systematically evaluate the effect of ionic strength on duplex stability for PNA having a charged backbone. Here we investigate the role of charge repulsion in PNA binding by synthesizing PNA strands having negatively or positively charged side chains, then measuring their duplex stability with DNA or RNA at varying salt concentrations. At low salt concentrations, positively charged PNA binds more strongly to DNA and RNA than does negatively charged PNA. However, at medium to high salt concentrations, this trend is reversed, and negatively charged PNA shows higher affinity for DNA and RNA than does positively charged PNA. These results show that charge screening by counterions in solution enables negatively charged side chains to be incorporated into the PNA backbone without reducing duplex stability with DNA and RNA. This research provides new insight into the role of electrostatics in PNA binding, and demonstrates that introduction of negatively charged side chains is not significantly detrimental to PNA binding affinity at physiological ionic strength. The ability to incorporate negative charge without sacrificing binding affinity is anticipated to enable the development of PNA therapeutics that take advantage of both the inherent benefits of PNA and the multitude of charge-based delivery technologies currently being developed for DNA and RNA. PMID:23484047

  15. Protein loops, solitons, and side-chain visualization with applications to the left-handed helix region

    NASA Astrophysics Data System (ADS)

    Lundgren, Martin; Niemi, Antti J.; Sha, Fan

    2012-06-01

    Folded proteins have a modular assembly. They are constructed from regular secondary structures like α helices and β strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe this modular structure. In complement to the widely employed Ramachandran plot that is based on toroidal geometry, our approach utilizes the geometry of a two sphere. Unlike the more conventional approaches that describe only a given peptide unit, ours is capable of describing the entire backbone environment including the neighboring peptide units. It maps the positions of each atom to the surface of the two-sphere exactly how these atoms are seen by an observer who is located at the position of the central Cα atom. At each level of side-chain atoms we observe a strong correlation between the positioning of the atom and the underlying local secondary structure with very little if any variation between the different amino acids. As a concrete example we analyze the left-handed helix region of nonglycyl amino acids. This region corresponds to an isolated and highly localized residue independent sector in the direction of the Cβ carbons on the two-sphere. We show that the residue independent localization extends to Cγ and Cδ carbons and to side-chain oxygen and nitrogen atoms in the case of asparagine and aspartic acid. When we extend the analysis to the side-chain atoms of the neighboring residues, we observe that left-handed β turns display a regular and largely amino acid independent structure that can extend to seven consecutive residues. This collective pattern is due to the presence of a backbone soliton. We show how one can use our visualization techniques to analyze and classify the different solitons in terms of selection rules that we describe in detail.

  16. On the source of entropic elastomeric force in polypeptides and proteins: Backbone configurational vs. side-chain solvational entropy

    SciTech Connect

    Luan, Chihao; Jaggard, J.; Harris, R.D.; Urry, D.W. )

    1989-01-01

    At physiological temperature in water, the relaxed state of the protein, elastin, and model elastomeric sequential polypeptides derived from this biological elastomer is the result of an inverse temperature transition. At lower temperatures, say at 20{degree}C, the hydrophobic side chains of the elastomers are hydrated with a low-entropy net of water. Following Flory and colleagues, thermoelasticity studies suggests that these polypeptide elastomers are dominantly entropic elastomers above the temperature of the inverse temperature transition. A central question becomes the source of the entropic elastomeric force. On stretching, hydrophobic side chains become exposed to water, resulting in an exothermic reaction of hydrophobic hydration. The issue addressed by the present report is whether this decrease in solvent entropy on stretching might make a major contribution to the entropic elastomeric restoring force. It has previously been argued that the free energy of solvation can be made very small by a 30% ethylene glycol (EG):70% water solvent mixture. This is demonstrated here using the repeating pentapeptide sequence of elastin (Val{sup 1}-Pro{sup 2}-Gly{sup 3} -Val{sup 4}-Gly{sup 5}){sub n} or poly(VPGVG) and its {gamma}-irradiation cross-linked elastomeric matrix. Differential scanning calorimetry of the inverse temperature transition of poly(VPGVG) shows the endothermic heat of the transition to become very small in EG/H{sub 2}O when compared with H{sub 2}O alone, which also indicates a very small entropy change for the transition on exposure of the hydrophobic side chains to the EG/H{sub 2}O solvent mixture. A similar result is found for the crosslinked elastomeric matrix. Significantly, however, in spite of the lower heats for hydrophobic solvation, the elastic modulus and the entropic elastomeric forces generated are greater in EG/H{sub 2}O.

  17. Protein loops, solitons, and side-chain visualization with applications to the left-handed helix region.

    PubMed

    Lundgren, Martin; Niemi, Antti J; Sha, Fan

    2012-06-01

    Folded proteins have a modular assembly. They are constructed from regular secondary structures like α helices and β strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe this modular structure. In complement to the widely employed Ramachandran plot that is based on toroidal geometry, our approach utilizes the geometry of a two sphere. Unlike the more conventional approaches that describe only a given peptide unit, ours is capable of describing the entire backbone environment including the neighboring peptide units. It maps the positions of each atom to the surface of the two-sphere exactly how these atoms are seen by an observer who is located at the position of the central C_{α} atom. At each level of side-chain atoms we observe a strong correlation between the positioning of the atom and the underlying local secondary structure with very little if any variation between the different amino acids. As a concrete example we analyze the left-handed helix region of nonglycyl amino acids. This region corresponds to an isolated and highly localized residue independent sector in the direction of the C_{β} carbons on the two-sphere. We show that the residue independent localization extends to C_{γ} and C_{δ} carbons and to side-chain oxygen and nitrogen atoms in the case of asparagine and aspartic acid. When we extend the analysis to the side-chain atoms of the neighboring residues, we observe that left-handed β turns display a regular and largely amino acid independent structure that can extend to seven consecutive residues. This collective pattern is due to the presence of a backbone soliton. We show how one can use our visualization techniques to analyze and classify the different solitons in terms of selection rules that we describe in detail.

  18. Influence of the side chain next to C-terminal benzimidazole in opioid pseudopeptides containing the Dmt-Tic pharmacophore.

    PubMed

    Balboni, Gianfranco; Trapella, Claudio; Sasaki, Yusuke; Ambo, Akihiro; Marczak, Ewa D; Lazarus, Lawrence H; Salvadori, Severo

    2009-09-10

    To improve the structure-activity studies of the lead delta opioid agonist H-Dmt-Tic-Asp*-Bid, we synthesized and pharmacologically characterized a series of analogues in which the side chain next to 1H-benzimidazole-2-yl (Bid) was substituted by those endowed with different chemical properties. Interesting results were obtained: (1) only Gly, Ala, and Asp resulted in delta agonism, (2) Phe yielded delta antagonism, (3) and all other residues except Glu (devoid of any activity) gave mu agonism.

  19. Phase behaviors, molecular and supramolecular structures in polymers containing rigid-rod backbones with cyanobiphenyl side chains

    NASA Astrophysics Data System (ADS)

    Ruan, Jrjeng

    One of the most important and challenging topics in materials chemistry involves designing nano-structures in synthetic materials via self-assembly for various highly technical applications. A specially designed combined liquid crystalline polymer containing a polyester backbone with cyanobiphenyl side chains has been studied in aspects of phase behaviors and crystal structures. The triclinic crystal phases identified in this series of polymer are all found to be constricted by 4-monomer unit cells. This discovery of 4-monomer triclinic unit cells motivates a search for the existence of supramolecular phases and understanding the possible molecular packing. A series of newly designed polyimides, which are composed of aromatic polyimide backbones with 4-cyanobiphenyl mesogens on the side chains has been synthesized. This series of polymers possesses a lesser degree of coupling between the backbones and side chains, which indicates the possibility of microphase separation between them. The representative polyimides of BPDA-7CBBP and BPDA-11CBBP in this series, in which 4-cyanobiphenyl side chains are connected onto the backbones through seven and eleven methylene units respectively have systematically studied in this research. Two crystal forms were recognized in BPDA-11CBBA, and one of them possesses six repeating units in one monoclinic unit cell. Moreover, the existence of a supramolecular phase has been proposed based on 2D WAXD fiber patterns. In the case of BPDA-7CBBP, three crystal forms were identified: two of them are constructed by triclinic lattices with large unit cells. The numbers of repeating units in those unit cells are seven and eight, respectively. Complicated phase behaviors including a second-order transition between the supramolecular phase and a high-order liquid crystal phase have been explored. The fact that large unit cells in both polymers with the numbers of repeating units in unit cells being 6, 7, and 8 leads to an important issue for

  20. Structure-Based Design of Novel Tetrahydro-Beta-Carboline Derivatives with a Hydrophilic Side Chain as Potential Phosphodiesterase Inhibitors

    PubMed Central

    Elhady, Ahmed K.; Sigler, Sara C.; Noureldin, Nazih; Canzoneri, Joshua C.; Ahmed, Nermin S.; Piazza, Gary A.; Abadi, Ashraf H.

    2015-01-01

    Tadalafil is a clinically approved phosphodiesterase-5 inhibitor for the treatment of erectile dysfunction and pulmonary arterial hypertension. It contains two chiral carbons, and the marketed isomer is the 6R, 12aR isomer with a methyl substituent on the terminal nitrogen of the piperazinedione ring. In this report, tadalafil analogues with an extended hydrophilic side chain on the piperazine nitrogen were designed to interact with particular hydrophilic residues in the binding pocket. This leads to analogues with moderate inhibitory activity on phosphodiesterase-5, even for isomers in which chiral carbons are of the S configuration.

  1. Proton clouds to measure long-range contacts between nonexchangeable side chain protons in solid-state NMR.

    PubMed

    Sinnige, Tessa; Daniëls, Mark; Baldus, Marc; Weingarth, Markus

    2014-03-26

    We show that selective labeling of proteins with protonated amino acids embedded in a perdeuterated matrix, dubbed 'proton clouds', provides general access to long-range contacts between nonexchangeable side chain protons in proton-detected solid-state NMR, which is important to study protein tertiary structure. Proton-cloud labeling significantly improves spectral resolution by simultaneously reducing proton line width and spectral crowding despite a high local proton density in clouds. The approach is amenable to almost all canonical amino acids. Our method is demonstrated on ubiquitin and the β-barrel membrane protein BamA.

  2. Influence of side-chain regiochemistry on the transistor performance of high-mobility, all-donor polymers.

    PubMed

    Fei, Zhuping; Pattanasattayavong, Pichaya; Han, Yang; Schroeder, Bob C; Yan, Feng; Kline, R Joseph; Anthopoulos, Thomas D; Heeney, Martin

    2014-10-29

    Three novel polythiophene isomers are reported whereby the only difference in structure relates to the regiochemistry of the solubilizing side chains on the backbone. This is demonstrated to have a significant impact on the optoelectronic properties of the polymers and their propensity to aggregate in solution. These differences are rationalized on the basis of differences in backbone torsion. The polymer with the largest effective conjugation length is demonstrated to exhibit the highest field-effect mobility, with peak values up to 4.6 cm(2) V(-1) s(-1). PMID:25302474

  3. Synthesis and characterisation of new types of side chain cholesteryl polymers.

    PubMed

    Wang, Bin; Du, Haiyan; Zhang, Junhua

    2011-01-01

    A series of cholesterol derivatives have been synthesised via the alkylation reaction of the 3-hydroxyl group with the aliphatic bromide compounds with different chain lengths, namely 3β-alkyloxy-cholesterol. The double bond between the C5 and C6 positions in these cholesterol derivatives was oxidised into epoxy, followed by an epoxy-ring-opening reaction with the treatment with acrylic acid, resulting in a series of 3β-alkyloxy-5α-hydroxy-6β-acryloyloxycholesterol, C(n)OCh (n=1, 2, 4, 6, 8, 10, 12), The acrylate group is connected to the C6 position, which is confirmed by the single crystal structure analysis. The corresponding polymers, PC(n)OCh, were prepared via free radical polymerisation. The structure of monomers and the resulting polymers were characterised with nuclear magnetic resonance (NMR), Fourier transform infrared spectroscopy (FT-IR) and gel permeation chromatography (GPC). The thermal properties of PC(n)OCh were studied using differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). To determine the secondary structure of polymers, circular dichroism (CD) spectra were performed. It was found that not all monomers produce high-molecular-weight polymers because of steric hindrance. However, all polymers have a helical structure, which can be enhanced by increasing the alkoxy chain length. In addition, increasing the alkoxy chain length decreases the glass transition temperature and increases the decomposition temperature of the polymers. PMID:21070795

  4. Synthesis and characterisation of new types of side chain cholesteryl polymers.

    PubMed

    Wang, Bin; Du, Haiyan; Zhang, Junhua

    2011-01-01

    A series of cholesterol derivatives have been synthesised via the alkylation reaction of the 3-hydroxyl group with the aliphatic bromide compounds with different chain lengths, namely 3β-alkyloxy-cholesterol. The double bond between the C5 and C6 positions in these cholesterol derivatives was oxidised into epoxy, followed by an epoxy-ring-opening reaction with the treatment with acrylic acid, resulting in a series of 3β-alkyloxy-5α-hydroxy-6β-acryloyloxycholesterol, C(n)OCh (n=1, 2, 4, 6, 8, 10, 12), The acrylate group is connected to the C6 position, which is confirmed by the single crystal structure analysis. The corresponding polymers, PC(n)OCh, were prepared via free radical polymerisation. The structure of monomers and the resulting polymers were characterised with nuclear magnetic resonance (NMR), Fourier transform infrared spectroscopy (FT-IR) and gel permeation chromatography (GPC). The thermal properties of PC(n)OCh were studied using differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). To determine the secondary structure of polymers, circular dichroism (CD) spectra were performed. It was found that not all monomers produce high-molecular-weight polymers because of steric hindrance. However, all polymers have a helical structure, which can be enhanced by increasing the alkoxy chain length. In addition, increasing the alkoxy chain length decreases the glass transition temperature and increases the decomposition temperature of the polymers.

  5. Molecular basis of an adult form of Sandhoff disease: substitution of glutamine for arginine at position 505 of the beta-chain of beta-hexosaminidase results in a labile enzyme.

    PubMed

    Bolhuis, P A; Ponne, N J; Bikker, H; Baas, F; Vianney de Jong, J M

    1993-09-01

    Sandhoff disease is a lysosomal storage disorder characterized by accumulation of GM2 ganglioside due to mutations in the beta-chain of beta-hexosaminidase. Hexosaminidase activity is negligible in infantile Sandhoff disease whereas residual activity is present in juvenile and adult forms. Here we report the molecular basis of the first described adult form of Sandhoff disease. Southern analysis of chromosomal DNA indicated the absence of chromosomal deletions in the gene encoding the beta-chain. Northern analysis of RNA from cultured fibroblasts demonstrated that at least one of the beta-chain alleles was transcribed into normal-length mRNA. Sequence analysis of the entire cDNA prepared from poly-adenylated RNA showed that only one point mutation was present, consisting of a G-->A transition at nucleotide position 1514. This mutation changes the electric charge at amino acid position 505 by substitution of glutamine for arginine in a highly conserved part of the beta-chain, present even in the slime mold Dictyostelium discoideum. The nucleotide transition generated a new restriction site for DdeI, which was present in only one of the alleles of the patient. Reverse transcription of mRNA followed by restriction with DdeI resulted in complete digestion at the mutation site, demonstrating that the second allele was of an mRNA-negative type. Transfection of COS cells with a cDNA construct containing the mutation but otherwise the normal sequence resulted in the expression of a labile form of beta-hexosaminidase. These results show that the patient's is a genetic compound, and that the lability of beta-hexosaminidase found in this form of Sandhoff disease is based on a single nucleotide transition. PMID:8357844

  6. Effect of Side Chains on Molecular Conformation of Anthracene-Ethynylene-Phenylene-Vinylene Oligomers: A Comparative Density Functional Study With and Without Dispersion Interaction.

    PubMed

    Dong, Chuanding; Hoppe, Harald; Beenken, Wichard J D

    2016-06-01

    Using density functional calculations with and without dispersion interaction, we studied the effects of linear octyl and branched 2-ethylhexyl side chains on the oligomer conformation of the conjugated copolymer poly(p-anthracene-ethynylene)-alt-poly(p-phenylene-vinylene). With dispersion included, the branched side chains can cause significant bending of the oligomer backbone, while without dispersion they induce mainly torsional disorder. The oligomers with mainly linear side chains keep good planarity when optimized with and without dispersion. Despite their dramatically different conformations, the calculated absorption spectra of the oligomers with various side chain combinations are very similar, indicating that the conformation of the copolymer is not the main reason for the experimentally observed different spectra of ordered and disordered phases.

  7. Stereoselective introduction of two chiral centers by a single diketoreductase: an efficient biocatalytic route for the synthesis of statin side chains.

    PubMed

    Wu, Xuri; Wang, Lili; Wang, Shuzhen; Chen, Yijun

    2010-06-01

    Statins, including atorvastatin (Lipitor), are the top-selling drugs in the world. The biocatalytic production of chiral side chains of statin drugs is of great interest to academia and industry. Stereoselective double reduction of a beta,delta-diketo ester catalyzed by a diketoreductase offers a simple and efficient route for the preparation of statin side chains. Comparison of different cofactor regeneration systems resulted in an easy and cost-effective process for this enzymatic reduction.

  8. Side chain dependence of intensity and wavenumber position of amide I' in IR and visible Raman spectra of XA and AX dipeptides.

    PubMed

    Measey, Thomas; Hagarman, Andrew; Eker, Fatma; Griebenow, Kai; Schweitzer-Stenner, Reinhard

    2005-04-28

    A series of AX and XA dipeptides in D2O have been investigated by FTIR, isotropic, and anisotropic Raman spectroscopy at acidic, neutral, and alkaline pD, to probe the influence of amino acid side chains on the amide I' band. We obtained a set of spectral parameters for each peptide, including intensities, wavenumbers, half-widths, and dipole moments, and found that these amide I' parameters are indeed dependent on the side chain. Side chains with similar characteristic properties were found to have similar effects on the amide I'. For example, dipeptides with aliphatic side chains were found to exhibit a downshift of the amide I' wavenumber, while those containing polar side chains experienced an increase in wavenumber. The N-terminal charge causes a substantial upshift of amide I', whereas the C-terminal charge causes a moderate decrease of the transition dipole moment. Density functional theory (DFT) calculations on the investigated dipeptides in vacuo yielded different correlations between theoretically and experimentally obtained wavenumbers for aliphatic/aromatic and polar/charged side chains, respectively. This might be indicative of a role of the hydration shell in transferring side chain-backbone interactions. For Raman bands, we found a correlation between amide I' depolarization ratio and wavenumber which reflects that some side chains (valine, histidine) have a significant influence on the Raman tensor. Altogether, the obtained data are of utmost importance for utilizing amide I as a tool for secondary structure analysis of polypeptides and proteins and providing an experimental basis for theoretical modeling of this important backbone mode. This is demonstrated by a rather accurate modeling for the amide I' band profiles of the IR, isotropic Raman, and anisotropic Raman spectra of the beta-amyloid fragment Abeta(1-82).

  9. Probing alkali metal-pi interactions with the side chain residue of tryptophan.

    PubMed

    Hu, Jiaxin; Barbour, Leonard J; Gokel, George W

    2002-04-16

    Feeble forces play a significant role in the organization of proteins. These include hydrogen bonding, hydrophobic interactions, salt bridge formation, and steric interactions. The alkali metal cation-pi interaction is a force of potentially profound importance but its consideration in biology has been limited by the lack of experimental evidence. Our previous studies of cation-pi interactions with Na(+) and K(+) involved the side arms of tryptophan (indole), tyrosine (phenol), and phenylalanine (benzene) as the arene donors. The receptor system possesses limiting steric constraints. In this report, we show that direct interactions between alkali metals and arenes occur at or within the van der Waals contact distance.

  10. Probing alkali metal–π interactions with the side chain residue of tryptophan

    PubMed Central

    Hu, Jiaxin; Barbour, Leonard J.; Gokel, George W.

    2002-01-01

    Feeble forces play a significant role in the organization of proteins. These include hydrogen bonding, hydrophobic interactions, salt bridge formation, and steric interactions. The alkali metal cation-π interaction is a force of potentially profound importance but its consideration in biology has been limited by the lack of experimental evidence. Our previous studies of cation–π interactions with Na+ and K+ involved the side arms of tryptophan (indole), tyrosine (phenol), and phenylalanine (benzene) as the arene donors. The receptor system possesses limiting steric constraints. In this report, we show that direct interactions between alkali metals and arenes occur at or within the van der Waals contact distance. PMID:11943874

  11. Side chain variations radically alter the diffusion of poly(2-alkyl-2-oxazoline) functionalised nanoparticles through a mucosal barrier.

    PubMed

    Mansfield, Edward D H; de la Rosa, Victor R; Kowalczyk, Radoslaw M; Grillo, Isabelle; Hoogenboom, Richard; Sillence, Katy; Hole, Patrick; Williams, Adrian C; Khutoryanskiy, Vitaliy V

    2016-08-16

    Functionalised nanomaterials are gaining popularity for use as drug delivery vehicles and, in particular, mucus penetrating nanoparticles may improve drug bioavailability via the oral route. To date, few polymers have been investigated for their muco-penetration, and the effects of systematic structural changes to polymer architectures on the penetration and diffusion of functionalised nanomaterials through mucosal tissue have not been reported. We investigated the influence of poly(2-oxazoline) alkyl side chain length on nanoparticle diffusion; poly(2-methyl-2-oxazoline), poly(2-ethyl-2-oxazoline), and poly(2-n-propyl-2-oxazoline) were grafted onto the surface of thiolated silica nanoparticles and characterised by FT-IR, Raman and NMR spectroscopy, thermogravimetric analysis, and small angle neutron scattering. Diffusion coefficients were determined in water and in a mucin dispersion (using Nanoparticle Tracking Analysis), and penetration through a mucosal barrier was assessed using an ex vivo fluorescence technique. The addition of a single methylene group in the side chain significantly altered the penetration and diffusion of the materials in both mucin dispersions and mucosal tissue. Nanoparticles functionalised with poly(2-methyl-2-oxazoline) were significantly more diffusive than particles with poly(2-ethyl-2-oxazoline) while particles with poly(2-n-propyl-2-oxazoline) showed no significant increase compared to the unfunctionalised particles. These data show that variations in the polymer structure can radically alter their diffusive properties with clear implications for the future design of mucus penetrating systems. PMID:27400181

  12. The power of hard-sphere models for proteins: Understanding side-chain conformations and predicting thermodynamic stability

    NASA Astrophysics Data System (ADS)

    Zhou, Alice; O'Hern, Corey; Regan, Lynne

    2013-03-01

    We seek to dramatically improve computational protein design using minimal models that include only the dominant physical interactions. By modeling proteins with hard-sphere interactions and stereochemical constraints, we are able to explain the side-chain dihedral angle distributions for Leu, Ile, and other hydrophobic residues that are observed in protein crystal structures. We also consider inter-residue interactions on the distribution of side-chain dihedral angles for residues in the hydrophobic core of T4 lysozyme. We calculate the energetic and entropic contributions to the free energy differences between wildtype T4 lysozyme and several mutants involving Leu to Ala substitutions. We find a strong correlation between the entropy difference and the decrease in the melting temperature of the mutatants. These results emphasize that considering both entropy and enthalpy is crucial for obtaining a quantitative understanding of protein stability. NSF DMR-1006537 and PHY-1019147, the Raymond and Beverly Sackler Institute for Biological, Physical and Engineering Sciences, and Howard Hughes Medical Institute International Research Fellowship

  13. Variation of the net charge, lipophilicity, and side chain flexibility in Dmt(1)-DALDA: Effect on Opioid Activity and Biodistribution.

    PubMed

    Novoa, Alexandre; Van Dorpe, Sylvia; Wynendaele, Evelien; Spetea, Mariana; Bracke, Nathalie; Stalmans, Sofie; Betti, Cecilia; Chung, Nga N; Lemieux, Carole; Zuegg, Johannes; Cooper, Matthew A; Tourwé, Dirk; De Spiegeleer, Bart; Schiller, Peter W; Ballet, Steven

    2012-11-26

    The influence of the side chain charges of the second and fourth amino acid residues in the peptidic μ opioid lead agonist Dmt-d-Arg-Phe-Lys-NH(2) ([Dmt(1)]-DALDA) was examined. Additionally, to increase the overall lipophilicity of [Dmt(1)]-DALDA and to investigate the Phe(3) side chain flexibility, the final amide bond was N-methylated and Phe(3) was replaced by a constrained aminobenzazepine analogue. The in vitro receptor binding and activity of the peptides, as well as their in vivo transport (brain in- and efflux and tissue biodistribution) and antinociceptive properties after peripheral administration (ip and sc) in mice were determined. The structural modifications result in significant shifts of receptor binding, activity, and transport properties. Strikingly, while [Dmt(1)]-DALDA and its N-methyl analogue, Dmt-d-Arg-Phe-NMeLys-NH(2), showed a long-lasting antinociceptive effect (>7 h), the peptides with d-Cit(2) generate potent antinociception more rapidly (maximal effect at 1h postinjection) but also lose their analgesic activity faster when compared to [Dmt(1)]-DALDA and [Dmt(1),NMeLys(4)]-DALDA.

  14. Solid-state NMR Study Reveals Collagen I Structural Modifications of Amino Acid Side Chains upon Fibrillogenesis*

    PubMed Central

    De Sa Peixoto, Paulo; Laurent, Guillaume; Azaïs, Thierry; Mosser, Gervaise

    2013-01-01

    In vivo, collagen I, the major structural protein in human body, is found assembled into fibrils. In the present work, we study a high concentrated collagen sample in its soluble, fibrillar, and denatured states using one and two dimensional {1H}-13C solid-state NMR spectroscopy. We interpret 13C chemical shift variations in terms of dihedral angle conformation changes. Our data show that fibrillogenesis increases the side chain and backbone structural complexity. Nevertheless, only three to five rotameric equilibria are found for each amino acid residue, indicating a relatively low structural heterogeneity of collagen upon fibrillogenesis. Using side chain statistical data, we calculate equilibrium constants for a great number of amino acid residues. Moreover, based on a 13C quantitative spectrum, we estimate the percentage of residues implicated in each equilibrium. Our data indicate that fibril formation greatly affects hydroxyproline and proline prolyl pucker ring conformation. Finally, we discuss the implication of these structural data and propose a model in which the attractive force of fibrillogenesis comes from a structural reorganization of 10 to 15% of the amino acids. These results allow us to further understand the self-assembling process and fibrillar structure of collagen. PMID:23341452

  15. Controlling the morphology of side chain liquid crystalline block copolymer thin films through variations in liquid crystalline content.

    PubMed

    Verploegen, Eric; Zhang, Tejia; Jung, Yeon Sik; Ross, Caroline; Hammond, Paula T

    2008-10-01

    In this paper, we describe methods for manipulating the morphology of side-chain liquid crystalline block copolymers through variations in the liquid crystalline content. By systematically controlling the covalent attachment of side chain liquid crystals to a block copolymer (BCP) backbone, the morphology of both the liquid crystalline (LC) mesophase and the phase-segregated BCP microstructures can be precisely manipulated. Increases in LC functionalization lead to stronger preferences for the anchoring of the LC mesophase relative to the substrate and the intermaterial dividing surface. By manipulating the strength of these interactions, the arrangement and ordering of the ultrathin film block copolymer nanostructures can be controlled, yielding a range of morphologies that includes perpendicular and parallel cylinders, as well as both perpendicular and parallel lamellae. Additionally, we demonstrate the utilization of selective etching to create a nanoporous liquid crystalline polymer thin film. The unique control over the orientation and order of the self-assembled morphologies with respect to the substrate will allow for the custom design of thin films for specific nanopatterning applications without manipulation of the surface chemistry or the application of external fields.

  16. Variation of the net charge, lipophilicity and side chain flexibility in Dmt1-DALDA: effect on opioid activity and biodistribution

    PubMed Central

    Novoa, Alexandre; Van Dorpe, Sylvia; Wynendaele, Evelien; Spetea, Mariana; Bracke, Nathalie; Stalmans, Sofie; Betti, Cecilia; Chung, Nga N.; Lemieux, Carole; Zuegg, Johannes; Cooper, Matthew A.; Tourwé, Dirk; De Spiegeleer, Bart; Schiller, Peter W.; Ballet, Steven

    2012-01-01

    The influence of the side chain charges of the second and fourth amino acid residues in the peptidic μ opioid lead agonist Dmt-D-Arg-Phe-Lys-NH2 ([Dmt1]-DALDA) was examined. Additionally, to increase the overall lipophilicity of [Dmt1]-DALDA and to investigate the Phe3 side chain flexibility, the final amide bond was N-methylated and Phe3 was replaced by a constrained aminobenzazepine analogue. The in vitro receptor binding and activity of the peptides, as well as their in vivo transport (brain in- and efflux and tissue biodistribution) and antinociceptive properties after peripheral administration (i.p. and s.c.) in mice were determined. The structural modifications result in significant shifts of receptor binding, activity and transport properties. Strikingly, while [Dmt1]-DALDA and its N-methyl analogue, Dmt-D-Arg-Phe-NMeLys-NH2, showed a long-lasting antinociceptive effect (>7h), the peptides with D-Cit2 generate potent antinociception more rapidly (maximal effect at 1h post-injection) but also lose their analgesic activity faster, when compared to [Dmt1]-DALDA and [Dmt1,NMeLys4]-DALDA. PMID:23102273

  17. 3D HCCH 3-TOCSY for Resonance Assignment of Methyl-Containing Side Chains in 13C-Labeled Proteins

    NASA Astrophysics Data System (ADS)

    Uhrín, Dušan; Uhrínová, Stanislava; Leadbeater, Claire; Nairn, Jacqueline; Price, Nicholas C.; Barlow, Paul N.

    2000-02-01

    Two 3D experiments, (H)CCH3-TOCSY and H(C)CH3-TOCSY, are proposed for resonance assignment of methyl-containing amino acid side chains. After the initial proton-carbon INEPT step, during which either carbon or proton chemical shift labeling is achieved (t1), the magnetization is spread along the amino acid side chains by a carbon spin lock. The chemical shifts of methyl carbons are labeled (t2) during the following constant time interval. Finally the magnetization is transferred, in a reversed INEPT step, to methyl protons for detection (t3). The proposed experiments are characterized by high digital resolution in the methyl carbon dimension (t2max = 28.6 ms), optimum sensitivity due to the use of proton decoupling during the long constant time interval, and an optional removal of CH2, or CH2 and CH, resonances from the F2F3 planes. The building blocks used in these experiments can be implemented in a range of heteronuclear experiments focusing on methyl resonances in proteins. The techniques are illustrated using a 15N, 13C-labeled E93D mutant of Schizosacharomyces pombe phosphoglycerate mutase (23.7 kDa).

  18. Synthesis and Photophysical Properties of Soluble Low-Bandgap Thienothiophene Polymers with Various Alkyl Side-Chain Lengths

    SciTech Connect

    Bae, W. J.; Scilla, C.; Duzhko, V. V.; Jo, Jang; Coughlin, E. B.

    2011-05-27

    We report the facile synthesis and characterization of a class of thienothiophene polymers with various lengths of alkyl side chains. A series of 2-alkylthieno[3,4-b]thiophene monomers (Ttx) have been synthesized in a two-step protocol in an overall yield of 28–37%. Poly(2-alkylthieno[3,4-b]thiophenes) (PTtx, alkyl: pentyl, hexyl, heptyl, octyl, and tridecyl) were synthesized by oxidative polymerization with FeCl₃ or via Grignard metathesis (GRIM) polymerization methods. The polymers are readily soluble in common organic solvents. The polymers synthesized by GRIM polymerization method (PTtx-G) have narrower molecular weight distribution (Ð) with lower molecular weight (Mn) than those synthesized by oxidative polymerization (PTtx-O). The band structures of the polymers with various lengths of alkyl side chains were investigated by UV–vis spectroscopy, cyclic voltammetry, and ultraviolet photoelectron spectroscopy. These low-bandgap polymers are good candidates for organic transistors, organic light-emitting diodes, and organic photovoltaic cells.

  19. Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity

    PubMed Central

    Ollikainen, Noah; de Jong, René M.; Kortemme, Tanja

    2015-01-01

    Interactions between small molecules and proteins play critical roles in regulating and facilitating diverse biological functions, yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited. One main difficulty, in addition to inaccuracies in energy functions, is the exquisite sensitivity of protein–ligand interactions to subtle conformational changes, coupled with the computational problem of sampling the large conformational search space of degrees of freedom of ligands, amino acid side chains, and the protein backbone. Here, we describe two benchmarks for evaluating the accuracy of computational approaches for re-engineering protein-ligand interactions: (i) prediction of enzyme specificity altering mutations and (ii) prediction of sequence tolerance in ligand binding sites. After finding that current state-of-the-art “fixed backbone” design methods perform poorly on these tests, we develop a new “coupled moves” design method in the program Rosetta that couples changes to protein sequence with alterations in both protein side-chain and protein backbone conformations, and allows for changes in ligand rigid-body and torsion degrees of freedom. We show significantly increased accuracy in both predicting ligand specificity altering mutations and binding site sequences. These methodological improvements should be useful for many applications of protein – ligand design. The approach also provides insights into the role of subtle conformational adjustments that enable functional changes not only in engineering applications but also in natural protein evolution. PMID:26397464

  20. Z-Selective olefin metathesis on peptides: investigation of side-chain influence, preorganization, and guidelines in substrate selection.

    PubMed

    Mangold, Shane L; O'Leary, Daniel J; Grubbs, Robert H

    2014-09-01

    Olefin metathesis has emerged as a promising strategy for modulating the stability and activity of biologically relevant compounds; however, the ability to control olefin geometry in the product remains a challenge. Recent advances in the design of cyclometalated ruthenium catalysts has led to new strategies for achieving such control with high fidelity and Z selectivity, but the scope and limitations of these catalysts on substrates bearing multiple functionalities, including peptides, remained unexplored. Herein, we report an assessment of various factors that contribute to both productive and nonproductive Z-selective metathesis on peptides. The influence of sterics, side-chain identity, and preorganization through peptide secondary structure are explored by homodimerization, cross metathesis, and ring-closing metathesis. Our results indicate that the amino acid side chain and identity of the olefin profoundly influence the activity of cyclometalated ruthenium catalysts in Z-selective metathesis. The criteria set forth for achieving high conversion and Z selectivity are highlighted by cross metathesis and ring-closing metathesis on diverse peptide substrates. The principles outlined in this report are important not only for expanding the scope of Z-selective olefin metathesis to peptides but also for applying stereoselective olefin metathesis in general synthetic endeavors. PMID:25102124

  1. Triblock Copolymers with Grafted Fluorine-Free Amphiphilic Non-Ionic Side Chains for Antifouling and Fouling-Release Applications

    SciTech Connect

    Y Cho; H Sundaram; C Weinman; M Paik; M Dimitriou; J Finlay; M Callow; J Callow; E Kramer; C Ober

    2011-12-31

    Fluorine-free, amphiphilic, nonionic surface active block copolymers (SABCs) were synthesized through chemical modification of a polystyrene-block-poly(ethylene-ran-butylene)-block-polyisoprene triblock copolymer precursor with selected amphiphilic nonionic Brij and other surfactants. Amphiphilicity was imparted by a hydrophobic aliphatic group combined with a hydrophilic poly(ethylene glycol) (PEG) group-containing moiety. The surfaces were characterized by dynamic water contact angle, atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and near edge X-ray absorption fine structure (NEXAFS) analysis. In biofouling assays, settlement (attachment) of both spores of the green alga Ulva and cells of the diatom Navicula on SABCs modified with Brij nonionic side chains was significantly reduced relative to a PDMS standard, with a nonionic surfactant combining a PEG group and an aliphatic moiety demonstrating the best performance. Additionally, a fouling-release assay using sporelings (young plants) of Ulva and Navicula suggested that the SABC derived from nonionic Brij side chains also out-performed PDMS as a fouling-release material. Good antifouling and fouling-release properties were not demonstrated for the other two amphiphilic surfaces derived from silicone and aromatic group containing nonionic surfactants included in this study. The results suggest that small differences in chemical surface functionality impart more significant changes with respect to the antifouling settlement and fouling-release performance of materials than overall wettability behavior.

  2. Fast side chain replacement in proteins using a coarse-grained approach for evaluating the effects of mutation during evolution.

    PubMed

    Grahnen, Johan A; Kubelka, Jan; Liberles, David A

    2011-08-01

    For high-throughput structural genomic and evolutionary bioinformatics approaches, there is a clear need for fast methods to evaluate substitutions structurally. Coarse-grained methods are both powerful and fast, and a coarse-grained approach to position the substituted side chains is presented. Through the application of a coarse-grained method, a speed-up on the single- residue replacement, of at least sevenfold is achieved compared with modern all-atom approaches. At the same time, this approach maintains a small median RMSD from the leading all-atom approach (as measured in coarse-grained space), and predicts the conformation of point mutants with similar accuracy and generates biologically realistic side chain angles. This method is also substantially more predictable in its run time, making it useful for high-throughput studies of protein structural evolution. To demonstrate the utility of this method, it has been implemented in a forward simulation of sequences threaded through the SH2 domains, with selective pressures to fold and bind specifically. The relative substitution rates across the protein structure and at the binding interface are reflective of those observed in SH2 domain evolution. The algorithm has been implemented in C++, with the source code and binaries (currently supported for Linux systems) freely available as SARA at http://www.wyomingbioinformatics.org/LiberlesGroup/SARA .

  3. Heterogeneous side chain conformation highlights a network of interactions implicated in hysteresis of the knotted protein, Minimal Tied Trefoil (MTTTm)

    PubMed Central

    Capraro, Dominique T.; Jennings, Patricia A.

    2015-01-01

    Hysteresis is a signature for a bistability in the native landscape of a protein with significant transition state barriers for the interconversion of stable species. Large global stability, as in GFP, contributes to the observation of this rare hysteretic phenomenon in folding. The signature for such behavior is non-coincidence in the unfolding and refolding transitions, despite waiting significantly longer than the time necessary for complete denaturation. Our work indicates that hysteresis in the knotted protein, the Minimal Tied Trefoil from Thermotoga maritma (MTTTm), is mediated by a network of side chain interactions within a tightly packed core. These initially identified interactions include proline 62 from a tight β-like turn, phenylalanine 65 at the beginning of the knotting loop, and histidine 114 that initiates the threading element. It is this tightly packed region and the knotting element that we propose is disrupted with prolonged incubation in the denatured state, and is involved in the observed hysteresis. Interestingly, the disruption is not linked to backbone interactions, but rather to the packing of side chains in this critical region. PMID:26291198

  4. Z-Selective olefin metathesis on peptides: investigation of side-chain influence, preorganization, and guidelines in substrate selection.

    PubMed

    Mangold, Shane L; O'Leary, Daniel J; Grubbs, Robert H

    2014-09-01

    Olefin metathesis has emerged as a promising strategy for modulating the stability and activity of biologically relevant compounds; however, the ability to control olefin geometry in the product remains a challenge. Recent advances in the design of cyclometalated ruthenium catalysts has led to new strategies for achieving such control with high fidelity and Z selectivity, but the scope and limitations of these catalysts on substrates bearing multiple functionalities, including peptides, remained unexplored. Herein, we report an assessment of various factors that contribute to both productive and nonproductive Z-selective metathesis on peptides. The influence of sterics, side-chain identity, and preorganization through peptide secondary structure are explored by homodimerization, cross metathesis, and ring-closing metathesis. Our results indicate that the amino acid side chain and identity of the olefin profoundly influence the activity of cyclometalated ruthenium catalysts in Z-selective metathesis. The criteria set forth for achieving high conversion and Z selectivity are highlighted by cross metathesis and ring-closing metathesis on diverse peptide substrates. The principles outlined in this report are important not only for expanding the scope of Z-selective olefin metathesis to peptides but also for applying stereoselective olefin metathesis in general synthetic endeavors.

