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Sample records for native-like protein structures

  1. Capturing native/native like structures with a physico-chemical metric (pcSM) in protein folding.

    PubMed

    Mishra, Avinash; Rao, Satyanarayan; Mittal, Aditya; Jayaram, B

    2013-08-01

    Specification of the three dimensional structure of a protein from its amino acid sequence, also called a "Grand Challenge" problem, has eluded a solution for over six decades. A modestly successful strategy has evolved over the last couple of decades based on development of scoring functions (e.g. mimicking free energy) that can capture native or native-like structures from an ensemble of decoys generated as plausible candidates for the native structure. A scoring function must be fast enough in discriminating the native from unfolded/misfolded structures, and requires validation on a large data set(s) to generate sufficient confidence in the score. Here we develop a scoring function called pcSM that detects true native structure in the top 5 with 93% accuracy from an ensemble of candidate structures. If we eliminate the native from ensemble of decoys then pcSM is able to capture near native structure (RMSD<=5Ǻ) in top 10 with 86% accuracy. The parameters considered in pcSM are a C-alpha Euclidean metric, secondary structural propensity, surface areas and an intramolecular energy function. pcSM has been tested on 415 systems consisting 142,698 decoys (public and CASP-largest reported hitherto in literature). The average rank for the native is 2.38, a significant improvement over that existing in literature. In-silico protein structure prediction requires robust scoring technique(s). Therefore, pcSM is easily amenable to integration into a successful protein structure prediction strategy. The tool is freely available at http://www.scfbio-iitd.res.in/software/pcsm.jsp. PMID:23665455

  2. Assessment of semiempirical enthalpy of formation in solution as an effective energy function to discriminate native-like structures in protein decoy sets.

    PubMed

    Urquiza-Carvalho, Gabriel Aires; Fragoso, Wallace Duarte; Rocha, Gerd Bruno

    2016-08-01

    In this work, we tested the PM6, PM6-DH+, PM6-D3, and PM7 enthalpies of formation in aqueous solution as scoring functions across 33 decoy sets to discriminate native structures or good models in a decoy set. In each set these semiempirical quantum chemistry methods were compared according to enthalpic and geometric criteria. Enthalpically, we compared the methods according to how much lower was the enthalpy of each native, when compared with the mean enthalpy of its set. Geometrically, we compared the methods according to the fraction of native contacts (Q), which is a measure of geometric closeness between an arbitrary structure and the native. For each set and method, the Q of the best decoy was compared with the Q0 , which is the Q of the decoy closest to the native in the set. It was shown that the PM7 method is able to assign larger energy differences between the native structure and the decoys in a set, arguably because of a better description of dispersion interactions, however PM6-DH+ was slightly better than the rest at selecting geometrically good models in the absence of a native structure in the set. © 2016 Wiley Periodicals, Inc. PMID:27249629

  3. Slipknotting upon native-like loop formation in a trefoil knot protein.

    PubMed

    Noel, Jeffrey K; Sułkowska, Joanna I; Onuchic, José N

    2010-08-31

    Protein knots and slipknots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Recent experimental results show that knotting, starting from a fully extended polypeptide, has not yet been observed. Understanding the nucleation process of folding knots is thus a natural challenge for both experimental and theoretical investigation. In this study, we employ energy landscape theory and molecular dynamics to elucidate the entire folding mechanism. The full free energy landscape of a knotted protein is mapped using an all-atom structure-based protein model. Results show that, due to the topological constraint, the protein folds through a three-state mechanism that contains (i) a precise nucleation site that creates a correctly twisted native loop (first barrier) and (ii) a rate-limiting free energy barrier that is traversed by two parallel knot-forming routes. The main route corresponds to a slipknot conformation, a collapsed configuration where the C-terminal helix adopts a hairpin-like configuration while threading, and the minor route to an entropically limited plug motion, where the extended terminus is threaded as through a needle. Knot formation is a late transition state process and results show that random (nonspecific) knots are a very rare and unstable set of configurations both at and below folding temperature. Our study shows that a native-biased landscape is sufficient to fold complex topologies and presents a folding mechanism generalizable to all known knotted protein topologies: knotting via threading a native-like loop in a preordered intermediate. PMID:20702769

  4. Release of Native-like Gaseous Proteins from Electrospray Droplets via the Charged Residue Mechanism: Insights from Molecular Dynamics Simulations.

    PubMed

    McAllister, Robert G; Metwally, Haidy; Sun, Yu; Konermann, Lars

    2015-10-01

    The mechanism whereby gaseous protein ions are released from charged solvent droplets during electrospray ionization (ESI) remains a matter of debate. Also, it is unclear to what extent electrosprayed proteins retain their solution structure. Molecular dynamics (MD) simulations offer insights into the temporal evolution of protein systems. Surprisingly, there have been no all-atom simulations of the protein ESI process to date. The current work closes this gap by investigating the behavior of protein-containing aqueous nanodroplets that carry excess positive charge. We focus on "native ESI", where proteins initially adopt their biologically active solution structures. ESI proceeds while the protein remains entrapped within the droplet. Protein release into the gas phase occurs upon solvent evaporation to dryness. Droplet shrinkage is accompanied by ejection of charge carriers (Na(+) for the conditions chosen here), keeping the droplet at ∼85% of the Rayleigh limit throughout its life cycle. Any remaining charge carriers bind to the protein as the final solvent molecules evaporate. The outcome of these events is largely independent of the initial protein charge and the mode of charge carrier binding. ESI charge states and collision cross sections of the MD structures agree with experimental data. Our results confirm the Rayleigh/charged residue model (CRM). Field emission of excess Na(+) plays an ancillary role by governing the net charge of the shrinking droplet. Models that envision protein ejection from the droplet are not supported. Most nascent CRM ions retain native-like conformations. For unfolded proteins ESI likely proceeds along routes that are different from the native state mechanism explored here. PMID:26325619

  5. Analysis of Native-Like Proteins and Protein Complexes Using Cation to Anion Proton Transfer Reactions (CAPTR)

    NASA Astrophysics Data System (ADS)

    Laszlo, Kenneth J.; Bush, Matthew F.

    2015-12-01

    Mass spectra of native-like protein complexes often exhibit narrow charge-state distributions, broad peaks, and contributions from multiple, coexisting species. These factors can make it challenging to interpret those spectra, particularly for mixtures with significant heterogeneity. Here we demonstrate the use of ion/ion proton transfer reactions to reduce the charge states of m/ z-selected, native-like ions of proteins and protein complexes, a technique that we refer to as cation to anion proton transfer reactions (CAPTR). We then demonstrate that CAPTR can increase the accuracy of charge state assignments and the resolution of interfering species in native mass spectrometry. The CAPTR product ion spectra for pyruvate kinase exhibit ~30 peaks and enable unambiguous determination of the charge state of each peak, whereas the corresponding precursor spectra exhibit ~6 peaks and the assigned charge states have an uncertainty of ±3%. 15+ bovine serum albumin and 21+ yeast enolase dimer both appear near m/ z 4450 and are completely unresolved in a mixture. After a single CAPTR event, the resulting product ions are baseline resolved. The separation of the product ions increases dramatically after each subsequent CAPTR event; 12 events resulted in a 3000-fold improvement in separation relative to the precursor ions. Finally, we introduce a framework for interpreting and predicting the figures of merit for CAPTR experiments. More generally, these results suggest that CAPTR strongly complements other mass spectrometry tools for analyzing proteins and protein complexes, particularly those in mixtures.

  6. Recombinant Minimalist Spider Wrapping Silk Proteins Capable of Native-Like Fiber Formation

    PubMed Central

    Xu, Lingling; Rainey, Jan K.; Meng, Qing; Liu, Xiang-Qin

    2012-01-01

    Spider silks are desirable biomaterials characterized by high tensile strength, elasticity, and biocompatibility. Spiders produce different types of silks for different uses, although dragline silks have been the predominant focus of previous studies. Spider wrapping silk, made of the aciniform protein (AcSp1), has high toughness because of its combination of high elasticity and tensile strength. AcSp1 in Argiope trifasciata contains a 200-aa sequence motif that is repeated at least 14 times. Here, we produced in E. coli recombinant proteins consisting of only one to four of the 200-aa AcSp1 repeats, designated W1 to W4. We observed that purified W2, W3 and W4 proteins could be induced to form silk-like fibers by shear forces in a physiological buffer. The fibers formed by W4 were ∼3.4 µm in diameter and up to 10 cm long. They showed an average tensile strength of 115 MPa, elasticity of 37%, and toughness of 34 J cm−3. The smaller W2 protein formed fewer fibers and required a higher protein concentration to form fibers, whereas the smallest W1 protein did not form silk-like fibers, indicating that a minimum of two of the 200-aa repeats was required for fiber formation. Microscopic examinations revealed structural features indicating an assembly of the proteins into spherical structures, fibrils, and silk-like fibers. CD and Raman spectral analysis of protein secondary structures suggested a transition from predominantly α-helical in solution to increasingly β-sheet in fibers. PMID:23209681

  7. Formation of local native-like tertiary structures in the slow refolding reaction of human carbonic anhydrase II as monitored by circular dichroism on tryptophan mutants.

    PubMed

    Andersson, D; Freskgård, P O; Jonsson, B H; Carlsson, U

    1997-04-15

    In the present study, near-UV CD kinetic measurements on mutants, in which one Trp residue had been replaced, were performed to probe the development of asymmetric environments around specific Trp residues during the refolding of human carbonic anhydrase II (HCAII). In addition, the formation of the active site was probed by the binding of a fluorescent sulfonamide inhibitor. The development of the individual Trp CD spectra during refolding was obtained by subtracting the CD spectrum of the mutant lacking one Trp from that of HCAII at different time points. The same method was used for the particular Trp residues to obtain the kinetic CD traces monitored at a specific wavelength (270 nm). Trp residues 16, 97, and 245 were analyzed. Trp16 probes the N-terminal domain (amino acid residues 1-25), and this part is forming its tertiary structure slower than the major domain (amino acid residues 26-260) of the protein molecule, which contains the active site and a dominating beta-sheet. An essentially native structure of the major domain seems to act as a template for the correct folding of the N terminus. Trp97 is located in a hydrophobic cluster comprising beta-strands 3-5 in the protein core. Previously, we have shown that this region is remarkably stable and compact, and stopped-flow fluorescence data indicate that Trp97 is buried in an apolar compact cluster within a few milliseconds [Svensson, M., Jonasson, P., Freskgård, P.-O., Jonsson, B.-H., Lindgren, M., Martensson, L.-G., Gentile, M., Bóren, K., & Carlsson, U. (1995) Biochemistry 34, 8606-8620; Jonasson, P., Aronsson, G., Carlsson, U., & Jonsson, B.-H. (1997) Biochemistry 36 (in press)]. Here it is shown that the development of the native tertiary structure at Trp97 occurs in the minute time domain. Trp245 is located in a long loop between the N-terminal domain and the core structure. Although this Trp has attained native-like fluorescence properties within the dead time of the CD experiment, it assumes a

  8. The TFE-induced transient native-like structure of the intrinsically disordered σ₄⁷⁰ domain of Escherichia coli RNA polymerase.

    PubMed

    Kaczka, Piotr; Winiewska, Maria; Zhukov, Igor; Rempoła, Bożenna; Bolewska, Krystyna; Łoziński, Tomasz; Ejchart, Andrzej; Poznańska, Anna; Wierzchowski, Kazimierz L; Poznański, Jarosław

    2014-12-01

    The transient folding of domain 4 of an E. coli RNA polymerase σ⁷⁰ subunit (rECσ₄⁷⁰) induced by an increasing concentration of 2,2,2-trifluoroethanol (TFE) in an aqueous solution was monitored by means of CD and heteronuclear NMR spectroscopy. NMR data, collected at a 30% TFE, allowed the estimation of the population of a locally folded rECσ₄⁷⁰ structure (CSI descriptors) and of local backbone dynamics ((15)N relaxation). The spontaneous organization of the helical regions of the initially unfolded protein into a TFE-induced 3D structure was revealed from structural constraints deduced from (15)N- to (13)C-edited NOESY spectra. In accordance with all the applied criteria, three highly populated α-helical regions, separated by much more flexible fragments, form a transient HLHTH motif resembling those found in PDB structures resolved for homologous proteins. All the data taken together demonstrate that TFE induces a transient native-like structure in the intrinsically disordered protein. PMID:25261014

  9. An early intermediate in the folding reaction of the B1 domain of protein G contains a native-like core.

    PubMed

    Park, S H; O'Neil, K T; Roder, H

    1997-11-25

    The folding kinetics of a 57-residue IgG binding domain of streptococcal protein G has been studied under varying solvent conditions, using stopped-flow fluorescence methods. Although GB1 has been cited as an example of a protein that obeys a two-state folding mechanism, the following kinetic observations suggest the presence of an early folding intermediate. Under stabilizing conditions (low denaturant concentrations, especially in the presence of sodium sulfate), the kinetics of folding shows evidence of a major unresolved fluorescence change during the 1.5 ms dead time of the stopped-flow experiment (burst phase). Together with some curvature in the rate profile for the single observable folding phase, this provides clear evidence of the rapid formation of compact states with native-like fluorescence for the single tryptophan at position 43. In refolding experiments at increasing denaturant concentrations, the amplitude of the sub-millisecond phase decreases sharply and the corresponding slope (m value) is only about 30% lower than that of the equilibrium unfolding curve indicative of a pre-equilibrium transition involving cooperative unfolding of an ensemble of compact intermediates. The dependence on guanidine hydrochloride concentration of both rates and amplitudes (including the equilibrium transition) is described quantitatively by a sequential three-state mechanism, U [symbol: see text] I [symbol: see text] N, where an intermediate (I) in rapid equilibrium with the unfolded state (U) precedes the rate-limiting formation of the native state (N). A 66-residue fragment of GB1 with an N-terminal extension containing five apolar side chains exhibits three-state kinetic behavior virtually identical to that of the 57-residue fragment. This is consistent with the presence of a well-shielded native-like core excluding the N-terminal tail in the early folding intermediate and argues against a mechanism involving random hydrophobic collapse, which would predict a

  10. Design and structure of two HIV-1 clade C SOSIP.664 trimers that increase the arsenal of native-like Env immunogens

    PubMed Central

    Julien, Jean-Philippe; Lee, Jeong Hyun; Ozorowski, Gabriel; Hua, Yuanzi; Torrents de la Peña, Alba; de Taeye, Steven W.; Nieusma, Travis; Cupo, Albert; Yasmeen, Anila; Golabek, Michael; Pugach, Pavel; Klasse, P. J.; Moore, John P.; Sanders, Rogier W.; Ward, Andrew B.; Wilson, Ian A.

    2015-01-01

    A key challenge in the quest toward an HIV-1 vaccine is design of immunogens that can generate a broadly neutralizing antibody (bnAb) response against the enormous sequence diversity of the HIV-1 envelope glycoprotein (Env). We previously demonstrated that a recombinant, soluble, fully cleaved SOSIP.664 trimer based on the clade A BG505 sequence is a faithful antigenic and structural mimic of the native trimer in its prefusion conformation. Here, we sought clade C native-like trimers with comparable properties. We identified DU422 and ZM197M SOSIP.664 trimers as being appropriately thermostable (Tm of 63.4 °C and 62.7 °C, respectively) and predominantly native-like, as determined by negative-stain electron microscopy (EM). Size exclusion chromatography, ELISA, and surface plasmon resonance further showed that these trimers properly display epitopes for all of the major bnAb classes, including quaternary-dependent, trimer-apex (e.g., PGT145) and gp120/gp41 interface (e.g., PGT151) epitopes. A cryo-EM reconstruction of the ZM197M SOSIP.664 trimer complexed with VRC01 Fab against the CD4 binding site at subnanometer resolution revealed a striking overall similarity to its BG505 counterpart with expected local conformational differences in the gp120 V1, V2, and V4 loops. These stable clade C trimers contribute additional diversity to the pool of native-like Env immunogens as key components of strategies to induce bnAbs to HIV-1. PMID:26372963

  11. Design and structure of two HIV-1 clade C SOSIP.664 trimers that increase the arsenal of native-like Env immunogens.

    PubMed

    Julien, Jean-Philippe; Lee, Jeong Hyun; Ozorowski, Gabriel; Hua, Yuanzi; Torrents de la Peña, Alba; de Taeye, Steven W; Nieusma, Travis; Cupo, Albert; Yasmeen, Anila; Golabek, Michael; Pugach, Pavel; Klasse, P J; Moore, John P; Sanders, Rogier W; Ward, Andrew B; Wilson, Ian A

    2015-09-22

    A key challenge in the quest toward an HIV-1 vaccine is design of immunogens that can generate a broadly neutralizing antibody (bnAb) response against the enormous sequence diversity of the HIV-1 envelope glycoprotein (Env). We previously demonstrated that a recombinant, soluble, fully cleaved SOSIP.664 trimer based on the clade A BG505 sequence is a faithful antigenic and structural mimic of the native trimer in its prefusion conformation. Here, we sought clade C native-like trimers with comparable properties. We identified DU422 and ZM197M SOSIP.664 trimers as being appropriately thermostable (Tm of 63.4 °C and 62.7 °C, respectively) and predominantly native-like, as determined by negative-stain electron microscopy (EM). Size exclusion chromatography, ELISA, and surface plasmon resonance further showed that these trimers properly display epitopes for all of the major bnAb classes, including quaternary-dependent, trimer-apex (e.g., PGT145) and gp120/gp41 interface (e.g., PGT151) epitopes. A cryo-EM reconstruction of the ZM197M SOSIP.664 trimer complexed with VRC01 Fab against the CD4 binding site at subnanometer resolution revealed a striking overall similarity to its BG505 counterpart with expected local conformational differences in the gp120 V1, V2, and V4 loops. These stable clade C trimers contribute additional diversity to the pool of native-like Env immunogens as key components of strategies to induce bnAbs to HIV-1. PMID:26372963

  12. A native-like intermediate serves as a branching point between the folding and aggregation pathways of the mouse prion protein

    PubMed Central

    Honda, Ryo P.; Xu, Ming; Yamaguchi, Kei-ichi; Roder, Heinrich; Kuwata, Kazuo

    2015-01-01

    SUMMARY Transient folding intermediates and/or partially unfolded equilibrium states are thought to play a key role in the formation of protein aggregates. However, there is only indirect evidence linking accumulation of folding intermediates to aggregation, and the underlying mechanism remains to be elucidated. Here we show that a partially unfolded state of the prion protein accumulates both as a stable equilibrium state at acidic pH (A-state) and as a late folding intermediate. With a time resolution of approximately 60 μs, we systematically studied the kinetics of folding and unfolding, starting from various initial conditions including the U-, N-, and A-states. Quantitative modeling showed that the observed kinetic data are completely consistent with a sequential four-state mechanism where the A-state is a late folding intermediate. Combined with previous evidence linking A-state accumulation to aggregation, the results indicate that this native-like state serves as a branching point between the folding and aggregation pathways. PMID:26256540

  13. Controlling the Ratio between Native-Like, Non-Native-Like, and Aggregated β-Lactoglobulin after Heat Treatment.

    PubMed

    Delahaije, Roy J B M; Gruppen, Harry; van Eijk van Boxtel, Evelien L; Cornacchia, Leonardo; Wierenga, Peter A

    2016-06-01

    The amount of heat-denatured whey protein is typically determined by pH 4.6 precipitation. Using this method, a significant amount of nondenatured protein was reported even after long heating times. Apparently, a fraction of the unfolded protein refolds into the "native" state rather than form aggregates. This fact is known and has been explained using kinetic models. How the conditions affect the refolding and aggregation is, however, not fully understood. Therefore, this study investigates the unfolding, refolding, and aggregation process of β-lactoglobulin using circular dichroism and size-exclusion chromatography to characterize different folding variants and to quantify their content. The proteins remaining in solution at pH 4.6 were confirmed to be native-like. The nonaggregated fraction contains proteins with a native-like and two types of non-native-like conformations. The nonaggregated fraction increased with decreasing temperature (60-90 °C) and concentration (1-50 g/L) and increasing electrostatic repulsion (pH 7-8; 0-50 mM). The native-like fraction in the nonaggregated fraction was independent of pH, ionic strength, and concentration but increased with decreasing temperature. PMID:27186663

  14. Influences of Membrane Mimetic Environments on Membrane Protein Structures

    PubMed Central

    Zhou, Huan-Xiang; Cross, Timothy A.

    2013-01-01

    The number of membrane protein structures in the Protein Data Bank is becoming significant and growing. Here, the transmembrane domain structures of the helical membrane proteins are evaluated to assess the influences of the membrane mimetic environments. Toward this goal, many of the biophysical properties of membranes are discussed and contrasted with those of the membrane mimetics commonly used for structure determination. Although the mimetic environments can perturb the protein structures to an extent that potentially gives rise to misinterpretation of functional mechanisms, there are also many structures that have a native-like appearance. From this assessment, an initial set of guidelines is proposed for distinguishing native-like from nonnative-like membrane protein structures. With experimental techniques for validation and computational methods for refinement and quality assessment and enhancement, there are good prospects for achieving native-like structures for these very important proteins. PMID:23451886

  15. A Native-Like SOSIP.664 Trimer Based on an HIV-1 Subtype B env Gene

    PubMed Central

    Pugach, Pavel; Ozorowski, Gabriel; Cupo, Albert; Ringe, Rajesh; Yasmeen, Anila; de Val, Natalia; Derking, Ronald; Kim, Helen J.; Korzun, Jacob; Golabek, Michael; de los Reyes, Kevin; Ketas, Thomas J.; Julien, Jean-Philippe; Burton, Dennis R.; Wilson, Ian A.; Sanders, Rogier W.; Klasse, P. J.

    2015-01-01

    ABSTRACT Recombinant trimeric mimics of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) spike should expose as many epitopes as possible for broadly neutralizing antibodies (bNAbs) but few, if any, for nonneutralizing antibodies (non-NAbs). Soluble, cleaved SOSIP.664 gp140 trimers based on the subtype A strain BG505 approach this ideal and are therefore plausible vaccine candidates. Here, we report on the production and in vitro properties of a new SOSIP.664 trimer derived from a subtype B env gene, B41, including how to make this protein in low-serum media without proteolytic damage (clipping) to the V3 region. We also show that nonclipped trimers can be purified successfully via a positive-selection affinity column using the bNAb PGT145, which recognizes a quaternary structure-dependent epitope at the trimer apex. Negative-stain electron microscopy imaging shows that the purified, nonclipped, native-like B41 SOSIP.664 trimers contain two subpopulations, which we propose represent an equilibrium between the fully closed and a more open conformation. The latter is different from the fully open, CD4 receptor-bound conformation and may represent an intermediate state of the trimer. This new subtype B trimer adds to the repertoire of native-like Env proteins that are suitable for immunogenicity and structural studies. IMPORTANCE The cleaved, trimeric envelope protein complex is the only neutralizing antibody target on the HIV-1 surface. Many vaccine strategies are based on inducing neutralizing antibodies. For HIV-1, one approach involves using recombinant, soluble protein mimics of the native trimer. At present, the only reliable way to make native-like, soluble trimers in practical amounts is via the introduction of specific sequence changes that confer stability on the cleaved form of Env. The resulting proteins are known as SOSIP.664 gp140 trimers, and the current paradigm is based on the BG505 subtype A env gene. Here, we describe the

  16. What makes a protein a protein? Hydrophobic core designs that specify stability and structural properties.

    PubMed Central

    Munson, M.; Balasubramanian, S.; Fleming, K. G.; Nagi, A. D.; O'Brien, R.; Sturtevant, J. M.; Regan, L.

    1996-01-01

    Here we describe how the systematic redesign of a protein's hydrophobic core alters its structure and stability. We have repacked the hydrophobic core of the four-helix-bundle protein, Rop, with altered packing patterns and various side chain shapes and sizes. Several designs reproduce the structure and native-like properties of the wild-type, while increasing the thermal stability. Other designs, either with similar sizes but different shapes, or with decreased sizes of the packing residues, destabilize the protein. Finally, overpacking the core with the larger side chains causes a loss of native-like structure. These results allow us to further define the roles of tight residue packing and the burial of hydrophobic surface area in the construction of native-like proteins. PMID:8844848

  17. Coexistence of Native-Like and Non-Native Cytochrome c on Anionic Liposomes with Different Cardiolipin Content.

    PubMed

    Pandiscia, Leah A; Schweitzer-Stenner, Reinhard

    2015-10-01

    We employed a combination of fluorescence, visible circular dichroism, and absorption spectroscopy to study the conformational changes of ferricytochrome c upon its binding to cardiolipin-containing small unilamellar vesicles. The measurements were performed as a function of the cardiolipin concentration, the cardiolipin content of the liposomes, and the NaCl concentration of the solvent. The data were analyzed with a novel model that combines a single binding step with a conformational equilibrium between native-like and non-native-like proteins bound to the membrane surface. The equilibrium between the two conformations, which themselves are comprised of structurally slightly different subconformations, shifts to the more non-native-like conformation with increasing cardiolipin concentration. For the binding isotherms described in this paper, we explicitly considered the enthalpic and entropic contributions of molecular crowding to protein binding at low lipid concentrations and high occupancy of the liposome surface. Increasing the CL content of liposomes increases the overall binding affinity but makes the conformational distribution much more susceptible to the influence of sodium and chloride ions, which shifts the equilibrium toward the more native-like state and directly inhibits binding, particularly to liposomes with 100% cardiolipin content. Spectroscopic evidence further suggests that a fraction of the non-native conformers adopts a pentacoordinated state similar to those obtained in class C peroxidases. On the basis of our results, we propose a hypothesis that describes the balance between facilitating and impeding forces controlling the peroxidase activity of cytochrome c in the inner membrane space of mitochondria. PMID:26369421

  18. Glycerol-induced folding of unstructured disulfide-deficient lysozyme into a native-like conformation.

    PubMed

    Sakamoto, Keiko; Hirai, Ken-Ichi; Kitamura, Yoshiaki; Yamazaki, Kouta; Yusa, Mitsunobu; Tokunaga, Naoki; Doi, Gakuji; Noda, Yasuo; Tachibana, Hideki; Segawa, Shin-Ichi

    2009-08-01

    2SS[6-127,64-80] variant of lysozyme which has two disulfide bridges, Cys6-Cys127 and Cys64-Cys80, and lacks the other two disulfide bridges, Cys30-Cys115 and Cys76-Cys94, was quite unstructured in water, but a part of the polypeptide chain was gradually frozen into a native-like conformation with increasing glycerol concentration. It was monitored from the protection factors of amide hydrogens against H/D exchange. In solution containing various concentrations of glycerol, H/D exchange reactions were carried out at pH* 3.0 and 4 degrees C. Then, (1)H-(15)N-HSQC spectra of partially deuterated protein were measured in a quenching buffer for H/D exchange (95% DMSO/5% D(2)O mixture at pH* 5.5 adjusted with dichloroacetate). In a solution of 10% glycerol, the protection factors were nearly equal to 10 at most of residues. With increasing glycerol concentration, some selected regions were further protected, and their protection factors reached about a 1000 in 30% glycerol solution. The highly protected residues were included in A-, B-, and C-helices and beta3-strand, and especially centered on Ile 55 and Leu 56. In 2SS[6-127,64-80], long-range interactions were recovered due to the preferential hydration by glycerol in the hydrophobic box of the alpha-domain. Glycerol-induced recovering of the native-like structure is discussed from the viewpoint of molten globules growing with the protein folding. (c) 2009 Wiley Periodicals, Inc. Biopolymers 91: 665-675, 2009.This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com. PMID:19353641

  19. Protein Structure

    ERIC Educational Resources Information Center

    Asmus, Elaine Garbarino

    2007-01-01

    Individual students model specific amino acids and then, through dehydration synthesis, a class of students models a protein. The students clearly learn amino acid structure, primary, secondary, tertiary, and quaternary structure in proteins and the nature of the bonds maintaining a protein's shape. This activity is fun, concrete, inexpensive and…

  20. Binding of inferred germline precursors of broadly neutralizing HIV-1 antibodies to native-like envelope trimers

    PubMed Central

    Sliepen, Kwinten; Medina-Ramírez, Max; Yasmeen, Anila; Moore, John P.; Klasse, Per Johan; Sanders, Rogier W.

    2016-01-01

    HIV-1 envelope glycoproteins (Env) and Env-based immunogens usually do not interact efficiently with the inferred germline precursors of known broadly neutralizing antibodies (bNAbs). This deficiency may be one reason why Env and Env-based immunogens are not efficient at inducing bNAbs. We evaluated the binding of 15 inferred germline precursors of bNAbs directed to different epitope clusters to three soluble native-like SOSIP.664 Env trimers. We found that native-like SOSIP.664 trimers bind to some inferred germline precursors of bNAbs, particularly ones involving the V1/V2 loops at the apex of the trimer. The data imply that native-like SOSIP.664 trimers will be an appropriate platform for structure-guided design improvements intended to create immunogens able to target the germline precursors of bNAbs. PMID:26433050

  1. HIV Neutralizing Antibodies Induced by Native-like Envelope Trimers

    PubMed Central

    Sanders, Rogier W.; van Gils, Marit J.; Derking, Ronald; Sok, Devin; Ketas, Thomas J.; Burger, Judith A.; Ozorowski, Gabriel; Cupo, Albert; Simonich, Cassandra; Goo, Leslie; Arendt, Heather; Kim, Helen J.; Lee, Jeong Hyun; Pugach, Pavel; Williams, Melissa; Debnath, Gargi; Moldt, Brian; van Breemen, Mariëlle J.; Isik, Gözde; Medina-Ramírez, Max; Back, Jaap Willem; Koff, Wayne; Julien, Jean-Philippe; Rakasz, Eva G.; Seaman, Michael S.; Guttman, Miklos; Lee, Kelly K.; Klasse, Per Johan; LaBranche, Celia; Schief, William R.; Wilson, Ian A.; Overbaugh, Julie; Burton, Dennis R.; Ward, Andrew B.; Montefiori, David C.; Dean, Hansi; Moore, John P.