  5. Aromatic substituents for prohibiting side-chain packing and π-π stacking in tin-cored tetrahedral stilbenoids

    NASA Astrophysics Data System (ADS)

    Kim, Cheolmin; Yoon, Min-Ju; Hong, Seok Hee; Park, Minjoon; Park, Kwangyong; Kim, Soo Young

    2016-05-01

    Tetrahedral structures comprising Sn-cored materials with five different types of substituents were synthesized. For the substituents, we employed methyl and tert-butyl as aliphatic groups, and naphthyl and phenyl as aromatic groups. The bandgap is in the range of 3.28 - 3.56 eV. The All the compounds with substituents showed bathochromical photoluminescence characteristics and exhibited aggregation-induced emission characteristics. Specifically, the compounds with aromatic substituents prohibited side-chain packing and π-π stacking. The energy levels of the highest occupied and lowest unoccupied molecular orbitals were measured to be 5.5 - 5.75 and 2.0 - 2.37 eV, respectively. The maximum luminance efficiencies and power efficiencies of the Sn-cored compound-based organic light-emitting diodes (OLEDs) were 0.38 - 0.71 cd/A and 0.15 - 0.28 lm/W. Therefore, it is expected that Sn-cored compounds with a tetrahedral structure, especially those containing aromatic substituents, can be used as an active material in blue OLEDs for prohibiting side-chain packing and π-π stacking. [Figure not available: see fulltext.

  6. Heterogeneous side chain conformation highlights a network of interactions implicated in hysteresis of the knotted protein, minimal tied trefoil

    NASA Astrophysics Data System (ADS)

    Burban, David J.; Haglund, Ellinor; Capraro, Dominique T.; Jennings, Patricia A.

    2015-09-01

    Hysteresis is a signature for a bistability in the native landscape of a protein with significant transition state barriers for the interconversion of stable species. Large global stability, as in GFP, contributes to the observation of this rare hysteretic phenomenon in folding. The signature for such behavior is non-coincidence in the unfolding and refolding transitions, despite waiting significantly longer than the time necessary for complete denaturation. Our work indicates that hysteresis in the knotted protein, the minimal tied trefoil from Thermotoga maritma (MTTTm), is mediated by a network of side chain interactions within a tightly packed core. These initially identified interactions include proline 62 from a tight β-like turn, phenylalanine 65 at the beginning of the knotting loop, and histidine 114 that initiates the threading element. It is this tightly packed region and the knotting element that we propose is disrupted with prolonged incubation in the denatured state, and is involved in the observed hysteresis. Interestingly, the disruption is not linked to backbone interactions, but rather to the packing of side chains in this critical region.

  7. Z-Selective Olefin Metathesis on Peptides: Investigation of Side-Chain Influence, Preorganization, and Guidelines in Substrate Selection

    PubMed Central

    2015-01-01

    Olefin metathesis has emerged as a promising strategy for modulating the stability and activity of biologically relevant compounds; however, the ability to control olefin geometry in the product remains a challenge. Recent advances in the design of cyclometalated ruthenium catalysts has led to new strategies for achieving such control with high fidelity and Z selectivity, but the scope and limitations of these catalysts on substrates bearing multiple functionalities, including peptides, remained unexplored. Herein, we report an assessment of various factors that contribute to both productive and nonproductive Z-selective metathesis on peptides. The influence of sterics, side-chain identity, and preorganization through peptide secondary structure are explored by homodimerization, cross metathesis, and ring-closing metathesis. Our results indicate that the amino acid side chain and identity of the olefin profoundly influence the activity of cyclometalated ruthenium catalysts in Z-selective metathesis. The criteria set forth for achieving high conversion and Z selectivity are highlighted by cross metathesis and ring-closing metathesis on diverse peptide substrates. The principles outlined in this report are important not only for expanding the scope of Z-selective olefin metathesis to peptides but also for applying stereoselective olefin metathesis in general synthetic endeavors. PMID:25102124

  8. Water molecules can control the side-chain rotamer distribution of an aryl peptide in a nonpolar environment.

    PubMed

    Radding, W

    1988-06-01

    With computer-controlled circular dichroism (CD) spectrophotometry it is possible to obtain difference CD spectra which result from small perturbations to the environment of a chiral molecule. In the experiments described here a dry iso-octane solution of cyclobis-N-methyl-L-phenylalanine (c-(NMe-L-Phe)2) has been perturbed by exposure to water vapor. The resulting difference spectrum shows that water coordination to c-(NMe-L-Phe)2 eliminates negative ellipticity in the 244 nm region, while it simultaneously creates positive CD intensity in the 212 nm region. These two features of the difference spectrum plus related features of other direct spectra imply that water coordinated with p-orbital unpaired electrons of the carbonyl interferes sterically with the chi = 180 degrees side-chain rotamer. It can be expected that in this way hydrogen bonding of any species to backbone carbonyls can control the rotamer distribution of aromatic side-chains, if one of the rotamers occludes unpaired electrons of the carbonyl. Such control may offer an on-off switch for electron transport through proteins.

  9. Crystallographic studies of V44 mutants of Clostridium pasteurianum rubredoxin: Effects of side-chain size on reduction potential

    SciTech Connect

    Park, Il Yeong; Eidsness, Marly K.; Lin, I-Jin; Gebel, Erika B.; Youn, Buhyun; Harley, Jill L.; Machonkin, Timothy E.; Frederick, Ronnie O.; Markley, John L.; Smith, Eugene T.; Ichiye, Toshiko; Kang, ChulHee

    2010-11-16

    Understanding the structural origins of differences in reduction potentials is crucial to understanding how various electron transfer proteins modulate their reduction potentials and how they evolve for diverse functional roles. Here, the high-resolution structures of several Clostridium pasteurianum rubredoxin (Cp Rd) variants with changes in the vicinity of the redox site are reported in order to increase this understanding. Our crystal structures of [V44L] (at 1.8 {angstrom} resolution), [V44A] (1.6 {angstrom}), [V44G] (2.0 {angstrom}) and [V44A, G45P] (1.5 {angstrom}) Rd (all in their oxidized states) show that there is a gradual decrease in the distance between Fe and the amide nitrogen of residue 44 upon reduction in the size of the side chain of residue 44; the decrease occurs from leucine to valine, alanine or glycine and is accompanied by a gradual increase in their reduction potentials. Mutation of Cp Rd at position 44 also changes the hydrogen-bond distance between the amide nitrogen of residue 44 and the sulfur of cysteine 42 in a size-dependent manner. Our results suggest that residue 44 is an important determinant of Rd reduction potential in a manner dictated by side-chain size. Along with the electric dipole moment of the 43-44 peptide bond and the 44-42 NHS type hydrogen bond, a modulation mechanism for solvent accessibility through residue 41 might regulate the redox reaction of the Rds. Proteins 2004.

  10. First observation of amino acid side chain dynamics in membrane proteins using high field deuterium nuclear magnetic resonance spectroscopy

    SciTech Connect

    Kinsey, R.A.; Kintanar, A.; Tsai, M.D.; Smith, R.L.; Janes, N.; Oldfield, E.

    1981-05-10

    The first deuterium NMR spectra of an individual membrane protein, bacteriohodopsin in the purple membrane of Halobacterium halobium R1 has been obtained. Biosynthetic isotopic enrichment with (gamma-2H6) valine and high field Fourier transform operation permitted rapid data acquisition on intact membranes, including measurement of relaxation times. At some temperatures high quality spectra could be obtained in less than 1 s. (U-14C)Valine tracer studies indicate that less than or equal to 2% of valine added to the growth medium is broken down and incorporated into other membrane constituents. The NMR results indicate that the valine side chain is a rather rigid structure. Motion about C alpha-C beta is slow (less than 10(5) s-1) at growth temperature, while motion about C beta-C gamma is as expected fast (much greater than 10(5) s-1) at all accessible temperatures. The activation energy for methyl group rotation from spin-lattice relaxation data between -75 and 53 degrees C is approximately 2.4 kcal/mol, in good agreement with previous 1H NMR studies on solid alkanes. Preliminary data on (gamma-2H6)valine-labeled Acholeplasma laidlawii B (PG9) cell membranes are also presented. Results strongly suggest that it should now be possible to observe in great detail the motions of any type of amino acid side chain in membrane proteins, including the effects of lipid composition on protein dynamics.

  11. New Insights into the Structure of (1→3,1→6)-β-D-Glucan Side Chains in the Candida glabrata Cell Wall

    PubMed Central

    Lowman, Douglas W.; West, Lara J.; Bearden, Daniel W.; Wempe, Michael F.; Power, Trevor D.; Ensley, Harry E.; Haynes, Ken; Williams, David L.; Kruppa, Michael D.

    2011-01-01

    β-glucan is a (1→3)-β-linked glucose polymer with (1→6)-β-linked side chains and a major component of fungal cell walls. β-glucans provide structural integrity to the fungal cell wall. The nature of the (1–6)-β-linked side chain structure of fungal (1→3,1→6)-β-D-glucans has been very difficult to elucidate. Herein, we report the first detailed structural characterization of the (1→6)-β-linked side chains of Candida glabrata using high-field NMR. The (1→6)-β-linked side chains have an average length of 4 to 5 repeat units spaced every 21 repeat units along the (1→3)-linked polymer backbone. Computer modeling suggests that the side chains have a bent curve structure that allows for a flexible interconnection with parallel (1→3)-β-D-glucan polymers, and/or as a point of attachment for proteins. Based on these observations we propose new approaches to how (1→6)-β-linked side chains interconnect with neighboring glucan polymers in a manner that maximizes fungal cell wall strength, while also allowing for flexibility, or plasticity. PMID:22096604

  12. Probing the carboxyester side chain in controlled deactivation (-)-δ(8)-tetrahydrocannabinols.

    PubMed

    Nikas, Spyros P; Sharma, Rishi; Paronis, Carol A; Kulkarni, Shashank; Thakur, Ganesh A; Hurst, Dow; Wood, JodiAnne T; Gifford, Roger S; Rajarshi, Girija; Liu, Yingpeng; Raghav, Jimit Girish; Guo, Jason Jianxin; Järbe, Torbjörn U C; Reggio, Patricia H; Bergman, Jack; Makriyannis, Alexandros

    2015-01-22

    We recently reported on a controlled deactivation/detoxification approach for obtaining cannabinoids with improved druggability. Our design incorporates a metabolically labile ester group at strategic positions within the THC structure. We have now synthesized a series of (-)-Δ(8)-THC analogues encompassing a carboxyester group within the 3-alkyl chain in an effort to explore this novel cannabinergic chemotype for CB receptor binding affinity, in vitro and in vivo potency and efficacy, as well as controlled deactivation by plasma esterases. We have also probed the chain's polar characteristics with regard to fast onset and short duration of action. Our lead molecule, namely 2-[(6aR,10aR)-6a,7,10,10a-tetrahydro-1-hydroxy-6,6,9-trimethyl-6H-dibenzo[b,d]pyran-3-yl]-2-methyl-propanoic acid 3-cyano-propyl ester (AM7438), showed picomolar affinity for CB receptors and is deactivated by plasma esterases while the respective acid metabolite is inactive. In further in vitro and in vivo experiments, the compound was found to be a remarkably potent and efficacious CB1 receptor agonist with relatively fast onset/offset of action. PMID:25470070

  13. Conformation-specific spectroscopy of capped glutamine-containing peptides: role of a single glutamine residue on peptide backbone preferences.

    PubMed

    Walsh, Patrick S; Dean, Jacob C; McBurney, Carl; Kang, Hyuk; Gellman, Samuel H; Zwier, Timothy S

    2016-04-28

    The conformational preferences of a series of short, aromatic-capped, glutamine-containing peptides have been studied under jet-cooled conditions in the gas phase. This work seeks a bottom-up understanding of the role played by glutamine residues in directing peptide structures that lead to neurodegenerative diseases. Resonant ion-dip infrared (RIDIR) spectroscopy is used to record single-conformation infrared spectra in the NH stretch, amide I and amide II regions. Comparison of the experimental spectra with the predictions of calculations carried out at the DFT M05-2X/6-31+G(d) level of theory lead to firm assignments for the H-bonding architectures of a total of eight conformers of four molecules, including three in Z-Gln-OH, one in Z-Gln-NHMe, three in Ac-Gln-NHBn, and one in Ac-Ala-Gln-NHBn. The Gln side chain engages actively in forming H-bonds with nearest-neighbor amide groups, forming C8 H-bonds to the C-terminal side, C9 H-bonds to the N-terminal side, and an amide-stacked geometry, all with an extended (C5) peptide backbone about the Gln residue. The Gln side chain also stabilizes an inverse γ-turn in the peptide backbone by forming a pair of H-bonds that bridge the γ-turn and stabilize it. Finally, the entire conformer population of Ac-Ala-Gln-NHBn is funneled into a single structure that incorporates the peptide backbone in a type I β-turn, stabilized by the Gln side chain forming a C7 H-bond to the central amide group in the β-turn not otherwise involved in a hydrogen bond. This β-turn backbone structure is nearly identical to that observed in a series of X-(AQ)-Y β-turns in the protein data bank, demonstrating that the gas-phase structure is robust to perturbations imposed by the crystalline protein environment.

  14. Multifunctional conjugated polymers with main-chain donors and side-chain acceptors for dye sensitized solar cells (DSSCs) and organic photovoltaic cells (OPVs).

    PubMed

    Chang, Dong Wook; Ko, Seo-Jin; Kim, Jin Young; Park, Su-Moon; Lee, Hyo Joong; Dai, Liming; Baek, Jong-Beom

    2011-11-15

    A novel multifunctional conjugated polymer (RCP-1) composed of an electron-donating backbone (carbazole) and an electron-accepting side chain (cyanoacetic acid) connected through conjugated vinylene and terthiophene has been synthesized and tested as a photosensitizer in two major molecule-based solar cells, namely dye sensitized solar cells (DSSCs) and organic photovoltaic cells (OPVs). Promising initial results on overall power conversion efficiencies of 4.11% and 1.04% are obtained from the basic structure of DSSCs and OPVs based on RCP-1, respectively. The well-defined donor (D)-acceptor (A) structure of RCP-1 has made it possible, for the first time, to reach over 4% of power conversion efficiency in DSSCs with an organic polymer sensitizer and good operation stability.

  15. Synthesis and characterization of side-chain cholesterol derivatives based on double bond

    NASA Astrophysics Data System (ADS)

    Yu, Yun-Long; Bai, Jun-Wei; Zhang, Jun-Hua

    2012-07-01

    After steps of esterification, epoxidation and ring-opening, a series of novel monomers of 5-hydroxyl-6-methacryloyloxy-3-alkylate, CnCOOCh (n = 1, 2, 3, 4, 5) were synthesized. After that, the corresponding polymers (PnCOOCh, n = 1, 2, 3, 4, 5) were obtained by free radical polymerization. The molecular structure, composition and thermal behaviors of monomers and polymers were confirmed by 1H NMR, FTIR, single crystal diffractometer, GPC, DSC and TGA. The results indicate that although their molecular weights are not high, all the polymers have high glass transition (Tg) and degradation temperature. In addition, Tg gradually decreases with increasing of alkyl chain lengths, and the degradation temperature increases with the increase of carbon number.

  16. Glutamine Modulates Macrophage Lipotoxicity

    PubMed Central

    He, Li; Weber, Kassandra J.; Schilling, Joel D.

    2016-01-01

    Obesity and diabetes are associated with excessive inflammation and impaired wound healing. Increasing evidence suggests that macrophage dysfunction is responsible for these inflammatory defects. In the setting of excess nutrients, particularly dietary saturated fatty acids (SFAs), activated macrophages develop lysosome dysfunction, which triggers activation of the NLRP3 inflammasome and cell death. The molecular pathways that connect lipid stress to lysosome pathology are not well understood, but may represent a viable target for therapy. Glutamine uptake is increased in activated macrophages leading us to hypothesize that in the context of excess lipids glutamine metabolism could overwhelm the mitochondria and promote the accumulation of toxic metabolites. To investigate this question we assessed macrophage lipotoxicity in the absence of glutamine using LPS-activated peritoneal macrophages exposed to the SFA palmitate. We found that glutamine deficiency reduced lipid induced lysosome dysfunction, inflammasome activation, and cell death. Under glutamine deficient conditions mTOR activation was decreased and autophagy was enhanced; however, autophagy was dispensable for the rescue phenotype. Rather, glutamine deficiency prevented the suppressive effect of the SFA palmitate on mitochondrial respiration and this phenotype was associated with protection from macrophage cell death. Together, these findings reveal that crosstalk between activation-induced metabolic reprogramming and the nutrient microenvironment can dramatically alter macrophage responses to inflammatory stimuli. PMID:27077881

  17. Glutamine as an immunoenhancing nutrient.

    PubMed

    Saito, H; Furukawa, S; Matsuda, T

    1999-01-01

    New strategies for immunonutritional support include administration of special nutrients such as glutamine. Glutamine is important in several key metabolic processes of immune cells and enterocytes. Exogenous glutamine augments the functions of lymphocytes and macrophages. Neutrophils also reportedly utilize glutamine at a significant rate. Our recent studies demonstrated that glutamine enhances neutrophil function. This article focuses on the effects of glutamine on neutrophil function in surgical stress. Enteral glutamine administration enhanced peritoneal and hepatic bacterial clearance in our rat peritonitis model. Furthermore, IV glutamine supplementation improved the outcome of animals with severe surgical stress. Our in vitro study revealed that supplemental glutamine augmented the bacterial killing function of neutrophils from postoperative patients. Glutamine increased phagocytosis of the neutrophils. In addition, glutamine dose-dependently increased production of reactive oxygen intermediates (ROI) by neutrophils. Thus, our studies suggest that glutamine supplementation may improve bactericidal function of neutrophils by increasing both phagocytosis and ROI production. In conclusion, glutamine plays an important role in neutrophil function. Glutamine may be useful for the prevention, and treatment, of severe infection in critical illness and trauma.

  18. Conformational analysis of the oligosaccharides related to side chains of holothurian fucosylated chondroitin sulfates.

    PubMed

    Gerbst, Alexey G; Dmitrenok, Andrey S; Ustyuzhanina, Nadezhda E; Nifantiev, Nikolay E

    2015-02-01

    Anionic polysaccharides fucosylated chondroitin sulfates (FCS) from holothurian species were shown to affect various biological processes, such as metastasis, angiogenesis, clot formation, thrombosis, inflammation, and some others. To understand the mechanism of FCSs action, knowledge about their spatial arrangement is required. We have started the systematic synthesis, conformational analysis, and study of biological activity of the oligosaccharides related to various fragments of these types of natural polysaccharides. In this communication, five molecules representing distinct structural fragments of chondroitin sulfate have been studied by means of molecular modeling and NMR. These are three disaccharides and two trisaccharides containing fucose and glucuronic acid residues with one sulfate group per each fucose residue or without it. Long-range C-H coupling constants were used for the verification of the theoretical models. The presence of two conformers for both linkage types was revealed. For the Fuc-GlA linkage, the dominant conformer was the same as described previously in a literature as the molecular dynamics (MD) average in a dodechasaccharide FCS fragment representing the backbone chain of the polysaccharide including GalNAc residues. This shows that the studied oligosaccharides, in addition to larger ones, may be considered as reliable models for Quantitative Structure-Activity Relationship (QSAR) studies to reveal pharmacophore fragments of FCS.

  19. Conformational Analysis of the Oligosaccharides Related to Side Chains of Holothurian Fucosylated Chondroitin Sulfates

    PubMed Central

    Gerbst, Alexey G.; Dmitrenok, Andrey S.; Ustyuzhanina, Nadezhda E.; Nifantiev, Nikolay E.

    2015-01-01

    Anionic polysaccharides fucosylated chondroitin sulfates (FCS) from holothurian species were shown to affect various biological processes, such as metastasis, angiogenesis, clot formation, thrombosis, inflammation, and some others. To understand the mechanism of FCSs action, knowledge about their spatial arrangement is required. We have started the systematic synthesis, conformational analysis, and study of biological activity of the oligosaccharides related to various fragments of these types of natural polysaccharides. In this communication, five molecules representing distinct structural fragments of chondroitin sulfate have been studied by means of molecular modeling and NMR. These are three disaccharides and two trisaccharides containing fucose and glucuronic acid residues with one sulfate group per each fucose residue or without it. Long-range C–H coupling constants were used for the verification of the theoretical models. The presence of two conformers for both linkage types was revealed. For the Fuc–GlA linkage, the dominant conformer was the same as described previously in a literature as the molecular dynamics (MD) average in a dodechasaccharide FCS fragment representing the backbone chain of the polysaccharide including GalNAc residues. This shows that the studied oligosaccharides, in addition to larger ones, may be considered as reliable models for Quantitative Structure-Activity Relationship (QSAR) studies to reveal pharmacophore fragments of FCS. PMID:25686272

  20. Probing the Carboxyester Side Chain in Controlled Deactivation (−)-Δ8-Tetrahydrocannabinols

    PubMed Central

    2015-01-01

    We recently reported on a controlled deactivation/detoxification approach for obtaining cannabinoids with improved druggability. Our design incorporates a metabolically labile ester group at strategic positions within the THC structure. We have now synthesized a series of (−)-Δ8-THC analogues encompassing a carboxyester group within the 3-alkyl chain in an effort to explore this novel cannabinergic chemotype for CB receptor binding affinity, in vitro and in vivo potency and efficacy, as well as controlled deactivation by plasma esterases. We have also probed the chain’s polar characteristics with regard to fast onset and short duration of action. Our lead molecule, namely 2-[(6aR,10aR)-6a,7,10,10a-tetrahydro-1-hydroxy-6,6,9-trimethyl-6H-dibenzo[b,d]pyran-3-yl]-2-methyl-propanoic acid 3-cyano-propyl ester (AM7438), showed picomolar affinity for CB receptors and is deactivated by plasma esterases while the respective acid metabolite is inactive. In further in vitro and in vivo experiments, the compound was found to be a remarkably potent and efficacious CB1 receptor agonist with relatively fast onset/offset of action. PMID:25470070

  1. Helical unwinding and side-chain unlocking unravel the outward open conformation of the melibiose transporter

    PubMed Central

    Wang, Li-Ying; Ravi, Vidhya M.; Leblanc, Gérard; Padrós, Esteve; Cladera, Josep; Perálvarez-Marín, Alex

    2016-01-01

    Molecular dynamics simulations have been used to study the alternate access mechanism of the melibiose transporter from Escherichia coli. Starting from the outward-facing partially occluded form, 2 out of 12 simulations produced an outward full open form and one partially open, whereas the rest yielded fully or partially occluded forms. The shape of the outward-open form resembles other outward-open conformations of secondary transporters. During the transporter opening, conformational changes in some loops are followed by changes in the periplasm region of transmembrane helix 7. Helical curvature relaxation and unlocking of hydrophobic and ionic locks promote the outward opening of the transporter making accessible the substrate binding site. In particular, FRET studies on mutants of conserved aromatic residues of extracellular loop 4 showed lack of substrate binding, emphasizing the importance of this loop for making crucial interactions that control the opening of the periplasmic side. This study indicates that the alternate access mechanism for the melibiose transporter fits better into a flexible gating mechanism rather than the archetypical helical rigid-body rocker-switch mechanism. PMID:27658476

  2. Unraveling the Interplay of Backbone Rigidity and Electron Rich Side-Chains on Electron Transfer in Peptides: The Realization of Tunable Molecular Wires

    PubMed Central

    2015-01-01

    Electrochemical studies are reported on a series of peptides constrained into either a 310-helix (1–6) or β-strand (7–9) conformation, with variable numbers of electron rich alkene containing side chains. Peptides (1 and 2) and (7 and 8) are further constrained into these geometries with a suitable side chain tether introduced by ring closing metathesis (RCM). Peptides 1, 4 and 5, each containing a single alkene side chain reveal a direct link between backbone rigidity and electron transfer, in isolation from any effects due to the electronic properties of the electron rich side-chains. Further studies on the linear peptides 3–6 confirm the ability of the alkene to facilitate electron transfer through the peptide. A comparison of the electrochemical data for the unsaturated tethered peptides (1 and 7) and saturated tethered peptides (2 and 8) reveals an interplay between backbone rigidity and effects arising from the electron rich alkene side-chains on electron transfer. Theoretical calculations on β-strand models analogous to 7, 8 and 9 provide further insights into the relative roles of backbone rigidity and electron rich side-chains on intramolecular electron transfer. Furthermore, electron population analysis confirms the role of the alkene as a “stepping stone” for electron transfer. These findings provide a new approach for fine-tuning the electronic properties of peptides by controlling backbone rigidity, and through the inclusion of electron rich side-chains. This allows for manipulation of energy barriers and hence conductance in peptides, a crucial step in the design and fabrication of molecular-based electronic devices. PMID:25122122

  3. Comparison of surface properties of random, block, and graft copolymers having perfluoroalkyl and silicone-containing side chains.

    PubMed

    Kim, Dong-Kwon; Lee, Soo-Bok

    2002-03-15

    Fluorosilicone copolymers of random, block, and graft with both perfluoroalkyl and silicone-containing side chains were synthesized, and their surface properties and surface modification effects on PVC film were compared. It can be confirmed that the fluorosilicone copolymers of random, block, and graft exhibit very low surface free energies of 9-13 dyn/cm, depending on the perfluoroalkyl group content and their molecular structure. The inherent surface free energies of the fluorosilicone copolymers are significantly influenced by their molecular structure and perfluoroalkyl group content. It can also be found that the fluorosilicone copolymers are very effective for lowering surface free energy. The surface free energy of a copolymer/PVC blend strongly varies with perfluoroalkyl group content as well as molecular structure. The molecular structure of a fluorosilicone copolymer is as important as the perfluoroalkyl group content for their inherent surface free energies and surface modification of other polymers.

  4. Tuning the pH-triggered self-assembly of dendritic peptide amphiphiles using fluorinated side chains.

    PubMed

    Appel, Ralph; Tacke, Sebastian; Klingauf, Jürgen; Besenius, Pol

    2015-01-28

    We report the synthesis of a series of anionic dendritic peptide amphiphiles of increasing hydrophobic character. By establishing state diagrams we describe their pH and ionic strength triggered self-assembly into supramolecular nanorods in water and highlight the impact of hydrophobic shielding in the supramolecular polymerisation process. Via the incorporation of fluorinated peptide side chains the pH-triggered monomer to polymer transition at physiological ionic strength is shifted from pH 5.0 to pH 7.4. We thereby show that compensating attractive non-covalent interactions and hydrophobic effects with repulsive electrostatic forces, a concept we refer to as frustrated growth, is a sensitive tool in order to manipulate one-dimensional supramolecular polymerisation processes in water. PMID:25410414

  5. Backbone and side-chain assignments of an effector membrane localization domain from Vibrio vulnificus MARTX toxin.

    PubMed

    Brothers, Michael C; Geissler, Brett; Hisao, Grant S; Wilson, Brenda A; Satchell, Karla J F; Rienstra, Chad M

    2014-10-01

    (1)H, (13)C, and (15)N chemical shift assignments are presented for the isolated four-helical bundle membrane localization domain from the domain of unknown function 5 (DUF5) effector (MLD(VvDUF5)) of the MARTX toxin from Vibrio vulnificus in its solution state. We have assigned 97% of all backbone and side-chain carbon atoms, including 96% of all backbone residues. Secondary chemical shift analysis using TALOS+ demonstrates four helices that align with those predicted by structure homology modeling using the MLDs of Pasteurella multocida toxin (PMT) and the clostridial TcdB and TcsL toxins as templates. Future studies will be towards solving the structure and determining the dynamics in the solution state.

  6. Electro-optical and pyroelectrical thermal analysis of novel nonlinear optical side-chain polymers with high thermal stability

    NASA Astrophysics Data System (ADS)

    Gerhard-Multhaupt, Reimund; Bauer, Stefan; Molzow, Wolf-Dietrich; Ren, W.; Wirges, Werner; Yilmaz, S.; Oertel, U.; Haenel, B.; Haeussler, L.; Komber, H.; Lunkwitz, K.

    1994-01-01

    Polymers containing nonlinear optical moieties were prepared on the basis of maleic anhydride copolymers. Azo dyes such as Disperse Red 1 (DR 1) were attached to the polymer backbones via esterification, amidization, or imidization. Optimal poling conditions for the side-chain polymers were determined by means of thermal analysis. After electrode poling with a bias voltage of 200 V at a temperature of 185 degree(s)C, the spin-coated samples were slowly cooled down to room temperature with the poling field still applied. The thermal stabilities of the poled polymer films were measured by means of electro-optical (EOTA) and pyro- electrical (PTA) thermal analysis and compared to the respective responses of DR 1/polymethylmethacrylate (PMMA) guest/host polymer samples. Both experimental techniques (EOTA and PTA) are discussed in some detail together with the experimental results.

  7. Power factor enhancement in solution-processed organic n-type thermoelectric materials through side chain design

    NASA Astrophysics Data System (ADS)

    Russ, Boris; Robb, Maxwell J.; Brunetti, Fulvio G.; Miller, Levi; Patel, Shrayesh; Ho, Victor; Urban, Jeffrey J.; Chabinyc, Michael L.; Hawker, Craig J.; Segalman, Rachel A.

    2014-03-01

    Building efficient organic thermoelectric architectures requires complementary p-type (hole transporting) and n-type (electron transporting) components. While several high performance hole-transporting polymers have been developed, the design of n-type organics has proven challenging, and thermoelectric studies of organic n-type systems are scarce. We investigate the properties of a series of charged perylene diimide (PDI) derivatives. Charged side chains in these materials enable both water solubility and self-doping. We show that changing the length of the alkyl spacer between the charged end groups and the PDI core dramatically improves thin film thermoelectric properties. The top derivatives in our study demonstrated the highest power factor reported for n-type solution-processed films. By complementing thermoelectric characterization of these variants with insight on the electronic and structural property changes from optical spectroscopy, EPR, and GIWAXS experiments, our findings shape a promising molecular design strategy for future enhancements in thermoelectric performance.

  8. Dielectric properties of liquid-crystal azomethine polymer with a side alkyl-substituted chain, doped with fullerene C60

    NASA Astrophysics Data System (ADS)

    Kovalev, D. S.; Kostromin, S. V.; Musteaţa, V.; Cozan, V.; Bronnikov, S. V.

    2016-04-01

    We studied the actual and imaginary components of the dielectric constant of liquid-crystal azomethine polymer with a side chain, doped with 0.5 wt % of fullerene C60, over a wide range of temperatures and frequencies; measurements were made by means of dielectric spectroscopy. By analyzing the frequency dependence of the dielectric constant, we detected the relaxation processes (α, β1, and β2) in the nanocomposite, corresponding to certain modes of molecular motion and described them by the Arrhenius equations (β1- and β2-processes) and the Vogel-Fulcher-Tamman equation (α-process). An antiplasticization effect is discovered after doping the polymer with fullerene C60, which manifests itself in increasing the glass transition temperature of the nanocomposite compared to this parameter typical of pure polymer.

  9. Crystal structure analysis of auromomycin apoprotein (macromomycin) shows importance of protein side chains to chromophore binding selectivity.

    PubMed

    Van Roey, P; Beerman, T A

    1989-09-01

    The crystal structure of macromomycin, the apoprotein of the antitumor antibiotic auromomycin, has been determined and refined at 1.6-A resolution. The overall structure is composed of a flattened seven-stranded antiparallel beta-barrel and two antiparallel beta-sheet ribbons. The barrel and the ribbons define a deep cleft that is the chromophore binding site. The cleft is very accessible and in this structure is occupied by two 2-methyl-2,4-pentanediol and two water molecules. The overall shape of the binding site is similar to that of the analogue actinoxanthin. Highly specific side chains that are not conserved between different analogues extend into the binding site and may be important to the chromophore binding specificity.

  10. Electrostatic Solvation Free Energy of Amino Acid Side Chain Analogs: Implications for the Validity of Electrostatic Linear Response in Water

    SciTech Connect

    Lin, Bin; Pettitt, Bernard M.

    2011-04-15

    Electrostatic free energies of solvation for 15 neutral amino acid side chain analogs are computed. We compare three methods of varying computational complexity and accuracy for three force fields: free energy simulations, Poisson-Boltzmann (PB), and linear response approximation (LRA) using AMBER, CHARMM, and OPLSAA force fields. We find that deviations from simulation start at low charges for solutes. The approximate PB and LRA produce an overestimation of electrostatic solvation free energies for most of molecules studied here. These deviations are remarkably systematic. The variations among force fields are almost as large as the variations found among methods. Our study confirms that success of the approximate methods for electrostatic solvation free energies comes from their ability to evaluate free energy differences accurately.

  11. In vitro and in vivo evidence for the inhibition of brassinosteroid synthesis by propiconazole through interference with side chain hydroxylation.

    PubMed

    Oh, Keimei; Matsumoto, Tadashi; Hoshi, Tomoki; Yoshizawa, Yuko

    2016-05-01

    We carried out the biochemical evaluation of the target site of propiconazole in BR biosynthesis. Applying BR biosynthesis intermediates to Arabidopsis seedlings grown in the presence of propiconazole under dark condition, we found that the target site of propiconazole in BR biosynthesis can be identified among the C22 and C23 side chain hydroxylation steps from campestanol to teasterone. Using differential spectra techniques to determine the binding affinity of propiconazole to CYP90D1, which is responsible for C23 hydroxylation of BR, we found that propiconazole induced typical type II binding spectra in response to purified recombinant CYP90D1 and the Kd value was found approximately 0.76 μM.

  12. Ozonolysis of surface-adsorbed methoxyphenols: kinetics of aromatic ring cleavage vs. alkene side-chain oxidation

    NASA Astrophysics Data System (ADS)

    O'Neill, E. M.; Kawam, A. Z.; Van Ry, D. A.; Hinrichs, R. Z.

    2014-01-01

    Lignin pyrolysis products, which include a variety of substituted methoxyphenols, constitute a major component of organics released by biomass combustion, and may play a central role in the formation of atmospheric brown carbon. Understanding the atmospheric fate of these compounds upon exposure to trace gases is therefore critical to predicting the chemical and physical properties of biomass burning aerosol. We used diffuse reflectance infrared spectroscopy to monitor the heterogeneous ozonolysis of 4-propylguaiacol, eugenol, and isoeugenol adsorbed on NaCl and α-Al2O3 substrates. Adsorption of gaseous methoxyphenols onto these substrates produced near-monolayer surface concentrations of 3 × 1018 molecules m-2. The subsequent dark heterogeneous ozonolysis of adsorbed 4-propylguaiacol cleaved the aromatic ring between the methoxy and phenol groups with the product conclusively identified by GC-MS and 1H-NMR. Kinetic analysis of eugenol and isoeugenol dark ozonolysis also suggested the formation of ring-cleaved products, although ozonolysis of the unsaturated substituent groups forming carboxylic acids and aldehydes was an order of magnitude faster. Average uptake coefficients for NaCl-adsorbed methoxyphenols were γ = 2.3 (± 0.8) × 10-7 and 2 (± 1) × 10-6 for ozonolysis of the aromatic ring and the unsaturated side chain, respectively, and reactions on α-Al2O3 were approximately two times slower. UV-visible radiation (λ > 300 nm) enhanced eugenol ozonolysis of the aromatic ring by a factor of 4(± 1) but had no effect on ozonolysis of the alkene side chain.

  13. Specificity of the basic side chains of Lys114, Lys125, and Arg129 of antithrombin in heparin binding.

    PubMed

    Schedin-Weiss, Sophia; Arocas, Véronique; Bock, Susan C; Olson, Steven T; Björk, Ingemar

    2002-10-15

    The anticoagulant polysaccharide heparin binds and activates the plasma proteinase inhibitor antithrombin through a pentasaccharide sequence. Lys114, Lys125, and Arg129 are the three most important residues of the inhibitor for pentasaccharide binding. To elucidate to what extent another positively charged side chain can fulfill the role of each of these residues, we have mutated Lys114 and Lys125 to Arg and Arg129 to Lys. Lys114 could be reasonably well replaced with Arg with only an approximately 15-fold decrease in pentasaccharide affinity, in contrast to an approximately 10(5)-fold decrease caused by substitution with an noncharged amino acid of comparable size. However, a loss of approximately one ionic interaction on mutation to Arg indicates that the optimal configuration of the network of basic residues of antithrombin that together interact with the pentasaccharide requires a Lys in position 114. Replacement of Lys125 with Arg caused an even smaller, approximately 3-fold, decrease in pentasaccharide affinity, compared with that of approximately 400-fold caused by mutation to a neutral amino acid. An Arg in position 125 is thus essentially equivalent to the wild-type Lys in pentasaccharide binding. Substitution of Arg129 with Lys decreased the pentasaccharide affinity an appreciable approximately 100-fold, a loss approaching that of approximately 400-fold caused by substitution with a neutral amino acid. Arg is thus specifically required in position 129 for high-affinity pentasaccharide binding. This requirement is most likely due to the ability of Arg to interact with other residues of antithrombin, primarily, Glu414 and Thr44, in a manner that appropriately positions the Arg side chain for keeping the pentasaccharide anchored to the activated state of the inhibitor. PMID:12369826

  14. Polarized optical spectroscopy applied to investigate two poly(phenylene-vinylene) polymers with different side chain structures

    NASA Astrophysics Data System (ADS)

    Pâlsson, Lars-Olof; Vaughan, Helen L.; Monkman, Andrew P.

    2006-10-01

    Two related poly(phenylene-vinylene) (PPV) light-emitting polymers have been investigated by means of polarized optical spectroscopy. The purpose of the investigation was to investigate the nature of the interactions in thin films and to examine what impact the difference in side chain structure and molecular weight in poly(2'-methoxy-5-2-ethyl-hexoxy)-1,4-phenylene vinylene (MEH-PPV) and poly(2-(3',7'-dimethyloctyloxy)-5-methoxy-1,4-phenylene-vinylene) (OC1C10-PPV) has on the electronic and optical properties of the two polymers. Aligning the polymers by dispersing them in anisotropic solvents and stretched films shows that the side chains have an impact on the relative orientations of the transition dipole moments. In anisotropic solvents the linear dichroism is larger for MEH-PPV than for the related polymer OC1C10-PPV, while in stretched films the opposite situation prevails. A lower polarization of the luminescence from OC1C10-PPV, relative to MEH-PPV, was also obtained independent of alignment medium used. The data therefore suggest that while mechanical stretching may align the OC1C10-PPV to a greater degree, the emitting species is distinct from the absorbing species. The circular dichroism (CD) spectra of both polymers undergo dramatic changes when the liquid phase and the solid state (film) are compared. The solution CD spectra shows no evidence of interchain interactions; instead the spectra of both systems indicate a helical conformation of the polymers. The CD spectra of films are dramatically different with the strong Cotton effect being observed. This points to the formation of an aggregate in the film, with an associated ground state interaction, an interchain species such as a physical dimer, or a more complex higher aggregate.

  15. Amide side chain amphiphilic polymers disrupt surface established bacterial bio-films and protect mice from chronic Acinetobacter baumannii infection.

    PubMed

    Uppu, Divakara S S M; Samaddar, Sandip; Ghosh, Chandradhish; Paramanandham, Krishnamoorthy; Shome, Bibek R; Haldar, Jayanta

    2016-01-01

    Bacterial biofilms represent the root-cause of chronic or persistent infections in humans. Gram-negative bacterial infections due to nosocomial and opportunistic pathogens such as Acinetobacter baumannii are more difficult to treat because of their inherent and rapidly acquiring resistance to antibiotics. Due to biofilm formation, A. baumannii has been noted for its apparent ability to survive on artificial surfaces for an extended period of time, therefore allowing it to persist in the hospital environment. Here we report, maleic anhydride based novel cationic polymers appended with amide side chains that disrupt surface established multi-drug resistant A. baumannii biofilms. More importantly, these polymers significantly (p < 0.0001) decrease the bacterial burden in mice with chronic A. baumannii burn wound infection. The polymers also show potent antibacterial efficacy against methicillin resistant Staphylococcus aureus (MRSA), vancomycin resistant Enterococci (VRE) and multi-drug resistant clinical isolates of A. baumannii with minimal toxicity to mammalian cells. We observe that optimal hydrophobicity dependent on the side chain chemical structure of these polymers dictate the selective toxicity to bacteria. Polymers interact with the bacterial cell membranes by causing membrane depolarization, permeabilization and energy depletion. Bacteria develop rapid resistance to erythromycin and colistin whereas no detectable development of resistance occurs against these polymers even after several passages. These results suggest the potential use of these polymeric biomaterials in disinfecting biomedical device surfaces after the infection has become established and also for the topical treatment of chronic bacterial infections.