    2015-01-01

    A challenge for HIV-1 immunogen design is inducing neutralizing antibodies (NAbs) against neutralization-resistant (Tier-2) viruses that dominate human transmissions. We show that a soluble recombinant HIV-1 envelope glycoprotein trimer that adopts a native conformation (BG505 SOSIP.664) induced NAbs potently against the sequence-matched Tier-2 virus in rabbits and similar but weaker responses in macaques. The trimer also consistently induced cross-reactive NAbs against more sensitive (Tier-1) viruses. Tier-2 NAbs recognized conformational epitopes that differed between animals and in some cases overlapped with those recognized by broadly neutralizing antibodies (bNAbs), whereas Tier-1 responses targeted linear V3 epitopes. A second trimer, B41 SOSIP.664, also induced a strong autologous Tier-2 NAb response in rabbits. Thus, native-like trimers represent a promising starting point for developing HIV-1 vaccines aimed at inducing bNAbs. PMID:26089353

  2. How native-like is non-native language processing?

    PubMed

    Clahsen, Harald; Felser, Claudia

    2006-12-01

    Following several decades of research on native language (L1) processing, psycholinguists have more recently begun to investigate how non-native language (L2) speakers comprehend and process language in real time. Regarding the traditional assumption that L2 learners have 'difficulty with grammar', this new research has revealed some unexpected similarities and differences between L1 and L2 processing. Specifically, it appears that L2 processing can become native-like in some linguistic subdomains (including certain aspects of grammar) but that L1 and L2 processing differences persist in the domain of complex syntax, even in highly proficient L2 speakers. Thus, more subtle linguistic distinctions seem to be required to understand the nature of non-native language processing. PMID:17071131

  3. Native like helices in a specially designed β peptide in the gas phase.

    PubMed

    Schubert, Franziska; Pagel, Kevin; Rossi, Mariana; Warnke, Stephan; Salwiczek, Mario; Koksch, Beate; von Helden, Gert; Blum, Volker; Baldauf, Carsten; Scheffler, Matthias

    2015-02-21

    In the natural peptides, helices are stabilized by hydrogen bonds that point backward along the sequence direction. Until now, there is only little evidence for the existence of analogous structures in oligomers of conformationally unrestricted β amino acids. We specifically designed the β peptide Ac-(β(2)hAla)6-LysH(+) to form native like helical structures in the gas phase. The design follows the known properties of the peptide Ac-Ala6-LysH(+) that forms a α helix in isolation. We perform ion-mobility mass-spectrometry and vibrational spectroscopy in the gas phase, combined with state-of-the-art density-functional theory simulations of these molecular systems in order to characterize their structure. We can show that the straightforward exchange of alanine residues for the homologous β amino acids generates a system that is generally capable of adopting native like helices with backward oriented H-bonds. By pushing the limits of theory and experiments, we show that one cannot assign a single preferred structure type due to the densely populated energy landscape and present an interpretation of the data that suggests an equilibrium of three helical structures. PMID:25611682

  4. Multipass Membrane Protein Structure Prediction Using Rosetta

    PubMed Central

    Yarov-Yarovoy, Vladimir; Schonbrun, Jack; Baker, David

    2006-01-01

    We describe the adaptation of the Rosetta de novo structure prediction method for prediction of helical transmembrane protein structures. The membrane environment is modeled by embedding the protein chain into a model membrane represented by parallel planes defining hydrophobic, interface, and polar membrane layers for each energy evaluation. The optimal embedding is determined by maximizing the exposure of surface hydrophobic residues within the membrane and minimizing hydrophobic exposure outside of the membrane. Protein conformations are built up using the Rosetta fragment assembly method and evaluated using a new membrane-specific version of the Rosetta low-resolution energy function in which residue–residue and residue–environment interactions are functions of the membrane layer in addition to amino acid identity, distance, and density. We find that lower energy and more native-like structures are achieved by sequential addition of helices to a growing chain, which may mimic some aspects of helical protein biogenesis after translocation, rather than folding the whole chain simultaneously as in the Rosetta soluble protein prediction method. In tests on 12 membrane proteins for which the structure is known, between 51 and 145 residues were predicted with root-mean-square deviation <4Å from the native structure. PMID:16372357

  5. A Native-Like Corneal Construct Using Donor Corneal Stroma for Tissue Engineering

    PubMed Central

    Lin, Jing; Yoon, Kyung-Chul; Zhang, Lili; Su, Zhitao; Lu, Rong; Ma, Ping; De Paiva, Cintia S.; Pflugfelder, Stephen C.; Li, De-Quan

    2012-01-01

    Tissue engineering holds great promise for corneal transplantation to treat blinding diseases. This study was to explore the use of natural corneal stroma as an optimal substrate to construct a native like corneal equivalent. Human corneal epithelium was cultivated from donor limbal explants on corneal stromal discs prepared by FDA approved Horizon Epikeratome system. The morphology, phenotype, regenerative capacity and transplantation potential were evaluated by hematoxylin eosin and immunofluorescent staining, a wound healing model, and the xeno-transplantation of the corneal constructs to nude mice. An optically transparent and stratified epithelium was rapidly generated on donor corneal stromal substrate and displayed native-like morphology and structure. The cells were polygonal in the basal layer and became flattened in superficial layers. The epithelium displayed a phenotype similar to human corneal epithelium in vivo. The differentiation markers, keratin 3, involucrin and connexin 43, were expressed in full or superficial layers. Interestingly, certain basal cells were immunopositive to antibodies against limbal stem/progenitor cell markers ABCG2 and p63, which are usually negative in corneal epithelium in vivo. It suggests that this bioengineered corneal epithelium shared some characteristics of human limbal epithelium in vivo. This engineered epithelium was able to regenerate in 4 days following from a 4mm-diameter wound created by a filter paper soaked with 1 N NaOH. This corneal construct survived well after xeno-transplantation to the back of a nude mouse. The transplanted epithelium remained multilayer and became thicker with a phenotype similar to human corneal epithelium. Our findings demonstrate that natural corneal stroma is an optimal substrate for tissue bioengineering, and a native-like corneal construct has been created with epithelium containing limbal stem cells. This construct may have great potential for clinical use in corneal

  6. Influences on the Design and Purification of Soluble, Recombinant Native-Like HIV-1 Envelope Glycoprotein Trimers

    PubMed Central

    Ringe, Rajesh P.; Yasmeen, Anila; Ozorowski, Gabriel; Go, Eden P.; Pritchard, Laura K.; Guttman, Miklos; Ketas, Thomas A.; Cottrell, Christopher A.; Wilson, Ian A.; Sanders, Rogier W.; Cupo, Albert; Crispin, Max; Lee, Kelly K.; Desaire, Heather; Ward, Andrew B.; Klasse, P. J.

    2015-01-01

    ABSTRACT We have investigated factors that influence the production of native-like soluble, recombinant trimers based on the env genes of two isolates of human immunodeficiency virus type 1 (HIV-1), specifically 92UG037.8 (clade A) and CZA97.012 (clade C). When the recombinant trimers based on the env genes of isolates 92UG037.8 and CZA97.012 were made according to the SOSIP.664 design and purified by affinity chromatography using broadly neutralizing antibodies (bNAbs) against quaternary epitopes (PGT145 and PGT151, respectively), the resulting trimers are highly stable and they are fully native-like when visualized by negative-stain electron microscopy. They also have a native-like (i.e., abundant) oligomannose glycan composition and display multiple bNAb epitopes while occluding those for nonneutralizing antibodies. In contrast, uncleaved, histidine-tagged Foldon (Fd) domain-containing gp140 proteins (gp140UNC-Fd-His), based on the same env genes, very rarely form native-like trimers, a finding that is consistent with their antigenic and biophysical properties and glycan composition. The addition of a 20-residue flexible linker (FL20) between the gp120 and gp41 ectodomain (gp41ECTO) subunits to make the uncleaved 92UG037.8 gp140-FL20 construct is not sufficient to create a native-like trimer, but a small percentage of native-like trimers were produced when an I559P substitution in gp41ECTO was also present. The further addition of a disulfide bond (SOS) to link the gp120 and gp41 subunits in the uncleaved gp140-FL20-SOSIP protein increases native-like trimer formation to ∼20 to 30%. Analysis of the disulfide bond content shows that misfolded gp120 subunits are abundant in uncleaved CZA97.012 gp140UNC-Fd-His proteins but very rare in native-like trimer populations. The design and stabilization method and the purification strategy are, therefore, all important influences on the quality of trimeric Env proteins and hence their suitability as vaccine components

  7. Extracting knowledge from protein structure geometry

    PubMed Central

    Røgen, Peter; Koehl, Patrice

    2013-01-01

    Protein structure prediction techniques proceed in two steps, namely the generation of many structural models for the protein of interest, followed by an evaluation of all these models to identify those that are native-like. In theory, the second step is easy, as native structures correspond to minima of their free energy surfaces. It is well known however that the situation is more complicated as the current force fields used for molecular simulations fail to recognize native states from misfolded structures. In an attempt to solve this problem we follow an alternate approach and derive a new potential from geometric knowledge extracted from native and misfolded conformers of protein structures. This new potential, MPP, has two main features that are key to its success. Firstly, it is composite in that it includes local and non local geometric information on proteins. At the short range level it captures and quantifies the mapping between the sequences and structures of short (7-mer) fragments of protein backbones through the introduction of a new local energy term. The local energy term is then augmented with a non local residue-based pairwise potential, and a solvent potential. Secondly, it is optimized to yield a maximized correlation between the energy of a structural model and its RMS to the native structure of the corresponding protein. We have shown that MPP yields high correlation values between RMS and energy and that it is able to retrieve the native structure of a protein from a set of high-resolution decoys. PMID:23280479

  8. Production of Influenza Virus HA1 Harboring Native-Like Epitopes by Pichia pastoris.

    PubMed

    Lin, Qingshan; Yang, Kunyu; He, Fangping; Jiang, Jie; Li, Tingting; Chen, Zhenqin; Li, Rui; Chen, Yixin; Li, Shaowei; Zhao, Qinjian; Xia, Ningshao

    2016-08-01

    The outbreak of the H5N1 highly pathogenic avian influenza which exhibits high variation had brought a serious threat to the safety of humanity. To overcome this high variation, hemagglutinin-based recombinant subunit vaccine with rational design has been considered as a substitute for traditional virion-based vaccine development. Here, we expressed HA1 part of the hemagglutinin protein using the Pichia pastoris expression system and attained a high yield of about 120 mg/L through the use of fed-batch scalable fermentation. HA1 protein in the culture supernatant was purified using two-step ion-exchange chromatography. The resultant HA1 protein was homogeneous in solution in a glycosylated form, as confirmed by endoglycosidase H treatment. Sedimentation velocity tests, silver staining of protein gels, and immunoblotting were used for verification. The native HA1 reacted well with conformational, cross-genotype, neutralizing monoclonal antibodies, whereas a loss of binding activity was noted with the denatured HA1 form. Moreover, the murine anti-HA1 serum exhibited a virus-capture capability in the hemagglutination inhibition assay, which suggests that HA1 harbors native-like epitopes. In conclusion, soluble HA1 was efficiently expressed and purified in this study. The functional glycosylated protein will be an alternative for the development of recombinant protein-based influenza vaccine. PMID:27040529

  9. Cytochrome c folds through foldon-dependent native-like intermediates in an ordered pathway

    PubMed Central

    Hu, Wenbing; Kan, Zhong-Yuan; Mayne, Leland; Englander, S. Walter

    2016-01-01

    Previous hydrogen exchange (HX) studies of the spontaneous reversible unfolding of Cytochrome c (Cyt c) under native conditions have led to the following conclusions. Native Cyt c (104 residues) is composed of five cooperative folding units, called foldons. The high-energy landscape is dominated by an energy ladder of partially folded forms that differ from each other by one cooperative foldon unit. The reversible equilibrium unfolding of native Cyt c steps up through these intermediate forms to the unfolded state in an energy-ordered sequence, one foldon unit at a time. To more directly study Cyt c intermediates and pathways during normal energetically downhill kinetic folding, the present work used HX pulse labeling analyzed by a fragment separation–mass spectrometry method. The results show that 95% or more of the Cyt c population folds by stepping down through the same set of foldon-dependent pathway intermediates as in energetically uphill equilibrium unfolding. These results add to growing evidence that proteins fold through a classical pathway sequence of native-like intermediates rather than through a vast number of undefinable intermediates and pathways. The present results also emphasize the condition-dependent nature of kinetic barriers, which, with less informative experimental methods (fluorescence, etc.), are often confused with variability in intermediates and pathways. PMID:26966231

  10. Cytochrome c folds through foldon-dependent native-like intermediates in an ordered pathway.

    PubMed

    Hu, Wenbing; Kan, Zhong-Yuan; Mayne, Leland; Englander, S Walter

    2016-04-01

    Previous hydrogen exchange (HX) studies of the spontaneous reversible unfolding of Cytochrome c (Cyt c) under native conditions have led to the following conclusions. Native Cyt c (104 residues) is composed of five cooperative folding units, called foldons. The high-energy landscape is dominated by an energy ladder of partially folded forms that differ from each other by one cooperative foldon unit. The reversible equilibrium unfolding of native Cyt c steps up through these intermediate forms to the unfolded state in an energy-ordered sequence, one foldon unit at a time. To more directly study Cyt c intermediates and pathways during normal energetically downhill kinetic folding, the present work used HX pulse labeling analyzed by a fragment separation-mass spectrometry method. The results show that 95% or more of the Cyt c population folds by stepping down through the same set of foldon-dependent pathway intermediates as in energetically uphill equilibrium unfolding. These results add to growing evidence that proteins fold through a classical pathway sequence of native-like intermediates rather than through a vast number of undefinable intermediates and pathways. The present results also emphasize the condition-dependent nature of kinetic barriers, which, with less informative experimental methods (fluorescence, etc.), are often confused with variability in intermediates and pathways. PMID:26966231

  11. Presenting native-like trimeric HIV-1 antigens with self-assembling nanoparticles.

    PubMed

    He, Linling; de Val, Natalia; Morris, Charles D; Vora, Nemil; Thinnes, Therese C; Kong, Leopold; Azadnia, Parisa; Sok, Devin; Zhou, Bin; Burton, Dennis R; Wilson, Ian A; Nemazee, David; Ward, Andrew B; Zhu, Jiang

    2016-01-01

    Structures of BG505 SOSIP.664 trimer in complex with broadly neutralizing antibodies (bNAbs) have revealed the critical role of trimeric context for immune recognition of HIV-1. Presentation of trimeric HIV-1 antigens on nanoparticles may thus provide promising vaccine candidates. Here we report the rational design, structural analysis and antigenic evaluation of HIV-1 trimer-presenting nanoparticles. We first demonstrate that both V1V2 and gp120 can be presented in native-like trimeric conformations on nanoparticles. We then design nanoparticles presenting various forms of stabilized gp140 trimer based on ferritin and a large, 60-meric E2p that displays 20 spikes mimicking virus-like particles (VLPs). Particle assembly is confirmed by electron microscopy (EM), while antigenic profiles are generated using representative bNAbs and non-NAbs. Lastly, we demonstrate high-yield gp140 nanoparticle production and robust stimulation of B cells carrying cognate VRC01 receptors by gp120 and gp140 nanoparticles. Together, our study provides an arsenal of multivalent immunogens for HIV-1 vaccine development. PMID:27349934

  12. Presenting native-like trimeric HIV-1 antigens with self-assembling nanoparticles

    PubMed Central

    He, Linling; de Val, Natalia; Morris, Charles D.; Vora, Nemil; Thinnes, Therese C.; Kong, Leopold; Azadnia, Parisa; Sok, Devin; Zhou, Bin; Burton, Dennis R.; Wilson, Ian A; Nemazee, David; Ward, Andrew B.; Zhu, Jiang

    2016-01-01

    Structures of BG505 SOSIP.664 trimer in complex with broadly neutralizing antibodies (bNAbs) have revealed the critical role of trimeric context for immune recognition of HIV-1. Presentation of trimeric HIV-1 antigens on nanoparticles may thus provide promising vaccine candidates. Here we report the rational design, structural analysis and antigenic evaluation of HIV-1 trimer-presenting nanoparticles. We first demonstrate that both V1V2 and gp120 can be presented in native-like trimeric conformations on nanoparticles. We then design nanoparticles presenting various forms of stabilized gp140 trimer based on ferritin and a large, 60-meric E2p that displays 20 spikes mimicking virus-like particles (VLPs). Particle assembly is confirmed by electron microscopy (EM), while antigenic profiles are generated using representative bNAbs and non-NAbs. Lastly, we demonstrate high-yield gp140 nanoparticle production and robust stimulation of B cells carrying cognate VRC01 receptors by gp120 and gp140 nanoparticles. Together, our study provides an arsenal of multivalent immunogens for HIV-1 vaccine development. PMID:27349934

  13. Structures of membrane proteins

    PubMed Central

    Vinothkumar, Kutti R.; Henderson, Richard

    2010-01-01

    In reviewing the structures of membrane proteins determined up to the end of 2009, we present in words and pictures the most informative examples from each family. We group the structures together according to their function and architecture to provide an overview of the major principles and variations on the most common themes. The first structures, determined 20 years ago, were those of naturally abundant proteins with limited conformational variability, and each membrane protein structure determined was a major landmark. With the advent of complete genome sequences and efficient expression systems, there has been an explosion in the rate of membrane protein structure determination, with many classes represented. New structures are published every month and more than 150 unique membrane protein structures have been determined. This review analyses the reasons for this success, discusses the challenges that still lie ahead, and presents a concise summary of the key achievements with illustrated examples selected from each class. PMID:20667175

  14. Solid state NMR strategy for characterizing native membrane protein structures.

    PubMed

    Murray, Dylan T; Das, Nabanita; Cross, Timothy A

    2013-09-17

    structural results. By combining the distance, torsional, and orientational restraints, we can characterize high resolution membrane protein structure in native-like lipid bilayer environments. PMID:23470103

  15. Simplified protein models can rival all atom simulations in predicting folding pathways and structure

    PubMed Central

    Adhikari, Aashish N.; Freed, Karl F.; Sosnick, Tobin R.

    2014-01-01

    We demonstrate the ability of simultaneously determining a protein’s folding pathway and structure using a properly formulated model without prior knowledge of the native structure. Our model employs a natural coordinate system for describing proteins and a search strategy inspired by the observation that real proteins fold in a sequential fashion by incrementally stabilizing native-like substructures or "foldons". Comparable folding pathways and structures are obtained for the twelve proteins recently studied using atomistic molecular dynamics simulations [K. Lindorff-Larsen, S. Piana, R.O. Dror, D. E. Shaw, Science 334, 517 (2011)], with our calculations running several orders of magnitude faster. We find that native-like propensities in the unfolded state do not necessarily determine the order of structure formation, a departure from a major conclusion of the MD study. Instead, our results support a more expansive view wherein intrinsic local structural propensities may be enhanced or overridden in the folding process by environmental context. The success of our search strategy validates it as an expedient mechanism for folding both in silico and in vivo. PMID:23889448

  16. Protein Structure Databases.

    PubMed

    Laskowski, Roman A

    2016-01-01

    Web-based protein structure databases come in a wide variety of types and levels of information content. Those having the most general interest are the various atlases that describe each experimentally determined protein structure and provide useful links, analyses, and schematic diagrams relating to its 3D structure and biological function. Also of great interest are the databases that classify 3D structures by their folds as these can reveal evolutionary relationships which may be hard to detect from sequence comparison alone. Related to these are the numerous servers that compare folds-particularly useful for newly solved structures, and especially those of unknown function. Beyond these are a vast number of databases for the more specialized user, dealing with specific families, diseases, structural features, and so on. PMID:27115626

  17. Second language processing shows increased native-like neural responses after months of no exposure.

    PubMed

    Morgan-Short, Kara; Finger, Ingrid; Grey, Sarah; Ullman, Michael T

    2012-01-01

    Although learning a second language (L2) as an adult is notoriously difficult, research has shown that adults can indeed attain native language-like brain processing and high proficiency levels. However, it is important to then retain what has been attained, even in the absence of continued exposure to the L2--particularly since periods of minimal or no L2 exposure are common. This event-related potential (ERP) study of an artificial language tested performance and neural processing following a substantial period of no exposure. Adults learned to speak and comprehend the artificial language to high proficiency with either explicit, classroom-like, or implicit, immersion-like training, and then underwent several months of no exposure to the language. Surprisingly, proficiency did not decrease during this delay. Instead, it remained unchanged, and there was an increase in native-like neural processing of syntax, as evidenced by several ERP changes--including earlier, more reliable, and more left-lateralized anterior negativities, and more robust P600s, in response to word-order violations. Moreover, both the explicitly and implicitly trained groups showed increased native-like ERP patterns over the delay, indicating that such changes can hold independently of L2 training type. The results demonstrate that substantial periods with no L2 exposure are not necessarily detrimental. Rather, benefits may ensue from such periods of time even when there is no L2 exposure. Interestingly, both before and after the delay the implicitly trained group showed more native-like processing than the explicitly trained group, indicating that type of training also affects the attainment of native-like processing in the brain. Overall, the findings may be largely explained by a combination of forgetting and consolidation in declarative and procedural memory, on which L2 grammar learning appears to depend. The study has a range of implications, and suggests a research program with

  18. Reconstructing Protein Structures by Neural Network Pairwise Interaction Fields and Iterative Decoy Set Construction

    PubMed Central

    Mirabello, Claudio; Adelfio, Alessandro; Pollastri, Gianluca

    2014-01-01

    Predicting the fold of a protein from its amino acid sequence is one of the grand problems in computational biology. While there has been progress towards a solution, especially when a protein can be modelled based on one or more known structures (templates), in the absence of templates, even the best predictions are generally much less reliable. In this paper, we present an approach for predicting the three-dimensional structure of a protein from the sequence alone, when templates of known structure are not available. This approach relies on a simple reconstruction procedure guided by a novel knowledge-based evaluation function implemented as a class of artificial neural networks that we have designed: Neural Network Pairwise Interaction Fields (NNPIF). This evaluation function takes into account the contextual information for each residue and is trained to identify native-like conformations from non-native-like ones by using large sets of decoys as a training set. The training set is generated and then iteratively expanded during successive folding simulations. As NNPIF are fast at evaluating conformations, thousands of models can be processed in a short amount of time, and clustering techniques can be adopted for model selection. Although the results we present here are very preliminary, we consider them to be promising, with predictions being generated at state-of-the-art levels in some of the cases. PMID:24970210

  19. BeEP Server: using evolutionary information for quality assessment of protein structure models

    PubMed Central

    Palopoli, Nicolas; Lanzarotti, Esteban; Parisi, Gustavo

    2013-01-01

    The BeEP Server (http://www.embnet.qb.fcen.uba.ar/embnet/beep.php) is an online resource aimed to help in the endgame of protein structure prediction. It is able to rank submitted structural models of a protein through an explicit use of evolutionary information, a criterion differing from structural or energetic considerations commonly used in other assessment programs. The idea behind BeEP (Best Evolutionary Pattern) is to benefit from the substitution pattern derived from structural constraints present in a set of homologous proteins adopting a given protein conformation. The BeEP method uses a model of protein evolution that takes into account the structure of a protein to build site-specific substitution matrices. The suitability of these substitution matrices is assessed through maximum likelihood calculations from which position-specific and global scores can be derived. These scores estimate how well the structural constraints derived from each structural model are represented in a sequence alignment of homologous proteins. Our assessment on a subset of proteins from the Critical Assessment of techniques for protein Structure Prediction (CASP) experiment has shown that BeEP is capable of discriminating the models and selecting one or more native-like structures. Moreover, BeEP is not explicitly parameterized to find structural similarities between models and given targets, potentially helping to explore the conformational ensemble of the native state. PMID:23729471

  20. Native-likeness in second language lexical categorization reflects individual language history and linguistic community norms

    PubMed Central

    Zinszer, Benjamin D.; Malt, Barbara C.; Ameel, Eef; Li, Ping

    2014-01-01

    Second language learners face a dual challenge in vocabulary learning: First, they must learn new names for the 100s of common objects that they encounter every day. Second, after some time, they discover that these names do not generalize according to the same rules used in their first language. Lexical categories frequently differ between languages (Malt et al., 1999), and successful language learning requires that bilinguals learn not just new words but new patterns for labeling objects. In the present study, Chinese learners of English with varying language histories and resident in two different language settings (Beijing, China and State College, PA, USA) named 67 photographs of common serving dishes (e.g., cups, plates, and bowls) in both Chinese and English. Participants’ response patterns were quantified in terms of similarity to the responses of functionally monolingual native speakers of Chinese and English and showed the cross-language convergence previously observed in simultaneous bilinguals (Ameel et al., 2005). For English, bilinguals’ names for each individual stimulus were also compared to the dominant name generated by the native speakers for the object. Using two statistical models, we disentangle the effects of several highly interactive variables from bilinguals’ language histories and the naming norms of the native speaker community to predict inter-personal and inter-item variation in L2 (English) native-likeness. We find only a modest age of earliest exposure effect on L2 category native-likeness, but importantly, we find that classroom instruction in L2 negatively impacts L2 category native-likeness, even after significant immersion experience. We also identify a significant role of both L1 and L2 norms in bilinguals’ L2 picture naming responses. PMID:25386149

  1. Second Language Processing Shows Increased Native-Like Neural Responses after Months of No Exposure

    PubMed Central

    Morgan-Short, Kara; Finger, Ingrid; Grey, Sarah; Ullman, Michael T.

    2012-01-01

    Although learning a second language (L2) as an adult is notoriously difficult, research has shown that adults can indeed attain native language-like brain processing and high proficiency levels. However, it is important to then retain what has been attained, even in the absence of continued exposure to the L2—particularly since periods of minimal or no L2 exposure are common. This event-related potential (ERP) study of an artificial language tested performance and neural processing following a substantial period of no exposure. Adults learned to speak and comprehend the artificial language to high proficiency with either explicit, classroom-like, or implicit, immersion-like training, and then underwent several months of no exposure to the language. Surprisingly, proficiency did not decrease during this delay. Instead, it remained unchanged, and there was an increase in native-like neural processing of syntax, as evidenced by several ERP changes—including earlier, more reliable, and more left-lateralized anterior negativities, and more robust P600s, in response to word-order violations. Moreover, both the explicitly and implicitly trained groups showed increased native-like ERP patterns over the delay, indicating that such changes can hold independently of L2 training type. The results demonstrate that substantial periods with no L2 exposure are not necessarily detrimental. Rather, benefits may ensue from such periods of time even when there is no L2 exposure. Interestingly, both before and after the delay the implicitly trained group showed more native-like processing than the explicitly trained group, indicating that type of training also affects the attainment of native-like processing in the brain. Overall, the findings may be largely explained by a combination of forgetting and consolidation in declarative and procedural memory, on which L2 grammar learning appears to depend. The study has a range of implications, and suggests a research program with

  2. How native-like can you possibly get: fMRI evidence for processing accent

    PubMed Central

    Ghazi-Saidi, Ladan; Dash, Tanya; Ansaldo, Ana I.

    2015-01-01

    Introduction: If ever attained, adopting native-like accent is achieved late in the learning process. Resemblance between L2 and mother tongue can facilitate L2 learning. In particular, cognates (phonologically and semantically similar words across languages), offer the opportunity to examine the issue of foreign accent in quite a unique manner. Methods: Twelve Spanish speaking (L1) adults learnt French (L2) cognates and practiced their native-like pronunciation by means of a computerized method. After consolidation, they were tested on L1 and L2 oral picture- naming during fMRI scanning. Results and Discussion: The results of the present study show that there is a specific impact of accent on brain activation, even if L2 words are cognates, and belong to a pair of closely related languages. Results point that the insula is a key component of accent processing, which is in line with reports from patients with foreign accent syndrome following damage to the insula (e.g., Katz et al., 2012; Moreno-Torres et al., 2013; Tomasino et al., 2013), and healthy L2 learners (Chee et al., 2004). Thus, the left insula has been consistently related to the integration of attentional and working memory abilities, together with fine-tuning of motor programming to achieve optimal articulation. PMID:26578931

  3. Structural characterization of a mutant peptide derived from ubiquitin: implications for protein folding.

    PubMed Central

    Zerella, R.; Chen, P. Y.; Evans, P. A.; Raine, A.; Williams, D. H.

    2000-01-01

    The formation of the N-terminal beta-hairpin of ubiquitin is thought to be an early event in the folding of this small protein. Previously, we have shown that a peptide corresponding to residues 1-17 of ubiquitin folds autonomously and is likely to have a native-like hairpin register. To investigate the causes of the stability of this fold, we have made mutations in the amino acids at the apex of the turn. We find that in a peptide where Thr9 is replaced by Asp, U(1-17)T9D, the native conformation is stabilized with respect to the wild-type sequence, so much so that we are able to characterize the structure of the mutant peptide fully by NMR spectroscopy. The data indicate that U(1-17)T9D peptide does indeed form a hairpin with a native-like register and a type I turn with a G1 beta-bulge, as in the full-length protein. The reason for the greater stability of the U(1-17)T9D mutant remains uncertain, but there are nuclear Overhauser effects between the side chains of Asp9 and Lys 11, which may indicate that a charge-charge interaction between these residues is responsible. PMID:11152124

  4. Quality assessment of modeled protein structure using physicochemical properties.

    PubMed

    Rana, Prashant Singh; Sharma, Harish; Bhattacharya, Mahua; Shukla, Anupam

    2015-04-01

    Physicochemical properties of proteins always guide to determine the quality of the protein structure, therefore it has been rigorously used to distinguish native or native-like structure from other predicted structures. In this work, we explore nine machine learning methods with six physicochemical properties to predict the Root Mean Square Deviation (RMSD), Template Modeling (TM-score), and Global Distance Test (GDT_TS-score) of modeled protein structure in the absence of its true native state. Physicochemical properties namely total surface area, euclidean distance (ED), total empirical energy, secondary structure penalty (SS), sequence length (SL), and pair number (PN) are used. There are a total of 95,091 modeled structures of 4896 native targets. A real coded Self-adaptive Differential Evolution algorithm (SaDE) is used to determine the feature importance. The K-fold cross validation is used to measure the robustness of the best predictive method. Through the intensive experiments, it is found that Random Forest method outperforms over other machine learning methods. This work makes the prediction faster and inexpensive. The performance result shows the prediction of RMSD, TM-score, and GDT_TS-score on Root Mean Square Error (RMSE) as 1.20, 0.06, and 0.06 respectively; correlation scores are 0.96, 0.92, and 0.91 respectively; R(2) are 0.92, 0.85, and 0.84 respectively; and accuracy are 78.82% (with ± 0.1 err), 86.56% (with ± 0.1 err), and 87.37% (with ± 0.1 err) respectively on the testing data set. The data set used in the study is available as supplement at http://bit.ly/RF-PCP-DataSets. PMID:25524475

  5. Folding of a large protein at high structural resolution.

    PubMed

    Walters, Benjamin T; Mayne, Leland; Hinshaw, James R; Sosnick, Tobin R; Englander, S Walter