  16. Dynamic properties of the native free antithrombin from molecular dynamics simulations: computational evidence for solvent- exposed Arg393 side chain.

    PubMed

    Tóth, László; Fekete, Attila; Balogh, Gábor; Bereczky, Zsuzsanna; Komáromi, István

    2015-09-01

    While antithrombin (AT) has small basal inhibitory activity, it reaches its full inhibitory potential against activated blood coagulation factors, FXa, FIXa, and FIIa (thrombin), via an allosteric and/or template (bridging) mechanism by the action of heparin, heparan sulfate, or heparin-mimetic pentasaccharides (PS). From the numerous X-ray structures available for different conformational states of AT, only indirect and incomplete conclusions can be drawn on the inherently dynamic properties of AT. As a typical example, the basal inhibitory activity of AT cannot be interpreted on the basis of "non-activated" free antithrombin X-ray structures since the Arg393 side chain, playing crucial role in antithrombin-proteinase interaction, is not exposed. In order to reveal the intrinsic dynamic properties and the reason of basal inhibitory activity of antithrombin, 2 μs molecular dynamics simulations were carried out on its native free-forms. It was shown from the simulation trajectories that the reactive center loop which is functioning as "bait" for proteases, even without any biasing potential can populate conformational state in which the Arg393 side chain is solvent exposed. It is revealed from the trajectory analysis that the peptide sequences correspond to the helix D extension, and new helix P formation can be featured with especially large root-mean-square fluctuations. Mutual information analyses of the trajectory showed remarkable (generalized) correlation between those regions of antithrombin which changed their conformations as the consequence of AT-PS complex formation. This suggests that allosteric information propagation pathways are present even in the non-activated native form of AT. PMID:25483839

  17. Protonated Dipeptide Losses from b 5 and b 4 Ions of Side Chain Hydroxyl Group Containing Pentapeptides

    NASA Astrophysics Data System (ADS)

    Atik, A. Emin; Yalcin, Talat

    2013-10-01

    In this study, C-terminal protonated dipeptide eliminations were reported for both b 5 and b 4 ions of side chain hydroxyl group (-OH) containing pentapeptides. The study utilized the model C-terminal amidated pentapeptides having sequences of XGGFL and AXVYI, where X represents serine (S), threonine (T), glutamic acid (E), aspartic acid (D), or tyrosine (Y) residue. Upon low-energy collision-induced dissociation (CID) of XGGFL (where X = S, T, E, D, and Y) model peptide series, the ions at m/z 279 and 223 were observed as common fragments in all b 5 and b 4 ion (except b 4 ion of YGGFL) mass spectra, respectively. By contrast, peptides, namely SMeGGFL-NH2 and EOMeGGFL-NH2, did not show either the ion at m/z 279 or the ion at m/z 223. It is shown that the side chain hydroxyl group is required for the possible mechanism to take place that furnishes the protonated dipeptide loss from b 5 and b 4 ions. In addition, the ions at m/z 295 and 281 were detected as common fragments in all b 5 and b 4 ion (except b 4 ion of AYVYI) mass spectra, respectively, for AXVYI model peptide series. The MS4 experiments exhibited that the fragment ions at m/z 279, 223, 295, and 281 entirely reflect the same fragmentation behavior of [M + H]+ ion generated from commercial dipeptides FL-OH, GF-OH, YI-OH, and VY-OH. These novel eliminations reported here for b 5 and b 4 ions can be useful in assigning the correct and reliable peptide sequences for high-throughput proteomic studies.

  18. II. Glutamine and glutamate.

    PubMed

    Tapiero, H; Mathé, G; Couvreur, P; Tew, K D

    2002-11-01

    Glutamine and glutamate with proline, histidine, arginine and ornithine, comprise 25% of the dietary amino acid intake and constitute the "glutamate family" of amino acids, which are disposed of through conversion to glutamate. Although glutamine has been classified as a nonessential amino acid, in major trauma, major surgery, sepsis, bone marrow transplantation, intense chemotherapy and radiotherapy, when its consumption exceeds its synthesis, it becomes a conditionally essential amino acid. In mammals the physiological levels of glutamine is 650 micromol/l and it is one of the most important substrate for ammoniagenesis in the gut and in the kidney due to its important role in the regulation of acid-base homeostasis. In cells, glutamine is a key link between carbon metabolism of carbohydrates and proteins and plays an important role in the growth of fibroblasts, lymphocytes and enterocytes. It improves nitrogen balance and preserves the concentration of glutamine in skeletal muscle. Deamidation of glutamine via glutaminase produces glutamate a precursor of gamma-amino butyric acid, a neurotransmission inhibitor. L-Glutamic acid is a ubiquitous amino acid present in many foods either in free form or in peptides and proteins. Animal protein may contain from 11 to 22% and plants protein as much as 40% glutamate by weight. The sodium salt of glutamic acid is added to several foods to enhance flavor. L-Glutamate is the most abundant free amino acid in brain and it is the major excitatory neurotransmitter of the vertebrate central nervous system. Most free L-glutamic acid in brain is derived from local synthesis from L-glutamine and Kreb's cycle intermediates. It clearly plays an important role in neuronal differentiation, migration and survival in the developing brain via facilitated Ca++ transport. Glutamate also plays a critical role in synaptic maintenance and plasticity. It contributes to learning and memory through use-dependent changes in synaptic efficacy and

  19. Dependence of Excited-State Properties of a Low-Bandgap Photovoltaic Copolymer on Side-Chain Substitution and Solvent.

    PubMed

    Zhao, Ning-Jiu; Zhang, Mao-Jie; Liang, Ran; Fu, Li-Min; Zhang, Wei; Ai, Xi-Cheng; Hou, Jian-Hui; Zhang, Jian-Ping

    2016-07-01

    The excited-state properties and chain conformations of a new low-bandgap copolymer based on benzo[1,2-b:4,5-b']dithiophene (BDT) and thieno[3,4-b]thiophene with meta-alkoxyphenyl-substituted side chains in solution were investigated comprehensively. Time-resolved spectroscopy suggested that the excited-state properties were sensitive to the conformations of the copolymer in solution. In addition, excited-state dynamics analyses revealed the photogeneration of triplet excited states by intersystem crossing (ISC) at a rate constant of ∼0.4×10(9)  s(-1) as a result of direct meta-alkoxyphenyl connection to the donor unit BDT irrespective to the macromolecular conformations. According to El-Sayed's rule, the fast ISC herein is correlated with the change of orbital types between singlet and triplet excited states as also shown by quantum chemical calculations. Our studies may shed light on the structure-property relationships of photovoltaic materials.

  20. Molecular Packing of High-Mobility Diketo Pyrrolo-Pyrrole Polymer Semiconductors with Branched Alkyl Side Chains

    SciTech Connect

    X Zhang; L Richter; D DeLongchamp; R Kline; M Hammond; I McCulloch; M Heeney; R Ashraf; J Smith; et al.

    2011-12-31

    We describe a series of highly soluble diketo pyrrolo-pyrrole (DPP)-bithiophene copolymers exhibiting field effect hole mobilities up to 0.74 cm{sup 2} V{sup -1} s{sup -1}, with a common synthetic motif of bulky 2-octyldodecyl side groups on the conjugated backbone. Spectroscopy, diffraction, and microscopy measurements reveal a transition in molecular packing behavior from a preferentially edge-on orientation of the conjugated plane to a preferentially face-on orientation as the attachment density of the side chains increases. Thermal annealing generally reduces both the face-on population and the misoriented edge-on domains. The highest hole mobilities of this series were obtained from edge-on molecular packing and in-plane liquid-crystalline texture, but films with a bimodal orientation distribution and no discernible in-plane texture exhibited surprisingly comparable mobilities. The high hole mobility may therefore arise from the molecular packing feature common to the entire polymer series: backbones that are strictly oriented parallel to the substrate plane and coplanar with other backbones in the same layer.

  1. Structure and dynamics of the aliphatic cholesterol side chain in membranes as studied by (2)H NMR spectroscopy and molecular dynamics simulation.

    PubMed

    Vogel, Alexander; Scheidt, Holger A; Baek, Dong Jae; Bittman, Robert; Huster, Daniel

    2016-02-01

    Cholesterol is an evolutionarily highly optimized molecule particularly known for its ability to condense the phospholipids in cellular membranes. Until recently, the accompanying increase in the chain order of the surrounding phospholipids was attributed to the planar and rigid tetracyclic ring structure of cholesterol. However, detailed investigations of cholesterol's aliphatic side chain demonstrated that this side chain is responsible for approximately half of the condensation effect. Therefore, we investigated the structure and dynamics of the aliphatic side chain of cholesterol using (2)H solid-state nuclear magnetic resonance (NMR) spectroscopy and microsecond timescale all-atom molecular dynamics (MD) simulations in four different model membranes: POPC, DPPC, PSM, and POPC/PSM (1 : 1 mol/mol) and at three different temperatures: 5 °C, 37 °C, and 50 °C. A cholesterol variant, in which 11 hydrogens of the aliphatic side chain were exchanged for deuterium, was used and the respective (2)H NMR spectra confirmed the axially asymmetric rotational diffusion of cholesterol in DPPC and PSM. Furthermore, NMR spectra indicated that some hydrogens showed an unexpected magnetic inequivalency. This finding was confirmed by all-atom molecular dynamics simulations and detailed analysis revealed that the hydrogens of the methylene groups at C22, C23, and C24 are magnetically inequivalent. This inequivalency is caused by steric clashes of the aliphatic side chain with the ring structure of cholesterol as well as the branched C21 methyl group. These excluded volume effects result in reduced conformational flexibility of the aliphatic side chain of cholesterol and explain its high order (order parameter of 0.78 for chain motions) and large contribution to the condensation effect. Additionally, the motional pattern of the side chain becomes highly anisotropic such that it shows larger fluctuations perpendicular to the ring plane of cholesterol with a biaxiality of the

  2. Toward Precise Interpretation of DEER-Based Distance Distributions: Insights from Structural Characterization of V1 Spin-Labeled Side Chains.

    PubMed

    Balo, Aidin R; Feyrer, Hannes; Ernst, Oliver P

    2016-09-20

    Pulsed electron paramagnetic resonance experiments can measure individual distances between two spin-labeled side chains in proteins in the range of ∼1.5-8 nm. However, the flexibility of traditional spin-labeled side chains leads to diffuse spin density loci and thus distance distributions with relatively broad peaks, thereby complicating the interpretation of protein conformational states. Here we analyzed the spin-labeled V1 side chain, which is internally anchored and hence less flexible. Crystal structures of V1-labeled T4 lysozyme constructs carrying the V1 side chain on α-helical segments suggest that V1 side chains adopt only a few discrete rotamers. In most cases, only one rotamer is observed at a given site, explaining the frequently observed narrow distance distribution for doubly V1-labeled proteins. We used the present data to derive guidelines that may allow distance interpretation of other V1-labeled proteins for higher-precision structural modeling. PMID:27532325

  3. Protein interactions with bottle-brush polymer layers: Effect of side chain and charge density ratio probed by QCM-D and AFM.

    PubMed

    Olanya, Geoffrey; Thormann, Esben; Varga, Imre; Makuska, Ricardas; Claesson, Per M

    2010-09-01

    Silica surfaces were coated with a range of cationic bottle-brush polymers with 45 units long poly(ethylene oxide) side chains, and their efficiency in reducing protein adsorption was probed by QCM-D, reflectometry and AFM. Preadsorbed layers formed by bottle-brush polymers with different side chain to charge ratio was exposed to two proteins with different net charge, lysozyme and BSA. The reduction in protein adsorption was found to depend on both the type of protein and on the nature of the polyelectrolyte layer. The most pronounced reduction in protein adsorption was achieved when the fraction of charged backbone segments was in the range 0.25-0.5 equivalent to a fraction of poly(ethylene oxide) side chains of 0.75-0.5. It was concluded that these polymers have enough electrostatic attachment points to ensure a strong binding to the surface, and at the same time a sufficient amount of poly(ethylene oxide) side chains to counteract protein adsorption. In contrast, a layer formed by a highly charged polyelectrolyte without side chains was unable to resists protein adsorption. On such a layer the adsorption of negatively charged BSA was strongly enhanced, and positively charged lysozyme adsorbed to a similar extent as to bare silica. AFM colloidal probe force measurement between silica surfaces with preadsorbed layers of bottle-brush polymers were conducted before and after exposure to BSA and lysozyme to gain insight into how proteins were incorporated in the bottle-brush polymer layers.

  4. Oxidative cleavage of the pentyl side-chain of cannabinoids. Identification of new biotransformation pathways in the metabolism of 4'-hydroxy-delta-9-tetrahydrocannabinol in the mouse.

    PubMed

    Harvey, D J

    1990-01-01

    During an investigation of the mechanisms leading to the formation of metabolites of cannabinoids in which the pentyl side chain is reduced to 2, 3 or 4 carbon atoms, the further metabolism of 4'-hydroxy-delta 9-tetrahydrocannabinol was investigated in vivo in mice. Metabolites were extracted with ethyl acetate, concentrated by chromatography on Sephadex LH-20 and identified by GC/MS. Ten metabolites were identified and a further two had tentative structural assignments made. The major metabolic route, in common with that seen with most cannabinoids, was hydroxylation at the allylic 11-position, followed by oxidation to a carboxylic acid. Additional hydroxylation occurred at C-8. Abundant metabolites were also formed by oxidative cleavage of the pentyl side chain. The major metabolites of this type had lost the terminal two carbon atoms to give compounds containing a carboxyethyl side chain. This is the major product normally produced by beta-oxidation of the acid formed from 5'-hydroxy-delta 9-tetrahydrocannabinol. Trace concentrations of two other acids that appeared to have a carboxypropyl side chain were also found. The results show that, in addition to beta-oxidation, initiated by hydroxylation at the 5'-carbon atom (omega-hydroxylation), at least one other oxidative route, initiated by omega-1-hydroxylation, is involved in the production of metabolites with two carbon atoms missing from the pentyl side chain. This pathway does not seem to have been characterized as a biotransformation mechanism in drug metabolism and a possible mechanism is suggested. PMID:1974198

  5. Exploiting Supramolecular Interactions for the Intramolecular Folding of Side-Chain Functionalized Polymers and Assembly of Anisotropic Colloids

    NASA Astrophysics Data System (ADS)

    Romulus, Joy

    The overarching goal presented in this thesis is the self-assembly of synthetic systems into higher ordered structures utilizing supramolecular chemistry. Noncovalent interactions including charge-transfer and hydrogen bonding as well as DNA hybridization are exploited to induce the assembly of polymers and colloids into well-defined architectures. This strategy provides a tunable handle on materials bulk properties that can be adjusted by simply changing variables such as temperature and solvent. A brief overview of design principles for the supramolecular assembly of side-chain functionalized polymers is presented. The polymerization technique selected was living ring-opening metathesis polymerization (ROMP), thus affording control over molecular weight and molecular weight distributions. ROMP also allowed for the incorporation of functional groups that were used to assemble the polymers into ordered structures. Charge-transfer motifs were exploited and shown to drive the assembly of random and alternating copolymers via intramolecular side-chain interactions. Incorporation of complementary hydrogen bonding motifs was shown to guide the single-chain folding of a multifunctional triblock copolymer into sheet-like structures. Precision over the size, shape, and monomer sequence were identified as key elements for efficient self-assembly. The self-assembly of colloids using DNA hybridization was also investigated. Previously, the majority of colloid-based research relied upon the self-assembly of spherical isotropic particles into closed-packed arrangements. In contrast, anisotropic particles may allow for the realization of open structures. By expanding upon a method to permanently cross-link DNA strands incubated on a colloidal surface, a new strategy to engineer patchy particles is described. These functional DNA-coated patches are demonstrated to direct particle assembly. The self-assembly of polymer and colloidal systems utilizing noncovalent interactions

  6. Quantum transport through a multi-quantum-dot-pair chain side-coupled with Majorana bound states

    NASA Astrophysics Data System (ADS)

    Zhao-Tan, Jiang; Cheng-Cheng, Zhong

    2016-06-01

    We investigate the quantum transport properties through a special kind of quantum dot (QD) system composed of a serially coupled multi-QD-pair (multi-QDP) chain and side-coupled Majorana bound states (MBSs) by using the Green functions method, where the conductance can be classified into two kinds: the electron tunneling (ET) conductance and the Andreev reflection (AR) one. First we find that for the nonzero MBS-QDP coupling a sharp AR-induced zero-bias conductance peak with the height of e 2/h is present (or absent) when the MBS is coupled to the far left (or the other) QDP. Moreover, the MBS-QDP coupling can suppress the ET conductance and strengthen the AR one, and further split into two sub-peaks each of the total conductance peaks of the isolated multi-QDPs, indicating that the MBS will make obvious influences on the competition between the ET and AR processes. Then we find that the tunneling rate Γ L is able to affect the conductances of leads L and R in different ways, demonstrating that there exists a Γ L-related competition between the AR and ET processes. Finally we consider the effect of the inter-MBS coupling on the conductances of the multi-QDP chains and it is shown that the inter-MBS coupling will split the zero-bias conductance peak with the height of e 2/h into two sub-peaks. As the inter-MBS coupling becomes stronger, the two sub-peaks are pushed away from each other and simultaneously become lower, which is opposite to that of the single QDP chain where the two sub-peaks with the height of about e 2/2h become higher. Also, the decay of the conductance sub-peaks with the increase of the MBS-QDP coupling becomes slower as the number of the QDPs becomes larger. This research should be an important extension in studying the transport properties in the kind of QD systems coupled with the side MBSs, which is helpful for understanding the nature of the MBSs, as well as the MBS-related QD transport properties. Project supported by the National Natural

  7. Deamidation Reactions of Asparagine- and Glutamine-Containing Dipeptides Investigated by Ion Spectroscopy

    NASA Astrophysics Data System (ADS)

    Kempkes, Lisanne J. M.; Martens, Jonathan; Grzetic, Josipa; Berden, Giel; Oomens, Jos

    2016-09-01

    Deamidation is a major fragmentation channel upon activation by collision induced dissociation (CID) for protonated peptides containing glutamine (Gln) and asparagine (Asn) residues. Here, we investigate these NH3-loss reactions for four Asn- and Gln-containing protonated peptides in terms of the resulting product ion structures using infrared ion spectroscopy with the free electron laser FELIX. The influence of the side chain length (Asn versus Gln) and of the amino acid sequence on the deamidation reaction has been examined. Molecular structures for the product ions are determined by comparison of experimental IR spectra with spectra predicted by density functional theory (DFT). The reaction mechanisms identified for the four dipeptides AlaAsn, AsnAla, AlaGln, and GlnAla are not the same. For all four dipeptides, primary deamidation takes place from the amide side chain (and not from the N-terminus) and, in most cases, resembles the mechanisms previously identified for the protonated amino acids asparagine and glutamine. Secondary fragmentation reactions of the deamidation products have also been characterized and provide further insight in - and confirmation of - the identified mechanisms. Overall, this study provides a comprehensive molecular structure map of the deamidation chemistry of this series of dipeptides.

  8. Deamidation Reactions of Asparagine- and Glutamine-Containing Dipeptides Investigated by Ion Spectroscopy

    NASA Astrophysics Data System (ADS)

    Kempkes, Lisanne J. M.; Martens, Jonathan; Grzetic, Josipa; Berden, Giel; Oomens, Jos

    2016-11-01

    Deamidation is a major fragmentation channel upon activation by collision induced dissociation (CID) for protonated peptides containing glutamine (Gln) and asparagine (Asn) residues. Here, we investigate these NH3-loss reactions for four Asn- and Gln-containing protonated peptides in terms of the resulting product ion structures using infrared ion spectroscopy with the free electron laser FELIX. The influence of the side chain length (Asn versus Gln) and of the amino acid sequence on the deamidation reaction has been examined. Molecular structures for the product ions are determined by comparison of experimental IR spectra with spectra predicted by density functional theory (DFT). The reaction mechanisms identified for the four dipeptides AlaAsn, AsnAla, AlaGln, and GlnAla are not the same. For all four dipeptides, primary deamidation takes place from the amide side chain (and not from the N-terminus) and, in most cases, resembles the mechanisms previously identified for the protonated amino acids asparagine and glutamine. Secondary fragmentation reactions of the deamidation products have also been characterized and provide further insight in - and confirmation of - the identified mechanisms. Overall, this study provides a comprehensive molecular structure map of the deamidation chemistry of this series of dipeptides.

  9. Immunomodulation. Part IV: Glutamine.

    PubMed

    Bell, Susan Givens

    2006-01-01

    Glutamine, a nonessential amino acid that appears to be conditionally essential during periods of physiologic stress, plays important physiologic roles in the immune system. However, neither enteral nor parenteral glutamine supplementation makes a difference in the rate of systemic infection or of NEC in very low birth weight infants. Thus, the search for agents to enhance the neonate's immune system and to serve as safe and effective adjuvants to antibiotics continues. Part V, the final article in this immunomodulation series, will explore the use of probiotics to support the neonatal immune system.

  10. The role of side chain entropy and mutual information for improving the de novo design of Kemp eliminases KE07 and KE70.

    PubMed

    Bhowmick, Asmit; Sharma, Sudhir C; Honma, Hallie; Head-Gordon, Teresa

    2016-07-28

    Side chain entropy and mutual entropy information between residue pairs have been calculated for two de novo designed Kemp eliminase enzymes, KE07 and KE70, and for their most improved versions at the end of laboratory directed evolution (LDE). We find that entropy, not just enthalpy, helped to destabilize the preference for the reactant state complex of the designed enzyme as well as favoring stabilization of the transition state complex for the best LDE enzymes. Furthermore, residues with the highest side chain couplings as measured by mutual information, when experimentally mutated, were found to diminish or annihilate catalytic activity, some of which were far from the active site. In summary, our findings demonstrate how side chain fluctuations and their coupling can be an important design feature for de novo enzymes, and furthermore could be utilized in the computational steps in lieu of or in addition to the LDE steps in future enzyme design projects.

  11. Parameterization of the Hamiltonian Dielectric Solvent (HADES) Reaction-Field Method for the Solvation Free Energies of Amino Acid Side-Chain Analogs.

    PubMed

    Zachmann, Martin; Mathias, Gerald; Antes, Iris

    2015-06-01

    Optimization of the Hamiltonian dielectric solvent (HADES) method for biomolecular simulations in a dielectric continuum is presented with the goal of calculating accurate absolute solvation free energies while retaining the model's accuracy in predicting conformational free-energy differences. The solvation free energies of neutral and polar amino acid side-chain analogs calculated by using HADES, which may optionally include nonpolar contributions, were optimized against experimental data to reach a chemical accuracy of about 0.5 kcal mol(-1). The new parameters were evaluated for charged side-chain analogs. The HADES results were compared with explicit-solvent, generalized Born, Poisson-Boltzmann, and QM-based methods. The potentials of mean force (PMFs) between pairs of side-chain analogs obtained by using HADES and explicit-solvent simulations were used to evaluate the effects of the improved parameters optimized for solvation free energies on intermolecular potentials.

  12. A study of phenylalanine side-chain dynamics in surface-adsorbed peptides using solid-state deuterium NMR and rotamer library statistics.

    PubMed

    Li, Kun; Emani, Prashant S; Ash, Jason; Groves, Michael; Drobny, Gary P

    2014-08-13

    Extracellular matrix proteins adsorbed onto mineral surfaces exist in a unique environment where the structure and dynamics of the protein can be altered profoundly. To further elucidate how the mineral surface impacts molecular properties, we perform a comparative study of the dynamics of nonpolar side chains within the mineral-recognition domain of the biomineralization protein salivary statherin adsorbed onto its native hydroxyapatite (HAP) mineral surface versus the dynamics displayed by the native protein in the hydrated solid state. Specifically, the dynamics of phenylalanine side chains (viz., F7 and F14) located in the surface-adsorbed 15-amino acid HAP-recognition fragment (SN15: DpSpSEEKFLRRIGRFG) are studied using deuterium magic angle spinning ((2)H MAS) line shape and spin-lattice relaxation measurements. (2)H NMR MAS spectra and T1 relaxation times obtained from the deuterated phenylalanine side chains in free and HAP-adsorbed SN15 are fitted to models where the side chains are assumed to exchange between rotameric states and where the exchange rates and a priori rotameric state populations are varied iteratively. In condensed proteins, phenylalanine side-chain dynamics are dominated by 180° flips of the phenyl ring, i.e., the "π flip". However, for both F7 and F14, the number of exchanging side-chain rotameric states increases in the HAP-bound complex relative to the unbound solid sample, indicating that increased dynamic freedom accompanies introduction of the protein into the biofilm state. The observed rotameric exchange dynamics in the HAP-bound complex are on the order of 5-6 × 10(6) s(-1), as determined from the deuterium MAS line shapes. The dynamics in the HAP-bound complex are also shown to have some solution-like behavioral characteristics, with some interesting deviations from rotameric library statistics.

  13. The effects of side-chain-induced disorder on the emission spectra and quantum yields of oligothiophene nano-aggregates. A combined experimental and MD-TDDFT study

    SciTech Connect

    Hong, Jiyun; Jeon, SuKyung; Kim, Janice J.; Devi, Diane; Chacon-Madrid, Kelly; Lee, Wynee; Koo, Seung Moh; Wildeman, Jurjen; Sfeir, Matthew Y.; Peteanu, Linda A.; Wen, Jin; Ma, Jing

    2014-07-24

    Oligomeric thiophenes are commonly-used components in organic electronics and solar cells. These molecules stack and/or aggregate readily under the processing conditions used to form thin films for these applications, significantly altering their optical and charge-transport properties. To determine how these effects depend on the substitution pattern of the thiophene main chains, nano-aggregates of three sexi-thiophene (6T) oligomers having different alkyl substitution patterns were formed using solvent poisoning techniques and studied using steady-state and time-resolved emission spectroscopy. The results indicate the substantial role played by the side-chain substituents in determining the emissive properties of these species. Both the measured spectral changes and their dependence on substitution are well modeled by combined quantum chemistry and molecular dynamics simulations. The simulations connect the side-chain-induced disorder, which determines the favorable chain packing configurations within the aggregates, with their measured electronic spectra.

  14. Supramolecular side-chain poly[2]pseudorotaxanes formed by orthogonal coordination-driven self-assembly and crown-ether-based host-guest interactions.

    PubMed

    Xing, Hao; Wei, Peifa; Yan, Xuzhou

    2014-06-01

    The themes of coordination-driven self-assembly, host-guest interactions, and supramolecular polymerization are unified in an orthogonal noninterfering fashion to deliver side-chain poly[2]pseudorotaxanes. Specifically, a bis(p-phenylene)-34-crown-10 derivative 1 bearing two pyridyl groups polymerizes into a side-chain poly[2]pseudorotaxane upon the addition of di-Pt(II) acceptor 4 in the presence of paraquat. Interestingly, by adding a competitive guest 3, the poly[2]pseudorotaxane can realize a conversion in one pot.

  15. Supramolecular side-chain poly[2]pseudorotaxanes formed by orthogonal coordination-driven self-assembly and crown-ether-based host-guest interactions.

    PubMed

    Xing, Hao; Wei, Peifa; Yan, Xuzhou

    2014-06-01

    The themes of coordination-driven self-assembly, host-guest interactions, and supramolecular polymerization are unified in an orthogonal noninterfering fashion to deliver side-chain poly[2]pseudorotaxanes. Specifically, a bis(p-phenylene)-34-crown-10 derivative 1 bearing two pyridyl groups polymerizes into a side-chain poly[2]pseudorotaxane upon the addition of di-Pt(II) acceptor 4 in the presence of paraquat. Interestingly, by adding a competitive guest 3, the poly[2]pseudorotaxane can realize a conversion in one pot. PMID:24819441

  16. Bis(thienothiophenyl) diketopyrrolopyrrole-based conjugated polymers with various branched alkyl side chains and their applications in thin-film transistors and polymer solar cells.

    PubMed

    Shin, Jicheol; Park, Gi Eun; Lee, Dae Hee; Um, Hyun Ah; Lee, Tae Wan; Cho, Min Ju; Choi, Dong Hoon

    2015-02-11

    New thienothiophene-flanked diketopyrrolopyrrole and thiophene-containing π-extended conjugated polymers with various branched alkyl side-chains were successfully synthesized. 2-Octyldodecyl, 2-decyltetradecyl, 2-tetradecylhexadecyl, 2-hexadecyloctadecyl, and 2-octadecyldocosyl groups were selected as the side-chain moieties and were anchored to the N-positions of the thienothiophene-flanked diketopyrrolopyrrole unit. All five polymers were found to be soluble owing to the bulkiness of the side chains. The thin-film transistor based on the 2-tetradecylhexadecyl-substituted polymer showed the highest hole mobility of 1.92 cm2 V(-1) s(-1) due to it having the smallest π-π stacking distance between the polymer chains, which was determined by grazing incidence X-ray diffraction. Bulk heterojunction polymer solar cells incorporating [6,6]-phenyl-C71-butyric acid methyl ester as the n-type molecule and the additive 1,8-diiodooctane (1 vol %) were also constructed from the synthesized polymers without thermal annealing; the device containing the 2-octyldodecyl-substituted polymer exhibited the highest power conversion efficiency of 5.8%. Although all the polymers showed similar physical properties, their device performance was clearly influenced by the sizes of the branched alkyl side-chain groups.

  17. Side Chain Engineering of Naphthalenediimide-Based N-type Polymer for High-Performance All-Polymer Solar Cell near 6% Efficiency

    NASA Astrophysics Data System (ADS)

    Lee, Changyeon; Kang, Hyunbum; Lee, Wonho; Kim, Taesu; Kim, Ki-Hyun; Woo, Han Young; Wang, Cheng; Kim, Bumjoon; Pusan National University (PNU) Collaboration; Lawrence Berkeley National Laboratory Collaboration

    2015-03-01

    Despite the attractive features of all-polymer solar cells (all-PSCs), i.e., enhanced absorption coefficients, the tunability of their energetic and chemical properties and their thermal and mechanical stabilities, they still face the great challenge of having significantly low power conversion efficiency (PCE) values of only 3-5%. The prominent origins of the poor efficiency of all-PSCs are the undesirable features of the bulk-heterojunction (BHJ) blend morphology including the phase-separated large-scale domain size, reduced ordering of the polymer chains. Tuning side alkyl chains of conjugated polymers is an effective route for manipulating the blend morphology in BHJ type solar cells. However, the role of side chains in all-PSCs is poorly understood. Herein, we report high-performing all-PSCs with 5.96% efficiency by developing a series of naphthalenediimide (NDI)-based polymer acceptors with different alkyl side chains. We demonstrated that the use of the PNDIT with hexyldecyl side chains produced highly-ordered polymer stackings with strong face-on geometry and at the same time, forming the optimal BHJ morphology with finely separated phase domains, all of which contributed together to induce well-balanced μe/ μh ratio and generate efficient all-PSCs with PCEs near 6%.

  18. Normal genes for the cholesterol side chain cleavage enzyme, P450scc, in congenital lipoid adrenal hyperplasia.

    PubMed Central

    Lin, D; Gitelman, S E; Saenger, P; Miller, W L

    1991-01-01

    Congenital lipoid adrenal hyperplasia is the most severe form of congenital adrenal hyperplasia. Affected individuals can synthesize no steroid hormones, and hence are all phenotypic females with a severe salt-losing syndrome that is fatal if not treated in early infancy. All previous studies have suggested that the disorder is in the cholesterol side chain cleavage enzyme (P450scc), which converts cholesterol to pregnenolone. A newborn patient was diagnosed by the lack of significant concentrations of adrenal or gonadal steroids either before or after stimulation with corticotropin (ACTH) or gonadotropin (hCG). The P450scc gene in this patient and in a previously described patient were grossly intact, as evidenced by Southern blotting patterns. Enzymatic (polymerase chain reaction) amplification and sequencing of the coding regions of their P450scc genes showed these were identical to the previously cloned human P450scc cDNA and gene sequences. Undetected compound heterozygosity was ruled out in the new patient by sequencing P450scc cDNA enzymatically amplified from gonadal RNA. Northern blots of gonadal RNA from this patient contained normal sized mRNAs for P450scc and also for adrenodoxin reductase, adrenodoxin, sterol carrier protein 2, endozepine, and GRP-78 (the precursor to steroidogenesis activator peptide). These studies show that lipoid CAH is not caused by lesions in the P450scc gene, and suggest that another unidentified factor is required for the conversion of cholesterol to pregnenolone, and is disordered in congenital lipoid adrenal hyperplasia. Images PMID:1661294

  19. Glutamine alimentation in catabolic state.

    PubMed

    Boelens, P G; Nijveldt, R J; Houdijk, A P; Meijer, S; van Leeuwen, P A

    2001-09-01

    Glutamine should be reclassified as a conditionally essential amino acid in the catabolic state because the body's glutamine expenditures exceed synthesis and low glutamine levels in plasma are associated with poor clinical outcome. After severe stress, several amino acids are mobilized from muscle tissue to supply energy and substrate to the host. Glutamine is one of the most important amino acids that provide this function. Glutamine acts as the preferred respiratory fuel for lymphocytes, hepatocytes and intestinal mucosal cells and is metabolized in the gut to citrulline, ammonium and other amino acids. Low concentrations of glutamine in plasma reflect reduced stores in muscle and this reduced availability of glutamine in the catabolic state seems to correlate with increased morbidity and mortality. Adding glutamine to the nutrition of clinical patients, enterally or parenterally, may reduce morbidity. Several excellent clinical trials have been performed to prove efficacy and feasibility of the use of glutamine supplementation in parenteral and enteral nutrition. The increased intake of glutamine has resulted in lower septic morbidity in certain critically ill patient populations. This review will focus on the efficacy and the importance of glutamine supplementation in diverse catabolic states.

  20. Clinical use of glutamine supplementation.

    PubMed

    Wernerman, Jan

    2008-10-01

    Endogenous production of glutamine may become insufficient during critical illness. The shortage of glutamine is reflected as a decrease in plasma concentration, which is a prognostic factor for poor outcome in sepsis. Because glutamine is a precursor for nucleotide synthesis, rapidly dividing cells are most likely to suffer from a shortage. Therefore, exogenous glutamine supplementation is necessary. In particular, when i.v. nutrition is given, extra glutamine supplementation becomes critical, because most present formulations for i.v. use do not contain any glutamine for technical reasons. The major part of endogenously produced glutamine comes from skeletal muscle. For patients staying a long time in the intensive care unit (ICU), the muscle mass decreases rapidly, which leaves a tissue of diminishing size to maintain the export of glutamine. The metabolic and nutritional adaptation in long-staying ICU patients is poorly studied and is one of the fields that needs more scientific evidence for clinical recommendations. To date, there is evidence to support the clinical use of glutamine supplementation in critically ill patients, in hematology patients, and in oncology patients. Strong evidence is presently available for i.v. glutamine supplementation to critically ill patients on parenteral nutrition. This must be regarded as the standard of care. For patients on enteral nutrition, more evidence is needed. To guide administration of glutamine, there are good arguments to use measurement of plasma glutamine concentration for guidance. This will give an indication for treatment as well as proper dosing. Most patients will have a normalized plasma glutamine concentration by adding 20-25 g/24 h. Furthermore, there are no reported adverse or negative effects attributable to glutamine supplementation.

  1. Main-Chain and Side-Chain Sequence-Regulated Vinyl Copolymers by Iterative Atom Transfer Radical Additions and 1:1 or 2:1 Alternating Radical Copolymerization.

    PubMed

    Soejima, Takamasa; Satoh, Kotaro; Kamigaito, Masami

    2016-01-27

    Main- and side-chain sequence-regulated vinyl copolymers were prepared by a combination of iterative atom transfer radical additions (ATRAs) of vinyl monomers for side-chain control and 1:1 or 2:1 alternating radical copolymerization of the obtained side-chain sequenced "oligomonomers" and vinyl comonomers for main-chain control. A complete set of sequence-regulated trimeric vinyl oligomers of styrene (S) and/or methyl acrylate (A) were first synthesized via iterative ATRAs of these monomers to a halide of monomeric S or A unit (X-S or X-A) under optimized conditions with appropriate ruthenium or copper catalysts, which were selected depending on the monomers and halides. The obtained halogen-capped oligomers were then converted into a series of maleimide (M)-ended oligomonomers with different monomer compositions and sequences (M-SSS, M-ASS, M-SAS, M-AAS, M-SSA, M-ASA, M-SAA, M-AAA) by a substitution reaction of the halide with furan-protected maleimide anion followed by deprotection of the furan units. These maleimide-ended oligomonomers were then radically copolymerized with styrene or limonene to enable the 1:1 or 2:1 monomer-sequence regulation in the main chain and finally result in the main- and side-chain sequence-regulated vinyl copolymers with high molecular weights in high yield. The properties of the sequence-regulated vinyl copolymers depended on not only the monomer compositions but also the monomer sequences. The solubility was highly affected by the outer monomer units in the side chains whereas the glass transition temperatures were primarily affected by the two successive monomer sequences. PMID:26761148

  2. The effects of regularly spaced glutamine substitutions on alpha-helical peptide structures: A DFT/ONIOM study

    NASA Astrophysics Data System (ADS)

    Roy, Dipankar; Dannenberg, J. J.

    2011-08-01

    The side-chains of the residues of glutamine (Q) and asparagine (N) contain amide groups. These can H-bond to each other in patterns similar to those of the backbone amides in α-helices. We show that mutating multiple Q's for alanines (A's) in a polyalanine helix stabilizes the helical structure, while similar mutations with multiple N's do not. We suggest that modification of peptides by incorporating Q's in such positions can make more robust helices that can be used to test the effects of secondary structures in biochemical experiments linked to proteins with variable structures such as tau and α-synuclein.

  3. Fluorinated Peptide Nucleic Acids with Fluoroacetyl Side Chain Bearing 5-(F/CF3)-Uracil: Synthesis and Cell Uptake Studies.

    PubMed

    Ellipilli, Satheesh; Palvai, Sandeep; Ganesh, Krishna N

    2016-08-01

    Fluorine incorporation into organic molecules imparts favorable physicochemical properties such as lipophilicity, solubility and metabolic stability necessary for drug action. Toward such applications using peptide nucleic acids (PNA), we herein report the chemical synthesis of fluorinated PNA monomers and biophysical studies of derived PNA oligomers containing fluorine in in the acetyl side chain (-CHF-CO-) bearing nucleobase uracil (5-F/5-CF3-U). The crystal structures of fluorinated racemic PNA monomers reveal interesting base pairing of enantiomers and packing arrangements directed by the chiral F substituent. Reverse phase HPLC show higher hydrophobicity of fluorinated PNA oligomers, dependent on the number and site of the fluorine substitution: fluorine on carbon adjacent to the carbonyl group induces higher lipophilicity than fluorine on nucleobase or in the backbone. The PNA oligomers containing fluorinated bases form hybrids with cDNA/RNA with slightly lower stability compared to that of unmodified aeg PNA, perhaps due to electronic effects. The uptake of fluorinated homooligomeric PNAs by HeLa cells was as facile as that of nonfluorinated PNA. In conjunction with our previous work on PNAs fluorinated in backbone and at N-terminus, it is evident that the fluorinated PNAs have potential to emerge as a new class of PNA analogues for applications in functional inhibition of RNA. PMID:27391099

  4. Tuning backbones and side-chains of cationic conjugated polymers for optical signal amplification of fluorescent DNA detection.