    2013-11-19

    Kinetic folding of the large two-domain maltose binding protein (MBP; 370 residues) was studied at high structural resolution by an advanced hydrogen-exchange pulse-labeling mass-spectrometry method (HX MS). Dilution into folding conditions initiates a fast molecular collapse into a polyglobular conformation (<20 ms), determined by various methods including small angle X-ray scattering. The compaction produces a structurally heterogeneous state with widespread low-level HX protection and spectroscopic signals that match the equilibrium melting posttransition-state baseline. In a much slower step (7-s time constant), all of the MBP molecules, although initially heterogeneously structured, form the same distinct helix plus sheet folding intermediate with the same time constant. The intermediate is composed of segments that are distant in the MBP sequence but adjacent in the native protein where they close the longest residue-to-residue contact. Segments that are most HX protected in the early molecular collapse do not contribute to the initial intermediate, whereas the segments that do participate are among the less protected. The 7-s intermediate persists through the rest of the folding process. It contains the sites of three previously reported destabilizing mutations that greatly slow folding. These results indicate that the intermediate is an obligatory step on the MBP folding pathway. MBP then folds to the native state on a longer time scale (~100 s), suggestively in more than one step, the first of which forms structure adjacent to the 7-s intermediate. These results add a large protein to the list of proteins known to fold through distinct native-like intermediates in distinct pathways. PMID:24191053

  6. Folding of a large protein at high structural resolution

    PubMed Central

    Walters, Benjamin T.; Mayne, Leland; Hinshaw, James R.; Sosnick, Tobin R.; Englander, S. Walter

    2013-01-01

    Kinetic folding of the large two-domain maltose binding protein (MBP; 370 residues) was studied at high structural resolution by an advanced hydrogen-exchange pulse-labeling mass-spectrometry method (HX MS). Dilution into folding conditions initiates a fast molecular collapse into a polyglobular conformation (<20 ms), determined by various methods including small angle X-ray scattering. The compaction produces a structurally heterogeneous state with widespread low-level HX protection and spectroscopic signals that match the equilibrium melting posttransition-state baseline. In a much slower step (7-s time constant), all of the MBP molecules, although initially heterogeneously structured, form the same distinct helix plus sheet folding intermediate with the same time constant. The intermediate is composed of segments that are distant in the MBP sequence but adjacent in the native protein where they close the longest residue-to-residue contact. Segments that are most HX protected in the early molecular collapse do not contribute to the initial intermediate, whereas the segments that do participate are among the less protected. The 7-s intermediate persists through the rest of the folding process. It contains the sites of three previously reported destabilizing mutations that greatly slow folding. These results indicate that the intermediate is an obligatory step on the MBP folding pathway. MBP then folds to the native state on a longer time scale (∼100 s), suggestively in more than one step, the first of which forms structure adjacent to the 7-s intermediate. These results add a large protein to the list of proteins known to fold through distinct native-like intermediates in distinct pathways. PMID:24191053

  7. HIV-1 VACCINES. HIV-1 neutralizing antibodies induced by native-like envelope trimers.

    PubMed

    Sanders, Rogier W; van Gils, Marit J; Derking, Ronald; Sok, Devin; Ketas, Thomas J; Burger, Judith A; Ozorowski, Gabriel; Cupo, Albert; Simonich, Cassandra; Goo, Leslie; Arendt, Heather; Kim, Helen J; Lee, Jeong Hyun; Pugach, Pavel; Williams, Melissa; Debnath, Gargi; Moldt, Brian; van Breemen, Mariëlle J; Isik, Gözde; Medina-Ramírez, Max; Back, Jaap Willem; Koff, Wayne C; Julien, Jean-Philippe; Rakasz, Eva G; Seaman, Michael S; Guttman, Miklos; Lee, Kelly K; Klasse, Per Johan; LaBranche, Celia; Schief, William R; Wilson, Ian A; Overbaugh, Julie; Burton, Dennis R; Ward, Andrew B; Montefiori, David C; Dean, Hansi; Moore, John P

    2015-07-10

    A challenge for HIV-1 immunogen design is the difficulty of inducing neutralizing antibodies (NAbs) against neutralization-resistant (tier 2) viruses that dominate human transmissions. We show that a soluble recombinant HIV-1 envelope glycoprotein trimer that adopts a native conformation, BG505 SOSIP.664, induced NAbs potently against the sequence-matched tier 2 virus in rabbits and similar but weaker responses in macaques. The trimer also consistently induced cross-reactive NAbs against more sensitive (tier 1) viruses. Tier 2 NAbs recognized conformational epitopes that differed between animals and in some cases overlapped with those recognized by broadly neutralizing antibodies (bNAbs), whereas tier 1 responses targeted linear V3 epitopes. A second trimer, B41 SOSIP.664, also induced a strong autologous tier 2 NAb response in rabbits. Thus, native-like trimers represent a promising starting point for the development of HIV-1 vaccines aimed at inducing bNAbs. PMID:26089353

  8. Structural Genomics of Protein Phosphatases

    SciTech Connect

    Almo,S.; Bonanno, J.; Sauder, J.; Emtage, S.; Dilorenzo, T.; Malashkevich, V.; Wasserman, S.; Swaminathan, S.; Eswaramoorthy, S.; et al

    2007-01-01

    The New York SGX Research Center for Structural Genomics (NYSGXRC) of the NIGMS Protein Structure Initiative (PSI) has applied its high-throughput X-ray crystallographic structure determination platform to systematic studies of all human protein phosphatases and protein phosphatases from biomedically-relevant pathogens. To date, the NYSGXRC has determined structures of 21 distinct protein phosphatases: 14 from human, 2 from mouse, 2 from the pathogen Toxoplasma gondii, 1 from Trypanosoma brucei, the parasite responsible for African sleeping sickness, and 2 from the principal mosquito vector of malaria in Africa, Anopheles gambiae. These structures provide insights into both normal and pathophysiologic processes, including transcriptional regulation, regulation of major signaling pathways, neural development, and type 1 diabetes. In conjunction with the contributions of other international structural genomics consortia, these efforts promise to provide an unprecedented database and materials repository for structure-guided experimental and computational discovery of inhibitors for all classes of protein phosphatases.

  9. A designed glycoprotein analogue of Gc-MAF exhibits native-like phagocytic activity.

    PubMed

    Bogani, Federica; McConnell, Elizabeth; Joshi, Lokesh; Chang, Yung; Ghirlanda, Giovanna

    2006-06-01

    Rational protein design has been successfully used to create mimics of natural proteins that retain native activity. In the present work, de novo protein engineering is explored to develop a mini-protein analogue of Gc-MAF, a glycoprotein involved in the immune system activation that has shown anticancer activity in mice. Gc-MAF is derived in vivo from vitamin D binding protein (VDBP) via enzymatic processing of its glycosaccharide to leave a single GalNAc residue located on an exposed loop. We used molecular modeling tools in conjunction with structural analysis to splice the glycosylated loop onto a stable three-helix bundle (alpha3W, PDB entry 1LQ7). The resulting 69-residue model peptide, MM1, has been successfully synthesized by solid-phase synthesis both in the aglycosylated and the glycosylated (GalNAc-MM1) form. Circular dichroism spectroscopy confirmed the expected alpha-helical secondary structure. The thermodynamic stability as evaluated from chemical and thermal denaturation is comparable with that of the scaffold protein, alpha3W, indicating that the insertion of the exogenous loop of Gc-MAF did not significantly perturb the overall structure. GalNAc-MM1 retains the macrophage stimulation activity of natural Gc-MAF; in vitro tests show an identical enhancement of Fc-receptor-mediated phagocytosis in primary macrophages. GalNAc-MM1 provides a framework for the development of mutants with increased activity that could be used in place of Gc-MAF as an immunomodulatory agent in therapy. PMID:16734450

  10. Protein structure mining using a structural alphabet.

    PubMed

    Tyagi, M; de Brevern, A G; Srinivasan, N; Offmann, B

    2008-05-01

    We present a comprehensive evaluation of a new structure mining method called PB-ALIGN. It is based on the encoding of protein structure as 1D sequence of a combination of 16 short structural motifs or protein blocks (PBs). PBs are short motifs capable of representing most of the local structural features of a protein backbone. Using derived PB substitution matrix and simple dynamic programming algorithm, PB sequences are aligned the same way amino acid sequences to yield structure alignment. PBs are short motifs capable of representing most of the local structural features of a protein backbone. Alignment of these local features as sequence of symbols enables fast detection of structural similarities between two proteins. Ability of the method to characterize and align regions beyond regular secondary structures, for example, N and C caps of helix and loops connecting regular structures, puts it a step ahead of existing methods, which strongly rely on secondary structure elements. PB-ALIGN achieved efficiency of 85% in extracting true fold from a large database of 7259 SCOP domains and was successful in 82% cases to identify true super-family members. On comparison to 13 existing structure comparison/mining methods, PB-ALIGN emerged as the best on general ability test dataset and was at par with methods like YAKUSA and CE on nontrivial test dataset. Furthermore, the proposed method performed well when compared to flexible structure alignment method like FATCAT and outperforms in processing speed (less than 45 s per database scan). This work also establishes a reliable cut-off value for the demarcation of similar folds. It finally shows that global alignment scores of unrelated structures using PBs follow an extreme value distribution. PB-ALIGN is freely available on web server called Protein Block Expert (PBE) at http://bioinformatics.univ-reunion.fr/PBE/. PMID:18004784

  11. Structure of giant muscle proteins

    PubMed Central

    Meyer, Logan C.; Wright, Nathan T.

    2013-01-01

    Giant muscle proteins (e.g., titin, nebulin, and obscurin) play a seminal role in muscle elasticity, stretch response, and sarcomeric organization. Each giant protein consists of multiple tandem structural domains, usually arranged in a modular fashion spanning 500 kDa to 4 MDa. Although many of the domains are similar in structure, subtle differences create a unique function of each domain. Recent high and low resolution structural and dynamic studies now suggest more nuanced overall protein structures than previously realized. These findings show that atomic structure, interactions between tandem domains, and intrasarcomeric environment all influence the shape, motion, and therefore function of giant proteins. In this article we will review the current understanding of titin, obscurin, and nebulin structure, from the atomic level through the molecular level. PMID:24376425

  12. Toolbox for Protein Structure Prediction.

    PubMed

    Roche, Daniel Barry; McGuffin, Liam James

    2016-01-01

    Protein tertiary structure prediction algorithms aim to predict, from amino acid sequence, the tertiary structure of a protein. In silico protein structure prediction methods have become extremely important, as in vitro-based structural elucidation is unable to keep pace with the current growth of sequence databases due to high-throughput next-generation sequencing, which has exacerbated the gaps in our knowledge between sequences and structures.Here we briefly discuss protein tertiary structure prediction, the biennial competition for the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and its role in shaping the field. We also discuss, in detail, our cutting-edge web-server method IntFOLD2-TS for tertiary structure prediction. Furthermore, we provide a step-by-step guide on using the IntFOLD2-TS web server, along with some real world examples, where the IntFOLD server can and has been used to improve protein tertiary structure prediction and aid in functional elucidation. PMID:26519323

  13. Arterivirus structural proteins and assembly

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This chapter reviews the structural characteristics of the Arteriviridae, including the basic molecular details of all of the proteins involved, the interactions of these proteins and where they occur, and further functional characterization. Most recent available literature has been focused on equi...

  14. APL: An angle probability list to improve knowledge-based metaheuristics for the three-dimensional protein structure prediction.

    PubMed

    Borguesan, Bruno; Barbachan e Silva, Mariel; Grisci, Bruno; Inostroza-Ponta, Mario; Dorn, Márcio

    2015-12-01

    Tertiary protein structure prediction is one of the most challenging problems in structural bioinformatics. Despite the advances in algorithm development and computational strategies, predicting the folded structure of a protein only from its amino acid sequence remains as an unsolved problem. We present a new computational approach to predict the native-like three-dimensional structure of proteins. Conformational preferences of amino acid residues and secondary structure information were obtained from protein templates stored in the Protein Data Bank and represented as an Angle Probability List. Two knowledge-based prediction methods based on Genetic Algorithms and Particle Swarm Optimization were developed using this information. The proposed method has been tested with twenty-six case studies selected to validate our approach with different classes of proteins and folding patterns. Stereochemical and structural analysis were performed for each predicted three-dimensional structure. Results achieved suggest that the Angle Probability List can improve the effectiveness of metaheuristics used to predicted the three-dimensional structure of protein molecules by reducing its conformational search space. PMID:26495908

  15. Structure Prediction of Membrane Proteins

    NASA Astrophysics Data System (ADS)

    Hu, Xiche

    Membrane proteins play a central role in many cellular and physiological processes. It is estimated that integral membrane proteins make up about 20-30% of the proteome (Krogh et al., 2001b; Stevens and Arkin, 2000; von Heijne, 1999). They are essential mediators of material and information transfer across cell membranes. Their functions include active and passive transport of molecules into and out of cells and organelles; transduction of energy among various forms (light, electrical, and chemical energy); as well as reception and transduction of chemical and electrical signals across membranes (Avdonin, 2005; Bockaert et al., 2002; Pahl, 1999; Rehling et al., 2004; Stack et al., 1995). Identifying these transmembrane (TM) proteins and deciphering their molecular mechanisms, then, is of great importance, particularly as applied to biomedicine. Membrane proteins are the targets of a large number of pharmacologically and toxicologically active substances, and are directly involved in their uptake, metabolism, and clearance (Bettler et al., 1998; Cohen, 2002; Heusser and Jardieu, 1997; Tibes et al., 2005; Xu et al., 2005). Despite the importance of membrane proteins, the knowledge of their high-resolution structures and mechanisms of action has lagged far behind in comparison to that of water-soluble proteins: less than 1% of all three-dimensional structures deposited in the Protein Data Bank are of membrane proteins. This unfortunate disparity stems from difficulties in overexpression and the crystallization of membrane proteins (Grisshammer and Tate, 1995; Michel, 1991).

  16. De Novo Protein Structure Prediction

    NASA Astrophysics Data System (ADS)

    Hung, Ling-Hong; Ngan, Shing-Chung; Samudrala, Ram

    An unparalleled amount of sequence data is being made available from large-scale genome sequencing efforts. The data provide a shortcut to the determination of the function of a gene of interest, as long as there is an existing sequenced gene with similar sequence and of known function. This has spurred structural genomic initiatives with the goal of determining as many protein folds as possible (Brenner and Levitt, 2000; Burley, 2000; Brenner, 2001; Heinemann et al., 2001). The purpose of this is twofold: First, the structure of a gene product can often lead to direct inference of its function. Second, since the function of a protein is dependent on its structure, direct comparison of the structures of gene products can be more sensitive than the comparison of sequences of genes for detecting homology. Presently, structural determination by crystallography and NMR techniques is still slow and expensive in terms of manpower and resources, despite attempts to automate the processes. Computer structure prediction algorithms, while not providing the accuracy of the traditional techniques, are extremely quick and inexpensive and can provide useful low-resolution data for structure comparisons (Bonneau and Baker, 2001). Given the immense number of structures which the structural genomic projects are attempting to solve, there would be a considerable gain even if the computer structure prediction approach were applicable to a subset of proteins.

  17. Protein interfacial structure and nanotoxicology

    NASA Astrophysics Data System (ADS)

    White, John W.; Perriman, Adam W.; McGillivray, Duncan J.; Lin, Jhih-Min

    2009-02-01

    Here we briefly recapitulate the use of X-ray and neutron reflectometry at the air-water interface to find protein structures and thermodynamics at interfaces and test a possibility for understanding those interactions between nanoparticles and proteins which lead to nanoparticle toxicology through entry into living cells. Stable monomolecular protein films have been made at the air-water interface and, with a specially designed vessel, the substrate changed from that which the air-water interfacial film was deposited. This procedure allows interactions, both chemical and physical, between introduced species and the monomolecular film to be studied by reflectometry. The method is briefly illustrated here with some new results on protein-protein interaction between β-casein and κ-casein at the air-water interface using X-rays. These two proteins are an essential component of the structure of milk. In the experiments reported, specific and directional interactions appear to cause different interfacial structures if first, a β-casein monolayer is attacked by a κ-casein solution compared to the reverse. The additional contrast associated with neutrons will be an advantage here. We then show the first results of experiments on the interaction of a β-casein monolayer with a nanoparticle titanium oxide sol, foreshadowing the study of the nanoparticle "corona" thought to be important for nanoparticle-cell wall penetration.

  18. Method for protein structure alignment

    DOEpatents

    Blankenbecler, Richard; Ohlsson, Mattias; Peterson, Carsten; Ringner, Markus

    2005-02-22

    This invention provides a method for protein structure alignment. More particularly, the present invention provides a method for identification, classification and prediction of protein structures. The present invention involves two key ingredients. First, an energy or cost function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. Second, a minimization of the energy or cost function by an iterative method, where in each iteration (1) a mean field method is employed for the assignment variables and (2) exact rotation and/or translation of atomic coordinates is performed, weighted with the corresponding assignment variables.

  19. A Real-Time All-Atom Structural Search Engine for Proteins

    PubMed Central

    Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F.

    2014-01-01

    Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new “designability”-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license). PMID:25079944

  20. Chemical Cross-Linking Stabilizes Native-Like HIV-1 Envelope Glycoprotein Trimer Antigens

    PubMed Central

    Schiffner, Torben; de Val, Natalia; Russell, Rebecca A.; de Taeye, Steven W.; de la Peña, Alba Torrents; Ozorowski, Gabriel; Kim, Helen J.; Nieusma, Travis; Brod, Florian; Cupo, Albert; Sanders, Rogier W.; Moore, John P.; Ward, Andrew B.

    2015-01-01

    ABSTRACT Major neutralizing antibody immune evasion strategies of the HIV-1 envelope glycoprotein (Env) trimer include conformational and structural instability. Stabilized soluble trimers such as BG505 SOSIP.664 mimic the structure of virion-associated Env but nevertheless sample different conformational states. Here we demonstrate that treating BG505 SOSIP.664 trimers with glutaraldehyde or a heterobifunctional cross-linker introduces additional stability with relatively modest effects on antigenicity. Thus, most broadly neutralizing antibody (bNAb) epitopes were preserved after cross-linking, whereas the binding of most weakly or nonneutralizing antibodies (non-NAb) was reduced. Cross-linking stabilized all Env conformers present within a mixed population, and individual conformers could be isolated by bNAb affinity chromatography. Both positive selection of cross-linked conformers using the quaternary epitope-specific bNAbs PGT145, PGT151, and 3BC315 and negative selection with non-NAbs against the V3 region enriched for trimer populations with improved antigenicity for bNAbs. Similar results were obtained using the clade B B41 SOSIP.664 trimer. The cross-linking method may, therefore, be useful for countering the natural conformational heterogeneity of some HIV-1 Env proteins and, by extrapolation, also vaccine immunogens from other pathogens. IMPORTANCE The development of a vaccine to induce protective antibodies against HIV-1 is of primary public health importance. Recent advances in immunogen design have provided soluble recombinant envelope glycoprotein trimers with near-native morphology and antigenicity. However, these trimers are conformationally flexible, potentially reducing B-cell recognition of neutralizing antibody epitopes. Here we show that chemical cross-linking increases trimer stability, reducing binding of nonneutralizing antibodies while largely maintaining neutralizing antibody binding. Cross-linking followed by positive or negative

  1. Protein Structure Comparison and Classification

    NASA Astrophysics Data System (ADS)

    Çamoǧlu, Orhan; Singh, Ambuj K.

    The success of genome projects has generated an enormous amount of sequence data. In order to realize the full value of the data, we need to understand its functional role and its evolutionary origin. Sequence comparison methods are incredibly valuable for this task. However, for sequences falling in the twilight zone (usually between 20 and 35% sequence similarity), we need to resort to structural alignment and comparison for a meaningful analysis. Such a structural approach can be used for classification of proteins, isolation of structural motifs, and discovery of drug targets.

  2. Explicit and implicit second language training differentially affect the achievement of native-like brain activation patterns.

    PubMed

    Morgan-Short, Kara; Steinhauer, Karsten; Sanz, Cristina; Ullman, Michael T

    2012-04-01

    It is widely believed that adults cannot learn a foreign language in the same way that children learn a first language. However, recent evidence suggests that adult learners of a foreign language can come to rely on native-like language brain mechanisms. Here, we show that the type of language training crucially impacts this outcome. We used an artificial language paradigm to examine longitudinally whether explicit training (that approximates traditional grammar-focused classroom settings) and implicit training (that approximates immersion settings) differentially affect neural (electrophysiological) and behavioral (performance) measures of syntactic processing. Results showed that performance of explicitly and implicitly trained groups did not differ at either low or high proficiency. In contrast, electrophysiological (ERP) measures revealed striking differences between the groups' neural activity at both proficiency levels in response to syntactic violations. Implicit training yielded an N400 at low proficiency, whereas at high proficiency, it elicited a pattern typical of native speakers: an anterior negativity followed by a P600 accompanied by a late anterior negativity. Explicit training, by contrast, yielded no significant effects at low proficiency and only an anterior positivity followed by a P600 at high proficiency. Although the P600 is reminiscent of native-like processing, this response pattern as a whole is not. Thus, only implicit training led to an electrophysiological signature typical of native speakers. Overall, the results suggest that adult foreign language learners can come to rely on native-like language brain mechanisms, but that the conditions under which the language is learned may be crucial in attaining this goal. PMID:21861686

  3. Explicit and Implicit Second Language Training Differentially Affect the Achievement of Native-like Brain Activation Patterns

    PubMed Central

    Morgan-Short, Kara; Steinhauer, Karsten; Sanz, Cristina; Ullman, Michael T.

    2013-01-01

    It is widely believed that adults cannot learn a foreign language in the same way that children learn a first language. However, recent evidence suggests that adult learners of a foreign language can come to rely on native-like language brain mechanisms. Here, we show that the type of language training crucially impacts this outcome. We used an artificial language paradigm to examine longitudinally whether explicit training (that approximates traditional grammar-focused classroom settings) and implicit training (that approximates immersion settings) differentially affect neural (electrophysiological) and behavioral (performance) measures of syntactic processing. Results showed that performance of explicitly and implicitly trained groups did not differ at either low or high proficiency. In contrast, electrophysiological (ERP) measures revealed striking differences between the groups’ neural activity at both proficiency levels in response to syntactic violations. Implicit training yielded an N400 at low proficiency, whereas at high proficiency, it elicited a pattern typical of native speakers: an anterior negativity followed by a P600 accompanied by a late anterior negativity. Explicit training, by contrast, yielded no significant effects at low proficiency and only an anterior positivity followed by a P600 at high proficiency. Although the P600 is reminiscent of native-like processing, this response pattern as a whole is not. Thus, only implicit training led to an electrophysiological signature typical of native speakers. Overall, the results suggest that adult foreign language learners can come to rely on native-like language brain mechanisms, but that the conditions under which the language is learned may be crucial in attaining this goal. PMID:21861686

  4. Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction

    PubMed Central

    Handl, Julia; Knowles, Joshua; Lovell, Simon C.

    2009-01-01

    Motivation: Decoy datasets, consisting of a solved protein structure and numerous alternative native-like structures, are in common use for the evaluation of scoring functions in protein structure prediction. Several pitfalls with the use of these datasets have been identified in the literature, as well as useful guidelines for generating more effective decoy datasets. We contribute to this ongoing discussion an empirical assessment of several decoy datasets commonly used in experimental studies. Results: We find that artefacts and sampling issues in the large majority of these data make it trivial to discriminate the native structure. This underlines that evaluation based on the rank/z-score of the native is a weak test of scoring function performance. Moreover, sampling biases present in the way decoy sets are generated or used can strongly affect other types of evaluation measures such as the correlation between score and root mean squared deviation (RMSD) to the native. We demonstrate how, depending on type of bias and evaluation context, sampling biases may lead to both over- or under-estimation of the quality of scoring terms, functions or methods. Availability: Links to the software and data used in this study are available at http://dbkgroup.org/handl/decoy_sets. Contact: simon.lovell@manchester.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19297350

  5. Sequence repeats and protein structure

    NASA Astrophysics Data System (ADS)

    Hoang, Trinh X.; Trovato, Antonio; Seno, Flavio; Banavar, Jayanth R.; Maritan, Amos

    2012-11-01

    Repeats are frequently found in known protein sequences. The level of sequence conservation in tandem repeats correlates with their propensities to be intrinsically disordered. We employ a coarse-grained model of a protein with a two-letter amino acid alphabet, hydrophobic (H) and polar (P), to examine the sequence-structure relationship in the realm of repeated sequences. A fraction of repeated sequences comprises a distinct class of bad folders, whose folding temperatures are much lower than those of random sequences. Imperfection in sequence repetition improves the folding properties of the bad folders while deteriorating those of the good folders. Our results may explain why nature has utilized repeated sequences for their versatility and especially to design functional proteins that are intrinsically unstructured at physiological temperatures.

  6. Sucralose Destabilization of Protein Structure.

    PubMed

    Chen, Lee; Shukla, Nimesh; Cho, Inha; Cohn, Erin; Taylor, Erika A; Othon, Christina M

    2015-04-16

    Sucralose is a commonly employed artificial sweetener that behaves very differently than its natural disaccharide counterpart, sucrose, in terms of its interaction with biomolecules. The presence of sucralose in solution is found to destabilize the native structure of two model protein systems: the globular protein bovine serum albumin and an enzyme staphylococcal nuclease. The melting temperature of these proteins decreases as a linear function of sucralose concentration. We correlate this destabilization to the increased polarity of the molecule. The strongly polar nature is manifested as a large dielectric friction exerted on the excited-state rotational diffusion of tryptophan using time-resolved fluorescence anisotropy. Tryptophan exhibits rotational diffusion proportional to the measured bulk viscosity for sucrose solutions over a wide range of concentrations, consistent with a Stokes-Einstein model. For sucralose solutions, however, the diffusion is dependent on the concentration, strongly diverging from the viscosity predictions, and results in heterogeneous rotational diffusion. PMID:26263149

  7. A protein structure data and analysis system.

    PubMed

    Tian, Hao; Sunderraman, Rajshekhar; Weber, Irene; Wang, Haibin; Yang, Hong

    2005-01-01

    In this paper, we present the design and implementation of a protein structure data and analysis system that is only used in the lab for analyzing the proprietary data. It is capable of storing public protein data, such as the data in Protein Data Bank (PDB) [1], and life scientists' proprietary data. This toolkit is targeted at life scientists who want to maintain proprietary protein structure data (may be incomplete), to search and query publicly known protein structures and to compare their structure data with others. The comparison functions can be used to find structure differences between two proteins at atom level, especially in mutant versions of proteins. The system can also be used as a tool of choosing better protein structure template in new protein's tertiary structure prediction. The system is developed in Java and the protein data is stored in a relational database (Oracle 9i). PMID:17282836

  8. Introduction to Protein Structure through Genetic Diseases

    ERIC Educational Resources Information Center

    Schneider, Tanya L.; Linton, Brian R.

    2008-01-01

    An illuminating way to learn about protein function is to explore high-resolution protein structures. Analysis of the proteins involved in genetic diseases has been used to introduce students to protein structure and the role that individual mutations can play in the onset of disease. Known mutations can be correlated to changes in protein…

  9. Amphipols Outperform Dodecylmaltoside Micelles in Stabilizing Membrane Protein Structure in the Gas Phase

    PubMed Central

    2014-01-01

    Noncovalent mass spectrometry (MS) is emerging as an invaluable technique to probe the structure, interactions, and dynamics of membrane proteins (MPs). However, maintaining native-like MP conformations in the gas phase using detergent solubilized proteins is often challenging and may limit structural analysis. Amphipols, such as the well characterized A8-35, are alternative reagents able to maintain the solubility of MPs in detergent-free solution. In this work, the ability of A8-35 to retain the structural integrity of MPs for interrogation by electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) is compared systematically with the commonly used detergent dodecylmaltoside. MPs from the two major structural classes were selected for analysis, including two β-barrel outer MPs, PagP and OmpT (20.2 and 33.5 kDa, respectively), and two α-helical proteins, Mhp1 and GalP (54.6 and 51.7 kDa, respectively). Evaluation of the rotationally averaged collision cross sections of the observed ions revealed that the native structures of detergent solubilized MPs were not always retained in the gas phase, with both collapsed and unfolded species being detected. In contrast, ESI-IMS-MS analysis of the amphipol solubilized MPs studied resulted in charge state distributions consistent with less gas phase induced unfolding, and the presence of lowly charged ions which exhibit collision cross sections comparable with those calculated from high resolution structural data. The data demonstrate that A8-35 can be more effective than dodecylmaltoside at maintaining native MP structure and interactions in the gas phase, permitting noncovalent ESI-IMS-MS analysis of MPs from the two major structural classes, while gas phase dissociation from dodecylmaltoside micelles leads to significant gas phase unfolding, especially for the α-helical MPs studied. PMID:25495802

  10. Solid State NMR and Protein-Protein Interactions in Membranes

    PubMed Central

    Miao, Yimin; Cross, Timothy A.

    2013-01-01

    Solid state NMR spectroscopy has evolved rapidly in recent years into an excellent tool for the characterization of membrane proteins and their complexes. In the past few years it has also become clear that the structure of membrane proteins, especially helical membrane proteins is determined, in part, by the membrane environment. Therefore, the modeling of this environment by a liquid crystalline lipid bilayer for solid state NMR has generated a unique tool for the characterization of native conformational states, local and global dynamics, and high resolution structure for these proteins. Protein-protein interactions can also benefit from this solid state NMR capability to characterize membrane proteins in a native-like environment. These complexes take the form of oligomeric structures and hetero-protein interactions both with water soluble proteins and other membrane proteins. PMID:24034903

  11. Solid state NMR and protein-protein interactions in membranes.

    PubMed

    Miao, Yimin; Cross, Timothy A

    2013-12-01

    Solid state NMR spectroscopy has evolved rapidly in recent years into an excellent tool for the characterization of membrane proteins and their complexes. In the past few years it has also become clear that the structure of membrane proteins, especially helical membrane proteins is determined, in part, by the membrane environment. Therefore, the modeling of this environment by a liquid crystalline lipid bilayer for solid state NMR has generated a unique tool for the characterization of native conformational states, local and global dynamics, and high-resolution structure for these proteins. Protein-protein interactions can also benefit from this solid state NMR capability to characterize membrane proteins in a native-like environment. These complexes take the form of oligomeric structures and hetero-protein interactions both with water-soluble proteins and other membrane proteins. PMID:24034903

  12. Protein structure alignment beyond spatial proximity

    PubMed Central

    Wang, Sheng; Ma, Jianzhu; Peng, Jian; Xu, Jinbo

    2013-01-01

    Protein structure alignment is a fundamental problem in computational structure biology. Many programs have been developed for automatic protein structure alignment, but most of them align two protein structures purely based upon geometric similarity without considering evolutionary and functional relationship. As such, these programs may generate structure alignments which are not very biologically meaningful from the evolutionary perspective. This paper presents a novel method DeepAlign for automatic pairwise protein structure alignment. DeepAlign aligns two protein structures using not only spatial proximity of equivalent residues (after rigid-body superposition), but also evolutionary relationship and hydrogen-bonding similarity. Experimental results show that DeepAlign can generate structure alignments much more consistent with manually-curated alignments than other automatic tools especially when proteins under consideration are remote homologs. These results imply that in addition to geometric similarity, evolutionary information and hydrogen-bonding similarity are essential to aligning two protein structures. PMID:23486213

  13. An Interactive Introduction to Protein Structure

    ERIC Educational Resources Information Center

    Lee, W. Theodore

    2004-01-01

    To improve student understanding of protein structure and the significance of noncovalent interactions in protein structure and function, students are assigned a project to write a paper complemented with computer-generated images. The assignment provides an opportunity for students to select a protein structure that is of interest and detail…

  14. Structure of CrgA, a cell division structural and regulatory protein from Mycobacterium tuberculosis, in lipid bilayers.