    PubMed

    Huang, Yan-Qin; Liu, Xing-Fen; Fan, Qu-Li; Wang, Lihua; Song, Shiping; Wang, Lian-Hui; Fan, Chunhai; Huang, Wei

    2009-06-15

    Three cationic conjugated polymers (CCPs) exhibiting different backbone geometries and charge densities were used to investigate how their conjugated backbone and side chain properties, together with the transitions of DNA amphiphilic properties, interplay in the CCP/DNA-C* (DNA-C*: fluorophore-labeled DNA) complexes to influence the optical signal amplification of fluorescent DNA detection based on Förster resonance energy transfer (FRET). By examining the FRET efficiencies to dsDNA-C* (dsDNA: double-stranded DNA) and ssDNA-C* (ssDNA: single-stranded DNA) for each CCP, twisted conjugated backbones and higher charge densities were proved to facilitate electrostatic attraction in CCP/dsDNA-C* complexes, and induced improved sensitivity to DNA hybridization. Especially, by using the CCP with twisted conjugated backbone and the highest charge density, a more than 7-fold higher efficiency of FRET to dsDNA-C* was found than to ssDNA-C*, indicating a high signal amplification for discriminating between dsDNA and ssDNA. By contrast, linear conjugated backbones and lower charge density were demonstrated to favor hydrophobic interactions in CCP/ssDNA-C* complexes. These findings provided guidelines for the design of novel sensitive CCP, which can be useful to recognize many other important DNA activities involving transitions of DNA amphiphilic properties like DNA hybridization, such as specific DNA binding with ions, some secondary or tertiary structural changes of DNA, and so forth.

  5. ABC triblock surface active block copolymer with grafted ethoxylated fluoroalkyl amphiphilic side chains for marine antifouling/fouling-release applications.

    PubMed

    Weinman, Craig J; Finlay, John A; Park, Daewon; Paik, Marvin Y; Krishnan, Sitaraman; Sundaram, Harihara S; Dimitriou, Michael; Sohn, Karen E; Callow, Maureen E; Callow, James A; Handlin, Dale L; Willis, Carl L; Kramer, Edward J; Ober, Christopher K

    2009-10-20

    An amphiphilic triblock surface-active block copolymer (SABC) possessing ethoxylated fluoroalkyl side chains was synthesized through the chemical modification of a polystyrene-block-poly(ethylene-ran-butylene)-block-polyisoprene polymer precursor. Bilayer coatings on glass slides consisting of a thin layer of the amphiphilic SABC spray coated on a thick layer of a polystyrene-block-poly(ethylene-ran-butylene)-block-polystyrene (SEBS) thermoplastic elastomer were prepared for biofouling assays with the green alga Ulva and the diatom Navicula. Dynamic water contact angle analysis and X-ray photoelectron spectroscopy (XPS) were used to characterize the surfaces. Additionally, the effect of the Young's modulus of the coating on the release properties of sporelings (young plants) of the green alga Ulva was examined through the use of two different SEBS thermoplastic elastomers possessing modulus values of an order of magnitude in difference. The amphiphilic SABC was found to reduce the settlement density of zoospores of Ulva as well as the strength of attachment of sporelings. The attachment strength of the sporelings was further reduced for the amphiphilic SABC on the "low"-modulus SEBS base layer. The weaker adhesion of diatoms, relative to a PDMS standard, further highlights the antifouling potential of this amphiphilic triblock hybrid copolymer.

  6. The mitochondrial environment is required for activity of the cholesterol side-chain cleavage enzyme, cytochrome P450scc.

    PubMed Central

    Black, S M; Harikrishna, J A; Szklarz, G D; Miller, W L

    1994-01-01

    Steroidogenesis is initiated by the conversion of cholesterol to pregnenolone by mitochondrial cytochrome P450scc [cholesterol, reduced-adrenal-ferredoxin:oxygen oxidoreductase (side-chain-cleaving); EC 1.14.15.6]. Several subsequent steroidal conversions occur in the endoplasmic reticulum (ER), but the last step in the production of glucocorticoids and mineralocorticoids again occurs in the mitochondria. Although cellular compartmentalization of steroidogenic enzymes appears to be a feature of all steroidogenic pathways, some reports indicate that cholesterol can be converted to pregnenolone outside the mitochondria. To investigate whether P450scc can function outside the mitochondria, we constructed vectors producing P450scc and various fusion enzymes of P450scc with electron-transport proteins and directed their expression to either the ER or the mitochondria. Whether targeted to mitochondria or to the ER, plasmid vectors encoding P450scc and fusion proteins of P450scc with either mitochondrial or microsomal electron-transport proteins produced immunodetectable protein. When expressed in mitochondria, all of these constructions converted 22-hydroxycholesterol to pregnenolone, but when expressed in the ER none of them produced pregnenolone. These results show that P450scc can function only in the mitochondria. Furthermore, it appears to be the mitochondrial environment that is required, rather than the specific mitochondrial electron-transport intermediates. Images PMID:8041774

  7. Neutral Pectin side chains of Amaranth (Amaranthus hypochondriacus) contain long, partially branched Arabinans and short galactans, both with terminal arabinopyranoses.

    PubMed

    Wefers, Daniel; Tyl, Catrin E; Bunzel, Mirko

    2015-01-21

    Amaranth is a pseudocereal of high nutritional value, including a high dietary fiber content. Amaranth dietary fiber was suggested to contain large amounts of neutral rhamnogalacturonan I side chains. In this study, endo-arabinanase and endo-galactanase were used to liberate arabinan and galactan oligosaccharides from amaranth fiber. The liberated oligosaccharides were identified by high-performance anion exchange chromatography with pulsed amperometric detection (HPAEC-PAD) and HPLC-MS(n) using standard compounds, which were isolated from amaranth, sugar beet, potato, and red clover sprouts and characterized by one- and two-dimensional NMR spectroscopy. It was demonstrated that insoluble amaranth arabinans have linear and branched areas, with the O-3 position being the dominant branching point. Minor amounts of branches at position O-2 and double substitution were also found. Amaranth arabinans were also demonstrated to contain terminal α-(1→5)-linked l-arabinopyranose units. In addition, it was evidenced that galactans from amaranth seeds are composed of β-(1→4)-linked d-galactopyranose units, which can also be terminated with l-arabinopyranose units. In direct comparison to structural elucidation of amaranth fiber by using methylation analysis, the advantage of the enzymatic approach over methylation analysis was demonstrated.

  8. The Identification of Two Arabinosyltransferases from Tomato Reveals Functional Equivalency of Xyloglucan Side Chain Substituents1[W][OPEN

    PubMed Central

    Schultink, Alex; Cheng, Kun; Park, Yong Bum; Cosgrove, Daniel J.; Pauly, Markus

    2013-01-01

    Xyloglucan (XyG) is the dominant hemicellulose present in the primary cell walls of dicotyledonous plants. Unlike Arabidopsis (Arabidopsis thaliana) XyG, which contains galactosyl and fucosyl substituents, tomato (Solanum lycopersicum) XyG contains arabinofuranosyl residues. To investigate the biological function of these differing substituents, we used a functional complementation approach. Candidate glycosyltransferases were identified from tomato by using comparative genomics with known XyG galactosyltransferase genes from Arabidopsis. These candidate genes were expressed in an Arabidopsis mutant lacking XyG galactosylation, and two of them resulted in the production of arabinosylated XyG, a structure not previously found in this plant species. These genes may therefore encode XyG arabinofuranosyltransferases. Moreover, the addition of arabinofuranosyl residues to the XyG of this Arabidopsis mutant rescued a growth and cell wall biomechanics phenotype, demonstrating that the function of XyG in plant growth, development, and mechanics has considerable flexibility in terms of the specific residues in the side chains. These experiments also highlight the potential of reengineering the sugar substituents on plant wall polysaccharides without compromising growth or viability. PMID:23893172

  9. Characterization of Kbot21 Reveals Novel Side Chain Interactions of Scorpion Toxins Inhibiting Voltage-Gated Potassium Channels

    PubMed Central

    ElFessi-Magouri, Rym; Peigneur, Steve; Othman, Houcemeddine; Srairi-Abid, Najet; ElAyeb, Mohamed; Tytgat, Jan; Kharrat, Riadh

    2015-01-01

    Scorpion toxins are important pharmacological tools for probing the physiological roles of ion channels which are involved in many physiological processes and as such have significant therapeutic potential. The discovery of new scorpion toxins with different specificities and affinities is needed to further characterize the physiology of ion channels. In this regard, a new short polypeptide called Kbot21 has been purified to homogeneity from the venom of Buthus occitanus tunetanus scorpion. Kbot21 is structurally related to BmBKTx1 from the venom of the Asian scorpion Buthus martensii Karsch. These two toxins differ by only two residues at position 13 (R /V) and 24 (D/N).Despite their very similar sequences, Kbot21 and BmBKTx1 differ in their electrophysiological activities. Kbot21 targets KV channel subtypes whereas BmBKTx1 is active on both big conductance (BK) and small conductance (SK) Ca2+-activated K+ channel subtypes, but has no effects on Kv channel subtypes. The docking model of Kbot21 with the Kv1.2 channel shows that the D24 and R13 side-chain of Kbot21 are critical for its interaction with KV channels. PMID:26398235

  10. Theoretical studies of salt-bridge formation by amino acid side chains in low and medium polarity environments.

    PubMed

    Nagy, Peter I; Erhardt, Paul W

    2010-12-16

    Salt-bridge formation between Asp/Glu···Lys and Asp/Glu···Arg side chains has been studied by model systems including formic and acetic acids as proton donors and methylamine, guanidine, and methylguanidine as proton acceptors. Calculations have been performed up to the CCSD(T)(CBS)//MP2/aug-cc-pvtz level with formic acid proton donors. Complexes formed with acetic acid were studied at the CCSD(T)/aug-cc-pvdz//MP2/aug-cc-pvdz level. Protein environments of low and moderate polarity were mimicked by a continuum solvent with dielectric constants (ε) set to 5 and 15, respectively. Free energy differences, ΔG(tot), were calculated for the neutral, hydrogen-bonded form and for the tautomeric ion pair. These values predict that a salt bridge is not favored for the Asp/Glu···Lys pair, even in an environment with ε as large as 15. In contrast, the Asp/Glu···Arg salt bridge is feasible even in an environment with ε = 5. Charge transfers for the complexes were calculated on the basis of CHELPG and AIM charges.

  11. Characterization of Kbot21 Reveals Novel Side Chain Interactions of Scorpion Toxins Inhibiting Voltage-Gated Potassium Channels.

    PubMed

    ElFessi-Magouri, Rym; Peigneur, Steve; Othman, Houcemeddine; Srairi-Abid, Najet; ElAyeb, Mohamed; Tytgat, Jan; Kharrat, Riadh

    2015-01-01

    Scorpion toxins are important pharmacological tools for probing the physiological roles of ion channels which are involved in many physiological processes and as such have significant therapeutic potential. The discovery of new scorpion toxins with different specificities and affinities is needed to further characterize the physiology of ion channels. In this regard, a new short polypeptide called Kbot21 has been purified to homogeneity from the venom of Buthus occitanus tunetanus scorpion. Kbot21 is structurally related to BmBKTx1 from the venom of the Asian scorpion Buthus martensii Karsch. These two toxins differ by only two residues at position 13 (R /V) and 24 (D/N).Despite their very similar sequences, Kbot21 and BmBKTx1 differ in their electrophysiological activities. Kbot21 targets KV channel subtypes whereas BmBKTx1 is active on both big conductance (BK) and small conductance (SK) Ca2+-activated K+ channel subtypes, but has no effects on Kv channel subtypes. The docking model of Kbot21 with the Kv1.2 channel shows that the D24 and R13 side-chain of Kbot21 are critical for its interaction with KV channels. PMID:26398235

  12. Neutral Pectin side chains of Amaranth (Amaranthus hypochondriacus) contain long, partially branched Arabinans and short galactans, both with terminal arabinopyranoses.

    PubMed

    Wefers, Daniel; Tyl, Catrin E; Bunzel, Mirko

    2015-01-21

    Amaranth is a pseudocereal of high nutritional value, including a high dietary fiber content. Amaranth dietary fiber was suggested to contain large amounts of neutral rhamnogalacturonan I side chains. In this study, endo-arabinanase and endo-galactanase were used to liberate arabinan and galactan oligosaccharides from amaranth fiber. The liberated oligosaccharides were identified by high-performance anion exchange chromatography with pulsed amperometric detection (HPAEC-PAD) and HPLC-MS(n) using standard compounds, which were isolated from amaranth, sugar beet, potato, and red clover sprouts and characterized by one- and two-dimensional NMR spectroscopy. It was demonstrated that insoluble amaranth arabinans have linear and branched areas, with the O-3 position being the dominant branching point. Minor amounts of branches at position O-2 and double substitution were also found. Amaranth arabinans were also demonstrated to contain terminal α-(1→5)-linked l-arabinopyranose units. In addition, it was evidenced that galactans from amaranth seeds are composed of β-(1→4)-linked d-galactopyranose units, which can also be terminated with l-arabinopyranose units. In direct comparison to structural elucidation of amaranth fiber by using methylation analysis, the advantage of the enzymatic approach over methylation analysis was demonstrated. PMID:25529336

  13. Dipolar dynamic frequency shifts in multiple-quantum spectra of methyl groups in proteins: correlation with side-chain motion.

    PubMed

    Tugarinov, Vitali; Ollerenshaw, Jason E; Kay, Lewis E

    2006-07-01

    Small deviations from the expected relative positions of multiplet components in double- and zero-quantum 1H-13C methyl correlation maps have been observed in spectra recorded on a 7-kDa protein. These dynamic frequency shifts (DFS) are the result of dipolar cross-correlations that derive from fields produced by the spins within the methyl groups. The shifts have been quantified and compared with values calculated from a Redfield analysis. Good agreement is noted between the signs of the predicted and experimentally observed relative shifts of lines in both F1 and F2 dimensions of spectra, as well as between the magnitudes of the calculated and observed shifts in the F2 (1H) dimension. The experimental DFS values show a reasonable correlation with 2H relaxation-derived measures of methyl side-chain dynamics, as expected from theory. This suggests that in cases where such shifts can be quantified, they can serve as qualitative measures of motion. PMID:16826549

  14. An effective strategy to increase hydroxide-ion conductivity through microphase separation induced by hydrophobic-side chains

    NASA Astrophysics Data System (ADS)

    Zeng, L.; Zhao, T. S.

    2016-01-01

    A highly conductive and durable anion exchange membrane (AEM) is an essential component for alkaline electrochemical conversion and storage systems. Contrary to the conventional wisdom that the ionic conductivity can be improved by increasing the ion exchange capacity (IEC) through a cross-linking process, in this work, a new approach to improve the ionic conductivity by enhancing the ionic mobility is adopted. The microstructure of quaternary ammonia poly (2, 6-dimethyl-1, 4-phenylene oxide) (QAPPO) is manipulated through grafting with hydrophobic side chains, which will drive the well-established hydrophilic/hydrophobic domains and nano-phase separated, well-connected ionic channels. As a result, the local hydroxide concentration is enhanced by the novel microstructure, thereby improving the ionic conductivity of the as-prepared ionomers. The as-prepared ionomers, denoted as self-aggregated QAPPO-CF, with an intermediate IEC value achieved an ionic conductivity of 65 mS cm-1 at 80 °C, outperforming the QAPPO with an even higher IEC value. This result suggests that the microphase separation is an effective approach to enhance the ionic conductivity.

  15. Synthesis, characterization, conformation and self-assembly behavior of polypeptide-based brush with oligo (ethylene glycol) side chains

    NASA Astrophysics Data System (ADS)

    Huang, Yugang; Luo, Weiang; Ye, Guodong

    2015-02-01

    A new polypeptide-based copolymer brush composed of poly (γ-propargyl-L-glutamate)-block-poly (propylene oxide)-block-poly (γ-propargyl-L-glutamate) backbone (PPLG-b-PPO-b-PPLG) and oligo (ethylene glycol) (PEG) side-chain was synthesized by combination of N-carboxyanhydride ring-opening polymerization and click chemistry. Nearly 100% grafting efficiency was achieved by copper-catalyzed azide-alkyne Huisgen 1,3-dipolar cycloaddition (CuAAc) reaction. The α-helical conformation adopted by the grafted polypeptide blocks in water was relatively stable and showed a reversible change in a heating-cooling circle from 5 to 70 °C. It displayed weak stability against elevated temperature but still reversible changes in the presence of 0.47 M NaCl. The brushes were amphiphilic and could self-assemble into thermo-sensitive micelles in water. Big micelles could break into small micelles upon heating due to the improved solubility.

  16. Microbial side-chain cleavage of phytosterols by mycobacteria in vegetable oil/aqueous two-phase system.

    PubMed

    Xu, Yang-Guang; Guan, Yi-Xin; Wang, Hai-Qing; Yao, Shan-Jing

    2014-09-01

    Microbial side-chain cleavage of natural sterols to 4-androstene-3,17-dione (AD) and 1,4-androstadiene-3,17-dione (ADD) by Mycobacteria has received much attention in pharmaceutical industry, while low yield of the reaction owing to the strong hydrophobicity of sterols is a tough problem to be solved urgently. Eight kinds of vegetable oils, i.e., sunflower, peanut, corn, olive, linseed, walnut, grape seed, and rice oil, were used to construct oil/aqueous biphasic systems in the biotransformation of phytosterols by Mycobacterium sp. MB 3683 cells. The results indicated that vegetable oils are suitable for phytosterol biotransformation. Specially, the yield of AD carried out in sunflower biphasic system (phase ratio of 1:9, oil to aqueous) was greatly increased to 84.8 % with 10 g/L feeding concentration after 120-h transformation at 30 °C and 200 rpm. Distribution coefficients of AD in different oil/aqueous systems were also determined. Because vegetable oils are of low cost and because of their eco-friendly characters, there is a great potential for the application of oil/aqueous two-phase systems in bacteria whole cell biocatalysis.

  17. Side-chain control of porosity closure in single- and multiple-peptide-based porous materials by cooperative folding

    NASA Astrophysics Data System (ADS)

    Martí-Gastaldo, C.; Antypov, D.; Warren, J. E.; Briggs, M. E.; Chater, P. A.; Wiper, P. V.; Miller, G. J.; Khimyak, Y. Z.; Darling, G. R.; Berry, N. G.; Rosseinsky, M. J.

    2014-04-01

    Porous materials are attractive for separation and catalysis—these applications rely on selective interactions between host materials and guests. In metal-organic frameworks (MOFs), these interactions can be controlled through a flexible structural response to the presence of guests. Here we report a MOF that consists of glycyl-serine dipeptides coordinated to metal centres, and has a structure that evolves from a solvated porous state to a desolvated non-porous state as a result of ordered cooperative, displacive and conformational changes of the peptide. This behaviour is driven by hydrogen bonding that involves the side-chain hydroxyl groups of the serine. A similar cooperative closure (reminiscent of the folding of proteins) is also displayed with multipeptide solid solutions. For these, the combination of different sequences of amino acids controls the framework's response to the presence of guests in a nonlinear way. This functional control can be compared to the effect of single-point mutations in proteins, in which exchange of single amino acids can radically alter structure and function.

  18. Restricted mobility of side chains on concave surfaces of solenoid proteins may impart heightened potential for intermolecular interactions.

    PubMed

    Ramya, L; Gautham, N; Chaloin, Laurent; Kajava, Andrey V

    2015-09-01

    Significant progress has been made in the determination of the protein structures with their number today passing over a hundred thousand structures. The next challenge is the understanding and prediction of protein-protein and protein-ligand interactions. In this work we address this problem by analyzing curved solenoid proteins. Many of these proteins are considered as "hub molecules" for their high potential to interact with many different molecules and to be a scaffold for multisubunit protein machineries. Our analysis of these structures through molecular dynamics simulations reveals that the mobility of the side-chains on the concave surfaces of the solenoids is lower than on the convex ones. This result provides an explanation to the observed preferential binding of the ligands, including small and flexible ligands, to the concave surface of the curved solenoid proteins. The relationship between the landscapes and dynamic properties of the protein surfaces can be further generalized to the other types of protein structures and eventually used in the computer algorithms, allowing prediction of protein-ligand interactions by analysis of protein surfaces.

  19. Compounds having aromatic rings and side-chain amide-functionality and a method for transporting monovalent anions across biological membranes using the same

    DOEpatents

    Davis, Jeffery T.; Sidorov, Vladimir; Kotch, Frank W.

    2008-04-08

    A compound containing at least two aromatic rings covalently bonded together, with each aromatic ring containing at least one oxyacetamide-based side chain, the compound being capable of forming a chloride ion channel across a lipid bilayer, and transporting chloride ion across the lipid bilayer.

  20. Pressure-dependent helix inversion of poly(quinoxaline-2,3-diyl)s containing chiral side chains in non-aqueous solvents.

    PubMed

    Nagata, Yuuya; Takeda, Ryohei; Suginome, Michinori

    2015-06-30

    Poly(quinoxaline-2,3-diyl)s with chiral (S)-2-butoxymethyl side chains dissolved in 1,2-dichloroethane experience a reversible pressure-dependent helix inversion from P- to M-helical structures between 0.1 MPa and 200 MPa.

  1. Impact of constitution of the terthiophene-vinylene conjugated side chain on the optical and photovoltaic properties of two-dimensional polythiophenes.

    PubMed

    Hsiow, Chuen-Yo; Raja, Rathinam; Wang, Chun-Yao; Lin, Yu-Hsiang; Yang, Yu-Wen; Hsieh, Yen-Ju; Rwei, Syang-Peng; Chiu, Wen-Yen; Huang, Ching-I; Wang, Leeyih

    2014-12-01

    The effects of the spatial arrangement of the conjugated side chains of two-dimensional polymers on their optical, electrochemical, molecular-packing, and photovoltaic characteristics were investigated. Accordingly, novel polythiophenes with horizontally (PBTTTV-h) and vertically (PBTTTV-v) grafted terthiophene–vinylene (TTV) conjugated side chains were synthesized that display two and one UV-vis peaks, respectively; the difference is due to the different constitutions of the conjugated side-chains. Because the spatial arrangement affects the molecular self-assembly, PBTTTV-h shows stronger crystallinity than PBTTTV-v, which enhances the charge mobility in devices. Moreover, PBTTTV-h has a lower HOMO energy level (−5.49 eV) than PBTTTV-v (−5.40 eV). Bulk heterojunction solar cells fabricated from PBTTTV-h/PC71BM and PBTTTV-v/PC71BM exhibit power conversion efficiencies of 4.75% and 4.00%, respectively, and Voc values of 800 and 730 mV, respectively, under AM1.5G illumination (100 mW cm(−2)). Thus, the architecture of the TTV conjugated side chains affects the optical, electrochemical, and photovoltaic properties; this study provides more ideas for improving 2-D conjugated polymers for semiconductor devices.

  2. The first example of a liquid crystalline side-chain polymer with bent-core mesogenic units: ferroelectric switching and spontaneous achiral symmetry breaking in an achiral polymer.

    PubMed

    Keith, Christina; Reddy, R Amaranatha; Tschierske, Carsten

    2005-02-21

    A dimethylsiloxane diluted polysiloxane side chain co-polymer with non-chiral banana-shaped mesogenic units shows an optically isotropic ferroelectric switching polar smectic C phase (SmCPF) consisting of a conglomerate of homogeneously chiral domains with opposite handedness.

  3. Probing the effects of the ester functional group, alkyl side chain length and anions on the bulk nanostructure of ionic liquids: a computational study.

    PubMed

    Fakhraee, Mostafa; Gholami, Mohammad Reza

    2016-04-14

    The effects of ester addition on nanostructural properties of biodegradable ILs composed of 1-alkoxycarbonyl-3-alkyl-imidazolium cations ([C1COOCnC1im](+), n = 1, 2, 4) combined with [Br](-), [NO3](-), [BF4](-), [PF6](-), [TfO](-), and [Tf2N](-) were explored by using the molecular dynamics (MD) simulations and quantum theory of atoms in molecules (QTAIM) analysis at 400 K. Various thermodynamic properties of these ILs were extensively computed in our earlier work (Ind. Eng. Chem. Res., 2015, 54, 11678-11700). Nano-scale segregation analysis demonstrates the formation of a small spherical island-like hydrocarbon within the continuous ionic domain for ILs with short alkyl side chain ([C1COOC1C1im]), and a sponge-like nanostructure for the compound with long alkyl side chain ([C1COOC4C1im]). Ester-functionalized ILs with ethyl side chain ([C1COOC2C1im]) are the turning point between two different morphologies. Non-polar channels were observed for [C1COOC4C1im] ILs composed of smaller anions such as [Br] and [NO3], whereas clustering organization was found for the other anions. Formation of the spherical micelle-like nanostructure was seen for lengthened cations. Finally, the incorporation of an ester group into the alkyl side chain of the cation leads to stronger segregation between charged and uncharged networks, which consequently increased the possibility of self-assembly and micelle formation. PMID:27001746

  4. Synthesis and photovoltaic properties of two-dimensional low-bandgap copolymers based on new benzothiadiazole derivatives with different conjugated arylvinylene side chains.

    PubMed

    Peng, Qiang; Lim, Siew-Lay; Wong, Ivy Hoi-Ka; Xu, Jun; Chen, Zhi-Kuan

    2012-09-17

    A new series of 2,1,3-benzothiadiazole (BT) acceptors with different conjugated aryl-vinylene side chains have been designed and used to build efficient low-bandgap (LBG) photovoltaic copolymers. Based on benzo[1,2-b:3,4-b']dithiophene and the resulting new BT derivatives, three two-dimensional (2D)-like donor (D)-acceptor (A) conjugated copolymers have been synthesised by Stille coupling polymerisation. These copolymers were characterised by NMR spectroscopy, gel-permeation chromatography, thermogravimetric analysis and differential scanning calorimetry. UV/Vis absorption and cyclic voltammetry measurements indicated that their optical and electrochemical properties can be facilely modified by changing the structures of the conjugated aryl-vinylene side chains. The copolymer with phenyl-vinylene side chains exhibited the best light harvesting and smallest bandgap of the three copolymers. The basic electronic structures of D-A model compounds of these copolymers were also studied by DFT calculations at the B3LYP/6-31G* level of theory. Polymer solar cells (PSCs) with a typical structure of indium tin oxide (ITO)/poly(3,4-ethylenedioxythiophene) (PEDOT):poly(styrenesulfonate) (PSS)/copolymer:[6,6]-phenyl-C(61) (C(71))-butyric acid-methyl ester (PCBM)/calcium (Ca)/aluminum (Al) were fabricated and measured under the illumination of AM1.5G at 100 mW cm(-2). The results showed that the device based on the copolymer with phenyl-vinylene side chains had the highest efficiency of 2.17 % with PC(71)BM as acceptor. The results presented herein indicate that all the prepared copolymers are promising candidates for roll-to-roll manufacturing of efficient PSCs. Suitable electronic, optical and photovoltaic properties of BT-based copolymers can also be achieved by fine-tuning the structures of the aryl-vinylene side chains for photovoltaic application.

  5. Evaluating Force Fields for the Computational Prediction of Ionized Arginine and Lysine Side-Chains Partitioning into Lipid Bilayers and Octanol.

    PubMed

    Sun, Delin; Forsman, Jan; Woodward, Clifford E

    2015-04-14

    Abundant peptides and proteins containing arginine (Arg) and lysine (Lys) amino acids can apparently permeate cell membranes with ease. However, the mechanisms by which these peptides and proteins succeed in traversing the free energy barrier imposed by cell membranes remain largely unestablished. Precise thermodynamic studies (both theoretical and experimental) on the interactions of Arg and Lys residues with model lipid bilayers can provide valuable clues to the efficacy of these cationic peptides and proteins. We have carried out molecular dynamics simulations to calculate the interactions of ionized Arg and Lys side-chains with the zwitterionic 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid bilayer for 10 widely used lipid/protein force fields: CHARMM36/CHARMM36, SLIPID/AMBER99SB-ILDN, OPLS-AA/OPLS-AA, Berger/OPLS-AA, Berger/GROMOS87, Berger/GROMOS53A6, GROMOS53A6/GROMOS53A6, nonpolarizable MARTINI, polarizable MARTINI, and BMW MARTINI. We performed umbrella sampling simulations to obtain the potential of mean force for Arg and Lys side-chains partitioning from water to the bilayer interior. We found significant differences between the force fields, both for the interactions between side-chains and bilayer surface, as well as the free energy cost for placing the side-chain at the center of the bilayer. These simulation results were compared with the Wimley-White interfacial scale. We also calculated the free energy cost for transferring ionized Arg and Lys side-chains from water to both dry and wet octanol. Our simulations reveal rapid diffusion of water molecules into octanol whereby the equilibrium mole fraction of water in the wet octanol phase was ∼25%. Surprisingly, our free energy calculations found that the high water content in wet octanol lowered the water-to-octanol partitioning free energies for cationic residues by only 0.6 to 0.7 kcal/mol. PMID:26574387

  6. Influence of the degree of unsaturation of the acyl side chain upon the interaction of analogues of 1-arachidonoylglycerol with monoacylglycerol lipase and fatty acid amide hydrolase

    SciTech Connect

    Vandevoorde, Severine; Saha, Bijali; Mahadevan, Anu; Razdan, Raj K.; Pertwee, Roger G.; Martin, Billy R.; Fowler, Christopher J. . E-mail: cf@pharm.umu.se

    2005-11-11

    Little is known as to the structural requirements of the acyl side chain for interaction of acylglycerols with monoacylglycerol lipase (MAGL), the enzyme chiefly responsible for the metabolism of the endocannabinoid 2-arachidonoylglycerol (2-AG) in the brain. In the present study, a series of twelve analogues of 1-AG (the more stable regioisomer of 2-AG) were investigated with respect to their ability to inhibit the metabolism of 2-oleoylglycerol by cytosolic and membrane-bound MAGL. In addition, the ability of the compounds to inhibit the hydrolysis of anandamide by fatty acid amide hydrolase (FAAH) was investigated. For cytosolic MAGL, compounds with 20 carbon atoms in the acyl chain and 2-5 unsaturated bonds inhibited the hydrolysis of 2-oleoylglycerol with similar potencies (IC{sub 50} values in the range 5.1-8.2 {mu}M), whereas the two compounds with a single unsaturated bond were less potent (IC{sub 50} values 19 and 21 {mu}M). The fully saturated analogue 1-monoarachidin did not inhibit the enzyme, whereas the lower side chain analogues 1-monopalmitin and 1-monomyristin inhibited the enzyme with IC{sub 50} values of 12 and 32 {mu}M, respectively. The 22-carbon chain analogue of 1-AG was also potent (IC{sub 50} value 4.5 {mu}M). Introduction of an {alpha}-methyl group for the C20:4, C20:3, and C22:4 compounds did not affect potency in a consistent manner. For the FAAH and the membrane-bound MAGL, there was no obvious relationship between the degree of unsaturation of the acyl side chain and the ability to inhibit the enzymes. It is concluded that increasing the number of unsaturated bonds on the acyl side chain of 1-AG from 1 to 5 has little effect on the affinity of acylglycerols for cytosolic MAGL.

  7. Autoantibodies against Cytochrome P450 Side-Chain Cleavage Enzyme in Dogs (Canis lupus familiaris) Affected with Hypoadrenocorticism (Addison's Disease).

    PubMed

    Boag, Alisdair M; Christie, Michael R; McLaughlin, Kerry A; Syme, Harriet M; Graham, Peter; Catchpole, Brian

    2015-01-01

    Canine hypoadrenocorticism likely arises from immune-mediated destruction of adrenocortical tissue, leading to glucocorticoid and mineralocorticoid deficiency. In humans with autoimmune Addison's disease (AAD) or autoimmune polyendocrine syndrome (APS), circulating autoantibodies have been demonstrated against enzymes associated with adrenal steroid synthesis. The current study investigates autoantibodies against steroid synthesis enzymes in dogs with spontaneous hypoadrenocorticism. Coding regions of canine CYP21A2 (21-hydroxylase; 21-OH), CYP17A1 (17-hydroxylase; 17-OH), CYP11A1 (P450 side-chain cleavage enzyme; P450scc) and HSD3B2 (3β hydroxysteroid dehydrogenase; 3βHSD) were amplified, cloned and expressed as 35S-methionine radiolabelled recombinant protein. In a pilot study, serum samples from 20 dogs with hypoadrenocorticism and four unaffected control dogs were screened by radio-immunoprecipitation assay. There was no evidence of reactivity against 21-OH, 17-OH or 3βHSD, but five dogs with hypoadrenocorticism showed immunoreactivity to P450scc compared with controls. Serum samples were subsequently obtained from 213 dogs diagnosed with hypoadrenocorticism and 110 dogs from a hospital control population. Thirty control dogs were randomly selected to establish a threshold for antibody positivity (mean + 3 × standard deviation). Dogs with hypoadrenocorticism were more likely to be P450scc autoantibody positive than hospital controls (24% vs. 1.2%, respectively; p = 0.0016). Sex was significantly associated with the presence of P450scc autoantibodies in the case population, with 30% of females testing positive compared with 17% of males (p = 0.037). Significant associations with breed (p = 0.015) and DLA-type (DQA1*006:01 allele; p = 0.017) were also found. This cross-sectional study indicates that P450scc autoantibodies are present in a proportion of dogs affected with hypoadrenocorticism.

  8. Autoantibodies against Cytochrome P450 Side-Chain Cleavage Enzyme in Dogs (Canis lupus familiaris) Affected with Hypoadrenocorticism (Addison's Disease).

    PubMed

    Boag, Alisdair M; Christie, Michael R; McLaughlin, Kerry A; Syme, Harriet M; Graham, Peter; Catchpole, Brian

    2015-01-01

    Canine hypoadrenocorticism likely arises from immune-mediated destruction of adrenocortical tissue, leading to glucocorticoid and mineralocorticoid deficiency. In humans with autoimmune Addison's disease (AAD) or autoimmune polyendocrine syndrome (APS), circulating autoantibodies have been demonstrated against enzymes associated with adrenal steroid synthesis. The current study investigates autoantibodies against steroid synthesis enzymes in dogs with spontaneous hypoadrenocorticism. Coding regions of canine CYP21A2 (21-hydroxylase; 21-OH), CYP17A1 (17-hydroxylase; 17-OH), CYP11A1 (P450 side-chain cleavage enzyme; P450scc) and HSD3B2 (3β hydroxysteroid dehydrogenase; 3βHSD) were amplified, cloned and expressed as 35S-methionine radiolabelled recombinant protein. In a pilot study, serum samples from 20 dogs with hypoadrenocorticism and four unaffected control dogs were screened by radio-immunoprecipitation assay. There was no evidence of reactivity against 21-OH, 17-OH or 3βHSD, but five dogs with hypoadrenocorticism showed immunoreactivity to P450scc compared with controls. Serum samples were subsequently obtained from 213 dogs diagnosed with hypoadrenocorticism and 110 dogs from a hospital control population. Thirty control dogs were randomly selected to establish a threshold for antibody positivity (mean + 3 × standard deviation). Dogs with hypoadrenocorticism were more likely to be P450scc autoantibody positive than hospital controls (24% vs. 1.2%, respectively; p = 0.0016). Sex was significantly associated with the presence of P450scc autoantibodies in the case population, with 30% of females testing positive compared with 17% of males (p = 0.037). Significant associations with breed (p = 0.015) and DLA-type (DQA1*006:01 allele; p = 0.017) were also found. This cross-sectional study indicates that P450scc autoantibodies are present in a proportion of dogs affected with hypoadrenocorticism. PMID:26618927

  9. Side-chain interactions in the regulatory domain of human glutamate dehydrogenase determine basal activity and regulation.

    PubMed

    Mastorodemos, Vasileios; Kanavouras, Konstantinos; Sundaram, Shobana; Providaki, Maria; Petraki, Zoe; Kokkinidis, Michael; Zaganas, Ioannis; Logothetis, Diomedes E; Plaitakis, Andreas

    2015-04-01

    Glutamate Dehydrogenase (GDH) is central to the metabolism of glutamate, a major excitatory transmitter in mammalian central nervous system (CNS). hGDH1 is activated by ADP and L-leucine and powerfully inhibited by GTP. Besides this housekeeping hGDH1, duplication led to an hGDH2 isoform that is expressed in the human brain dissociating its function from GTP control. The novel enzyme has reduced basal activity (4-6% of capacity) while remaining remarkably responsive to ADP/L-leucine activation. While the molecular basis of this evolutionary adaptation remains unclear, substitution of Ser for Arg443 in hGDH1 is shown to diminish basal activity (< 2% of capacity) and abrogate L-leucine activation. To explore whether the Arg443Ser mutation disrupts hydrogen bonding between Arg443 and Ser409 of adjacent monomers in the regulatory domain ('antenna'), we replaced Ser409 by Arg or Asp in hGDH1. The Ser409Arg-1 change essentially replicated the Arg443Ser-1 mutation effects. Molecular dynamics simulation predicted that Ser409 and Arg443 of neighboring monomers come in close proximity in the open conformation and that introduction of Ser443-1 or Arg409-1 causes them to separate with the swap mutation (Arg409/Ser443) reinstating their proximity. A swapped Ser409Arg/Arg443Ser-1 mutant protein, obtained in recombinant form, regained most of the wild-type hGDH1 properties. Also, when Ser443 was replaced by Arg443 in hGDH2 (as occurs in hGDH1), the Ser443Arg-2 mutant acquired most of the hGDH1 properties. Hence, side-chain interactions between 409 and 443 positions in the 'antenna' region of hGDHs are crucial for basal catalytic activity, allosteric regulation, and relative resistance to thermal inactivation. PMID:25620628

  10. Nuclear Magnetic Resonance Observation of α-Synuclein Membrane Interaction by Monitoring the Acetylation Reactivity of Its Lysine Side Chains.

    PubMed

    Lee, Jung Ho; Ying, Jinfa; Bax, Ad

    2016-09-01

    The interaction between α-synuclein (αS) protein and lipid membranes is key to its role in synaptic vesicle homeostasis and plays a role in initiating fibril formation, which is implicated in Parkinson's disease. The natural state of αS inside the cell is generally believed to be intrinsically disordered, but chemical cross-linking experiments provided evidence of a tetrameric arrangement, which was reported to be rich in α-helical secondary structure based on circular dichroism (CD). Cross-linking relies on chemical modification of the protein's Lys C(ε) amino groups, commonly by glutaraldehyde, or by disuccinimidyl glutarate (DSG), with the latter agent preferred for cellular assays. We used ultra-high-resolution homonuclear decoupled nuclear magnetic resonance experiments to probe the reactivity of the 15 αS Lys residues toward N-succinimidyl acetate, effectively half the DSG cross-linker, which results in acetylation of Lys. The intensities of both side chain and backbone amide signals of acetylated Lys residues provide direct information about the reactivity, showing a difference of a factor of 2.5 between the most reactive (K6) and the least reactive (K102) residue. The presence of phospholipid vesicles decreases reactivity of most Lys residues by up to an order of magnitude at high lipid:protein stoichiometries (500:1), but only weakly at low ratios. The decrease in Lys reactivity is found to be impacted by lipid composition, even for vesicles that yield similar αS CD signatures. Our data provide new insight into the αS-bilayer interaction, including the pivotal state in which the available lipid surface is limited. Protection of Lys C(ε) amino groups by αS-bilayer interaction will strongly impact quantitative interpretation of DSG cross-linking experiments.

  11. Vanadium(V) complex with Schiff-base ligand containing a flexible amino side chain: Synthesis, structure and reactivity.