    PubMed

    Das, Nabanita; Dai, Jian; Hung, Ivan; Rajagopalan, Malini R; Rajagopalan, Malini R; Zhou, Huan-Xiang; Cross, Timothy A

    2015-01-13

    The 93-residue transmembrane protein CrgA in Mycobacterium tuberculosis is a central component of the divisome, a large macromolecular machine responsible for cell division. Through interactions with multiple other components including FtsZ, FtsQ, FtsI (PBPB), PBPA, and CwsA, CrgA facilitates the recruitment of the proteins essential for peptidoglycan synthesis to the divisome and stabilizes the divisome. CrgA is predicted to have two transmembrane helices. Here, the structure of CrgA was determined in a liquid-crystalline lipid bilayer environment by solid-state NMR spectroscopy. Oriented-sample data yielded orientational restraints, whereas magic-angle spinning data yielded interhelical distance restraints. These data define a complete structure for the transmembrane domain and provide rich information on the conformational ensembles of the partially disordered N-terminal region and interhelical loop. The structure of the transmembrane domain was refined using restrained molecular dynamics simulations in an all-atom representation of the same lipid bilayer environment as in the NMR samples. The two transmembrane helices form a left-handed packing arrangement with a crossing angle of 24° at the conserved Gly39 residue. This helix pair exposes other conserved glycine and alanine residues to the fatty acyl environment, which are potential sites for binding CrgA's partners such as CwsA and FtsQ. This approach combining oriented-sample and magic-angle spinning NMR spectroscopy in native-like lipid bilayers with restrained molecular dynamics simulations represents a powerful tool for structural characterization of not only isolated membrane proteins, but their complexes, such as those that form macromolecular machines. PMID:25548160

  15. Structure of CrgA, a cell division structural and regulatory protein from Mycobacterium tuberculosis, in lipid bilayers

    PubMed Central

    Das, Nabanita; Dai, Jian; Hung, Ivan; Rajagopalan, Malini; Zhou, Huan-Xiang; Cross, Timothy A.

    2015-01-01

    The 93-residue transmembrane protein CrgA in Mycobacterium tuberculosis is a central component of the divisome, a large macromolecular machine responsible for cell division. Through interactions with multiple other components including FtsZ, FtsQ, FtsI (PBPB), PBPA, and CwsA, CrgA facilitates the recruitment of the proteins essential for peptidoglycan synthesis to the divisome and stabilizes the divisome. CrgA is predicted to have two transmembrane helices. Here, the structure of CrgA was determined in a liquid–crystalline lipid bilayer environment by solid-state NMR spectroscopy. Oriented-sample data yielded orientational restraints, whereas magic-angle spinning data yielded interhelical distance restraints. These data define a complete structure for the transmembrane domain and provide rich information on the conformational ensembles of the partially disordered N-terminal region and interhelical loop. The structure of the transmembrane domain was refined using restrained molecular dynamics simulations in an all-atom representation of the same lipid bilayer environment as in the NMR samples. The two transmembrane helices form a left-handed packing arrangement with a crossing angle of 24° at the conserved Gly39 residue. This helix pair exposes other conserved glycine and alanine residues to the fatty acyl environment, which are potential sites for binding CrgA’s partners such as CwsA and FtsQ. This approach combining oriented-sample and magic-angle spinning NMR spectroscopy in native-like lipid bilayers with restrained molecular dynamics simulations represents a powerful tool for structural characterization of not only isolated membrane proteins, but their complexes, such as those that form macromolecular machines. PMID:25548160

  16. Structure Prediction of Protein Complexes

    NASA Astrophysics Data System (ADS)

    Pierce, Brian; Weng, Zhiping

    Protein-protein interactions are critical for biological function. They directly and indirectly influence the biological systems of which they are a part. Antibodies bind with antigens to detect and stop viruses and other infectious agents. Cell signaling is performed in many cases through the interactions between proteins. Many diseases involve protein-protein interactions on some level, including cancer and prion diseases.

  17. Design of a minimal protein oligomerization domain by a structural approach.

    PubMed Central

    Burkhard, P.; Meier, M.; Lustig, A.

    2000-01-01

    Because of the simplicity and regularity of the alpha-helical coiled coil relative to other structural motifs, it can be conveniently used to clarify the molecular interactions responsible for protein folding and stability. Here we describe the de novo design and characterization of a two heptad-repeat peptide stabilized by a complex network of inter- and intrahelical salt bridges. Circular dichroism spectroscopy and analytical ultracentrifugation show that this peptide is highly alpha-helical and 100% dimeric tinder physiological buffer conditions. Interestingly, the peptide was shown to switch its oligomerization state from a dimer to a trimer upon increasing ionic strength. The correctness of the rational design principles used here is supported by details of the atomic structure of the peptide deduced from X-ray crystallography. The structure of the peptide shows that it is not a molten globule but assumes a unique, native-like conformation. This de novo peptide thus represents an attractive model system for the design of a molecular recognition system. PMID:11206050

  18. Design of a minimal protein oligomerization domain by a structural approach.

    PubMed

    Burkhard, P; Meier, M; Lustig, A

    2000-12-01

    Because of the simplicity and regularity of the alpha-helical coiled coil relative to other structural motifs, it can be conveniently used to clarify the molecular interactions responsible for protein folding and stability. Here we describe the de novo design and characterization of a two heptad-repeat peptide stabilized by a complex network of inter- and intrahelical salt bridges. Circular dichroism spectroscopy and analytical ultracentrifugation show that this peptide is highly alpha-helical and 100% dimeric tinder physiological buffer conditions. Interestingly, the peptide was shown to switch its oligomerization state from a dimer to a trimer upon increasing ionic strength. The correctness of the rational design principles used here is supported by details of the atomic structure of the peptide deduced from X-ray crystallography. The structure of the peptide shows that it is not a molten globule but assumes a unique, native-like conformation. This de novo peptide thus represents an attractive model system for the design of a molecular recognition system. PMID:11206050

  19. PDBFlex: exploring flexibility in protein structures.

    PubMed

    Hrabe, Thomas; Li, Zhanwen; Sedova, Mayya; Rotkiewicz, Piotr; Jaroszewski, Lukasz; Godzik, Adam

    2016-01-01

    The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software. PMID:26615193

  20. PDBFlex: exploring flexibility in protein structures

    PubMed Central

    Hrabe, Thomas; Li, Zhanwen; Sedova, Mayya; Rotkiewicz, Piotr; Jaroszewski, Lukasz; Godzik, Adam

    2016-01-01

    The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software. PMID:26615193

  1. [Protein structure: Folding and prions].

    PubMed

    Rey-Gayo, Antonio; Calbo Torrecilla, Francisco

    2002-04-01

    Transmissible spongiform encephalopathies have become a subject of prime social concern in recent years because of its relation to "mad cow disease" and their potential for transmission to humans. Among the most important scientific aspects of these diseases are the peculiar characteristics of the agent involved in their transmission. In this article we briefly describe the outstanding features of prions, the most widely accepted hypothesis for these diseases. We focus on the molecular characteristics of this protein, coded in the genome of the affected host, and describe the conformational alterations in the protein's tertiary structure that have been blamed for its pathologic activity. Our aim is to summarize the state-of-the-art knowledge on prions, the hypotheses proposed to explain mechanisms of disease transmission without agents containing genetic material, and some specific peculiarities of this new infectious agent. The links between this knowledge and possible therapeutic strategies to overcome the disease justify, once again, close interaction among chemistry, molecular biology, and medicine. PMID:11996702

  2. Sucralose Destabilization of Protein Structure

    NASA Astrophysics Data System (ADS)

    Cho, Inha; Chen, Lee; Shukla, Nimesh; Othon, Christina

    2015-03-01

    Sucralose is a commonly employed artificial sweetener. Sucralose behaves very differently than its natural disaccharide counterpart, sucrose, in terms of its interaction with biomolecules. The presence of sucralose in solution is found to destabilize the native structure of the globular protein Bovine Serum Albumin (BSA). The melting temperature decreases as a linear function of sucralose concentration. We correlate this destabilization with the increased polarity of the sucralose molecule as compared to sucrose. The strongly polar nature is observed as a large dielectric friction exerted on the excited state rotational diffusion of tryptophan using time-resolved fluorescence anisotropy. Tryptophan exhibits rotational diffusion proportional to the measured bulk viscosity for sucrose solutions over a wide range of concentrations, consistent with a Stokes-Einstein diffusional model. For sucralose solutions however, the diffusion is linearly dependent with the concentration, strongly diverging from the viscosity predictions. The polar nature of sucralose causes a dramatically different interaction with biomolecules than natural disaccharide molecules. Connecticut Space Grant Consortium.

  3. Constrained Peptides as Miniature Protein Structures

    PubMed Central

    Yin, Hang

    2012-01-01

    This paper discusses the recent developments of protein engineering using both covalent and noncovalent bonds to constrain peptides, forcing them into designed protein secondary structures. These constrained peptides subsequently can be used as peptidomimetics for biological functions such as regulations of protein-protein interactions. PMID:25969758

  4. Infrared Structural Biology: Detect Functionally Important Structural Motions of Proteins

    NASA Astrophysics Data System (ADS)

    Xie, Aihua

    Proteins are dynamic. Lack of dynamic structures of proteins hampers our understanding of protein functions. Infrared structural biology (IRSB) is an emerging technology. There are several advantages of IRSB for mechanistic studies of proteins: (1) its excellent dynamic range (detecting structural motions from picoseconds to >= seconds); (2) its high structural sensitivity (detect tiny but functionally important structural motions such as proton transfer and changes in hydrogen bonding interaction); (3) its ability to detect different structural motions simultaneously. Successful development of infrared structural biology demands not only new experimental techniques (from infrared technologies to chemical synthesis and cell biology), but also new data processing (how to translate infrared signals into quantitative structural information of proteins). These topics will be discussed as well as examples of how to use IRSB to study structure-function relationship of proteins. This work was supported by NSF DBI1338097 and OCAST HR10-078.

  5. Exploring Salt Bridge Structures of Gas-Phase Protein Ions using Multiple Stages of Electron Transfer and Collision Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Zhang, Zhe; Browne, Shaynah J.; Vachet, Richard W.

    2014-04-01

    The gas-phase structures of protein ions have been studied by electron transfer dissociation (ETD) and collision-induced dissociation (CID) after electrospraying these proteins from native-like solutions into a quadrupole ion trap mass spectrometer. Because ETD can break covalent bonds while minimally disrupting noncovalent interactions, we have investigated the ability of this dissociation technique together with CID to probe the sites of electrostatic interactions in gas-phase protein ions. By comparing spectra from ETD with spectra from ETD followed by CID, we find that several proteins, including ubiquitin, CRABP I, azurin, and β-2-microglobulin, appear to maintain many of the salt bridge contacts known to exist in solution. To support this conclusion, we also performed calculations to consider all possible salt bridge patterns for each protein, and we find that the native salt bridge pattern explains the experimental ETD data better than nearly all other possible salt bridge patterns. Overall, our data suggest that ETD and ETD/CID of native protein ions can provide some insight into approximate location of salt bridges in the gas phase.

  6. Exploring Salt Bridge Structures of Gas-Phase Protein Ions using Multiple Stages of Electron Transfer and Collision Induced Dissociation

    PubMed Central

    Zhang, Zhe; Browne, Shaynah J.; Vachet, Richard W.

    2014-01-01

    The gas-phase structures of protein ions have been studied by electron transfer dissociation (ETD) and collision-induced dissociation (CID) after electrospraying these proteins from native-like solutions into a quadrupole ion trap mass spectrometer. Because ETD can break covalent bonds while minimally disrupting non-covalent interactions, we have investigated the ability of this dissociation technique together with CID to probe the sites of electrostatic interactions in gas phase protein ions. By comparing spectra from ETD with spectra from ETD followed by CID, we find that several proteins, including ubiquitin, CRABP I, azurin, and β-2-microglobulin, appear to maintain many of the salt bridge contacts known to exist in solution. To support this conclusion, we also performed calculations to consider all possible salt bridge patterns for each protein, and we find that the native salt bridge pattern explains the experimental ETD data better than nearly all other possible salt bridge patterns. Overall, our data suggest that ETD and ETD/CID of native protein ions can provide some insight into approximate location of salt bridges in the gas phase. PMID:24496600

  7. Practical lessons from protein structure prediction

    PubMed Central

    Ginalski, Krzysztof; Grishin, Nick V.; Godzik, Adam; Rychlewski, Leszek

    2005-01-01

    Despite recent efforts to develop automated protein structure determination protocols, structural genomics projects are slow in generating fold assignments for complete proteomes, and spatial structures remain unknown for many protein families. Alternative cheap and fast methods to assign folds using prediction algorithms continue to provide valuable structural information for many proteins. The development of high-quality prediction methods has been boosted in the last years by objective community-wide assessment experiments. This paper gives an overview of the currently available practical approaches to protein structure prediction capable of generating accurate fold assignment. Recent advances in assessment of the prediction quality are also discussed. PMID:15805122

  8. Structural templates for comparative protein docking

    PubMed Central

    Anishchenko, Ivan; Kundrotas, Petras J.; Tuzikov, Alexander V.; Vakser, Ilya A.