    PubMed

    Nica, Simona; Rudolph, Manfred; Lippold, Ines; Buchholz, Axel; Görls, Helmar; Plass, Winfried

    2015-06-01

    The Schiff-base ligand (H2salhyhNH3)Cl (1) derived from salicylaldehyde and 6-aminohexanoic acid hydrazide hydrochloride reacts with ammonium metavanadate in methanol solution to yield the dioxidovanadium(V) complex [VO2(salhyhNH3)] (2). The utilized hydrazone ligand contains a flexible and protonated amino side chain. Crystallization from methanol affords complex 2 in the monoclinic space group P21/n, whereas crystallization from a methanol/water mixture 1:1 yields crystals, containing a water molecule of crystallization per two formula units (2⋅1/2H2O), in the orthorhombic space group Pbcn. In both cases the protonated amino group compensates the negative charge on the dioxidovanadium moiety and is involved in an extensive hydrogen bonding network particularly including the oxido groups from neighboring vanadium complexes. The reactivity of complex 2 toward protonation in aqueous solution has been investigated by spectrophotometric titrations and is characterized by two subsequent protonation steps at the hydrazide nitrogen atom of the ligand system and an oxido group leading to the formation of an oxidohydroxidovanadium(V) species with corresponding pKa values of 3.2 and 2.9, respectively. With larger excess of acid the oxidohydroxidovanadium(V) species starts to form the corresponding anhydride. The formation of the anhydride is strongly favored in the presence of methanol. The reaction of complex 2 with hydrogen peroxide in methanol solution leads to the formation of an oxidoperoxidovanadium(V) species, whereas in aqueous solution the addition of one equivalent of acid is required. Complex 2 catalyzes the oxidation of methylphenylsulfane to the corresponding sulfoxide in methanol/dichloromethane mixture using hydrogen peroxide as oxidant at room temperature.

  12. Inter-helical interactions in membrane proteins: analysis based on the local backbone geometry and the side chain interactions.

    PubMed

    Jha, Anupam Nath; Vishveshwara, Saraswathi

    2009-06-01

    The availability of a significant number of the structures of helical membrane proteins has prompted us to investigate the mode of helix-helix packing. In the present study, we have considered a dataset of alpha-helical membrane proteins representing structures solved from all the known superfamilies. We have described the geometry of all the helical residues in terms of local coordinate axis at the backbone level. Significant inter-helical interactions have been considered as contacts by weighing the number of atom-atom contacts, including all the side-chain atoms. Such a definition of local axis and the contact criterion has allowed us to investigate the inter-helical interaction in a systematic and quantitative manner. We show that a single parameter (designated as alpha), which is derived from the parameters representing the mutual orientation of local axes, is able to accurately capture the details of helix-helix interaction. The analysis has been carried out by dividing the dataset into parallel, anti-parallel, and perpendicular orientation of helices. The study indicates that a specific range of alpha value is preferred for interactions among the anti-parallel helices. Such a preference is also seen among interacting residues of parallel helices, however to a lesser extent. No such preference is seen in the case of perpendicular helices, the contacts that arise mainly due to the interaction of surface helices with the end of the trans-membrane helices. The study supports the prevailing view that the anti-parallel helices are well packed. However, the interactions between helices of parallel orientation are non-trivial. The packing in alpha-helical membrane proteins, which is systematically and rigorously investigated in this study, may prove to be useful in modeling of helical membrane proteins.

  13. Nucleic Acid Ligands With Protein-like Side Chains: Modified Aptamers and Their Use as Diagnostic and Therapeutic Agents

    PubMed Central

    Rohloff, John C; Gelinas, Amy D; Jarvis, Thale C; Ochsner, Urs A; Schneider, Daniel J; Gold, Larry; Janjic, Nebojsa

    2014-01-01

    Limited chemical diversity of nucleic acid libraries has long been suspected to be a major constraining factor in the overall success of SELEX (Systematic Evolution of Ligands by EXponential enrichment). Despite this constraint, SELEX has enjoyed considerable success over the past quarter of a century as a result of the enormous size of starting libraries and conformational richness of nucleic acids. With judicious introduction of functional groups absent in natural nucleic acids, the “diversity gap” between nucleic acid–based ligands and protein-based ligands can be substantially bridged, to generate a new class of ligands that represent the best of both worlds. We have explored the effect of various functional groups at the 5-position of uracil and found that hydrophobic aromatic side chains have the most profound influence on the success rate of SELEX and allow the identification of ligands with very low dissociation rate constants (named Slow Off-rate Modified Aptamers or SOMAmers). Such modified nucleotides create unique intramolecular motifs and make direct contacts with proteins. Importantly, SOMAmers engage their protein targets with surfaces that have significantly more hydrophobic character compared with conventional aptamers, thereby increasing the range of epitopes that are available for binding. These improvements have enabled us to build a collection of SOMAmers to over 3,000 human proteins encompassing major families such as growth factors, cytokines, enzymes, hormones, and receptors, with additional SOMAmers aimed at pathogen and rodent proteins. Such a large and growing collection of exquisite affinity reagents expands the scope of possible applications in diagnostics and therapeutics. PMID:25291143

  14. Effects of hydrophobic helix length and side chain chemistry on biomimicry in peptoid analogues of SP-C.

    PubMed

    Brown, Nathan J; Wu, Cindy W; Seurynck-Servoss, Shannon L; Barron, Annelise E

    2008-02-12

    The hydrophobic proteins of lung surfactant (LS), SP-B and SP-C, are critical constituents of an effective surfactant replacement therapy for the treatment of respiratory distress syndrome. Because of concerns and difficulties associated with animal-derived surfactants, recent investigations have focused on the creation of synthetic analogues of the LS proteins. However, creating an accurate mimic of SP-C that retains its biophysical surface activity is extraordinarily challenging given the lipopeptide's extreme hydrophobicity and propensity to misfold and aggregate. One successful approach that overcomes these difficulties is the use of poly-N-substituted glycines, or peptoids, to mimic SP-C. To develop a non-natural, bioactive mimic of SP-C and to investigate the effects of side chain chemistry and length of the helical hydrophobic region, we synthesized, purified, and performed in vitro testing of two classes of peptoid SP-C mimics: those having a rigid alpha-chiral aromatic helix and those having a biomimetic alpha-chiral aliphatic helix. The length of the two classes of mimics was also systematically altered. Circular dichroism spectroscopy gave evidence that all of the peptoid-based mimics studied here emulated SP-C's secondary structure, forming stable helical structures in solution. Langmuir-Wilhelmy surface balance, fluorescence microscopy, and pulsating bubble surfactometry experiments provide evidence that the aromatic-based SP-C peptoid mimics, in conjunction with a synthetic lipid mixture, have superior surface activity and biomimetic film morphology in comparison to the aliphatic-based mimics and that there is an increase in surface activity corresponding to increasing helical length.

  15. Sequence-specific, nanomolar peptide binding via cucurbit[8]uril-induced folding and inclusion of neighboring side chains.

    PubMed

    Smith, Lauren C; Leach, David G; Blaylock, Brittney E; Ali, Omar A; Urbach, Adam R

    2015-03-18

    This paper describes the molecular recognition of the tripeptide Tyr-Leu-Ala by the synthetic receptor cucurbit[8]uril (Q8) in aqueous buffer with nanomolar affinity and exceptional specificity. This combination of characteristics, which also applies to antibodies, is desirable for applications in biochemistry and biotechnology but has eluded supramolecular chemists for decades. Building on prior knowledge that Q8 binds to peptides with N-terminal aromatic residues, a library screen of 105 peptides was designed to test the effects of residues adjacent to N-terminal Trp, Phe, or Tyr. The screen used tetramethylbenzobis(imidazolium) (MBBI) as a fluorescent indicator and resulted in the unexpected discovery that MBBI can serve not only as a turn-off sensor via the simultaneous inclusion of a Trp residue but also as a turn-on sensor via the competitive displacement of MBBI upon binding of Phe- or Tyr-terminated peptides. The unusual fluorescence response of the Tyr series prompted further investigation by (1)H NMR spectroscopy, electrospray ionization mass spectrometry, and isothermal titration calorimetry. From these studies, a novel binding motif was discovered in which only 1 equiv of peptide binds to Q8, and the side chains of both the N-terminal Tyr residue and its immediate neighbor bind within the Q8 cavity. For the peptide Tyr-Leu-Ala, the equilibrium dissociation constant value is 7.2 nM, whereas that of its sequence isomer Tyr-Ala-Leu is 34 μM. The high stability, recyclability, and low cost of Q8 combined with the straightforward incorporation of Tyr-Leu-Ala into recombinant proteins should make this system attractive for the development of biological applications.

  16. Functional modeling identifies paralogous solanesyl-diphosphate synthases that assemble the side chain of plastoquinone-9 in plastids.

    PubMed

    Block, Anna; Fristedt, Rikard; Rogers, Sara; Kumar, Jyothi; Barnes, Brian; Barnes, Joshua; Elowsky, Christian G; Wamboldt, Yashitola; Mackenzie, Sally A; Redding, Kevin; Merchant, Sabeeha S; Basset, Gilles J

    2013-09-20

    It is a little known fact that plastoquinone-9, a vital redox cofactor of photosynthesis, doubles as a precursor for the biosynthesis of a vitamin E analog called plastochromanol-8, the physiological significance of which has remained elusive. Gene network reconstruction, GFP fusion experiments, and targeted metabolite profiling of insertion mutants indicated that Arabidopsis possesses two paralogous solanesyl-diphosphate synthases, AtSPS1 (At1g78510) and AtSPS2 (At1g17050), that assemble the side chain of plastoquinone-9 in plastids. Similar paralogous pairs were detected throughout terrestrial plant lineages but were not distinguished in the literature and genomic databases from mitochondrial homologs involved in the biosynthesis of ubiquinone. The leaves of the atsps2 knock-out were devoid of plastochromanol-8 and displayed severe losses of both non-photoactive and photoactive plastoquinone-9, resulting in near complete photoinhibition at high light intensity. Such a photoinhibition was paralleled by significant damage to photosystem II but not to photosystem I. In contrast, in the atsps1 knock-out, a small loss of plastoquinone-9, restricted to the non-photoactive pool, was sufficient to eliminate half of the plastochromanol-8 content of the leaves. Taken together, these results demonstrate that plastochromanol-8 originates from a subfraction of the non-photoactive pool of plastoquinone-9. In contrast to other plastochromanol-8 biosynthetic mutants, neither the single atsps knock-outs nor the atsps1 atsps2 double knock-out displayed any defects in tocopherols accumulation or germination.

  17. Potentiometric and spectroscopic study of the complexation of copper(II) ions by tripeptides containing aromatic side-chains

    NASA Astrophysics Data System (ADS)

    Ghalem, S.; Fan, B.-T.; Xiao, L.

    1998-01-01

    The complexation of copper(II) ions with L,L-Gly-Phe-Phe, L,L-Phe-Gly-Phe and L,L-Phe-Phe-Gly was studied by potentiometric and spectroscopic measurements. Only four complexes have been found for each copper(II)-tripeptide system, and no species with two ligand molecules was observed. The results show influences of aromatic side-chains. These influences are dependent upon the location of two aromatic rings in studied tripeptides. The stabilization or destabilization of a given complex is probably the result of several different effects, including steric hindrance, hydrophobic effect, electrodonor effect and π-d interaction. The spectroscopic measurements, e.s.r and electronic absorption, are useful to determine the complex structures. La complexation du cuivre(II) par Gly-Phe-Phe-L,L, Phe-Gly-Phe-L,L et Phe-Phe-Gly-L,L a été étudiée par potentiométrie et par spectroscopies. Seulement quatre espèces ont été mises en évidence pour chaque système Cu(II)-tripeptide. Aucun complexe contenant deux molécules de ligand n'a été observé. Les résultats obtenus montrent des influences évidentes liées aux chaînes latérales aromatiques. Ces influences dépendent des positions des résidus phénylalanines. La stabilisation ou déstabilisation d'un complexe est probablement le résultat d'un ensemble de différents effets : effet stérique, effet hydrophobe, électrodonneur et l'interaction π-d. Les spectroscopies RPE et visible ont été utilisées pour la détermination structurale des complexes.

  18. Interrelationships between glutamine and citrulline metabolism

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This article analyzes the contribution of glutamine to the synthesis of citrulline and reviews the evidence that glutamine supplementation increases citrulline production. Glutamine supplementation has been proposed in the treatment of critically ill patients; however, a recent large multicenter ran...

  19. Poly(quinoxaline-2,3-diyl)s bearing (S)-3-octyloxymethyl side chains as an efficient amplifier of alkane solvent effect leading to switch of main-chain helical chirality.

    PubMed

    Nagata, Yuuya; Nishikawa, Tsuyoshi; Suginome, Michinori

    2014-11-12

    Poly(quinoxaline-2,3-diyl) containing (S)-3-octyloxymethyl side chains was synthesized to investigate the induction of a single-handed helical sense to the main chain in various alkane solvents. The polymer showed an efficient solvent dependent helix inversion between n-octane (M-helix) and cyclooctane (P-helix). After a screening of alkane solvents, it was found that linear alkanes having large molecular aspect ratios induced M-helical structure, and branched or cyclic alkanes having small molecular aspect ratios induced P-helical structure. A polymer ligand containing (S)-3-octyloxymethyl side chains and diphenylphosphino pendants also exhibited solvent-dependent helical inversion between n-octane and cyclooctane, leading to the highly enantioselective production of the both enantiomeric product in a palladium-catalyzed asymmetric hydrosilylation reaction of styrene (R-product 94% ee in n-octane and S-product 90% ee in cyclooctane). PMID:25343492

  20. Active site-directed inhibitors of cytochrome P-450scc. Structural and mechanistic implications of a side chain-substituted series of amino-steroids.

    PubMed

    Sheets, J J; Vickery, L E

    1983-10-10

    A series of analogues of cholesterol, each having a shortened side chain and a primary amine group, were prepared and tested for their effects on bovine adrenocortical cholesterol side chain cleavage cytochrome P-450 (P-450scc). A previous study had shown that one derivative, 22-amino-23,24-bisnor-5-cholen-3 beta-ol, is a potent competitive inhibitor of the enzyme and forms a complex in which the steroid ring binds to the cholesterol site and the side chain amine forms a bond with the heme iron (Sheets, J. J., and Vickery, L. E. (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 5773-5777). In the studies reported here, the 23-amine derivative, 23-amino-24-nor-5-cholen-3 beta-ol, was found to be an equally potent inhibitor and to be competitive with respect to cholesterol (Ki = 38 nM). Binding of the 23-amine to P-450scc also caused formation of a low spin complex with an absorption maximum at 422 nm, indicative of a nitrogen-donor ligand. Other derivatives in which the side chain amine was linked closer to the steroid, 17 beta-amino-5-androsten-3 beta-ol and (20 R + S)-20-amino-5-pregnen-3 beta-ol, were found to be only very weak inhibitors (I50 greater than 100 microM) and did not produce the 422 nm spectral form when bound. Derivatives in which the amine was attached a greater distance from the steroid ring, 24-amino-5-cholen-3 beta-ol and 25-amino-26,27-bisnor-5-cholesten-3 beta-ol, caused a progressive decrease in inhibitory potency and a failure to produce the 422 nm form on binding. The dependence of the type of interaction of these amino-steroids with P-450scc upon the amine position establishes that the steroid binding site and the heme catalytic site of the enzyme are fixed within a specific distance of one another. The heme appears to be located sufficiently close to the position that the side chain of cholesterol would occupy to allow for direct attack of an iron-bound oxidant to occur during hydroxylation and side chain cleavage.

  1. Side-chain Engineering of Benzo[1,2-b:4,5-b’]dithiophene Core-structured Small Molecules for High-Performance Organic Solar Cells

    PubMed Central

    Yin, Xinxing; An, Qiaoshi; Yu, Jiangsheng; Guo, Fengning; Geng, Yongliang; Bian, Linyi; Xu, Zhongsheng; Zhou, Baojing; Xie, Linghai; Zhang, Fujun; Tang, Weihua

    2016-01-01

    Three novel small molecules have been developed by side-chain engineering on benzo[1,2-b:4,5-b’]dithiophene (BDT) core. The typical acceptor-donor-acceptor (A-D-A) structure is adopted with 4,8-functionalized BDT moieties as core, dioctylterthiophene as π bridge and 3-ethylrhodanine as electron-withdrawing end group. Side-chain engineering on BDT core exhibits small but measurable effect on the optoelectronic properties of small molecules. Theoretical simulation and X-ray diffraction study reveal the subtle tuning of interchain distance between conjugated backbones has large effect on the charge transport and thus the photovoltaic performance of these molecules. Bulk-heterojunction solar cells fabricated with a configuration of ITO/PEDOT:PSS/SM:PC71BM/PFN/Al exhibit a highest power conversion efficiency (PCE) of 6.99% after solvent vapor annealing. PMID:27140224

  2. Highly efficient stabilisation of meta-ethynylpyridine polymers with amide side chains in water by coordination of rare-earth metals.

    PubMed

    Makida, Hiroki; Abe, Hajime; Inouye, Masahiko

    2015-02-14

    An amphiphilic meta-ethynylpyridine polymer with chiral amide side chains was developed. The polymer was prepared by sequential Sonogashira reactions, and the product was soluble in polar and apolar solvents. The additive effects of metal salts on the polymer were examined in water and aqueous EtOH on the basis of UV-vis and CD spectra. The enhancement of the positive Cotton effect and hypochromism around 360 nm occurred by the addition of various metal salts, indicating the coordination of the cations to the amide side chains of the polymer to stabilise the helical structure. Among them, rare-earth metal salts, especially Sc(OTf)3 showed more efficient additive effects probably because of its strong coordination ability even in water. Positive cooperativity was observed for the coordination of Sc(OTf)3 to the polymer in aqueous EtOH.

  3. Backbone and side-chain resonance assignment of the A147T polymorph of mouse TSPO in complex with a high-affinity radioligand.

    PubMed

    Jaremko, Mariusz; Jaremko, Łukasz; Giller, Karin; Becker, Stefan; Zweckstetter, Markus

    2016-04-01

    The integral polytopic membrane protein TSPO is the target for numerous endogenous and synthetic ligands. However, the affinity of many ligands is influenced by a common polymorphism in TSPO, in which an alanine at position 147 is replaced by threonine, thereby complicating the use of several radioligands for clinical diagnosis. In contrast, the best-characterized TSPO ligand (R)-PK11195 binds with similar affinity to both variants of mitochondrial TSPO (wild-type and A147T variant). Here we report the (1)H, (13)C, (15)N backbone and side-chain resonance assignment of the A147T polymorph of TSPO from Mus Musculus in complex with (R)-PK11195 in DPC detergent micelles. More than 90 % of all resonances were sequence-specifically assigned, demonstrating the ability to obtain high-quality spectral data for both the backbone and the side-chains of medically relevant integral membrane proteins.

  4. Low half-wave voltage Y-branch electro-optic polymer modulator based on side-chain polyurethane-imide

    NASA Astrophysics Data System (ADS)

    Tang, Jie; Wang, Long-De; Li, Ruo-Zhou; Zhang, Qiang; Zhang, Tong

    2016-06-01

    A Y-branch electro-optic (EO) polymer modulator has been designed and fabricated. High performance side-chain polyurethane-imide (PUI) with a high EO coefficient of larger than 50 pm/V and a moderate glass-transition temperature (Tg) of 206∘C is used as EO polymer core layer of the modulator. The fabricated phase modulator exhibits a low half-wave voltage of 1.94 V at 1550 nm in single arm modulation with 1 cm EO interaction length and 2 cm total length. The results show that the modulator fabricated by side-chain PUI EO materials possesses potential applications in low driving voltage and low cost optical systems.

  5. Effects of Side-Chain and Electron Exchange Correlation on the Band Structure of Perylene Diimide Liquid Crystals: A Density Functional Study

    SciTech Connect

    Arantes, J. T.; Lima, M. P.; Fazzio, A.; Xiang, H.; Wei, S. H.; Dalpian, G. M.

    2009-04-01

    The structural and electronic properties of perylene diimide liquid crystal PPEEB are studied using ab initio methods based on the density functional theory (DFT). Using available experimental crystallographic data as a guide, we propose a detailed structural model for the packing of solid PPEEB. We find that due to the localized nature of the band edge wave function, theoretical approaches beyond the standard method, such as hybrid functional (PBE0), are required to correctly characterize the band structure of this material. Moreover, unlike previous assumptions, we observe the formation of hydrogen bonds between the side chains of different molecules, which leads to a dispersion of the energy levels. This result indicates that the side chains of the molecular crystal not only are responsible for its structural conformation but also can be used for tuning the electronic and optical properties of these materials.

  6. Side-chain Engineering of Benzo[1,2-b:4,5-b’]dithiophene Core-structured Small Molecules for High-Performance Organic Solar Cells

    NASA Astrophysics Data System (ADS)

    Yin, Xinxing; An, Qiaoshi; Yu, Jiangsheng; Guo, Fengning; Geng, Yongliang; Bian, Linyi; Xu, Zhongsheng; Zhou, Baojing; Xie, Linghai; Zhang, Fujun; Tang, Weihua

    2016-05-01

    Three novel small molecules have been developed by side-chain engineering on benzo[1,2-b:4,5-b’]dithiophene (BDT) core. The typical acceptor-donor-acceptor (A-D-A) structure is adopted with 4,8-functionalized BDT moieties as core, dioctylterthiophene as π bridge and 3-ethylrhodanine as electron-withdrawing end group. Side-chain engineering on BDT core exhibits small but measurable effect on the optoelectronic properties of small molecules. Theoretical simulation and X-ray diffraction study reveal the subtle tuning of interchain distance between conjugated backbones has large effect on the charge transport and thus the photovoltaic performance of these molecules. Bulk-heterojunction solar cells fabricated with a configuration of ITO/PEDOT:PSS/SM:PC71BM/PFN/Al exhibit a highest power conversion efficiency (PCE) of 6.99% after solvent vapor annealing.

  7. A Polyurethane Surface Modifier: Contrasting Amphiphilic and Contraphilic Surfaces Driven by block and random Soft Blocks having Trifluoroethoxymethyl and PEG Side Chains

    PubMed Central

    Zhang, Wei; Fujiwara, Tomoko; Taşkent, Hűmeyra; Zheng, Ying; Brunson, Kennard; Gamble, Lara; Wynne, Kenneth J.

    2013-01-01

    A conventional MDI-BD-PTMO polyurethane was modified using 2 wt.% polyurethanes (U) having copolyoxetane soft blocks with hydrophobic 3F, CF3CH2OCH2- and hydrophilic MEn, CH3O(CH2CH2O)nCH2-, n = 3, 7) side chains. In contrast to neat 3F-co-MEn-U, 2 wt.% 3F-co-MEn-U compositions have physically stable morphologies and wetting behavior. Surface composition (XPS) and amphiphilic or contraphilic wetting are controlled by the 3F-co-MEn polyoxetane soft block architecture and MEn side chain length. Importantly, θrec can be tuned for 2 wt.% 3F-co-MEn-U compositions independent of swelling, which is controlled by the bulk polyurethane. AFM imaging led to a new morphological model whereby fluorous/PEG-hard block nano-aggregates combine to form near surface features culminating in micron scale texturing. PMID:24204100

  8. Hexakis(m-phenylene ethynylene) Macrocycles with Multiple H-Bonding Side Chains and Modified Cavities: Altered Stacking Strength and Persistent Tubular Assembly.

    PubMed

    Zhong, Yulong; Wang, Qiuhua; Yang, Yi; Lu, Zhonglin; He, Lan; Gong, Bing

    2016-05-01

    Hexakis(m-phenylene ethynylene) macrocycles 1 bearing multiple hydrogen-bonding side chains and containing inner cavities modified with different functional groups are synthesized based on Pd-catalyzed (Sonogashira) coupling of monomeric building blocks to trimeric precursors that are recombined and coupled to give macrocycles with different substitution patterns of inward-pointing groups. Examining four representative macrocycles indicates that they all undergo the same helical tubular assembly previously observed for macrocycle 1a but with different stacking strengths.

  9. Pyroacm Resin: An Acetamidomethyl Derived Resin for Solid Phase Synthesis of Peptides through Side Chain Anchoring of C-Terminal Cysteine Residues.

    PubMed

    Juvekar, Vinayak; Gong, Young Dae

    2016-02-19

    The design, synthesis and utilization of an efficient acetamidomethyl derived resin for the peptide synthesis is presented using established Fmoc and Boc protocols via side chain anchoring. Cleavage of the target peptide from the resin is performed using carboxymethylsulfenyl chloride under mild conditions which gave in situ thiol-sulfenyl protection of the cysteine residues. The utility of the resin is successfully demonstrated through applications to the syntheses of model peptides and natural products Riparin 1.1 and Riparin 1.2.

  10. Application of palladium-catalyzed carboxyl anhydride-boronic acid cross coupling in the synthesis of novel bile acids analogs with modified side chains.

    PubMed

    Mayorquín-Torres, Martha C; Flores-Álamo, Marcos; Iglesias-Arteaga, Martin A

    2015-09-01

    Palladium-catalyzed cross coupling of 4-methoxycarbonyl phenyboronic acid with acetylated bile acids in which the carboxyl functions was activated by formation of a mixed anhydride with pivalic anhydride afforded the cross coupled compounds, which were converted in novel side chain modified bile acids by one pot carbonyl reduction/removal of the protecting acetyl groups by Wolff-Kishner reduction. Unambiguous assignments of the NMR signals and crystal characterization of the heretofore unknown compounds are provided.

  11. Bismuth(III) triflate-catalyzed direct conversion of corticosteroids into highly functionalized 17-ketosteroids by cleavage of the C17-dihydroxyacetone side chain.

    PubMed

    Pinto, Rui M A; Salvador, Jorge A R; Le Roux, Christophe; Paixão, José A

    2009-11-01

    The use of bismuth(III) triflate as catalyst for the direct conversion of corticosteroids into highly functionalized 17-ketosteroids by cleavage of the C17-dihydroxyacetone side chain is reported. This catalytic process is very chemoselective, since functionalities of the starting corticosteroids, such as Delta(4)-3-keto, Delta(1,4)-3-keto, 11beta-hydroxyl, and 9beta,11beta-epoxide, remained intact. PMID:19799442

  12. Formation of a Three-Electron Sulfur-Sulfur Bond as a Probe for Interaction between Side Chains of Methionine Residues.

    PubMed

    Filipiak, Piotr; Bobrowski, Krzysztof; Hug, Gordon L; Pogocki, Dariusz; Schöneich, Christian; Marciniak, Bronislaw

    2016-09-15

    The mechanism of oxidation processes of l-Met-(Pro)n-l-Met peptides that contain two Met residues located on the N- and C-terminal and separated by a defined number (n = 0-4) of proline residues was investigated in aqueous solutions using pulse radiolysis. The use of such peptides allowed for distance control between the sulfur atoms located in the side chains of the Met residues. The formation of a contact between the side chains of the Met residues was probed by the observation of transients with σ*-type 2c-3e S∴S and S∴O bonds as well as of α-(alkylthio)alkyl radicals (αS). This approach enabled the monitoring, in real time, of the efficiency and kinetics of interactions between methionine side chains. Such knowledge is important, inter alia, for long-distance electron transfer processes because methionine side chains can serve as relay stations and also for many aspects of protein folding when the formation of a contact between two amino acid residues in an unfolded polypeptide chain plays a central role in protein-folding mechanisms. The yields of these transients (measured as G-values) were found to be dependent on the number of Pro residues; however, they were not dependent in a simple way on the average distance ⟨rS-S⟩ between the sulfur atoms in Met residues. A decrease in the yield of the (S∴S)(+) species with an increase in the number of Pro residues in the bridge occurred at the expense of an increase in the yields of the intramolecular three-electron-bonded (S∴O)(+) radical cations and αS radicals. A detailed understanding of these trends in the chemical yields was developed by modeling the underlying chemical kinetics with Langevin dynamical simulations of the various oligoproline peptide chains and combining them with a simple statistical mechanical theory on the end-to-end contact rates for polymer chains. This analysis showed that the formation of a contact between terminal Met residues in the peptides with 0-2 Pro residues was

  13. Itraconazole Side Chain Analogues: Structure–Activity Relationship Studies for Inhibition of Endothelial Cell Proliferation, Vascular Endothelial Growth Factor Receptor 2 (VEGFR2) Glycosylation, and Hedgehog Signaling

    PubMed Central

    Shi, Wei; Nacev, Benjamin A.; Aftab, Blake T.; Head, Sarah; Rudin, Charles M.; Liu, Jun O.

    2012-01-01

    Itraconazole is an antifungal drug that was recently found to possess potent antiangiogenic activity and anti-hedgehog (Hh) pathway activity. To search for analogues of itraconazole with greater potency and to understand the structure–activity relationship in both antiangiogenic and Hh targeting activity, 25 itraconazole side chain analogues were synthesized and assayed for inhibition of endothelial cell proliferation and Gli1 transcription in a medulloblastoma (MB) culture. Through this analysis, we have identified analogues with increased potency for inhibiting endothelial cell proliferation and the Hh pathway, as well as VEGFR2 glycosylation that was recently found to be inhibited by itraconazole. An SAR analysis of these activities revealed that potent activity of the analogues against VEGFR2 glycosylation was generally driven by side chains of at least four carbons in composition with branching at the α or β position. SAR trends for targeting the Hh pathway were divergent from those related to HUVEC proliferation or VEGFR2 glycosylation. These results also suggest that modification of the sec-butyl side chain can lead to enhancement of the biological activity of itraconazole. PMID:21936514

  14. Effect of side-chain structure of rigid polyimide dispersant on mechanical properties of single-walled carbon nanotube/cyanate ester composite.

    PubMed

    Yuan, Wei; Li, Weifeng; Mu, Yuguang; Chan-Park, Mary B

    2011-05-01

    Three kinds of polymer, polyimide without side-chain (PI), polyimide-graft-glyceryl 4-nonylphenyl ether (PI-GNE), and polyimide-graft-bisphenol A diglyceryl acrylate (PI-BDA), have been synthesized and used to disperse single-walled carbon nanotubes (SWNTs) and to improve the interfacial bonding between SWNTs and cyanate ester (CE) matrix. Visual observation, UV-vis-near-IR (UV-vis-NIR) spectra, and atomic force microscopy (AFM) images show that both PI-GNE and PI-BDA are highly effective at dispersing and debundling SWNTs in DMF, whereas PI is less effective. Interaction between SWNTs and PI, PI-GNE or PI-BDA was confirmed by computer simulation and Raman spectra. A series of CE-based composite films reinforced with different loadings of SWNTs, SWNTs/PI, SWNTs/PI-GNE and SWNTs/PI-BDA were prepared by solution casting. It was found that, because of the unique side-chain structure of PI-BDA, SWNTs/PI-BDA disperse better in CE matrix than do SWNTs/PI-GNE, SWNTs/PI, and SWNTs. As a result, SWNTs/PI-BDA/CE composites have the greatest improvement in mechanical properties of the materials tested. These results imply that the choice of side-chain on a dispersant is very important to the dispersion of SWNTs in matrix and the filler/matrix interfacial adhesion, which are two key requirements for achieving effective reinforcement. PMID:21526794

  15. Exploration on natural product anibamine side chain modification toward development of novel CCR5 antagonists and potential anti-prostate cancer agents.

    PubMed

    Xu, Guoyan G; Zaidi, Saheem A; Zhang, Feng; Singh, Shilpa; Raborg, Thomas J; Yuan, Yunyun; Zhang, Yan

    2015-09-01

    Prostate cancer is one of the leading causes of death among males in the world. Prostate cancer cells have been shown to express upregulated chemokine receptor CCR5, a G protein-coupled receptor (GPCR) that relates to the inflammation process. Anibamine, a natural product containing a pyridine ring and two aliphatic side chains, was shown to carry a binding affinity of 1 μM at CCR5 as an antagonist with potential anti-cancer activity. However, it is not drug-like according to the Lipinski's rule of five mainly due to its two long aliphatic side chains. In our effort to improve its drug-like property, a series of anibamine derivatives were designed and synthesized by placement of aromatic side chains through an amide linkage to the pyridine ring. The newly synthesized compounds were tested for their CCR5 affinity and antagonism, and potential anti-proliferation activity against prostate cancer cell lines. Basal cytotoxicity was finally studied for compounds showing potent anti-proliferation activity. It was found that compounds with hydrophobic substitutions on the aromatic systems seemed to carry more promising CCR5 binding and prostate cancer cell proliferation inhibition activities.

  16. Odd-even effect of repeating aminoethylene units in the side chain of N-substituted polyaspartamides on gene transfection profiles.

    PubMed

    Uchida, Hirokuni; Miyata, Kanjiro; Oba, Makoto; Ishii, Takehiko; Suma, Tomoya; Itaka, Keiji; Nishiyama, Nobuhiro; Kataoka, Kazunori

    2011-10-01

    A series of the N-substituted polyaspartamides possessing repeating aminoethylene units in the side chain was prepared in this study to identify polyplexes with effective endosomal escape and low cytotoxicity. All cationic N-substituted polyaspartamides showed appreciably lower cytotoxicity than that of commercial transfection reagents. Interestingly, a distinctive odd-even effect of the repeating aminoethylene units in the polymer side chain on the efficiencies of endosomal escape and transfection to several cell lines was observed. The polyplexes from the polymers with an even number of repeating aminoethylene units (PA-Es) achieved an order of magnitude higher transfection efficiency, without marked cytotoxicity, than those of the polymers with an odd number of repeating aminoethylene units (PA-Os). This odd-even effect agreed well with the buffering capacity of these polymers as well as their capability to disrupt membrane integrity selectively at endosomal pH, leading to highly effective endosomal escape of the PA-E polyplexes. Furthermore, the formation of a polyvalent charged array with precise spacing between protonated amino groups in the polymer side chain was shown to be essential for effective disruption of the endosomal membrane, thus facilitating transport of the polyplex into the cytoplasm. These data provide useful knowledge for designing polycations to construct safe and efficient nonviral gene carriers.

  17. Computational modeling of the side chain dihedral angle distributions of methionine using hard-sphere repulsive and short-range attractive interactions

    NASA Astrophysics Data System (ADS)

    Virrueta, Alejandro; O'Hern, Corey; Regan, Lynne

    Methionine (Met) is a versatile amino acid found frequently both in protein cores and at protein-protein interfaces. Thus, a complete description of the structure of Met is tantamount to a fundamental understanding of protein structure and design. In previous work, we showed that our hard-sphere dipeptide model is able to recapitulate the side chain dihedral angle distributions observed in high-resolution protein crystal structures for the 8 amino acids we have studied to date: Val, Thr, Ser, Leu, Ile, Cys, Tyr, and Phe. Using the same approach, we can predict the observed Met side chain dihedral angle distributions P (χ1) and P (χ2) , but not P (χ3) . In this manuscript, we investigate the possible origins of the discrepancy and identify the minimal additions to the hard-sphere dipeptide model necessary to quantitatively predict P (χ3) of Met. We find that applying a Lennard-Jones potential with weak attraction between hydrogen atoms is sufficient to achieve predictions that match the observed χ3 side chain dihedral angle probability distributions for Met, Nle, and Mse without negatively affecting our results for the 8 previously studied amino acids. A. V. is supported by an NSF Graduate Research Fellowship and a Ford Foundation Fellowship.

  18. The effects of side-chain-induced disorder on the emission spectra and quantum yields of oligothiophene nano-aggregates. A combined experimental and MD-TDDFT study

    DOE PAGES

    Hong, Jiyun; Jeon, SuKyung; Kim, Janice J.; Devi, Diane; Chacon-Madrid, Kelly; Lee, Wynee; Koo, Seung Moh; Wildeman, Jurjen; Sfeir, Matthew Y.; Peteanu, Linda A.; et al

    2014-07-24

    Oligomeric thiophenes are commonly-used components in organic electronics and solar cells. These molecules stack and/or aggregate readily under the processing conditions used to form thin films for these applications, significantly altering their optical and charge-transport properties. To determine how these effects depend on the substitution pattern of the thiophene main chains, nano-aggregates of three sexi-thiophene (6T) oligomers having different alkyl substitution patterns were formed using solvent poisoning techniques and studied using steady-state and time-resolved emission spectroscopy. The results indicate the substantial role played by the side-chain substituents in determining the emissive properties of these species. Both the measured spectral changesmore » and their dependence on substitution are well modeled by combined quantum chemistry and molecular dynamics simulations. The simulations connect the side-chain-induced disorder, which determines the favorable chain packing configurations within the aggregates, with their measured electronic spectra.« less

  19. Right on TARGET: glutamine metabolism in cancer

    PubMed Central

    Ratnikov, Boris; Jeon, Young Joo; Smith, Jeffrey W.; Ronai, Ze'ev A.

    2015-01-01

    Recent studies highlight the importance of glutamine metabolism in metabolic reprogramming, which underlies cancer cell addiction to glutamine. Examples for the dependence on glutamine metabolism are seen across different tumor types as during different phases of cancer development, progression and response to therapy. In this perspective, we assess the possibility of targeting glutamine metabolism as a therapeutic modality for cancer. PMID:26425657

  20. Defective peroxisomal cleavage of the C27-steroid side chain in the cerebro-hepato-renal syndrome of Zellweger.

    PubMed Central

    Kase, B F; Björkhem, I; Hågå, P; Pedersen, J I

    1985-01-01

    only slow incorporation of radioactivity into 24-OH-THCA and into the C29-dicarboxylic acid. From the specific activity decay curve of 14C in cholic acid obtained after intravenous injection of 14C-cholic acid, the pool size of cholic acid was calculated to be 24 mg/m2 and the daily production rate to 9 mg/m2 per d. This corresponds to a reduction of approximately 85 and 90%, respectively, when compared with normal infants. It is concluded that liver peroxisomes are essential in the normal conversion of THCA to cholic acid. In the Zellweger syndrome this conversion is defective and as a consequence the accumulated THCA is either excreted as such or transformed into other metabolites by hydroxylation or side chain elongation. The accumulation of THCA, as well as the similar rate of conversion of 5 beta-cholestane-3 alpha,7 alpha.12 alpha-triol and THCA into cholic acid, support the contention that the 26-hydroxylase pathway with intermediate formation of THCA is the most important pathway for formation of cholic acid in man. PMID:3973012

  1. Coordinate developmental expression of genes regulating sterol economy and cholesterol side-chain cleavage in the porcine ovary.

    PubMed

    LaVoie, H A; Benoit, A M; Garmey, J C; Dailey, R A; Wright, D J; Veldhuis, J D

    1997-08-01

    To investigate the coordinate developmental expression of low-density lipoprotein (LDL) receptor, 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase, sterol carrier protein 2 (SCP2), steroidogenic acute regulatory protein (StAR), and cytochrome P450 side-chain cleavage (P450scc) enzyme messages throughout the pig estrous cycle, RNase protection analysis was performed using homologous (partially cloned) porcine sequences. Total RNA was isolated from ovarian tissues from unstimulated prepubertal gilts and gilts stimulated with eCG (Day -3) and hCG (Day 0) to induce follicular growth and ovulation. Specific transcripts (relative to 18S rRNA) were quantified in immature ovaries, preovulatory follicles (> or = 5 mm), corpora lutea (CL), and corpora albicantia. As an index of steroidogenesis, tissue progesterone content (per microgram protein) was low in the unstimulated ovary and preovulatory follicles, and it began to increase 4 days post-hCG, peaked at 12 days, and returned to preovulatory concentrations by 20 days post-hCG. HMG-CoA reductase mRNA was expressed at low levels and did not change significantly throughout the estrous cycle. The amount of LDL receptor mRNA increased approximately 6-fold after eCG stimulation and was expressed at similar concentrations in both preovulatory follicles and functional CL. Expression of SCP2 mRNA did not differ among the four tissue types but tended to be highest in midcycle (Day 12) CL compared other stages of CL (p = 0.007). StAR mRNA expression was minimal in unstimulated ovaries, was higher in preovulatory follicles (p = 0.014), and then rose again in CL (p = 0.009 compared with unstimulated ovary). P450scc mRNA concentrations were low in unstimulated ovaries, increased in preovulatory follicles (p = 0.044), and increased further in CL (p = 0.001 compared with preovulatory follicles). P450scc and StAR mRNA levels correlated with progesterone levels (r = +0.37, p = 0.025, and r = +0.71, p < 0.001, respectively). The

  2. Exogenous glutamine: the clinical evidence.

    PubMed

    Bongers, Thomas; Griffiths, Richard D; McArdle, Anne

    2007-09-01

    We know that critically ill patients suffering from undernutrition with a limited nutritional reserve have a poorer outcome. Furthermore, having a low body mass index has been shown to be an independent predictor of excess mortality in multiple organ failure. Therefore, nutritional support has gained increasing interest in critical illness with the hope of preventing or attenuating the effects of malnutrition. A negative nitrogen balance is the characteristic metabolic feature in critical illness, with the major protein loss derived from skeletal muscle. In particular, glutamine concentrations are rapidly reduced in plasma and muscle. Over the last 20 yrs or so, increasing evidence is emerging to support the use of glutamine supplementation in critical illness. Clinical trials have found a mortality and morbidity advantage with glutamine supplementation. The advantage appears to be greater the more glutamine is given and greater again when given parenterally. Various modes of action have been postulated. Glutamine seems to have an effect on the immune system, antioxidant status, glucose metabolism, and heat shock protein response. However, the benefit of exogenous glutamine on morbidity and mortality is not universally accepted. This review critically appraises the current clinical evidence regarding glutamine supplementation in critical illness.

  3. Intra-residue interactions in proteins: interplay between serine or cysteine side chains and backbone conformations, revealed by laser spectroscopy of isolated model peptides.

    PubMed

    Alauddin, Mohammad; Biswal, Himansu S; Gloaguen, Eric; Mons, Michel

    2015-01-21

    Intra-residue interactions play an important role in proteins by influencing local folding of the backbone. Taking advantage of the capability of gas phase experiments to provide relevant information on the intrinsic H-bonding pattern of isolated peptide chains, the intra-residue interactions of serine and cysteine residues, i.e., OH/SH···OC(i) C6 and NH(i···)O/S C5 interactions in Ser/Cys residues, are probed by laser spectroscopy of isolated peptides. The strength of these local side chain-main chain interactions, elegantly documented from their IR spectral features for well-defined conformations of the main chain, demonstrates that a subtle competition exists between the two types of intra-residue bond: the C6 H-bond is the major interaction with Ser, in contrast to Cys where C5 interaction takes over. The restricted number of conformers observed in the gas phase experiment with Ser compared to Cys (where both extended and folded forms are observed) also suggests a significant mediation role of these intra-residue interactions on the competition between the several main chain folding patterns. PMID:25482851

  4. Imidazolium-Functionalized Poly(arylene ether sulfone) Anion-Exchange Membranes Densely Grafted with Flexible Side Chains for Fuel Cells.

    PubMed

    Guo, Dong; Lai, Ao Nan; Lin, Chen Xiao; Zhang, Qiu Gen; Zhu, Ai Mei; Liu, Qing Lin

    2016-09-28

    With the intention of optimizing the performance of anion-exchange membranes (AEMs), a set of imidazolium-functionalized poly(arylene ether sulfone)s with densely distributed long flexible aliphatic side chains were synthesized. The membranes made from the as-synthesized polymers are robust, transparent, and endowed with microphase segregation capability. The ionic exchange capacity (IEC), hydroxide conductivity, water uptake, thermal stability, and alkaline resistance of the AEMs were evaluated in detail for fuel cell applications. Morphological observation with the use of atomic force microscopy and small-angle X-ray scattering reveals that the combination of high-local-density-type and side-chain-type architectures induces distinguished nanophase separation in the AEMs. The as-prepared membranes have advantages in effective water management and ionic conductivity over traditional main-chain polymers. Typically, the conductivity and IEC were in the ranges of 57.3-112.5 mS cm(-1) and 1.35-1.84 mequiv g(-1) at 80 °C, respectively. Furthermore, the membranes exhibit good thermal and alkaline stability and achieve a peak power density of 114.5 mW cm(-2) at a current density of 250.1 mA cm(-2). Therefore, the present polymers containing clustered flexible pendent aliphatic imidazolium promise to be attractive AEM materials for fuel cells. PMID:27579786

  5. Clusters of isoleucine, leucine, and valine side chains define cores of stability in high-energy states of globular proteins: Sequence determinants of structure and stability.

    PubMed

    Kathuria, Sagar V; Chan, Yvonne H; Nobrega, R Paul; Özen, Ayşegül; Matthews, C Robert

    2016-03-01

    Measurements of protection against exchange of main chain amide hydrogens (NH) with solvent hydrogens in globular proteins have provided remarkable insights into the structures of rare high-energy states that populate their folding free-energy surfaces. Lacking, however, has been a unifying theory that rationalizes these high-energy states in terms of the structures and sequences of their resident proteins. The Branched Aliphatic Side Chain (BASiC) hypothesis has been developed to explain the observed patterns of protection in a pair of TIM barrel proteins. This hypothesis supposes that the side chains of isoleucine, leucine, and valine (ILV) residues often form large hydrophobic clusters that very effectively impede the penetration of water to their underlying hydrogen bond networks and, thereby, enhance the protection against solvent exchange. The linkage between the secondary and tertiary structures enables these ILV clusters to serve as cores of stability in high-energy partially folded states. Statistically significant correlations between the locations of large ILV clusters in native conformations and strong protection against exchange for a variety of motifs reported in the literature support the generality of the BASiC hypothesis. The results also illustrate the necessity to elaborate this simple hypothesis to account for the roles of adjacent hydrocarbon moieties in defining stability cores of partially folded states along folding reaction coordinates.

  6. Synthesis and properties of side-chain-type ion exchange membrane PEEK-g-StSO 3Na for bipolar membranes

    NASA Astrophysics Data System (ADS)

    Huang, Xuehong; Huang, Dengbin; Ou, Xiaojuan; Ding, Fuchuan; Chen, Zhen

    2012-01-01

    Side-chain-type ion exchange membranes (PEEK-g-StSO3Na) were prepared by grafting poly (ether ether ketone) (PEEK) containing propenyl groups with sodium sulfonic styrene (StSO3Na) and KH570. PEEK was synthesized by the aromatic nucleophilic polycondensation reaction of 4,4‧-difluorobenzophenone, bisphenol A and diallylbisphenol A. The synthesized copolymers with the -SO3Na group on the side chain of polymers possessed high molecular weights. The cross-linking reaction was carried out through a sol-gel reaction of the trimethoxysilane group. The copolymer membranes exhibited excellent mechanical properties due to their aromatic structure extending through the backbone and flexible StSO3Na aliphatic chains. The ion exchange capacities (IECs) of the membranes ranged from 2.27 to 2.50 mmol g-1 and the water content ranged from 107.2 to 126.1%, with both parameters increasing with StSO3Na grafting degree. The H+ permeability of copolymer membranes increased with increasing IEC, reaching value above 0.3056 mol/L at 2 h, which is higher than that of Nafion® 117 at the same measurement condition. They displayed reasonably high H+ permeability due to the higher acidity of benzoyl sulfonic acid group, the larger interchain spacing, which is available for water occupation, and the lower AC impedance of the bipolar membrane.

  7. Imidazolium-Functionalized Poly(arylene ether sulfone) Anion-Exchange Membranes Densely Grafted with Flexible Side Chains for Fuel Cells.

    PubMed

    Guo, Dong; Lai, Ao Nan; Lin, Chen Xiao; Zhang, Qiu Gen; Zhu, Ai Mei; Liu, Qing Lin

    2016-09-28

    With the intention of optimizing the performance of anion-exchange membranes (AEMs), a set of imidazolium-functionalized poly(arylene ether sulfone)s with densely distributed long flexible aliphatic side chains were synthesized. The membranes made from the as-synthesized polymers are robust, transparent, and endowed with microphase segregation capability. The ionic exchange capacity (IEC), hydroxide conductivity, water uptake, thermal stability, and alkaline resistance of the AEMs were evaluated in detail for fuel cell applications. Morphological observation with the use of atomic force microscopy and small-angle X-ray scattering reveals that the combination of high-local-density-type and side-chain-type architectures induces distinguished nanophase separation in the AEMs. The as-prepared membranes have advantages in effective water management and ionic conductivity over traditional main-chain polymers. Typically, the conductivity and IEC were in the ranges of 57.3-112.5 mS cm(-1) and 1.35-1.84 mequiv g(-1) at 80 °C, respectively. Furthermore, the membranes exhibit good thermal and alkaline stability and achieve a peak power density of 114.5 mW cm(-2) at a current density of 250.1 mA cm(-2). Therefore, the present polymers containing clustered flexible pendent aliphatic imidazolium promise to be attractive AEM materials for fuel cells.

  8. Side-chain conducting and phase-separated polymeric binders for high-performance silicon anodes in lithium-ion batteries.

    PubMed

    Park, Sang-Jae; Zhao, Hui; Ai, Guo; Wang, Cheng; Song, Xiangyun; Yuca, Neslihan; Battaglia, Vincent S; Yang, Wanli; Liu, Gao

    2015-02-25

    Here we describe a class of electric-conducting polymers that conduct electrons via the side chain π-π stacking. These polymers can be designed and synthesized with different chemical moieties to perform different functions, extremely suitable as a conductive polymer binder for lithium battery electrodes. A class of methacrylate polymers based on a polycyclic aromatic hydrocarbon side moiety, pyrene, was synthesized and applied as an electrode binder to fabricate a silicon (Si) electrode. The electron mobilities for PPy and PPyE are characterized as 1.9 × 10(-4) and 8.5 × 10(-4) cm(2) V(-1) s(-1), respectively. These electric conductive polymeric binders can maintain the electrode mechanical integrity and Si interface stability over a thousand cycles of charge and discharge. The as-assembled batteries exhibit a high capacity and excellent rate performance due to the self-assembled solid-state nanostructures of the conductive polymer binders. These pyrene-based methacrylate binders also enhance the stability of the solid electrolyte interphase (SEI) of a Si electrode over long-term cycling. The physical properties of this polymer are further tailored by incorporating ethylene oxide moieties at the side chains to enhance the adhesion and adjust swelling to improve the stability of the high loading Si electrode.

  9. Site-specific protonation kinetics of acidic side chains in proteins determined by pH-dependent carboxyl (13)C NMR relaxation.

    PubMed

    Wallerstein, Johan; Weininger, Ulrich; Khan, M Ashhar I; Linse, Sara; Akke, Mikael

    2015-03-01

    Proton-transfer dynamics plays a critical role in many biochemical processes, such as proton pumping across membranes and enzyme catalysis. The large majority of enzymes utilize acid-base catalysis and proton-transfer mechanisms, where the rates of proton transfer can be rate limiting for the overall reaction. However, measurement of proton-exchange kinetics for individual side-chain carboxyl groups in proteins has been achieved in only a handful of cases, which typically have involved comparative analysis of mutant proteins in the context of reaction network modeling. Here we describe an approach to determine site-specific protonation and deprotonation rate constants (kon and koff, respectively) of carboxyl side chains, based on (13)C NMR relaxation measurements as a function of pH. We validated the method using an extensively studied model system, the B1 domain of protein G, for which we measured rate constants koff in the range (0.1-3) × 10(6) s(-1) and kon in the range (0.6-300) × 10(9) M(-1) s(-1), which correspond to acid-base equilibrium dissociation constants (Ka) in excellent agreement with previous results determined by chemical shift titrations. Our results further reveal a linear free-energy relationship between log kon and pKa, which provides information on the free-energy landscape of the protonation reaction, showing that the variability among residues in these parameters arises primarily from the extent of charge stabilization of the deprotonated state by the protein environment. We find that side-chain carboxyls with extreme values of koff or kon are involved in hydrogen bonding, thus providing a mechanistic explanation for the observed stabilization of the protonated or deprotonated state.

  10. Mass transport in low Tg azo-polymers: Effect on the surface relief grating induction and stability of additional side chain groups able to generate physical interactions

    NASA Astrophysics Data System (ADS)

    Luca, Alina Raicu; Moleavin, Ioana-Andreea; Hurduc, Nicolae; Hamel, Matthieu; Rocha, Licinio

    2014-01-01

    The nanostructuration ability of low glass transition temperature (Tg) azo-polysiloxanes films is investigated at working temperatures close or higher than the film Tg. The behavior of materials incorporating additional side chain nitrobenzene or naphthalene groups and as a result presenting different Tg is compared in terms of the surface modulation dynamics and stability of the induced topographic modifications. This comparison is carried out under light exposure and in dark environment. We demonstrate the ability to optically generate surface modulations on these materials even at operating temperatures corresponding to the film Tg. Along with a modification of the opto-mechanic properties correlated with the materials chemical structure, a collapse of the surface structures occurring with different dynamics in materials of similar Tg is highlighted. These observations suggest the existence of an additional mechanism rather than a purely thermal redistribution of the polymer chains in the films.

  11. New theories for smectic and nematic liquid-crystal polymers: Backbone LCPs (liquid crystalline polymers) and their mixtures and side-chain LCPs

    SciTech Connect

    Dowell, F.

    1987-01-01

    A summary of predictions and explanations from statistical-physics theories for both backbone and side-chain liquid crystalline polymers (LCPs) and for mixtures with backbone LCPs are presented. Trends in the thermodynamic and molecular ordering properties have been calculated as a function of pressure, density, temperature, and molecule chemical structures (including degree of polymerization and the following properties of the chemical structures of the repeat units: lengths and shapes, intra-chain rotation energies, dipole moments, site-site polarizabilities and Lennard-Jones potentials, etc.) in nematic and multiple smectic-A LC phases and in the isotropic liquid phase. The theoretical results are found to be in good agreement with existing experimental data. These theories can also be applied to combined LCPs. Since these theories have no ad hoc or arbitrarily adjustable parameters, these theories can be used to design new LCPs and new solvents as well as to predict and explain properties. 27 refs., 4 tabs.

  12. Regulation of Glutamine Transport in Escherichia coli.

    PubMed Central

    Willis, R C; Iwata, K K; Furlong, C E

    1975-01-01

    The formation of the high-affinity (Km equal to 0.2 muM) L-glutamine transport system of Escherichia coli strain 7 (Lin) appears to be subject to the same major control as the glutamine synthetase (EC 6.3.1.2) of this gram-negative organism. Culture of cells under nitrogen-limited conditions provides maximum derepression of both the glutamine synthetase and the glutamine transport system. Nutritional conditions providing a rich supply of ammonium salts or available sources of nitrogen, i.e., conditions which repress the formation of glutamine synthetase, provide three- and 20-fold repression, respectively, of the glutamine transport system. Culture of cells with glutamine supplements of 2 mM does not increase the repression of high-affinity glutamine transport system beyond the level observed in the absence of glutamine. A second kinetically distinct low-affinity component of glutamine. A second kinetically distinct low-affinity component of glutamine uptake is observed in cells cultured with a glutamine-depleted nutrient broth. This second component is associated with the appearance of glutaminase A (EC 3.5.1.2) and asparaginase I (EC 3.5.1.1), a periplasmic enzyme. Parallel changes were observed in the levels of the high-affinity glutamine transport system and the glutamine synthetase when cells were cultured with the carbon sources: glucose, glycerol, or succinate. PMID:238938

  13. Gas-phase models of γ turns: Effect of side-chain/backbone interactions investigated by IR/UV spectroscopy and quantum chemistry

    NASA Astrophysics Data System (ADS)

    Chin, Wutharath; Piuzzi, François; Dognon, Jean-Pierre; Dimicoli, Iliana; Mons, Michel

    2005-08-01

    The conformations of laser-desorbed jet-cooled short peptide chains Ac -Phe-Xxx-NH2 (Xxx =Gly, Ala, Val, and Pro) have been investigated by IR/UV double resonance spectroscopy and density-functional-theory (DFT) quantum chemistry calculations. Singly γ-folded backbone conformations (βL-γ) are systematically observed as the most stable conformers, showing that in these two-residue peptide chains, the local conformational preference of each residue is retained (βL for Phe and γ turn for Xxx). Besides, β turns are also spontaneously formed but appear as minor conformers. The theoretical analysis suggests negligible inter-residue interactions of the main conformers, which enables us to consider these species as good models of γ turns. In the case of valine, two similar types of γ turns, differing by the strength of their hydrogen bond, have been found both experimentally and theoretically. This observation provides evidence for a strong flexibility of the peptide chain, whose minimum-energy structures are controlled by side-chain/backbone interactions. The qualitative conformational difference between the present species and the reversed sequence Ac -Xxx-Phe-NH2 is also discussed.

  14. Three-component synthesis of highly functionalized aziridines containing a peptide side chain and their one-step transformation into β-functionalized α-ketoamides

    PubMed Central

    Huck, Lena; González, Juan F; de la Cuesta, Elena

    2016-01-01

    Summary A sequential three-component process is described, starting from 3-arylmethylene-2,5-piperazinediones and involving a one-pot sequence of reactions achieving regioselective opening of the 2,5-diketopiperazine ring and diastereoselective generation of an aziridine ring. This method allows the preparation of N-unprotected, trisubstituted aziridines bearing a peptide side chain under mild conditions. Their transformation into β-trifluoroacetamido-α-ketoamide and α,β-diketoamide frameworks was also achieved in a single step. PMID:27559422

  15. A new approach to the side chain formation of 24-alkyl-22-hydroxy steroids: application to the preparation of early brassinolide biosynthetic precursors.

    PubMed

    Hurski, Alaksiej L; Zhabinskii, Vladimir N; Khripach, Vladimir A

    2012-06-01

    A new synthetic route to 22S-hydroxy-24R-methyl steroids has been developed and applied for the preparation of cathasterone, (22S)-hydroxycampesterol, and 6-deoxocathasterone, which are precursors in the early stages of the biosynthesis of brassinolide. The construction of the steroid side chain with the correct stereochemistry at C-24 is based on the use of Claisen rearrangement. The introduction of the 22-hydroxyl group has been achieved by epoxidation of the Δ(22)-double bond, nucleophilic opening of the intermediate mesyl epoxide with sodium sulfide, and desulfurization of the formed tetrahydrothiophenes with Raney nickel.

  16. Functional role of residue 193 (chymotrypsin numbering) in serine proteases: influence of side chain length and beta-branching on the catalytic activity of blood coagulation factor XIa.

    PubMed

    Schmidt, Amy E; Sun, Mao-fu; Ogawa, Taketoshi; Bajaj, S Paul; Gailani, David

    2008-02-01

    In serine proteases, Gly193 (chymotrypsin numbering) is conserved with rare exception. Mutants of blood coagulation proteases have been reported with Glu, Ala, Arg or Val substitutions for Gly193. To further understand the role of Gly193 in protease activity, we replaced it with Ala or Val in coagulation factor XIa (FXIa). For comparison to the reported FXIa Glu193 mutant, we prepared FXIa with Asp (short side chain) or Lys (opposite charge) substitutions. Binding of p-aminobenzamidine (pAB) and diisopropylfluorphosphate (DFP) were impaired 1.6-36-fold and 35-478-fold, respectively, indicating distortion of, or altered accessibility to, the S1 and oxyanion-binding sites. Val or Asp substitutions caused the most impairment. Salt bridge formation between the amino terminus of the mature protease moiety at Ile16 and Asp194, essential for catalysis, was impaired 1.4-4-fold. Mutations reduced catalytic efficiency of tripeptide substrate hydrolysis 6-280-fold, with Val or Asp causing the most impairment. Further studies were directed toward macromolecular interactions with the FXIa mutants. kcat for factor IX activation was reduced 8-fold for Ala and 400-1100-fold for other mutants, while binding of the inhibitors antithrombin and amyloid beta-precursor protein Kunitz domain (APPI) was impaired 13-2300-fold and 22-27000-fold, respectively. The data indicate that beta-branching of the side chain of residue 193 is deleterious for interactions with pAB, DFP and amidolytic substrates, situations where no S2'-P2' interactions are involved. When an S2'-P2' interaction is involved (factor IX, antithrombin, APPI), beta-branching and increased side chain length are detrimental. Molecular models indicate that the mutants have impaired S2' binding sites and that beta-branching causes steric conflicts with the FXIa 140-loop, which could perturb the local tertiary structure of the protease domain. In conclusion, enzyme activity is impaired in FXIa when Gly193 is replaced by a non

  17. A new approach to the side chain formation of 24-alkyl-22-hydroxy steroids: application to the preparation of early brassinolide biosynthetic precursors.

    PubMed

    Hurski, Alaksiej L; Zhabinskii, Vladimir N; Khripach, Vladimir A

    2012-06-01

    A new synthetic route to 22S-hydroxy-24R-methyl steroids has been developed and applied for the preparation of cathasterone, (22S)-hydroxycampesterol, and 6-deoxocathasterone, which are precursors in the early stages of the biosynthesis of brassinolide. The construction of the steroid side chain with the correct stereochemistry at C-24 is based on the use of Claisen rearrangement. The introduction of the 22-hydroxyl group has been achieved by epoxidation of the Δ(22)-double bond, nucleophilic opening of the intermediate mesyl epoxide with sodium sulfide, and desulfurization of the formed tetrahydrothiophenes with Raney nickel. PMID:22487564

  18. Three-component synthesis of highly functionalized aziridines containing a peptide side chain and their one-step transformation into β-functionalized α-ketoamides.

    PubMed

    Huck, Lena; González, Juan F; de la Cuesta, Elena; Menéndez, J Carlos

    2016-01-01

    A sequential three-component process is described, starting from 3-arylmethylene-2,5-piperazinediones and involving a one-pot sequence of reactions achieving regioselective opening of the 2,5-diketopiperazine ring and diastereoselective generation of an aziridine ring. This method allows the preparation of N-unprotected, trisubstituted aziridines bearing a peptide side chain under mild conditions. Their transformation into β-trifluoroacetamido-α-ketoamide and α,β-diketoamide frameworks was also achieved in a single step. PMID:27559422

  19. Molecular structures and antiproliferative activity of side-chain saturated and homologated analogs of 2-chloro-3-(n-alkylamino)-1,4-napthoquinone

    NASA Astrophysics Data System (ADS)

    Pal, Sanjima; Jadhav, Mahesh; Weyhermüller, Thomas; Patil, Yogesh; Nethaji, M.; Kasabe, Umesh; Kathawate, Laxmi; Konkimalla, V. Badireenath; Salunke-Gawali, Sunita

    2013-10-01

    Side chain homologated derivatives of 2-chloro-3-(n-alkylamino)-1,4-naphthoquinone {n-alkyl: pentyl; L-5, hexyl; L-6, heptyl; L-7 and octyl; L-8} have been synthesized and characterized by elemental analysis, FT-IR, 1H NMR, UV-visible spectroscopy and LC-MS. Compounds, L-4, {n-alkyl: butyl; L-4}, L-6 and L-8 have been characterized by single crystal X-ray diffraction studies. The single crystal X-ray structures reveal that L-4 and L-8 crystallizes in P21 space group, while L-6 in P21/c space group. Molecules of L-4 and L-8 from polymeric chains through Csbnd H⋯O and Nsbnd H⋯O close contacts. L-6 is a dimer formed by Nsbnd H⋯O interaction. Slipped π-π stacking interactions are observed between quinonoid and benzenoid rings of L-4 and L-8. Orientations of alkyl group in L-4 and L-8 is on same side of the chain and polymeric chains run opposite to one another to form zip like structure to the alkyl groups. Antiproliferative activities of L-1 to L-8{n-alkyl: methyl; L-1, ethyl; L-2, propyl; L-3 and butyl; L-4} were studied in cancer cells of colon (COLO205), brain (U87MG) and pancreas (MIAPaCa2) where L-1, L-2 and L-3 were active in MIAPaCa2 (L-1 = L-2 > L-3) and COLO205 (L-2 = L-3 > L-1) and inactive in U87MG. From antiproliferative studies with compounds L-1 to L-8 it can be concluded that homologation of 2-chloro-3-(n-alkylamino)-1,4-napthoquinone with saturated methyl groups yielded tissue specific compounds such as L-2 (for MIAPaCa2) and L-3 (for COLO205) with optimal activity.

  20. Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the united residue (UNRES) force field for protein simulations

    PubMed Central

    Sieradzan, Adam K.; Krupa, Paweł; Scheraga, Harold A.; Liwo, Adam; Czaplewski, Cezary

    2015-01-01

    The UNited RESidue (UNRES) model of polypeptide chains is a coarse-grained model in which each amino-acid residue is reduced to two interaction sites, namely a united peptide group (p) located halfway between the two neighboring α-carbon atoms (Cαs), which serve only as geometrical points, and a united side chain (SC) attached to the respective Cα. Owing to this simplification, millisecond Molecular Dynamics simulations of large systems can be performed. While UNRES predicts overall folds well, it reproduces the details of local chain conformation with lower accuracy. Recently, we implemented new knowledge-based torsional potentials (Krupa et. al. J. Chem. Theory Comput., 2013, 9, 4620–4632) that depend on the virtual-bond dihedral angles involving side chains: Cα ⋯ Cα ⋯ Cα ⋯ SC (τ(1)), SC ⋯ Cα ⋯ Cα ⋯ Cα (τ(2)), and SC ⋯ Cα ⋯ Cα ⋯ SC (τ(3)) in the UNRES force field. These potentials resulted in significant improvement of the simulated structures, especially in the loop regions. In this work, we introduce the physics-based counterparts of these potentials, which we derived from the all-atom energy surfaces of terminally-blocked amino-acid residues by Boltzmann integration over the angles λ(1) and λ(2) for rotation about the Cα ⋯ Cα virtual-bond angles and over the side-chain angles χ. The energy surfaces were, in turn, calculated by using the semiempirical AM1 method of molecular quantum mechanics. Entropy contribution was evaluated with use of the harmonic approximation from Hessian matrices. One-dimensional Fourier series in the respective virtual-bond-dihedral angles were fitted to the calculated potentials, and these expressions have been implemented in the UNRES force field. Basic calibration of the UNRES force field with the new potentials was carried out with eight training proteins, by selecting the optimal weight of the new energy terms and reducing the weight of the regular torsional terms. The force field was

  1. (Ala)(4)-X-(Ala)4 as a model system for the optimization of the χ1 and χ2 amino acid side-chain dihedral empirical force field parameters.

    PubMed

    Shim, Jihyun; Zhu, Xiao; Best, Robert B; MacKerell, Alexander D

    2013-03-15

    Amino acid side-chain fluctuations play an essential role in the structure and function of proteins. Accordingly, in theoretical studies of proteins, it is important to have an accurate description of their conformational properties. Recently, new side-chain torsion parameters were introduced into the CHARMM and Amber additive force fields and evaluated based on the conformational properties of the individual side-chains using protein simulations in explicit solvent. While effective for validation, molecular dynamics simulations of proteins must be extended into the microsecond regime to obtain full convergence of the side-chain conformations, limiting their use for force field optimization. To address this, we systematically test the utility of explicit solvent simulations of (Ala)(4)-X-(Ala)(4) peptides, where X represents the amino acids, as model systems for the optimization of χ(1) and χ(2) side-chain parameters. The effect of (Ala)(4)-X-(Ala)(4) backbone conformation was tested by constraining the backbone in the α-helical, C5, C7(eq), and PPII conformations and performing exhaustive sampling using Hamiltonian replica exchange simulations. Rotamer distributions from protein and the (Ala)(4)-X-(Ala)(4) simulations showed the highest correlation for the C7(eq) and PPII conformations, although agreement was the best for the α-helical conformation for Asn. Hydrogen bond analysis indicates the utility of the C7(eq) and PPII conformations to be due to specific side-chain-backbone hydrogen bonds not being oversampled, thereby allowing sampling of a range of side-chain conformations consistent with the distributions occurring in full proteins. It is anticipated that the (Ala)(4)-X-(Ala)(4) model system will allow for iterative force field optimization targeting condensed-phase conformational distributions of side-chains.

  2. Modeling the effects of structure and dynamics of the nitroxide side-chain on the ESR spectra of spin labeled proteins

    PubMed Central

    Tombolato, Fabio; Ferrarini, Alberta; Freed, Jack H.

    2010-01-01

    In a companion paper (Tombolato, F.; Ferrarini, A.; Freed, J.H., ... ) a study of the conformational dynamics of methanethiosulfonate spin probes linked at a surface exposed α-helix has been presented. Here, on the basis of this analysis, X-band ESR spectra of these spin labels are simulated, within the framework of the Stochastic Liouville Equation methodology. Slow reorientations of the whole protein are superimposed on fast chain motions, which have been identified with conformational jumps and fluctuations in the minima of the chain torsional potential. Fast chain motions are introduced in the SLE for the protein reorientations through partially averaged magnetic tensors and relaxation times calculated according to the motional narrowing theory. The 72R1 and 72R2 mutants of T4 lysozyme, which bear the spin label at a solvent-exposed helix site, have been taken as test systems. For the side-chain of the R2 spin label, only a few non-interconverting conformers are possible, whose mobility is limited to torsional fluctuations, yielding almost identical spectra, typical of slightly mobile nitroxides. In the case of R1, more complex spectra result from the simultaneous presence of constrained and mobile chain conformers, with relative weights which can depend on the local environment. The model provides an explanation for the experimentally observed dependence of the spectral lineshapes on temperature, solvent, and pattern of substituents in the pyrroline ring. The relatively simple methodology presented here allows the introduction of realistic features of the spin probe dynamics into the simulation of ESR spectra of spin labeled proteins; moreover, it provides suggestions for a proper account of such dynamics in more sophisticated approaches. PMID:17181284

  3. Reversible competitive α-ketoheterocycle inhibitors of fatty acid amide hydrolase containing additional conformational constraints in the acyl side chain: orally active, long-acting analgesics.

    PubMed

    Ezzili, Cyrine; Mileni, Mauro; McGlinchey, Nicholas; Long, Jonathan Z; Kinsey, Steven G; Hochstatter, Dustin G; Stevens, Raymond C; Lichtman, Aron H; Cravatt, Benjamin F; Bilsky, Edward J; Boger, Dale L

    2011-04-28

    A series of α-ketooxazoles containing conformational constraints in the C2 acyl side chain of 2 (OL-135) were examined as inhibitors of fatty acid amide hydrolase (FAAH). Only one of the two possible enantiomers displayed potent FAAH inhibition (S vs R enantiomer), and their potency is comparable or improved relative to 2, indicating that the conformational restriction in the C2 acyl side chain is achievable. A cocrystal X-ray structure of the α-ketoheterocycle 12 bound to a humanized variant of rat FAAH revealed its binding details, confirmed that the (S)-enantiomer is the bound active inhibitor, shed light on the origin of the enantiomeric selectivity, and confirmed that the catalytic Ser241 is covalently bound to the electrophilic carbonyl as a deprotonated hemiketal. Preliminary in vivo characterization of the inhibitors 12 and 14 is reported demonstrating that they raise brain anandamide levels following either intraperitoneal (ip) or oral (po) administration indicative of effective in vivo FAAH inhibition. Significantly, the oral administration of 12 caused dramatic accumulation of anandamide in the brain, with peak levels achieved between 1.5 and 3 h, and these elevations were maintained over 9 h. Additional studies of these two representative members of the series (12 and 14) in models of thermal hyperalgesia and neuropathic pain are reported, including the demonstration that 12 administered orally significantly attenuated mechanical (>6 h) and cold (>9 h) allodynia for sustained periods consistent with its long-acting effects in raising the endogenous concentration of anandamide.

  4. Introduction of a methoxymethyl side chain into p-phenylenediamine attenuates its sensitizing potency and reduces the risk of allergy induction

    SciTech Connect

    Goebel, Carsten; Troutman, John; Hennen, Jenny; Rothe, Helga; Schlatter, Harald; Gerberick, G. Frank; Blömeke, Brunhilde

    2014-02-01

    The strong sensitizing potencies of the most important primary intermediates of oxidative hair dyes, p-phenylenediamine (PPD) and p-toluylenediamine (PTD, i.e. 2-methyl-PPD) are well established. They are considered as the key sensitizers in hair dye allergic contact dermatitis. While modification of their molecular structure is expected to alter their sensitizing properties, it may also impair their color performance. With introduction of a methoxymethyl side chain we found the primary intermediate 2-methoxymethyl-p-phenylenediamine (ME-PPD) with excellent hair coloring performance but significantly reduced sensitizing properties compared to PPD and PTD: In vitro, ME-PPD showed an attenuated innate immune response when analyzed for its protein reactivity and dendritic cell activation potential. In vivo, the effective concentration of ME-PPD necessary to induce an immune response 3-fold above vehicle control (EC3 value) in the local lymph node assay (LLNA) was 4.3%, indicating a moderate skin sensitizing potency compared to values of 0.1 and 0.17% for PPD and PTD, respectively. Finally, assessing the skin sensitizing potency of ME-PPD under consumer hair dye usage conditions through a quantitative risk assessment (QRA) indicated an allergy induction risk negligible compared to PPD or PTD. - Highlights: • Methoxymethyl side chain in p-phenylenediamine reduces its strong skin sensitizing properties. • Reduced protein reactivity and dendritic cell activation. • Reduced skin sensitizing potency in local lymph node assay (LLNA). • Negligible allergy induction risk under hair dye usage conditions.

  5. Graft copolymer composed of cationic backbone and bottle brush-like side chains as a physically adsorbed coating for protein separation by capillary electrophoresis.

    PubMed

    Zhou, Dan; Xiang, Lina; Zeng, Rongju; Cao, Fuhu; Zhu, Xiaoxi; Wang, Yanmei

    2011-12-01

    To stabilize electroosmotic flow (EOF) and suppress protein adsorption onto the silica capillary inner wall, a cationic hydroxyethylcellulose-graft-poly (poly(ethylene glycol) methyl ether methacrylate) (cat-HEC-g-PPEGMA) graft copolymer composed of cationic backbone and bottle brush-like side chains was synthesized for the first time and used as a novel physically adsorbed coating for protein separation by capillary electrophoresis. Reversed (anodal) and very stable EOF was obtained in cat-HEC-g-PPEGMA-coated capillary at pH 2.2-7.8. The effects of degree of cationization, PEGMA grafting ratio, PEGMA molecular mass, and buffer pH on the separation of basic proteins were investigated. A systematic comparative study of protein separation in bare and HEC-coated capillaries and in cat-HEC-g-PPEGMA-coated capillary was also performed. The basic proteins can be well separated in cat-HEC-g-PPEGMA-coated capillary over the pH range of 2.8-6.8 with good repeatability and high separation efficiency, because the coating combines good protein-resistant property of bottle brush-like PPEGMA side chains with excellent coating ability of cat-HEC backbone. Besides its success in separation of basic proteins, the cat-HEC-g-PPEGMA coating was also superior in the fast separation of other protein samples, such as protein mixture, egg white, and saliva, which indicates that it is a promising coating for further proteomics analysis. PMID:22038787

  6. Grafting of a functionalized side-chain liquid crystal polymer on carbon fiber surfaces: Novel coupling agents for fiber/polymer matrix composites

    SciTech Connect

    Le Bonheur, V.; Stupp, S.I. )

    1993-09-01

    The authors studied covalent grafting to functionalized carbon fibers of a specially designed liquid crystalline monomer and its corresponding side-chain liquid crystalline polymer containing pendant chemical functions on their mesogenic groups. From a materials point of view these liquid crystalline compounds could act as coupling agents at fiber/polymer matrix interfaces, offering a mechanism to control composite properties not only through bonding but also through their [open quotes]spontaneous[close quotes] molecular orientation in interfacial regions. The grafting methodology for both monomer and polymer to fiber surfaces involved esterification through carbodiimide chemistry in solution. Carboxylic acid groups found on functionalized carbon fiber surfaces were esterified to phenolic functions in the side chains of the experimental polymer. Following grafting procedures the fibers were analyzed by scanning electron microscopy (SEM) and by contact angle measurements. SEM micrographs of fibers grafted with polymer revealed the presence of strongly attached polymeric material on the graphitic surface after rigorous extraction with polymer solvent. Contact angle measurements and polar/dispersive free energy analysis indicated also a smaller polar component of the surface free energy of fibers possibly due to the hydrophobic polymer backbone grafted on the carbon surfaces. On the basis of results, it is concluded that the esterification reaction grafted the polyphenolic liquid-crystal polymer on graphite fiber surfaces. 24 refs., 8 figs., 4 tabs.

  7. Effects of short-side-chain perfluorosulfonic acid ionomers as binders on the performance of low Pt loading fuel cell cathodes

    NASA Astrophysics Data System (ADS)

    Park, Young-Chul; Kakinuma, Katsuyoshi; Uchida, Hiroyuki; Watanabe, Masahiro; Uchida, Makoto

    2015-02-01

    We investigated the effects of short-side-chain (SSC) perfluorosulfonic acid ionomers on the electrochemical properties, fuel cell performance and ionomer distribution of a highly dispersed Pt/GCB catalyst with a low Pt loading, 0.05 mg cm-2. The SSC ionomers in the cathode catalyst layers (CLs) resulted in an improvement of the Pt utilization (UPt) and Pt effectiveness (EfPt) values compared with those for the conventional long-side-chain (LSC) ionomer. Furthermore, the SSC ionomers with high ion exchange capacity (IEC), e.g., SSC-1.43 and SSC-1.80 ionomers, exhibited significantly enhanced cell performance under low to medium relative humidity (RH) conditions. This result is ascribed to the higher proton conductivity of the SSC ionomers and more effective trapping of water that is produced during the oxygen reduction reaction (ORR) than those of the LSC ionomer. It was also found that the SSC ionomers showed better continuity and uniformity on the Pt and carbon particles than the LSC ionomer, which might have led to improvement of both the mass transport and the proton-conducting network in the CLs. The application of the SSC ionomers as binders demonstrated an increase of the performance at the low Pt loading fuel cell cathode over a wide range of humidity.

  8. Stimulation of cholesterol side-chain cleavage by a luteinizing-hormone-releasing hormone (luliberin) agonist (ICI 118630) in rat Leydig cells.

    PubMed Central

    Sullivan, M H; Cooke, B A

    1983-01-01

    The action of a luliberin (luteinizing-hormone-releasing hormone) agonist (ICI 118630) and lutropin (luteinizing hormone) on the activity of the cytochrome P-450 cholesterol side-chain cleavage enzyme in rat Leydig cells has been investigated. This has been carried out by studying the metabolism of exogenous (22R)-22- and 25-hydroxycholesterol to testosterone. It was found that both hydroxycholesterols increased testosterone production to higher levels than achieved by lutropin alone. Addition of luliberin agonist but not lutropin was found to increase further the metabolism of the hydroxycholesterol to testosterone; this occurred in the presence of saturating and subsaturating levels of the hydroxycholesterols. This effect of luliberin agonist was potentiated in the presence of lutropin. The protein synthesis inhibitor, cycloheximide, inhibited the luliberin agonist-induced stimulation of the hydroxycholesterol metabolism. At low calcium levels (1.1 microM), testosterone production was increased by addition of (22R)-22-hydroxycholesterol but the luliberin agonist effect was negated. The calmodulin inhibitor trifluoperazine inhibited (22R)-22-hydroxycholesterol-stimulated steroidogenesis and negated the luliberin agonist effect. These results indicate that luliberin agonist specifically increases the synthesis of the cytochrome P-450 cholesterol side-chain cleavage enzyme in rat testis Leydig cells. PMID:6230077

  9. Gauche(+) side-chain orientation as a key factor in the search for an immunogenic peptide mixture leading to a complete fully protective vaccine.

    PubMed

    Bermúdez, Adriana; Calderon, Dayana; Moreno-Vranich, Armando; Almonacid, Hannia; Patarroyo, Manuel A; Poloche, Andrés; Patarroyo, Manuel E

    2014-04-11

    Topological and stereo-electron characteristics are essential in major histocompability class II-peptide-T-cell receptor (MHC-p-TCR) complex formation for inducing an appropriate immune response. Modified high activity binding peptides (mHABPs) were synthesised for complete full protection antimalarial vaccine development producing a large panel of individually fully protection-inducing protein structures (FPIPS) and very high long-lasting antibody-inducing (VHLLAI) mHABPs. Most of those which did not interfere, compete, inhibit or suppress their individual VHLLAI or FPIPS activity contained or displayed a polyproline II-like (PPIIL) structure when mixed. Here we show that amino acid side-chains located in peptide binding region (PBR) positions p3 and p7 displayed specific electron charges and side-chain gauche(+) orientation for interacting with the TCR. Based on the above, and previously described physicochemical principles, non-interfering, long-lasting, full protection-inducing, multi-epitope, multistage, minimal subunit-based chemically synthesised mHABP mixtures can be designed for developing vaccines against diseases scourging humankind, malaria being one of them. PMID:24582630

  10. Context-dependent effects on the hydrophilicity/hydrophobicity of side-chains during reversed-phase high-performance liquid chromatography: Implications for prediction of peptide retention behaviour

    PubMed Central

    Mant, C.T.; Hodges, R.S.

    2009-01-01

    The present study set out to investigate whether observed relative hydrophilicity/hydrophobicity values of positively charged side-chains (with Lys and Arg as representative side-chains) or hydrophobic side-chains (with Ile as the representative side-chain) were context-dependent, i.e., did such measured values vary depending on characteristics of the peptides within which such side-chains are substituted (overall peptide hydrophobicity, number of positive charges) and/or properties of the mobile phase (anionic counterions of varying hydrophobicity and concentration)? Reversed-phase high-performance liquid chromatography (RP-HPLC) was applied to two series of four synthetic peptide analogues (+1, +2, +3 and +4 net charge), the only difference between the two peptide series being the substitution of one hydrophobic Ile residue for a Gly residue, in the presence of anionic ion-pairing reagents of varying hydrophobicity (HCOOH ≈ H3PO4 < TFA < PFPA < HFBA) and concentration (2–50 mM). RP-HPLC of these peptide series revealed that the relative hydrophilicity of Lys and Arg side-chains in the peptides increased with peptide hydrophobicity. In addition the relative hydrophobicity of Ile decreased dramatically with an increase in the number of positive charges in the peptide, this hydrophobicity decrease being of greater magnitude as the hydrophobicity of the anionic ion-pairing reagent increased. These results have significant implications in the prediction of peptide retention times for proteomic applications. PMID:16814308

  11. Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states

    PubMed Central

    Baranowski, Maciej; Ołldziej, Stanisław; Scheraga, Harold A.; Liwo, Adam; Czaplewski, Cezary

    2013-01-01

    The UNited RESidue (UNRES) coarse-grained model of polypeptide chains, developed in our laboratory, enables us to carry out millisecond-scale molecular-dynamics simulations of large proteins effectively. It performs well in ab initio predictions of protein structure, as demonstrated in the last Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP10). However, the resolution of the simulated structure is too coarse, especially in loop regions, which results from insufficient specificity of the model of local interactions. To improve the representation of local interactions, in this work we introduced new side-chain-backbone correlation potentials, derived from a statistical analysis of loop regions of 4585 proteins. To obtain sufficient statistics, we reduced the set of amino-acid-residue types to five groups, derived in our earlier work on structurally optimized reduced alphabets, based on a statistical analysis of the properties of amino-acid structures. The new correlation potentials are expressed as one-dimensional Fourier series in the virtual-bond-dihedral angles involving side-chain centroids. The weight of these new terms was determined by a trial-and-error method, in which Multiplexed Replica Exchange Molecular Dynamics (MREMD) simulations were run on selected test proteins. The best average root-mean-square deviations (RMSDs) of the calculated structures from the experimental structures below the folding-transition temperatures were obtained with the weight of the new side-chain-backbone correlation potentials equal to 0.57. The resulting conformational ensembles were analyzed in detail by using the Weighted Histogram Analysis Method (WHAM) and Ward's minimum-variance clustering. This analysis showed that the RMSDs from the experimental structures dropped by 0.5 Å on average, compared to simulations without the new terms, and the deviation of individual residues in the loop region of the computed

  12. Critical Roles of Hydrophobicity and Orientation of Side Chains for Inactivation of Sarcoplasmic Reticulum Ca2+-ATPase with Thapsigargin and Thapsigargin Analogs*

    PubMed Central

    Winther, Anne-Marie L.; Liu, Huizhen; Sonntag, Yonathan; Olesen, Claus; le Maire, Marc; Soehoel, Helmer; Olsen, Carl-Erik; Christensen, S. Brøgger; Nissen, Poul; Møller, Jesper V.

    2010-01-01

    Thapsigargin (Tg), a specific inhibitor of sarco/endoplasmic Ca2+-ATPases (SERCA), binds with high affinity to the E2 conformation of these ATPases. SERCA inhibition leads to elevated calcium levels in the cytoplasm, which in turn induces apoptosis. We present x-ray crystallographic and intrinsic fluorescence data to show how Tg and chemical analogs of the compound with modified or removed side chains bind to isolated SERCA 1a membranes. This occurs by uptake via the membrane lipid followed by insertion into a resident intramembranous binding site with few adaptative changes. Our binding data indicate that a balanced hydrophobicity and accurate positioning of the side chains, provided by the central guaianolide ring structure, defines a pharmacophore of Tg that governs both high affinity and access to the protein-binding site. Tg analogs substituted with long linkers at O-8 extend from the binding site between transmembrane segments to the putative N-terminal Ca2+ entry pathway. The long chain analogs provide a rational basis for the localization of the linker, the presence of which is necessary for enabling prostate-specific antigen to cleave peptide-conjugated prodrugs targeting SERCA of cancer cells (Denmeade, S. R., Jakobsen, C. M., Janssen, S., Khan, S. R., Garrett, E. S., Lilja, H., Christensen, S. B., and Isaacs, J. T. (2003) J. Natl. Cancer Inst. 95, 990–1000). Our study demonstrates the usefulness of a simple in vitro system to test and direct development toward the formulation of new Tg derivatives with improved properties for SERCA targeting. Finally, we propose that the Tg binding pocket may be a regulatory site that, for example, is sensitive to cholesterol. PMID:20551329

  13. Clusters of branched aliphatic side chains serve as cores of stability in the native state of the HisF TIM barrel protein.

    PubMed

    Gangadhara, Basavanapura N; Laine, Jennifer M; Kathuria, Sagar V; Massi, Francesca; Matthews, C Robert

    2013-03-25

    Imidazole-3-glycerol phosphate synthase is a heterodimeric allosteric enzyme that catalyzes consecutive reactions in imidazole biosynthesis through its HisF and HisH subunits. The unusually slow unfolding reaction of the isolated HisF TIM barrel domain from the thermophilic bacteria, Thermotoga maritima, enabled an NMR-based site-specific analysis of the main-chain hydrogen bonds that stabilize its native conformation. Very strong protection against exchange with solvent deuterium in the native state was found in a subset of buried positions in α-helices and pervasively in the underlying β-strands associated with a pair of large clusters of isoleucine, leucine and valine (ILV) side chains located in the α7(βα)8(βα)1-2 and α2(βα)3-6β7 segments of the (βα)8 barrel. The most densely packed region of the large cluster, α3(βα)4-6β7, correlates closely with the core of stability previously observed in computational, protein engineering and NMR dynamics studies, demonstrating a key role for this cluster in determining the thermodynamic and structural properties of the native state of HisF. When considered with the results of previous studies where ILV clusters were found to stabilize the hydrogen-bonded networks in folding intermediates for other TIM barrel proteins, it appears that clusters of branched aliphatic side chains can serve as cores of stability across the entire folding reaction coordinate of one of the most common motifs in biology.

  14. Composition of the epicuticular waxes coating the adaxial side of Phyllostachys aurea leaves: Identification of very-long-chain primary amides.

    PubMed

    Racovita, Radu C; Jetter, Reinhard

    2016-10-01

    The present study presents comprehensive chemical analyses of cuticular wax mixtures of the bamboo Phyllostachys aurea. The epicuticular and intracuticular waxes were sampled selectively from the adaxial side of leaves on young and old plants and investigated by gas chromatography-mass spectrometry and flame ionization detection. The epi- and intracuticular layers on young and old leaves had wax loads ranging from 1.7 μg/cm(2) to 1.9 μg/cm(2). Typical very-long-chain aliphatic wax constituents were found with characteristic chain length patterns, including alkyl esters (primarily C48), alkanes (primarily C29), fatty acids (primarily C28 and C16), primary alcohols (primarily C28) and aldehydes (primarily C30). Alicyclic wax components were identified as tocopherols and triterpenoids, including substantial amounts of triterpenoid esters. Alkyl esters, alkanes, fatty acids and aldehydes were found in greater amounts in the epicuticular layer, while primary alcohols and most terpenoids accumulated more in the intracuticular wax. Alkyl esters occurred as mixtures of metamers, combining C20 alcohol with various acids into shorter ester homologs (C36C40), and a wide range of alcohols with C22 and C24 acids into longer esters (C42C52). Primary amides were identified, with a characteristic chain length profile peaking at C30. The amides were present exclusively in the epicuticular layer and thus at or near the surface, where they may affect plant-herbivore or plant-pathogen interactions. PMID:27402630

  15. Optimal design of ethanol supply chains considering carbon trading effects and multiple technologies for side-product exploitation.

    PubMed

    Ortiz-Gutiérrez, R A; Giarola, S; Bezzo, F

    2013-01-01

    This work proposes a spatially explicit mixed integer linear programming modelling framework representing the dynamic evolution of a bioethanol supply chain (SC) under increasing biofuel demand and greenhouse gas (GHG) emission savings over time. Key features of the proposed framework comprise: (i) the incorporation of available set-aside rural surfaces for energy crop cultivation; (ii) the acknowledgement ofan economic value to the overall GHG emissions through the introduction of an Emission Trading System. Multiple technological options are assessed to exploit the co-product Distiller's Dried Grains with Solubles either as animal fodder (standard usage) or as fuel for heat and power generation or as raw material for biogas production (and hence heat and power). Bioethanol production in Northern Italy is chosen as a demonstrative case study. PMID:24350473

  16. Synthesis of dendrigraft poly(ϵ-caprolactone)s using side hydroxyl groups for the grafting of branch chains.

    PubMed

    Cheng, Juan; Ling, Xiujun; Zhong, Zhenlin; Zhuo, Renxi

    2011-11-15

    Dendrigraft poly(ϵ-caprolactone)s with high molecular weight and narrow polydispersity are synthesized via a convenient generation-growth approach. Copolymerization of ϵ-caprolactone (CL) and 4-(2-benzoxyethoxy)-ϵ-caprolactone (BECL) with stannous octanoate as a catalyst affords a functionalized poly(ϵ-caprolactone) (PCL) with benzyl-protected hydroxyl side groups. After removal of benzyl groups by palladium-catalyzed hydrogenolysis, the graft copolymerization of CL and BECL onto the hydroxyl-bearing linear polyester (zero-generation) affords the first-generation graft polyester. Further deprotection and graft polymerization cycles led to dendrigraft polyesters. Molecular weights are multiplied in each graft copolymerization. The second-generation dendrigraft poly(ϵ-caprolactone) has an M(w) of 236 000 g·mol(-1) and M(w) /M(n) of 1.53. PMID:21928304

  17. Side-chain effects on the solution-phase conformations and charge photogeneration dynamics of low-bandgap copolymers

    NASA Astrophysics Data System (ADS)

    Huo, Ming-Ming; Liang, Ran; Xing, Ya-Dong; Hu, Rong; Zhao, Ning-Jiu; Zhang, Wei; Fu, Li-Min; Ai, Xi-Cheng; Zhang, Jian-Ping; Hou, Jian-Hui

    2013-09-01

    Solution-phase conformations and charge photogeneration dynamics of a pair of low-bandgap copolymers based on benzo[1,2-b:4,5-b']dithiophene (BDT) and thieno[3,4-b]thiophene (TT), differed by the respective carbonyl (-C) and ester (-E) substituents at the TT units, were comparatively investigated by using near-infrared time-resolved absorption (TA) spectroscopy at 25 °C and 120 °C. Steady-state and TA spectroscopic results corroborated by quantum chemical analyses prove that both PBDTTT-C and PBDTTT-E in chlorobenzene solutions are self-aggregated; however, the former bears a relatively higher packing order. Specifically, PBDTTT-C aggregates with more π-π stacked domains, whereas PBDTTT-E does with more random coils interacting strongly at the chain intersections. At 25 °C, the copolymers exhibit comparable exciton lifetimes (˜1 ns) and fluorescence quantum yields (˜2%), but distinctly different charge photogeneration dynamics: PBDTTT-C on photoexcitation gives rise to a branching ratio of charge separated (CS) over charge transfer (CT) states more than 20% higher than PBDTTT-E does, correlating with their photovoltaic performance. Temperature and excitation-wavelength dependent exciton/charge dynamics suggest that the CT states localize at the chain intersections that are survivable up to 120 °C, and that the excitons and the CS states inhabit the stretched strands and the also thermally robust orderly stacked domains. The stable self-aggregation structures and the associated primary charge dynamics of the PBDTTT copolymers in solutions are suggested to impact intimately on the morphologies and the charge photogeneration efficiency of the solid-state photoactive layers.

  18. Synthesis of novel polymethacrylates with siloxyl bridging perfluoroalkyl side-chains for hydrophobic application on cotton fabrics

    NASA Astrophysics Data System (ADS)

    Cai, Lu; Dai, Li; Yuan, Yanhua; Liu, Anqi; Zhanxiong, Li

    2016-05-01

    Three novel fluorinated methacrylate monomers with siloxyl bridging perfluoroalkyl groups were synthesized and characterized. Afterwards, the corresponding polymethacrylate latexes, namely monofluoroalkylsiloxyl polymethacrylate (PMFSMA), bisfluoroalkylsiloxyl polymethacrylate (PBFSMA) and trisfluoroalkylsiloxyl polymethacrylate (PTFSMA), were prepared and coated onto cotton fabrics to make them water-repellent. Particle size, particle size distribution, zeta potential and high-resolution transmission electron microscope (TEM) were tested to assess the emulsion stability and particle morphology. Thermal properties of PTFSMA were evaluated by thermal-gravimetric analysis (TGA). Surface properties of the coated cotton fabrics were characterized by Fourier transform infrared spectroscopy (FT-IR), scanning electron microscope (SEM), water contact angle (WCA), adhesive force and X-ray photoelectron spectroscopy (XPS). It was found that the incorporation of more perfluoroalkyl chains and the annealing process could decrease the surface free energy of polymer film to 13.7 mN/m. Furthermore, the EDS spectra of PTFSMA film after annealing showed an enrichment of fluorine in the film-air interface.

  19. The influence of novel gemini surfactants containing cycloalkyl side-chains on the structural phases of DNA in solution.

    PubMed

    Pietralik, Zuzanna; Kumita, Janet R; Dobson, Christopher M; Kozak, Maciej

    2015-07-01

    Very important to gene therapy is the delivery system of the nucleic acids (called a vector), which will enhance the efficiency of the transport of new DNA into cells whilst protecting against damage. A promising alternative to the currently used viral vectors are the systems based on amphiphilic compounds - lipoplexes. Among them, gemini surfactants, which consist of two hydrophobic chains and two cationic heads connected by a linker - spacer group, appear to be promising candidates. The subject of this study involves two gemini surfactants, alkoxy derivatives of bis-imidazolium quaternary salts, differing in the length of their spacer groups and how they interact with two types of salmon sperm DNA (low and high molecular weight (MW)) or plasmid DNA (pDNA). The mixtures of gemini surfactants with nucleic acids of differing p/n ratios (positive-to-negative charge ratio) were characterised by small angle X-ray scattering (SAXS) of synchrotron radiation, dynamic light scattering (DLS), circular dichroism (CD) spectroscopy, atomic force microscopy (AFM), transmission electron microscopy (TEM) and gel electrophoresis techniques. This analysis allows for the selection of the most suitable and promising candidates for non-viral vectors in gene therapy, determination of the conditions needed to form stable complexes, identification of conformational changes in the DNA molecules upon interactions with gemini surfactants and in some cases, determination of the structures formed in these lipoplexes.

  20. Significant Improvement of Semiconducting Performance of the Diketopyrrolopyrrole-Quaterthiophene Conjugated Polymer through Side-Chain Engineering via Hydrogen-Bonding.

    PubMed

    Yao, Jingjing; Yu, Chenmin; Liu, Zitong; Luo, Hewei; Yang, Yang; Zhang, Guanxin; Zhang, Deqing

    2016-01-13

    Three diketopyrrolopyrrole (DPP)-quaterthiophene conjugated polymers, pDPP4T-1, pDPP4T-2, and pDPP4T-3, in which the molar ratios of the urea-containing alkyl chains vs branching alkyl chains are 1:30, 1:20, and 1:10, respectively, were prepared and investigated. In comparison with pDPP4T without urea groups in the alkyl side chains and pDPP4T-A, pDPP4T-B, and pDPP4T-C containing both linear and branched alkyl chains, thin films of pDPP4T-1, pDPP4T-2, and pDPP4T-3 exhibit higher hole mobilities; thin-film mobility increases in the order pDPP4T-1 < pDPP4T-2 < pDPP4T-3, and hole mobility of a thin film of pDPP4T-3 can reach 13.1 cm(2) V(-1) s(-1) after thermal annealing at just 100 °C. The incorporation of urea groups in the alkyl side chains also has an interesting effect on the photovoltaic performances of DPP-quaterthiophene conjugated polymers after blending with PC71BM. Blended thin films of pDPP4T-1:PC71BM, pDPP4T-2:PC71BM, and pDPP4T-3:PC71BM exhibit higher power conversion efficiencies (PCEs) than pDPP4T:PC71BM, pDPP4T-A:PC71BM, pDPP4T-B:PC71BM, and pDPP4T-C:PC71BM. The PCE of pDPP4T-1:PC71BM reaches 6.8%. Thin films of pDPP4T-1, pDPP4T-2, and pDPP4T-3 and corresponding thin films with PC71BM were characterized with AFM, GIXRD, and STEM. The results reveal that the lamellar packing order of the alkyl chains is obviously enhanced for thin films of pDPP4T-1, pDPP4T-2, and pDPP4T-3; after thermal annealing, slight inter-chain π-π stacking emerges for pDPP4T-2 and pDPP4T-3. Blends of pDPP4T-1, pDPP4T-2, and pDPP4T-3 with PC71BM show a more pronounced micro-phase separation. These observations suggest that the presence of urea groups may further facilitate the assemblies of these conjugated polymers into nanofibers and ordered aggregation of PC71BM. PMID:26669732

  1. Activation of R235A mutant orotidine 5'-monophosphate decarboxylase by the guanidinium cation: effective molarity of the cationic side chain of Arg-235.

    PubMed

    Barnett, Shonoi A; Amyes, Tina L; Wood, B McKay; Gerlt, John A; Richard, John P

    2010-02-01

    The R235A mutation at yeast orotidine 5'-monophosphate decarboxylase (OMPDC) results in a 1300-fold increase in K(m) and a 14-fold decrease in k(cat) for decarboxylation of orotidine 5'-monophosphate, corresponding to a 5.8 kcal/mol destabilization of the transition state. There is strong activation of this mutant enzyme by added guanidinium cation (Gua(+)): 1 M Gua(+) stabilizes the transition state by ca. 3 kcal/mol. This stabilization is due to the binding of Gua(+) to the binary E(mut) x OMP complex, with a K(d) of 50 mM, to form the 9-fold more reactive ternary E(mut) x OMP x Gua(+) complex. The "effective molarity" of the cationic side chain of Arg-235 at the wild-type enzyme is calculated to be 160 M.

  2. Evidence of a Structural Defect in Ice VII and the Side Chain Dependent Response of Small Model Peptides to Increased Pressure

    PubMed Central

    Scott, J. Nathan; Vanderkooi, Jane M.

    2014-01-01

    The effect of high pressure on the OH stretch of dilute HOD in D2O was examined using high pressure FTIR. It was found that at pressures directly above the ice VI to ice VII transition, ice VII displays a splitting in the OH absorption indicative of differing hydrogen bonding environments. This result is contrary to published structures of ice VII in which each OH oscillator should experience an identical electronic environment. The anomalous band was found to decrease in absorbance and finally disappear at ~43.0 kbar. In addition, the pressure response of the amide I′ and II′ bands of three small model peptides was examined. Analysis of these bands’ response to increased pressure indicates significant side chain dependence of their structural rearrangement, which may play a role in the composition of full length proteins of barophilic organisms. PMID:21740637

  3. Discovery of 2-azetidinone and 1H-pyrrole-2,5-dione derivatives containing sulfonamide group at the side chain as potential cholesterol absorption inhibitors.

    PubMed

    Yuan, Xinrui; Lu, Peng; Xue, Xiaojian; Qin, Hui; Fan, Chen; Wang, Yubin; Zhang, Qi

    2016-02-01

    Cholesterol absorption inhibitor (CAI) targeting Niemann-Pick C1-like1 protein was developed for the treatment of hyperlipidaemia and only ezetimibe was approved so far. For developing novel CAIs, we synthesized sixteen 2-azetidinone derivatives and thirteen 1H-pyrrole-2,5-dione derivatives containing sulfonamide group at the side chain, and their inhibitory activity of cholesterol absorption was evaluated in Caco-2 cell line in vitro. Furthermore, top six compounds were measured by cytotoxicity and partition coefficient, and 2-azetidinone analogue 9e was selected for in vivo study. Finally, 9e considerably reduced total cholesterol, LDL-C, FFA and triglyceride in the serum and increased the rate of HDL-C to total cholesterol, suggesting it could regulate the lipid metabolism and act as a potent CAI.

  4. In-vitro and in-vivo antimicrobial activities of a novel cephalosporin derivative, CP6162, possessing a dihydroxypyridone moiety at the C-3 side chain.

    PubMed

    Orikasa, Y; Hara, T; Miyata, A; Tamura, A; Kawaharajo, K; Matsumoto, T; Komiya, I; Iwamatsu, K; Shibahara, S; Inouye, S

    1991-01-01

    The antibacterial activity of a novel cephalosporin derivative, CP6162, possessing a dihydroxypyridone moiety at the C-3 side chain, was evaluated in vitro and in vivo, with ceftazidime, aztreonam and cefoperazone as the reference antibiotics. CP6162 showed weak or little activity against Gram-positive bacteria, but potent activity against clinical isolates of the Gram-negative species including strains of Pseudomonas aeruginosa, Ps. cepacia, Acinetobacter sp., Xanthomonas maltophilia, Serratia marcescens, Enterobacter cloacae and Citrobacter freundii, which were resistant to the reference antibiotics. The MICs of CP6162 were only slightly affected by the high producers of beta-lactamases except for cephalosporinase-producing C. freundii. It was, however, affected by the presence of ferric ion. CP6162 showed in-vivo activity paralleling the in-vitro activity, and also showed pharmacokinetic parameters similar to those of ceftazidime in mice and rats.

  5. Structure of epiglucan, a highly side-chain/branched (1 --> 3;1 --> 6)-beta-glucan from the micro fungus Epicoccum nigrum Ehrenb. ex Schlecht.

    PubMed

    Schmid, F; Stone, B A; McDougall, B M; Bacic, A; Martin, K L; Brownlee, R T; Chai, E; Seviour, R J

    2001-03-22

    The extracellular fungal polysaccharide, epiglucan, synthesised by Epicoccum nigrum is a side-chain/branched (1 --> 3;1 --> 6)-D-beta-glucan. Methylation analysis, 13C DEPT NMR and specific enzymic digestion data show slight variation in branching frequency among the epiglucans from the three strains examined. The (1 --> 3)-beta-linked backbone has (1 --> 6)-beta-linked branches at frequencies greater than the homologous glucans, scleroglucan and schizophyllan, from Sclerotium spp. and Schizophyllum commune, respectively. The structural analyses do not allow a distinction to be made between structures I and II. [structures: see text] Epiglucan displays non-Newtonian shear thinning rheological properties, typical of these glucans. PMID:11322730

  6. Analyzing sites of OH radical attack (ring vs. side chain) in oxidation of substituted benzenes via dual stable isotope analysis (δ(13)C and δ(2)H).

    PubMed

    Zhang, Ning; Geronimo, Inacrist; Paneth, Piotr; Schindelka, Janine; Schaefer, Thomas; Herrmann, Hartmut; Vogt, Carsten; Richnow, Hans H

    2016-01-15

    OH radicals generated by the photolysis of H2O2 can degrade aromatic contaminants by either attacking the aromatic ring to form phenolic products or oxidizing the substituent. We characterized these competing pathways by analyzing the carbon and hydrogen isotope fractionation (εC and εH) of various substituted benzenes. For benzene and halobenzenes that only undergo ring addition, low values of εC (-0.7‰ to -1.0‰) were observed compared with theoretical values (-7.2‰ to -8‰), possibly owing to masking effect caused by pre-equilibrium between the substrate and OH radical preceding the rate-limiting step. In contrast, the addition of OH radicals to nitrobenzene ring showed a higher εC (-3.9‰), probably due to the lower reactivity. Xylene isomers, anisole, aniline, N,N-dimethylaniline, and benzonitrile yielded normal εH values (-2.8‰ to -29‰) indicating the occurrence of side-chain reactions, in contrast to the inverse εH (11.7‰ to 30‰) observed for ring addition due to an sp(2) to sp(3) hybridization change at the reacting carbon. Inverse εH values for toluene (14‰) and ethylbenzene (30‰) were observed despite the formation of side-chain oxidation products, suggesting that ring addition has a larger contribution to isotope fractionation. Dual element isotope slopes (∆δ(2)H/∆δ(13)C) therefore allow identification of significant degradation pathways of aromatic compounds by photochemically induced OH radicals. Issues that should be addressed in future studies include quantitative determination of the contribution of each competing pathway to the observed isotope fractionation and characterization of physical processes preceding the reaction that could affect isotope fractionation.

  7. Altered Backbone and Side-Chain Interactions Result in Route Heterogeneity during the Folding of Interleukin-1β (IL-1β)

    PubMed Central

    Capraro, Dominique T.; Lammert, Heiko; Heidary, David K.; Roy, Melinda; Gross, Larry A.; Onuchic, José N.; Jennings, Patricia A.

    2013-01-01

    Deletion of the β-bulge trigger-loop results in both a switch in the preferred folding route, from the functional loop packing folding route to barrel closure, as well as conversion of the agonist activity of IL-1β into antagonist activity. Conversely, circular permutations of IL-1β conserve the functional folding route as well as the agonist activity. These two extremes in the folding-functional interplay beg the question of whether mutations in IL-1β would result in changes in the populations of heterogeneous folding routes and the signaling activity. A series of topologically equivalent water-mediated β-strand bridging interactions within the pseudosymmetric β-trefoil fold of IL-1β highlight the backbone water interactions that stabilize the secondary and tertiary structure of the protein. Additionally, conserved aromatic residues lining the central cavity appear to be essential for both stability and folding. Here, we probe these protein backbone-water molecule and side chain-side chain interactions and the role they play in the folding mechanism of this geometrically stressed molecule. We used folding simulations with structure-based models, as well as a series of folding kinetic experiments to examine the effects of the F42W core mutation on the folding landscape of IL-1β. This mutation alters water-mediated backbone interactions essential for maintaining the trefoil fold. Our results clearly indicate that this perturbation in the primary structure alters a structural water interaction and consequently modulates the population of folding routes accessed during folding and signaling activity. PMID:23972849

  8. Activity of 3-Ketosteroid 9α-Hydroxylase (KshAB) Indicates Cholesterol Side Chain and Ring Degradation Occur Simultaneously in Mycobacterium tuberculosis*

    PubMed Central

    Capyk, Jenna K.; Casabon, Israël; Gruninger, Robert; Strynadka, Natalie C.; Eltis, Lindsay D.

    2011-01-01

    Mycobacterium tuberculosis (Mtb), a significant global pathogen, contains a cholesterol catabolic pathway. Although the precise role of cholesterol catabolism in Mtb remains unclear, the Rieske monooxygenase in this pathway, 3-ketosteroid 9α-hydroxylase (KshAB), has been identified as a virulence factor. To investigate the physiological substrate of KshAB, a rhodococcal acyl-CoA synthetase was used to produce the coenzyme A thioesters of two cholesterol derivatives: 3-oxo-23,24-bisnorchol-4-en-22-oic acid (forming 4-BNC-CoA) and 3-oxo-23,24-bisnorchola-1,4-dien-22-oic acid (forming 1,4-BNC-CoA). The apparent specificity constant (kcat/Km) of KshAB for the CoA thioester substrates was 20–30 times that for the corresponding 17-keto compounds previously proposed as physiological substrates. The apparent KmO2 was 90 ± 10 μm in the presence of 1,4-BNC-CoA, consistent with the value for two other cholesterol catabolic oxygenases. The Δ1 ketosteroid dehydrogenase KstD acted with KshAB to cleave steroid ring B with a specific activity eight times greater for a CoA thioester than the corresponding ketone. Finally, modeling 1,4-BNC-CoA into the KshA crystal structure suggested that the CoA moiety binds in a pocket at the mouth of the active site channel and could contribute to substrate specificity. These results indicate that the physiological substrates of KshAB are CoA thioester intermediates of cholesterol side chain degradation and that side chain and ring degradation occur concurrently in Mtb. This finding has implications for steroid metabolites potentially released by the pathogen during infection and for the design of inhibitors for cholesterol-degrading enzymes. The methodologies and rhodococcal enzymes used to generate thioesters will facilitate the further study of cholesterol catabolism. PMID:21987574

  9. Modification of residue 42 of the active site loop with a lysine-mimetic side chain rescues isochorismate-pyruvate lyase activity in Pseudomonas aeruginosa PchB.

    PubMed

    Olucha, José; Meneely, Kathleen M; Lamb, Audrey L

    2012-09-25

    PchB is an isochorismate-pyruvate lyase from Pseudomonas aeruginosa. A positively charged lysine residue is located in a flexible loop that behaves as a lid to the active site, and the lysine residue is required for efficient production of salicylate. A variant of PchB that lacks the lysine at residue 42 has a reduced catalytic free energy of activation of up to 4.4 kcal/mol. Construction of a lysine isosteric residue bearing a positive charge at the appropriate position leads to the recovery of 2.5-2.7 kcal/mol (about 60%) of the 4.4 kcal/mol by chemical rescue. Exogenous addition of ethylamine to the K42A variant leads to a neglible recovery of activity (0.180 kcal/mol, roughly 7% rescue), whereas addition of propylamine caused an additional modest loss in catalytic power (0.056 kcal/mol, or 2% loss). This is consistent with the view that (a) the lysine-42 residue is required in a specific conformation to stabilize the transition state and (b) the correct conformation is achieved for a lysine-mimetic side chain at site 42 in the course of loop closure, as expected for transition-state stabilization by the side chain ammonio function. That the positive charge is the main effector of transition state stabilization is shown by the construction of a lysine-isosteric residue capable of exerting steric effects and hydrogen bonding but not electrostatic effects, leading to a modest increase of catalytic power (0.267-0.505 kcal/mol of catalytic free energy, or roughly 6-11% rescue). PMID:22970849

  10. Influence of the side-chain length on the cellular uptake and the cytotoxicity of rhenium triscarbonyl derivatives: a bimodal infrared and luminescence quantitative study.

    PubMed

    Clède, Sylvain; Lambert, François; Saint-Fort, Rénette; Plamont, Marie-Aude; Bertrand, Hélène; Vessières, Anne; Policar, Clotilde

    2014-07-01

    Rhenium triscarbonyl complexes fac-[Re(CO)3 (N^N)] with appropriate ancillary N^N ligands are relevant for fluorescent bio-imaging. Recently, we have shown that [Re(CO)3 ] cores can also be efficiently mapped inside cells using their IR signature and that they can thus be used in a bimodal approach. To describe them we have coined the term SCoMPIs for single-core multimodal probes for imaging. In the context of the use of these SCoMPIs in bio-imaging, the questions of their cellular uptake and cytotoxicity are critical. We report here a series of compounds derived from the [Re(CO)3 Cl(pyta)] core (pyta=4-(2-pyridyl)-1,2,3-triazole). The pyta ligand is of interest because it can be easily functionalized. Aliphatic side chains (C4 , C8 , and C12 ) were appended to this core. A correlative study involving IR and luminescence was performed to monitor and quantify their cellular internalization. We studied the relationship between lipophilicity (log P(o/w)), cytotoxicity (IC50 ), and cellular uptake, and we showed that both uptake and cytotoxicity increase with the length of the side chain, with a higher uptake for the C12 derivative. This study stresses the distinction that has to be made between apparent toxicity, determined as an incubation concentration IC50 , and intrinsic toxicity. Indeed, the intrinsic toxicity of a compound can remain hidden if it is not cell permeable. Therefore it must be kept in mind that IC50 values are composite values, reflecting both cellular uptake and intrinsic toxicity.

  11. Plasma glutamine levels and falciparum malaria.

    PubMed

    Cowan, G; Planche, T; Agbenyega, T; Bedu-Addo, G; Owusu-Ofori, A; Adebe-Appiah, J; Agranoff, D; Woodrow, C; Castell, L; Elford, B; Krishna, S

    1999-01-01

    Glutamine deficiency is associated with increased rates of sepsis and mortality, which can be prevented by glutamine supplementation. Changes in glutamine concentration were examined in Ghanaian children with acute falciparum malaria and control cases. The mean (SD) plasma glutamine concentration was lower in patients with acute malaria (401 (82) mumol/L, n = 50) than in control patients (623 (67) mumol/L, n = 7; P < 0.001). Plasma glutamine concentrations all rose in convalescence. The mean (SD) increase in plasma glutamine was 202 (123) mumol/L (n = 18; P < 0.001) compared with acute infection. We conclude that acute falciparum malaria is associated with large decreases in plasma glutamine and these falls may increase susceptibility to sepsis and dyserythropoeisis.

  12. Effects of surface-active block copolymers with oxyethylene and fluoroalkyl side chains on the antifouling performance of silicone-based films.

    PubMed

    Martinelli, Elisa; Gunes, Deniz; Wenning, Brandon M; Ober, Christopher K; Finlay, John A; Callow, Maureen E; Callow, James A; Di Fino, Alessio; Clare, Anthony S; Galli, Giancarlo

    2016-01-01

    Block copolymers made from a poly(dimethyl siloxane) (Si) and a poly(meth)acrylate carrying oxyethylene (EG) or fluoroalkyl (AF) side chains were synthesized and incorporated as surface-active components into a silicone matrix to produce cross-linked films with different surface hydrophilicity/phobicity. Near-edge X-ray absorption fine structure (NEXAFS) studies showed that film surfaces containing Si-EG were largely populated by the siloxane, with the oxyethylene chains present only to a minor extent. In contrast, the fluorinated block was selectively segregated to the polymer-air interface in films containing Si-AF as probed by NEXAFS and X-ray photoelectron spectroscopy (XPS) analyses. Such differences in surface composition were reflected in the biological performance of the coatings. While the films with Si-EG showed a higher removal of both Ulva linza sporelings and Balanus amphitrite juveniles than the silicone control, those with Si-AF exhibited excellent antifouling properties, preventing the settlement of cyprids of B. amphitrite.

  13. Pyrrolo-dC oligonucleotides bearing alkynyl side chains with terminal triple bonds: synthesis, base pairing and fluorescent dye conjugates prepared by the azide-alkyne "click" reaction.

    PubMed

    Seela, Frank; Sirivolu, Venkata Ramana

    2008-05-01

    5-(Octa-1,7-diynyl)-2'-deoxyuridine was converted into the furano-dU derivative 7 by copper-catalyzed cyclization; the pyrolodC-derivative 3 was formed upon ammonolysis. The bicyclic nucleosides 3 and 7 as well as the corresponding non-cyclic precursors 4 and 6 all containing terminal C[triple bond]C bonds were conjugated with the non-fluorescent 3-azido-7-hydroxycoumarin 5 employing the copper(I)-catalyzed Huisgen-Sharpless-Meldal cycloaddition "click reaction". Strongly fluorescent 1H-1,2,3-triazole conjugates (30-33) are formed incorporating two fluorescent reporters-the pyrdC nucleoside and the coumarin moiety. Oligonucleotides incorporating 6-alkynyl and 6-alkyl 7H-pyrrolo[2,3-d]pyrimidin-2(3H)-one nucleosides (3 and 2f) have been prepared by solid-phase synthesis using the phosphoramidite building blocks 10 and 13 ; the pyrrolo-dC oligonucleotides are formed during ammonia treatment. The duplex stability of oligonucleotides containing 3 and related derivatives was studied. Oligonucleotides with terminal triple bonded nucleosides such as 3 are more stabilizing than those lacking a side chain with terminal unsaturation; open-chain derivatives (4) are even more efficient. The click reaction was also performed on oligonucleotides containing the pyrdC-derivative and the fluorescence properties of nucleosides, oligonucleotides and their coumarin conjugates were studied. PMID:18421402

  14. Effects of surface-active block copolymers with oxyethylene and fluoroalkyl side chains on the antifouling performance of silicone-based films.

    PubMed

    Martinelli, Elisa; Gunes, Deniz; Wenning, Brandon M; Ober, Christopher K; Finlay, John A; Callow, Maureen E; Callow, James A; Di Fino, Alessio; Clare, Anthony S; Galli, Giancarlo

    2016-01-01

    Block copolymers made from a poly(dimethyl siloxane) (Si) and a poly(meth)acrylate carrying oxyethylene (EG) or fluoroalkyl (AF) side chains were synthesized and incorporated as surface-active components into a silicone matrix to produce cross-linked films with different surface hydrophilicity/phobicity. Near-edge X-ray absorption fine structure (NEXAFS) studies showed that film surfaces containing Si-EG were largely populated by the siloxane, with the oxyethylene chains present only to a minor extent. In contrast, the fluorinated block was selectively segregated to the polymer-air interface in films containing Si-AF as probed by NEXAFS and X-ray photoelectron spectroscopy (XPS) analyses. Such differences in surface composition were reflected in the biological performance of the coatings. While the films with Si-EG showed a higher removal of both Ulva linza sporelings and Balanus amphitrite juveniles than the silicone control, those with Si-AF exhibited excellent antifouling properties, preventing the settlement of cyprids of B. amphitrite. PMID:26769148

  15. From polymers to proteins: the effect of side chains and broken symmetry on the formation of secondary structures within a Wang-Landau approach.

    PubMed

    Škrbić, Tatjana; Badasyan, Artem; Hoang, Trinh Xuan; Podgornik, Rudolf; Giacometti, Achille

    2016-05-25

    We use a micro-canonical Wang-Landau technique to study the equilibrium properties of a single flexible homopolymer where consecutive monomers are represented by impenetrable hard spherical beads tangential to each other, and non-consecutive monomers interact via a square-well potential. To mimic the characteristics of a protein-like system, the model is then refined in two different directions. Firstly, by allowing partial overlap between consecutive beads, we break the spherical symmetry and thus provide a severe constraint on the possible conformations of the chain. Alternatively, we introduce additional spherical beads at specific positions in the direction normal to the backbone, to represent the steric hindrance of the side chains in real proteins. Finally, we consider also a combination of these two ingredients. In all three systems, we obtain the full phase diagram in the temperature-interaction range plane and find the presence of helicoidal structures at low temperatures in the intermediate range of interactions. The effect of the range of the square-well attraction is highlighted, and shown to play a role similar to that found in simple liquids and polymers. Perspectives in terms of protein folding are finally discussed. PMID:27137225

  16. A roundabout approach to control morphological orientation and solar-cell performance by modulating side-chain branching position in benzodithiophene-based polymers.

    PubMed

    Lee, Kyu Cheol; Song, Seyeong; Lee, Junghoon; Kim, Dong Suk; Kim, Jin Young; Yang, Changduk

    2015-04-27

    To be meaningful to guide the rational design of novel high-performance conjugated semiconductors, we prepared three benzo[1,2-b:4,5-b']dithiophene (BDT)-based polymers by systematically moving the branching point of the alkyl chain. The effect of side-chain engineering was thoroughly investigated by a range of techniques. We demonstrate that a subtle change in the branching position in the BDT core can have a critical impact on polymer packing and preferential backbone orientation in thin films; copolymers made from BDT and thieno[3,4-c]pyrrole-4,6-dione units (TPD) adopt more of a face-on orientation as the branching point is shifted closer to the backbone, which can be correlated with a dramatic difference in solar-cells performance. The high short-circuit current density (11.6 mA cm(-2) ) for the copolymer with one carbon atom between the alkoxylated oxygen atom and the branching point results from its predominantly face-on orientation and smoother surface in thin films, which results in power conversion efficiencies as high as 4.56 %.

  17. RXR partial agonist produced by side chain repositioning of alkoxy RXR full agonist retains antitype 2 diabetes activity without the adverse effects.

    PubMed

    Kawata, Kohei; Morishita, Ken-ichi; Nakayama, Mariko; Yamada, Shoya; Kobayashi, Toshiki; Furusawa, Yuki; Arimoto-Kobayashi, Sakae; Oohashi, Toshitaka; Makishima, Makoto; Naitou, Hirotaka; Ishitsubo, Erika; Tokiwa, Hiroaki; Tai, Akihiro; Kakuta, Hiroki

    2015-01-22

    We previously reported RXR partial agonist CBt-PMN (1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydro-2-naphthyl)-1H-benzotriazole-5-carboxylic acid: 5, EC50 = 143 nM, Emax = 75%), which showed a potent glucose-lowering effect without causing serious adverse effects. However, it remains important to elucidate the structural requirements for RXR efficacy and the glucose-lowering effect because RXR-permissive heterodimers such as PPAR/RXR or LXR/RXR are reported to be activated differently depending upon the chemical structure of RXR agonists. In this work, we show that an RXR partial agonist, NEt-4IB (6-[ethyl-(4-isobutoxy-3-isopropylphenyl)amino]pyridine-3-carboxylic acid: 8b, EC50 = 169 nM, Emax = 55%), can be obtained simply by repositioning the side chains (interchanging the isobutoxy and isopropoxy groups) at the hydrophobic moiety of the RXR full agonist NEt-3IB (6-[ethyl-(3-isobutoxy-4-isopropylphenyl)amino]pyridine-3-carboxylic acid: 7b, EC50 = 19 nM). NEt-4IB (8b) showed antitype 2 diabetes activity without the above side effects upon repeated oral administration to mice at 10 mg/kg/day, similarly to 5. PMID:25486327

  18. A Computational Study of the Mechanism of Succinimide Formation in the Asn-His Sequence: Intramolecular Catalysis by the His Side Chain.

    PubMed

    Takahashi, Ohgi; Manabe, Noriyoshi; Kirikoshi, Ryota

    2016-01-01

    The rates of deamidation reactions of asparagine (Asn) residues which occur spontaneously and nonenzymatically in peptides and proteins via the succinimide intermediate are known to be strongly dependent on the nature of the following residue on the carboxyl side (Xxx). The formation of the succinimide intermediate is by far the fastest when Xxx is glycine (Gly), the smallest amino acid residue, while extremely slow when Xxx is bulky such as isoleucine (Ile) and valine (Val). In this respect, it is very interesting to note that the succinimide formation is definitely accelerated when Xxx is histidine (His) despite its large size. In this paper, we computationally show that, in an Asn-His sequence, the His side-chain imidazole group (in the neutral Nε-protonated form) can specifically catalyze the formation of the tetrahedral intermediate in the succinimide formation by mediating a proton transfer. The calculations were performed for Ace-Asn-His-Nme (Ace = acetyl, Nme = methylamino) as a model compound by the density functional theory with the B3LYP functional and the 6-31+G(d,p) basis set. We also show that the tetrahedral intermediate, once protonated at the NH₂ group, easily releases an ammonia molecule to give the succinimide species. PMID:27005609

  19. Glutamine supplementation in the newborn infant.

    PubMed

    Parimi, Prabhu S; Kalhan, Satish C

    2007-02-01

    Glutamine is a non-essential amino acid that can be synthesized de novo from glutamate. This synthesis can be increased by intravenous infusion of carbon precursors (alpha-ketoglutarate or amino acids) in adults and in infants. The metabolism of glutamine is highly compartmentalized between the splanchnic tissues and the periphery, so that orally administered glutamine is completely metabolized in the splanchnic compartment. Data from studies in adults and children show that plasma levels of glutamine decline during acute stress and illness. Because of its importance in several physiological functions (the demonstrated benefits of supplemental glutamine in adult burns and trauma patients and the inhibitory effect on proteolysis in the skeletal muscle in vitro), it has been suggested that during 'acute stress' the demands of glutamine outweigh its de novo synthesis, resulting in a fall in plasma glutamine levels. As a consequence, glutamine has been considered a 'conditionally essential' amino acid. Because of its instability in solution, glutamine is not routinely added to the parenteral amino acid mixtures. A number of clinical trials of parenteral and enteral supplementation of glutamine have been performed. The outcome measures examined have varied between acute effects and long-term complex clinical events such as mortality and risk of infections. Although acute studies in LBW babies have shown some beneficial effects such as changes in protein metabolism and activation of immune system, these have not been translated into prolonged advantages such as reduction in mortality or in nosocomial infection. The reasons for these differences are discussed.

  20. Endogenous glutamine production in critically ill patients: the effect of exogenous glutamine supplementation

    PubMed Central

    2014-01-01

    Introduction Glutamine rate of appearance (Ra) may be used as an estimate of endogenous glutamine production. Recently a technique employing a bolus injection of isotopically labeled glutamine was introduced, with the potential to allow for multiple assessments of the glutamine Ra over time in critically ill patients, who may not be as metabolically stable as healthy individuals. Here the technique was used to evaluate the endogenous glutamine production in critically ill patients in the fed state with and without exogenous glutamine supplementation intravenously. Methods Mechanically ventilated patients (n = 11) in the intensive care unit (ICU) were studied on two consecutive days during continuous parenteral feeding. To allow the patients to be used as their own controls, they were randomized for the reference measurement during basal feeding without supplementation, before or after the supplementation period. Glutamine Ra was determined by a bolus injection of 13C-glutamine followed by a period of frequent sampling to establish the decay-curve for the glutamine tracer. Exogenous glutamine supplementation was given by intravenous infusion of a glutamine containing dipeptide, L-alanyl-L-glutamine, 0.28 g/kg during 20 hours. Results A 14% increase of endogenous glutamine Ra was seen at the end of the intravenous supplementation period as compared to the basal measurements (P = 0.009). Conclusions The bolus injection technique to measure glutamine Ra to estimate the endogenous production of glutamine in critically ill patients was demonstrated to be useful for repetitive measurements. The hypothesized attenuation of endogenous glutamine production during L-alanyl-L-glutamine infusion given as a part of full nutrition was not seen. PMID:24731231

  1. The fragmentations of [M-H]- anions derived from underivatised peptides. The side-chain loss of H2S from Cys. A joint experimental and theoretical study.

    PubMed

    Bilusich, Daniel; Brinkworth, Craig S; McAnoy, Andrew M; Bowie, John H

    2003-01-01

    Loss of H2S is the characteristic Cys side-chain fragmentation of the [M-H]- anions of Cys-containing peptides. A combination of experiment and theory suggests that this reaction is initiated from the Cys enolate anion as follows: RNH-(-)C(CH2SH)CONHR' Ø [RNHC(=CH2)CONHR' (HS-)] Ø [RNHC(=CH2)CO-HNR'-H]-+H2S. This process is facile. Calculations at the HF/6-31G(d)//AM1 level of theory indicate that the initial anion needs only > or =20.1 kcal mol(-1) of excess energy to effect loss of H2S. Loss of CH2S is a minor process, RNHCH(CH2SH)CON(-)-R' Ø RNHCH(CH2S-)CONHR' Ø RNH -CHCONHR+CH2S, requiring an excess energy of > or =50.2 kcal mol(-1). When Cys occupies the C-terminal end of a peptide, the major fragmentation from the [M-H]- species involves loss of (H2S+CO2). A deuterium-labelling study suggests that this could either be a charge-remote reaction (a process which occurs remote from and uninfluenced by the charged centre in the molecule), or an anionic reaction initiated from the C-terminal CO2- group. These processes have barriers requiring the starting material to have an excess energy of > or =79.6 (charge-remote) or > or =67.1 (anion-directed) kcal mol(-1), respectively, at the HF/6-31G(d)//AM1 level of theory. The corresponding losses of CH2O and H2O from the [M-H]- anions of Ser-containing peptides require > or =35.6 and > or =44.4 kcal mol(-1) of excess energy (calculated at the AM1 level of theory), explaining why loss of CH2O is the characteristic side-chain loss of Ser in the negative ion mode. PMID:14608618

  2. Roles of aromatic side chains and template effects of the hydrophobic cavity of a self-assembled peptide nanoarchitecture for anisotropic growth of gold nanocrystals.

    PubMed

    Tomizaki, Kin-ya; Kishioka, Kohei; Kobayashi, Hiroki; Kobayashi, Akitsugu; Yamada, Naoki; Kataoka, Shunsuke; Imai, Takahito; Kasuno, Megumi

    2015-11-15

    Gold nanocrystals are promising as catalysts and for use in sensing/imaging systems, photonic/plasmonic devices, electronics, drug delivery systems, and for photothermal therapy due to their unique physical, chemical, and biocompatible properties. The use of various organic templates allows control of the size, shape, structure, surface modification and topology of gold nanocrystals; in particular, currently the synthesis of gold nanorods requires a cytotoxic surfactant to control morphology. To control the shape of gold nanocrystals, we previously demonstrated the de novo design and synthesis of a β-sheet-forming nonapeptide (RU006: Ac-AIAKAXKIA-NH2, X=L-2-naphthylalanine, Nal) and the fabrication of gold nanocrystals by mixing RU006 and HAuCl4 in water. The reaction afforded ultrathin gold nanoribbons 50-100 nm wide, several nanometers high, and microns long. To understand the mechanism underlying gold nanoribbon formation by the RU006 system, we here report (i) the effects of replacement of the Nal aromatic side chain in the RU006 sequence with other aromatic moieties, (ii) the electrochemical properties of aromatic side chains in the de novo designed template peptides to estimate the redox potential and number of electrons participating in the gold crystallization process, and (iii) the stoichiometry of the RU006 system for gold nanoribbon synthesis. Interestingly, RU006 bearing a naphthalene moiety (oxidation peak potential of 1.50 V vs Ag/Ag(+)) and an analog [Ant(6)]-RU006 bearing a bulky anthracene moiety (oxidation peak potential of 1.05 V vs Ag/Ag(+)) allowed the growth of anisotropic (ribbon-like) and isotropic (round) gold nanocrystals, respectively. This trend in morphology of gold nanocrystals was attributed to spatially-arranged hydrophobic cavities sufficiently large to accommodate the gold precursor and to allow directed crystal growth driven by cross-linking reactions among the naphthalene rings. Support for this mechanism was obtained by

  3. Vibrational analysis of amino acids and short peptides in hydrated media. VIII. Amino acids with aromatic side chains: L-phenylalanine, L-tyrosine, and L-tryptophan.

    PubMed

    Hernández, Belén; Pflüger, Fernando; Adenier, Alain; Kruglik, Sergei G; Ghomi, Mahmoud

    2010-11-25

    Four out of the 20 natural α-amino acids (α-AAs) contain aromatic rings in their side chains. In a recent paper (J. Phys. Chem. B 2010, 114, 9072-9083), we have analyzed the structural and vibrational features of l-histidine, one of the potent elements of this series. Here, we report on the three remaining members of this family, i.e., l-phenylalanine, l-tyrosine, and l-tryptophan. Their solution (H(2)O and D(2)O) Raman scattering and Fourier transform infrared absorption attenuated total reflection (FT-IR ATR) spectra were measured at room temperature from the species corresponding to those existing at physiological conditions. Because of the very low water solubility of tyrosine, special attention was paid to avoid any artifact concerning the report of the vibrational spectra corresponding to nondissolved powder of this AA in aqueous solution. Finally, we could obtain for the first time the Raman and FT-IR spectra of tyrosine at very low concentration (2.3 mM) upon long accumulation time. To clarify this point, those vibrational spectra of tyrosine recorded either in the solid phase or in a heterogeneous state, where dissolved and nondissolved species of this AA coexist in aqueous solution, are also provided as Supporting Information . To carry out a discussion on the general geometrical and vibrational behavior of these AAs, we resorted to quantum mechanical calculations at the DFT/B3LYP/6-31++G* level, allowing (i) determination of potential energy surfaces of these AAs in a continuum solvent as a function of the torsion angles χ(1) and χ(2), defining the conformation of each aromatic side chain around C(α)-C(β) and C(β)-C(γ) bonds, respectively; (ii) analysis of geometrical features of the AAs surrounded by clusters of n explicit (n = 5-7) water molecules interacting with the backbone and aromatic rings; and (iii) assignment of the observed vibrational modes by means of the theoretical data provided by the lowest energy conformers of explicitly

  4. Roles of aromatic side chains and template effects of the hydrophobic cavity of a self-assembled peptide nanoarchitecture for anisotropic growth of gold nanocrystals.

    PubMed

    Tomizaki, Kin-ya; Kishioka, Kohei; Kobayashi, Hiroki; Kobayashi, Akitsugu; Yamada, Naoki; Kataoka, Shunsuke; Imai, Takahito; Kasuno, Megumi

    2015-11-15

    Gold nanocrystals are promising as catalysts and for use in sensing/imaging systems, photonic/plasmonic devices, electronics, drug delivery systems, and for photothermal therapy due to their unique physical, chemical, and biocompatible properties. The use of various organic templates allows control of the size, shape, structure, surface modification and topology of gold nanocrystals; in particular, currently the synthesis of gold nanorods requires a cytotoxic surfactant to control morphology. To control the shape of gold nanocrystals, we previously demonstrated the de novo design and synthesis of a β-sheet-forming nonapeptide (RU006: Ac-AIAKAXKIA-NH2, X=L-2-naphthylalanine, Nal) and the fabrication of gold nanocrystals by mixing RU006 and HAuCl4 in water. The reaction afforded ultrathin gold nanoribbons 50-100 nm wide, several nanometers high, and microns long. To understand the mechanism underlying gold nanoribbon formation by the RU006 system, we here report (i) the effects of replacement of the Nal aromatic side chain in the RU006 sequence with other aromatic moieties, (ii) the electrochemical properties of aromatic side chains in the de novo designed template peptides to estimate the redox potential and number of electrons participating in the gold crystallization process, and (iii) the stoichiometry of the RU006 system for gold nanoribbon synthesis. Interestingly, RU006 bearing a naphthalene moiety (oxidation peak potential of 1.50 V vs Ag/Ag(+)) and an analog [Ant(6)]-RU006 bearing a bulky anthracene moiety (oxidation peak potential of 1.05 V vs Ag/Ag(+)) allowed the growth of anisotropic (ribbon-like) and isotropic (round) gold nanocrystals, respectively. This trend in morphology of gold nanocrystals was attributed to spatially-arranged hydrophobic cavities sufficiently large to accommodate the gold precursor and to allow directed crystal growth driven by cross-linking reactions among the naphthalene rings. Support for this mechanism was obtained by

  5. Simple Approaches for Estimating Vicinal 1H- 1H Coupling-Constants and for Obtaining Stereospecific Resonance Assignments in Leucine Side Chains

    NASA Astrophysics Data System (ADS)

    Constantine, K. L.; Friedrichs, M. S.; Mueller, L.

    An approach for deriving stereospecific δ-methyl assignments and χ 2 dihedral angle constraints for leucine residues, based on easily recognized patterns of 1H- 1H spin-spin coupling constants and intraresidue nuclear-Overhauser-effect spectroscopy (NOESY) cross-peak intensities, is described. The approach depends on resolved H γ and/or δ-methyl resonances and on initially obtaining stereospecific assignments for H β2 and H β3. As part of the overall strategy, a method is presented for obtaining qualitative or, in favorable cases, semiquantitative estimates of vicinal 1H- 1H coupling constants from peak intensities measured in a short-mixing-time 1H- 1H total correlation spectroscopy (TOCSY) experiment. This method of estimating 1H- 1H spin-spin coupling constants is generally applicable to all side-chain types. The approach is illustrated for several leucine residues within uniformly 15N-labeled and 15N/ 13C-double-labeled isolated light-chain variable domain of the anti-digoxin antibody 26-10. Estimates of 3Jαβ and 3Jβγ coupling constants are derived from a three-dimensional (3D) 13C-edited TOCSY-heteronuclear multiple-quantum coherence (HMQC) spectrum. These data are combined with information from 3D 15N-edited NOESY and 3D 13C-edited NOESY spectra to yield stereospecific H β2, H β3, and δ-methyl assignments, as well as constraints on χ (1) and χ 2 dihedral angles. Although the overall approach is illustrated using 3D 15N-edited and 13C-edited data, it is equally applicable to analysis of two-dimensional 1H- 1H NOESY and TOCSY spectra.

  6. Glutamine metabolism and cycling in Neurospora crassa.

    PubMed Central

    Mora, J

    1990-01-01

    Evidence for the existence of a glutamine cycle in Neurospora crassa is reviewed. Through this cycle glutamine is converted into glutamate by glutamate synthase and catabolized by the glutamine transaminase-omega-amidase pathway, the products of which (2-oxoglutarate and ammonium) are the substrates for glutamate dehydrogenase-NADPH, which synthesizes glutamate. In the final step ammonium is assimilated into glutamine by the action of a glutamine synthetase (GS), which is formed by two distinct polypeptides, one catalytically very active (GS beta), and the other (GS alpha) less active but endowed with the capacity to modulate the activity of GS alpha. Glutamate synthase uses the amide nitrogen of glutamine to synthesize glutamate; glutamate dehydrogenase uses ammonium, and both are required to maintain the level of glutamate. The energy expended in the synthesis of glutamine drives the cycle. The glutamine cycle is not futile, because it is necessary to drive an effective carbon flow to support growth; in addition, it facilitates the allocation of nitrogen or carbon according to cellular demands. The glutamine cycle which dissipates energy links catabolism and anabolism and, in doing so, buffers variations in the nutrient supply and drives energy generation and carbon flow for optimal cell function. PMID:2145504

  7. Introduction of a methoxymethyl side chain into p-phenylenediamine attenuates its sensitizing potency and reduces the risk of allergy induction.

    PubMed

    Goebel, Carsten; Troutman, John; Hennen, Jenny; Rothe, Helga; Schlatter, Harald; Gerberick, G Frank; Blömeke, Brunhilde

    2014-02-01

    The strong sensitizing potencies of the most important primary intermediates of oxidative hair dyes, p-phenylenediamine (PPD) and p-toluylenediamine (PTD, i.e. 2-methyl-PPD) are well established. They are considered as the key sensitizers in hair dye allergic contact dermatitis. While modification of their molecular structure is expected to alter their sensitizing properties, it may also impair their color performance. With introduction of a methoxymethyl side chain we found the primary intermediate 2-methoxymethyl-p-phenylenediamine (ME-PPD) with excellent hair coloring performance but significantly reduced sensitizing properties compared to PPD and PTD: In vitro, ME-PPD showed an attenuated innate immune response when analyzed for its protein reactivity and dendritic cell activation potential. In vivo, the effective concentration of ME-PPD necessary to induce an immune response 3-fold above vehicle control (EC3 value) in the local lymph node assay (LLNA) was 4.3%, indicating a moderate skin sensitizing potency compared to values of 0.1 and 0.17% for PPD and PTD, respectively. Finally, assessing the skin sensitizing potency of ME-PPD under consumer hair dye usage conditions through a quantitative risk assessment (QRA) indicated an allergy induction risk negligible compared to PPD or PTD. PMID:24333256

  8. Theoretical studies on interactions between low energy electrons and protein-DNA fragments: valence anions of AT-amino acids side chain complexes.

    PubMed

    Szyperska, Anna; Gajewicz, Agnieszka; Mazurkiewicz, Kamil; Leszczynski, Jerzy; Rak, Janusz

    2011-11-21

    Electron attachment to trimeric complexes that mimic most frequent hydrogen bonding interactions between an amino acid side chain (AASC) and the Watson-Crick (WC) 9-methyladenine-1-methylthymine (MAMT) base pair has been studied at the B3LYP/6-31++G(d,p) level of theory. Although the neutral trimers will not occur in the gas phase due to unfavorable free energy of stabilization (G(stab)) they should form a protein-DNA complex where entropy changes related to formation of such a complex will more than balance its disadvantageous G(stab). The most stable neutrals possess an identical pattern of hydrogen bonds (HBs). In addition, the proton-acceptor (N7) and proton-donor (N10) atoms of adenine involved in those HBs are located in the main groove of DNA. All neutral structures support the adiabatically stable valence anions in which the excess electron is localized on a π* orbital of thymine. The vertical detachment energies (VDEs) of anions corresponding to the most stable neutrals are substantially smaller than that of the isolated WC MAMT base pair. Hence, electron transfer from the anionic thymine to the phosphate group and as a consequence formation of a single strand break (SSB) should proceed more efficiently in a protein-dsDNA complex than in the naked dsDNA as far as electron attachment to thymine is concerned.

  9. Role of the 7 alpha-methoxy and side-chain carboxyl of moxalactam in beta-lactamase stability and antibacterial activity.

    PubMed Central

    Murakami, K; Yoshida, T

    1981-01-01

    The effects of the alpha-carboxyl of the phenylmalonyl side chain and the 7 alpha-methoxy group in moxalactam (6059-S) (7 beta-[2-carboxy-2-(4-hydroxyphenyl) acetamido]-7 alpha-methoxy-3[[(1-methyl-1H-tetrazol-5-y])thio] methyl]-1-oxa-1-dethia-3-cephem-4-carboxylic acid) and in the 1-sulfur congener on the stability to beta-lactamase were investigated by spectrophotometric and microbiological assays. The 7 alpha-methoxy substituent stabilized the compounds against penicillinase hydrolysis, and the alpha-carboxyl group stabilized them against cephalosporinase. An exception is the beta-lactamase produced by Proteus vulgaris, an inducible cephalosporinase, which hydrolyzed compounds having the alpha-carboxyl group but not those having the 7 alpha-methoxy group. Both substituents exerted their stabilizing effects independently, and compounds with both substituents, e.g., moxalactam (6059-S) and its 1-sulfur congener, were resistant to both penicillinases and cephalosporinases. The stabilization of the compounds to beta-lactamase hydrolysis improved their antibacterial activity against beta-lactamase-producing strains. PMID:6454378

  10. Side-chain H and C resonance assignment in protonated/partially deuterated proteins using an improved 3D 13C-detected HCC-TOCSY

    NASA Astrophysics Data System (ADS)

    Hu, Kaifeng; Vögeli, Beat; Pervushin, Konstantin

    2005-06-01

    We propose the use of 13C-detected 3D HCC-TOCSY experiments for assignment of 1H and 13C resonances in protonated and partially deuterated proteins. The experiments extend 2D C-13-start and C-13-observe TOCSY type experiments proposed earlier [J. Biomol. NMR 26 (2) (2003) 167]. Introduction of the third 1H dimension to 2D TOCSY: (i) reduces the peak overlap and (ii) increases the sensitivity per unit time, even for highly deuterated (>85%) protein samples, which makes this improved method an attractive tool for the side-chain H and C assignment of average sized proteins with natural isotope abundance as well as large partially deuterated proteins. The experiments are demonstrated with a 16 kDa 15N, 13C-labeled non-deuterated apo-CcmE and a 48 kDa uniformly 15N, 13C-labeled and fractionally (˜90%) deuterated dimeric sFkpA. It is predicted that this method should be suitable for the assignment of methyl 13C and 1H chemical shifts of methyl protonated, highly deuterated and 13C-labeled proteins with even higher molecular weight.

  11. Supramolecular phase-selective gelation by peptides bearing side-chain azobenzenes: effect of ultrasound and potential for dye removal and oil spill remediation.

    PubMed

    Bachl, Jürgen; Oehm, Stefan; Mayr, Judith; Cativiela, Carlos; Marrero-Tellado, José Juan; Díaz, David Díaz

    2015-05-22

    Phase selective gelation (PSG) of organic phases from their non-miscible mixtures with water was achieved using tetrapeptides bearing a side-chain azobenzene moiety. The presence of the chromophore allowed PSG at the same concentration as the minimum gelation concentration (MGC) necessary to obtain the gels in pure organic phases. Remarkably, the presence of the water phase during PSG did not impact the thermal, mechanical, and morphological properties of the corresponding organogels. In the case of miscible oil/water mixtures, the entire mixture was gelled, resulting in the formation of quasi-hydrogels. Importantly, PSG could be triggered at room temperature by ultrasound treatment of the mixture or by adding ultrasound-aided concentrated solution of the peptide in an oil-phase to a mixture of the same oil and water. Moreover, the PSG was not affected by the presence of salts or impurities existing in water from natural sources. The process could be scaled-up, and the oil phases (e.g., aromatic solvents, gasoline, diesel fuel) recovered almost quantitatively after a simple distillation process, which also allowed the recovery and reuse of the gelator. Finally, these peptidic gelators could be used to quantitatively remove toxic dyes from aqueous solutions.

  12. The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35

    NASA Astrophysics Data System (ADS)

    Gsponer, Jörg; Haberthür, Urs; Caflisch, Amedeo

    2003-04-01

    Understanding the early steps of aggregation at atomic detail might be crucial for the rational design of therapeutics preventing diseases associated with amyloid deposits. In this paper, aggregation of the heptapeptide GNNQQNY, from the N-terminal prion-determining domain of the yeast protein Sup35, was studied by 20 molecular dynamics runs for a total simulation time of 20 μs. The simulations generate in-register parallel packing of GNNQQNY -strands that is consistent with x-ray diffraction and Fourier transform infrared data. The statistically preferred aggregation pathway does not correspond to a purely downhill profile of the energy surface because of the presence of enthalpic barriers that originate from out-of-register interactions. The parallel -sheet arrangement is favored over the antiparallel because of side-chain contacts; in particular, stacking interactions of the tyrosine rings and hydrogen bonds between amide groups. No ordered aggregation was found in control simulations with the mutant sequence SQNGNQQRG in accord with experimental data and the strong sequence dependence of aggregation.

  13. Sterol side chain reductase 2 is a key enzyme in the biosynthesis of cholesterol, the common precursor of toxic steroidal glycoalkaloids in potato.

    PubMed

    Sawai, Satoru; Ohyama, Kiyoshi; Yasumoto, Shuhei; Seki, Hikaru; Sakuma, Tetsushi; Yamamoto, Takashi; Takebayashi, Yumiko; Kojima, Mikiko; Sakakibara, Hitoshi; Aoki, Toshio; Muranaka, Toshiya; Saito, Kazuki; Umemoto, Naoyuki

    2014-09-01

    Potatoes (Solanum tuberosum) contain α-solanine and α-chaconine, two well-known toxic steroidal glycoalkaloids (SGAs). Sprouts and green tubers accumulate especially high levels of SGAs. Although SGAs were proposed to be biosynthesized from cholesterol, the biosynthetic pathway for plant cholesterol is poorly understood. Here, we identify sterol side chain reductase 2 (SSR2) from potato as a key enzyme in the biosynthesis of cholesterol and related SGAs. Using in vitro enzyme activity assays, we determined that potato SSR2 (St SSR2) reduces desmosterol and cycloartenol to cholesterol and cycloartanol, respectively. These reduction steps are branch points in the biosynthetic pathways between C-24 alkylsterols and cholesterol in potato. Similar enzymatic results were also obtained from tomato SSR2. St SSR2-silenced potatoes or St SSR2-disrupted potato generated by targeted genome editing had significantly lower levels of cholesterol and SGAs without affecting plant growth. Our results suggest that St SSR2 is a promising target gene for breeding potatoes with low SGA levels. PMID:25217510

  14. Comb-shaped conjugates comprising hydroxypropyl cellulose backbones and low-molecular-weight poly(N-isopropylacryamide) side chains for smart hydrogels: synthesis, characterization, and biomedical applications.

    PubMed

    Xu, F J; Zhu, Y; Liu, F S; Nie, J; Ma, J; Yang, W T

    2010-03-17

    Hydroxypropyl cellulose (HPC) possesses a lower critical solution temperature (LCST) above 40 °C, while the poly(N-isopropylacrylamide) (P(NIPAAm)) exhibits a LCST of about 32 °C. Herein, comb-shaped copolymer conjugates of HPC backbones and low-molecular-weight P(NIPAAm) side chains (HPC-g-P(NIPAAm) or HPN) were prepared via atom transfer radical polymerization (ATRP) from the bromoisobutyryl-functionalized HPC biopolymers. By changing the composition ratio of HPC and P(NIPAAm), the LCSTs of HPNs can be adjusted to be lower than the body temperature. The MTT assay from the HEK293 cell line indicated that HPNs possess reduced cytotoxicity. Some of the hydroxyl groups of HPNs were used as cross-linking sites for the preparation of stable HPN hydrogels. In comparison with the HPC hydrogels, the cross-linked HPN hydrogels possess interconnected pore structures and higher swelling ratios. The in vitro release kinetics of fluorescein isothiocyanate-labeled dextran and BSA (or dextran-FITC and BSA-FITC) as model drugs from the hydrogels showed that the HPN hydrogels are suitable for long-term sustained release of macromolecular drugs at body temperature.

  15. Supramolecular Phase-Selective Gelation by Peptides Bearing Side-Chain Azobenzenes: Effect of Ultrasound and Potential for Dye Removal and Oil Spill Remediation

    PubMed Central

    Bachl, Jürgen; Oehm, Stefan; Mayr, Judith; Cativiela, Carlos; Marrero-Tellado, José Juan; Díaz Díaz, David

    2015-01-01

    Phase selective gelation (PSG) of organic phases from their non-miscible mixtures with water was achieved using tetrapeptides bearing a side-chain azobenzene moiety. The presence of the chromophore allowed PSG at the same concentration as the minimum gelation concentration (MGC) necessary to obtain the gels in pure organic phases. Remarkably, the presence of the water phase during PSG did not impact the thermal, mechanical, and morphological properties of the corresponding organogels. In the case of miscible oil/water mixtures, the entire mixture was gelled, resulting in the formation of quasi-hydrogels. Importantly, PSG could be triggered at room temperature by ultrasound treatment of the mixture or by adding ultrasound-aided concentrated solution of the peptide in an oil-phase to a mixture of the same oil and water. Moreover, the PSG was not affected by the presence of salts or impurities existing in water from natural sources. The process could be scaled-up, and the oil phases (e.g., aromatic solvents, gasoline, diesel fuel) recovered almost quantitatively after a simple distillation process, which also allowed the recovery and reuse of the gelator. Finally, these peptidic gelators could be used to quantitatively remove toxic dyes from aqueous solutions. PMID:26006247

  16. Porous silica particles grafted with an amphiphilic side-chain polymer as a stationary phase in reversed-phase high-performance liquid chromatography.

    PubMed

    Shahruzzaman, Md; Takafuji, Makoto; Ihara, Hirotaka

    2015-07-01

    The amphiphilic polymer-grafted silica was newly prepared as a stationary phase in high-performance liquid chromatography. Poly(4-vinylpyridine) with a trimethoxysilyl group at one end was grafted onto porous silica particles and the pyridyl side chains were quaternized with 1-bromooctadecane. The obtained poly(octadecylpyridinium)-grafted silica was characterized by elemental analysis, diffuse reflectance infrared Fourier transform spectroscopy and Brunauer-Emmett-Teller analysis. The degree of quaternization of the pyridyl groups on the obtained stationary phase was estimated to be 70%. The selective retention behaviors of polycyclic aromatic hydrocarbons including some positional isomers were investigated using poly(octadecylpyridinium)-grafted silica as an amphiphilic polymer stationary phase in high-performance liquid chromatography and results were compared with commercially available polymeric octadecylated silica and phenyl-bonded silica columns. The results indicate that the selectivity toward polycyclic aromatic hydrocarbons exhibited by the amphiphilic polymer stationary phase is higher than the corresponding selectivity exhibited by a conventional phenyl-bonded silica column. However, compared with the polymeric octadecylated silica phase, the new stationary phase presents similar retention behavior for polycyclic aromatic hydrocarbons but different retention behavior particularly for positional isomers of disubstituted benzenes as the aggregation structure of amphiphilic polymers on the surface of silica substrate has been altered during mobile phase variation.

  17. Supramolecular phase-selective gelation by peptides bearing side-chain azobenzenes: effect of ultrasound and potential for dye removal and oil spill remediation.

    PubMed

    Bachl, Jürgen; Oehm, Stefan; Mayr, Judith; Cativiela, Carlos; Marrero-Tellado, José Juan; Díaz, David Díaz

    2015-01-01

    Phase selective gelation (PSG) of organic phases from their non-miscible mixtures with water was achieved using tetrapeptides bearing a side-chain azobenzene moiety. The presence of the chromophore allowed PSG at the same concentration as the minimum gelation concentration (MGC) necessary to obtain the gels in pure organic phases. Remarkably, the presence of the water phase during PSG did not impact the thermal, mechanical, and morphological properties of the corresponding organogels. In the case of miscible oil/water mixtures, the entire mixture was gelled, resulting in the formation of quasi-hydrogels. Importantly, PSG could be triggered at room temperature by ultrasound treatment of the mixture or by adding ultrasound-aided concentrated solution of the peptide in an oil-phase to a mixture of the same oil and water. Moreover, the PSG was not affected by the presence of salts or impurities existing in water from natural sources. The process could be scaled-up, and the oil phases (e.g., aromatic solvents, gasoline, diesel fuel) recovered almost quantitatively after a simple distillation process, which also allowed the recovery and reuse of the gelator. Finally, these peptidic gelators could be used to quantitatively remove toxic dyes from aqueous solutions. PMID:26006247

  18. Synthesis of 24-nor-5 beta-cholan-23-oic acid derivatives: a convenient and efficient one-carbon degradation of the side chain of natural bile acids.

    PubMed

    Schteingart, C D; Hofmann, A F

    1988-10-01

    An efficient procedure for obtaining nor-bile acids from natural (C24) bile acids is described. Treatment of formylated bile acids with sodium nitrite in a mixture of trifluoroacetic anhydride with trifluoroacetic acid gives, through a "second order" Beckmann rearrangement, 24-nor-23-nitriles. These compounds, on alkaline hydrolysis, afford the corresponding nor-bile acids in high yields. The sequence was successfully applied to the synthesis of 3 alpha-hydroxy-24-nor-5 beta-cholan-23-oic (norlithocholic) acid, 3 alpha,6 alpha- (norhyodeoxycholic), 3 alpha,7 alpha- (norchenodeoxycholic), 3 alpha,7 beta- (norursodeoxycholic), and 3 alpha,12 alpha-dihydroxy-24-nor-5 beta-cholan-23-oic (nordeoxycholic) acids, as well as 3 alpha,7 alpha,12 alpha-trihydroxy-24-nor-5 beta-cholan-23-oic (norcholic) acid. 13C-NMR spectra of their methyl esters are reported. The procedure provides a more rapid alternative to the Barbier-Wieland degradation for shortening by one methylene group the side chain of natural (C24) bile acids.

  19. Backbone and side chain NMR assignments of Geobacillus stearothermophilus ZapA allow identification of residues that mediate the interaction of ZapA with FtsZ.

    PubMed

    Nogueira, Maria Luiza C; Sforça, Mauricio Luis; Chin, Yanni K-Y; Mobli, Mehdi; Handler, Aaron; Gorbatyuk, Vitaliy Y; Robson, Scott A; King, Glenn F; Gueiros-Filho, Frederico J; Zeri, Ana Carolina de Mattos

    2015-10-01

    Bacterial division begins with the formation of a contractile protein ring at midcell, which constricts the bacterial envelope to generate two daughter cells. The central component of the division ring is FtsZ, a tubulin-like protein capable of self-assembling into filaments which further associate into a higher order structure known as the Z ring. Proteins that bind to FtsZ play a crucial role in the formation and regulation of the Z ring. One such protein is ZapA, a widely conserved 21 kDa homodimeric protein that associates with FtsZ filaments and promotes their bundling. Although ZapA was discovered more than a decade ago, the structural details of its interaction with FtsZ remain unknown. In this work, backbone and side chain NMR assignments for the Geobacillus stearothermophilus ZapA homodimer are described. We titrated FtsZ into (15)N(2)H-ZapA and mapped ZapA residues whose resonances are perturbed upon FtsZ binding. This information provides a structural understanding of the interaction between FtsZ and ZapA.

  20. Nine hydrophobic side chains are key determinants of the thermodynamic stability and oligomerization status of tumour suppressor p53 tetramerization domain.

    PubMed Central

    Mateu, M G; Fersht, A R

    1998-01-01

    The contribution of almost each amino acid side chain to the thermodynamic stability of the tetramerization domain (residues 326-353) of human p53 has been quantitated using 25 mutants with single-residue truncations to alanine (or glycine). Truncation of either Leu344 or Leu348 buried at the tetramer interface, but not of any other residue, led to the formation of dimers of moderate stability (8-9 kcal/mol of dimer) instead of tetramers. One-third of the substitutions were moderately destabilizing (<3.9 kcal/mol of tetramer). Truncations of Arg333, Asn345 or Glu349 involved in intermonomer hydrogen bonds, Ala347 at the tetramer interface or Thr329 were more destabilizing (4.1-5.7 kcal/mol). Strongly destabilizing (8.8- 11.7 kcal/mol) substitutions included those of Met340 at the tetramer interface and Phe328, Arg337 and Phe338 involved peripherally in the hydrophobic core. Truncation of any of the three residues involved centrally in the hydrophobic core of each primary dimer either prevented folding (Ile332) or allowed folding only at high protein concentration or low temperature (Leu330 and Phe341). Nine hydrophobic residues per monomer constitute critical determinants for the stability and oligomerization status of this p53 domain. PMID:9582268

  1. Phenyl propenoic side chain degradation of ferulic acid by Pycnoporus cinnabarinus - elucidation of metabolic pathways using [5-2H]-ferulic acid.

    PubMed

    Krings, U; Pilawa, S; Theobald, C; Berger, R G

    2001-02-23

    The white-rot fungus Pycnoporous cinnabarinus (DMS-1184) was submerged cultured for 22 days under controlled conditions in a bioreactor. After 6, 9, and 15 days of culture the growth medium was supplemented with [5-2H]-labelled ferulic acid (I). The major phenolic compounds identified labelled were four lignans, the methyl esters of ferulic (I) and vanillic acid (VIII), (E)-coniferyl aldehyde (II), (E)-coniferyl alcohol (III), vanillic acid (VIII), vanillin (IX) and vanillyl alcohol (X). The detection of considerable amounts of labelled 4-hydroxy-3-methoxyacetophenone (VII) in the late growth phase suggested the increasing formation and decarboxylation of free 4-hydroxy-3-methoxybenzoylacetic acid (VI) and, thus, a beta-oxidation-like degradation of ferulic acid (I) or its methyl ester to vanillic acid (VIII). 4-Hydroxy-3-methoxybenzoylacetic acid methyl ester (VI) and 3-hydroxy-(4-hydroxy-3-methoxyphenyl)-propanoic acid methyl ester (V) were synthesised and then identified as metabolites in the culture medium. The fungal degradation of the phenyl propenoic side chain of ferulic acid (I), a principal key step of lignin decomposition, appeared to proceed analogous to fatty acids. PMID:11173097

  2. Sterol Side Chain Reductase 2 Is a Key Enzyme in the Biosynthesis of Cholesterol, the Common Precursor of Toxic Steroidal Glycoalkaloids in Potato[W][OPEN

    PubMed Central

    Sawai, Satoru; Ohyama, Kiyoshi; Yasumoto, Shuhei; Seki, Hikaru; Sakuma, Tetsushi; Yamamoto, Takashi; Takebayashi, Yumiko; Kojima, Mikiko; Sakakibara, Hitoshi; Aoki, Toshio; Muranaka, Toshiya; Saito, Kazuki; Umemoto, Naoyuki

    2014-01-01

    Potatoes (Solanum tuberosum) contain α-solanine and α-chaconine, two well-known toxic steroidal glycoalkaloids (SGAs). Sprouts and green tubers accumulate especially high levels of SGAs. Although SGAs were proposed to be biosynthesized from cholesterol, the biosynthetic pathway for plant cholesterol is poorly understood. Here, we identify sterol side chain reductase 2 (SSR2) from potato as a key enzyme in the biosynthesis of cholesterol and related SGAs. Using in vitro enzyme activity assays, we determined that potato SSR2 (St SSR2) reduces desmosterol and cycloartenol to cholesterol and cycloartanol, respectively. These reduction steps are branch points in the biosynthetic pathways between C-24 alkylsterols and chol