    2014-01-01

    Structural characterization of protein-protein interactions is important for understanding life processes. Because of the inherent limitations of experimental techniques, such characterization requires computational approaches. Along with the traditional protein-protein docking (free search for a match between two proteins), comparative (template-based) modeling of protein-protein complexes has been gaining popularity. Its development puts an emphasis on full and partial structural similarity between the target protein monomers and the protein-protein complexes previously determined by experimental techniques (templates). The template-based docking relies on the quality and diversity of the template set. We present a carefully curated, non-redundant library of templates containing 4,950 full structures of binary complexes and 5,936 protein-protein interfaces extracted from the full structures at 12Å distance cut-off. Redundancy in the libraries was removed by clustering the PDB structures based on structural similarity. The value of the clustering threshold was determined from the analysis of the clusters and the docking performance on a benchmark set. High structural quality of the interfaces in the template and validation sets was achieved by automated procedures and manual curation. The library is included in the Dockground resource for molecular recognition studies at http://dockground.bioinformatics.ku.edu. PMID:25488330

  9. Crystal structures of MBP fusion proteins.

    PubMed

    Waugh, David S

    2016-03-01

    Although chaperone-assisted protein crystallization remains a comparatively rare undertaking, the number of crystal structures of polypeptides fused to maltose-binding protein (MBP) that have been deposited in the Protein Data Bank (PDB) has grown dramatically during the past decade. Altogether, 102 fusion protein structures were detected by Basic Local Alignment Search Tool (BLAST) analysis. Collectively, these structures comprise a range of sizes, space groups, and resolutions that are typical of the PDB as a whole. While most of these MBP fusion proteins were equipped with short inter-domain linkers to increase their rigidity, fusion proteins with long linkers have also been crystallized. In some cases, surface entropy reduction mutations in MBP appear to have facilitated the formation of crystals. A comparison of the structures of fused and unfused proteins, where both are available, reveals that MBP-mediated structural distortions are very rare. PMID:26682969

  10. The interface of protein structure, protein biophysics, and molecular evolution

    PubMed Central

    Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

    2012-01-01

    Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

  11. NAPS: Network Analysis of Protein Structures.

    PubMed

    Chakrabarty, Broto; Parekh, Nita

    2016-07-01

    Traditionally, protein structures have been analysed by the secondary structure architecture and fold arrangement. An alternative approach that has shown promise is modelling proteins as a network of non-covalent interactions between amino acid residues. The network representation of proteins provide a systems approach to topological analysis of complex three-dimensional structures irrespective of secondary structure and fold type and provide insights into structure-function relationship. We have developed a web server for network based analysis of protein structures, NAPS, that facilitates quantitative and qualitative (visual) analysis of residue-residue interactions in: single chains, protein complex, modelled protein structures and trajectories (e.g. from molecular dynamics simulations). The user can specify atom type for network construction, distance range (in Å) and minimal amino acid separation along the sequence. NAPS provides users selection of node(s) and its neighbourhood based on centrality measures, physicochemical properties of amino acids or cluster of well-connected residues (k-cliques) for further analysis. Visual analysis of interacting domains and protein chains, and shortest path lengths between pair of residues are additional features that aid in functional analysis. NAPS support various analyses and visualization views for identifying functional residues, provide insight into mechanisms of protein folding, domain-domain and protein-protein interactions for understanding communication within and between proteins. URL:http://bioinf.iiit.ac.in/NAPS/. PMID:27151201

  12. Protein folding and misfolding: mechanism and principles.

    PubMed

    Englander, S Walter; Mayne, Leland; Krishna, Mallela M G

    2007-11-01

    Two fundamentally different views of how proteins fold are now being debated. Do proteins fold through multiple unpredictable routes directed only by the energetically downhill nature of the folding landscape or do they fold through specific intermediates in a defined pathway that systematically puts predetermined pieces of the target native protein into place? It has now become possible to determine the structure of protein folding intermediates, evaluate their equilibrium and kinetic parameters, and establish their pathway relationships. Results obtained for many proteins have serendipitously revealed a new dimension of protein structure. Cooperative structural units of the native protein, called foldons, unfold and refold repeatedly even under native conditions. Much evidence obtained by hydrogen exchange and other methods now indicates that cooperative foldon units and not individual amino acids account for the unit steps in protein folding pathways. The formation of foldons and their ordered pathway assembly systematically puts native-like foldon building blocks into place, guided by a sequential stabilization mechanism in which prior native-like structure templates the formation of incoming foldons with complementary structure. Thus the same propensities and interactions that specify the final native state, encoded in the amino-acid sequence of every protein, determine the pathway for getting there. Experimental observations that have been interpreted differently, in terms of multiple independent pathways, appear to be due to chance misfolding errors that cause different population fractions to block at different pathway points, populate different pathway intermediates, and fold at different rates. This paper summarizes the experimental basis for these three determining principles and their consequences. Cooperative native-like foldon units and the sequential stabilization process together generate predetermined stepwise pathways. Optional misfolding errors

  13. Structure of mutant human oncogene protein determined

    SciTech Connect

    Baum, R.

    1989-01-16

    The protein encoded by a mutant human oncogene differs only slightly in structure from the native protein that initiates normal cell division, a finding that may complicate efforts to develop inhibitors of the mutant protein. Previously, the x-ray structure of the protein encoded by the normal c-Ha-ras gene, a protein believed to signal cells to start or stop dividing through its interaction with guanosine triphosphate (GTP), was reported. The structure of the protein encoded by a transforming c-Ha-ras oncogene, in which a valine codon replaces the normal glycine codon at position 12 in the gene, has now been determined. The differences in the structures of the mutant and normal proteins are located primarily in a loop that interacts with the /beta/-phosphate of a bound guanosine diphosphate (GDP) molecule.

  14. Structural alphabets for protein structure classification: a comparison study.

    PubMed

    Le, Quan; Pollastri, Gianluca; Koehl, Patrice

    2009-03-27

    Finding structural similarities between proteins often helps reveal shared functionality, which otherwise might not be detected by native sequence information alone. Such similarity is usually detected and quantified by protein structure alignment. Determining the optimal alignment between two protein structures, however, remains a hard problem. An alternative approach is to approximate each three-dimensional protein structure using a sequence of motifs derived from a structural alphabet. Using this approach, structure comparison is performed by comparing the corresponding motif sequences or structural sequences. In this article, we measure the performance of such alphabets in the context of the protein structure classification problem. We consider both local and global structural sequences. Each letter of a local structural sequence corresponds to the best matching fragment to the corresponding local segment of the protein structure. The global structural sequence is designed to generate the best possible complete chain that matches the full protein structure. We use an alphabet of 20 letters, corresponding to a library of 20 motifs or protein fragments having four residues. We show that the global structural sequences approximate well the native structures of proteins, with an average coordinate root mean square of 0.69 A over 2225 test proteins. The approximation is best for all alpha-proteins, while relatively poorer for all beta-proteins. We then test the performance of four different sequence representations of proteins (their native sequence, the sequence of their secondary-structure elements, and the local and global structural sequences based on our fragment library) with different classifiers in their ability to classify proteins that belong to five distinct folds of CATH. Without surprise, the primary sequence alone performs poorly as a structure classifier. We show that addition of either secondary-structure information or local information from the

  15. Comparative Protein Structure Modeling Using Modeller

    PubMed Central

    Eswar, Narayanan; Marti-Renom, Marc A.; Madhusudhan, M.S.; Eramian, David; Shen, Min-yi; Pieper, Ursula

    2014-01-01

    Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate three-dimensional (3-D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3-D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3-D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. PMID:18428767

  16. Template-based structure modeling of protein-protein interactions

    PubMed Central

    Szilagyi, Andras; Zhang, Yang

    2014-01-01

    The structure of protein-protein complexes can be constructed by using the known structure of other protein complexes as a template. The complex structure templates are generally detected either by homology-based sequence alignments or, given the structure of monomer components, by structure-based comparisons. Critical improvements have been made in recent years by utilizing interface recognition and by recombining monomer and complex template libraries. Encouraging progress has also been witnessed in genome-wide applications of template-based modeling, with modeling accuracy comparable to high-throughput experimental data. Nevertheless, bottlenecks exist due to the incompleteness of the proteinprotein complex structure library and the lack of methods for distant homologous template identification and full-length complex structure refinement. PMID:24721449

  17. A new protein structure representation for efficient protein function prediction.

    PubMed

    Maghawry, Huda A; Mostafa, Mostafa G M; Gharib, Tarek F

    2014-12-01

    One of the challenging problems in bioinformatics is the prediction of protein function. Protein function is the main key that can be used to classify different proteins. Protein function can be inferred experimentally with very small throughput or computationally with very high throughput. Computational methods are sequence based or structure based. Structure-based methods produce more accurate protein function prediction. In this article, we propose a new protein structure representation for efficient protein function prediction. The representation is based on three-dimensional patterns of protein residues. In the analysis, we used protein function based on enzyme activity through six mechanistically diverse enzyme superfamilies: amidohydrolase, crotonase, haloacid dehalogenase, isoprenoid synthase type I, and vicinal oxygen chelate. We applied three different classification methods, naïve Bayes, k-nearest neighbors, and random forest, to predict the enzyme superfamily of a given protein. The prediction accuracy using the proposed representation outperforms a recently introduced representation method that is based only on the distance patterns. The results show that the proposed representation achieved prediction accuracy up to 98%, with improvement of about 10% on average. PMID:25343279

  18. Protein Structures Revealed at Record Pace

    ScienceCinema

    Greg Hura

    2010-01-08

    The structure of a protein in days -- not months or years -- ushers in a new era in genomics research. Berkeley Lab scientists have developed a high-throughput protein pipeline that could expedite the development of biofuels and elucidate how proteins carry out lifes vital functions.

  19. Protein Structures Revealed at Record Pace

    ScienceCinema

    Hura, Greg

    2013-05-29

    The structure of a protein in days -- not months or years -- ushers in a new era in genomics research. Berkeley Lab scientists have developed a high-throughput protein pipeline that could expedite the development of biofuels and elucidate how proteins carry out lifes vital functions.

  20. Protein Structures Revealed at Record Pace

    SciTech Connect

    Hura, Greg

    2009-01-01

    The structure of a protein in days -- not months or years -- ushers in a new era in genomics research. Berkeley Lab scientists have developed a high-throughput protein pipeline that could expedite the development of biofuels and elucidate how proteins carry out lifes vital functions.

  1. Protein Structures Revealed at Record Pace

    SciTech Connect

    Greg Hura

    2009-07-09

    The structure of a protein in days -- not months or years -- ushers in a new era in genomics research. Berkeley Lab scientists have developed a high-throughput protein pipeline that could expedite the development of biofuels and elucidate how proteins carry out lifes vital functions.

  2. Predicting protein dynamics from structural ensembles

    NASA Astrophysics Data System (ADS)

    Copperman, J.; Guenza, M. G.

    2015-12-01

    The biological properties of proteins are uniquely determined by their structure and dynamics. A protein in solution populates a structural ensemble of metastable configurations around the global fold. From overall rotation to local fluctuations, the dynamics of proteins can cover several orders of magnitude in time scales. We propose a simulation-free coarse-grained approach which utilizes knowledge of the important metastable folded states of the protein to predict the protein dynamics. This approach is based upon the Langevin Equation for Protein Dynamics (LE4PD), a Langevin formalism in the coordinates of the protein backbone. The linear modes of this Langevin formalism organize the fluctuations of the protein, so that more extended dynamical cooperativity relates to increasing energy barriers to mode diffusion. The accuracy of the LE4PD is verified by analyzing the predicted dynamics across a set of seven different proteins for which both relaxation data and NMR solution structures are available. Using experimental NMR conformers as the input structural ensembles, LE4PD predicts quantitatively accurate results, with correlation coefficient ρ = 0.93 to NMR backbone relaxation measurements for the seven proteins. The NMR solution structure derived ensemble and predicted dynamical relaxation is compared with molecular dynamics simulation-derived structural ensembles and LE4PD predictions and is consistent in the time scale of the simulations. The use of the experimental NMR conformers frees the approach from computationally demanding simulations.

  3. The Critical Period for Second Language Pronunciation: Is There Such a Thing? Ten Case Studies of Late Starters who Attained a Native-like Hebrew Accent

    ERIC Educational Resources Information Center

    Abu-Rabia, Salim; Kehat, Simona

    2004-01-01

    This paper investigates the critical period hypothesis (CPH) for the acquisition of a second language sound system (phonology) in a naturalistic setting. Ten cases of successful late-starters with a native-like Hebrew pronunciation are presented in an effort to determine possible variables that may account for their exceptional accomplishment. The…

  4. Genome-wide Membrane Protein Structure Prediction

    PubMed Central

    Piccoli, Stefano; Suku, Eda; Garonzi, Marianna; Giorgetti, Alejandro

    2013-01-01

    Transmembrane proteins allow cells to extensively communicate with the external world in a very accurate and specific way. They form principal nodes in several signaling pathways and attract large interest in therapeutic intervention, as the majority pharmaceutical compounds target membrane proteins. Thus, according to the current genome annotation methods, a detailed structural/functional characterization at the protein level of each of the elements codified in the genome is also required. The extreme difficulty in obtaining high-resolution three-dimensional structures, calls for computational approaches. Here we review to which extent the efforts made in the last few years, combining the structural characterization of membrane proteins with protein bioinformatics techniques, could help describing membrane proteins at a genome-wide scale. In particular we analyze the use of comparative modeling techniques as a way of overcoming the lack of high-resolution three-dimensional structures in the human membrane proteome. PMID:24403851

  5. Protein structures in SDS micelle-protein complexes.

    PubMed Central

    Parker, W; Song, P S

    1992-01-01

    Sodium dodecyl sulfate (SDS) is used more often than any other detergent as an excellent denaturing or "unfolding" detergent. However, formation of ordered structure (alpha-helix or beta-sheet) in certain peptides is known to be induced by interaction with SDS micelles. The SDS-induced structures formed by these peptides are amphiphilic, having both a hydrophobic and a hydrophilic face. Previous work in this area has revealed that SDS induces helical folding in a wide variety of non-helical proteins. Here, we describe the interaction of several structurally unrelated proteins with SDS micelles and the correlation of these structures to helical amphiphilic regions present in the primary sequence. It is likely that the ability of native nonordered protein structures to form induced amphiphilic ordered structures is rather common. PMID:1600087

  6. How special is the biochemical function of native proteins?

    PubMed Central

    Skolnick, Jeffrey; Gao, Mu; Zhou, Hongyi

    2016-01-01

    Native proteins perform an amazing variety of biochemical functions, including enzymatic catalysis, and can engage in protein-protein and protein-DNA interactions that are essential for life. A key question is how special are these functional properties of proteins. Are they extremely rare, or are they an intrinsic feature? Comparison to the properties of compact conformations of artificially generated compact protein structures selected for thermodynamic stability but not any type of function, the artificial (ART) protein library, demonstrates that a remarkable number of the properties of native-like proteins are recapitulated. These include the complete set of small molecule ligand-binding pockets and most protein-protein interfaces. ART structures are predicted to be capable of weakly binding metabolites and cover a significant fraction of metabolic pathways, with the most enriched pathways including ancient ones such as glycolysis. Native-like active sites are also found in ART proteins. A small fraction of ART proteins are predicted to have strong protein-protein and protein-DNA interactions. Overall, it appears that biochemical function is an intrinsic feature of proteins which nature has significantly optimized during evolution. These studies raise questions as to the relative roles of specificity and promiscuity in the biochemical function and control of cells that need investigation. PMID:26962440

  7. Website on Protein Interaction and Protein Structure Related Work

    NASA Technical Reports Server (NTRS)

    Samanta, Manoj; Liang, Shoudan; Biegel, Bryan (Technical Monitor)

    2003-01-01

    In today's world, three seemingly diverse fields - computer information technology, nanotechnology and biotechnology are joining forces to enlarge our scientific knowledge and solve complex technological problems. Our group is dedicated to conduct theoretical research exploring the challenges in this area. The major areas of research include: 1) Yeast Protein Interactions; 2) Protein Structures; and 3) Current Transport through Small Molecules.

  8. Protein-protein interface prediction based on hexagon structure similarity.

    PubMed

    Guo, Fei; Ding, Yijie; Li, Shuai Cheng; Shen, Chao; Wang, Lusheng

    2016-08-01

    Studies on protein-protein interaction are important in proteome research. How to build more effective models based on sequence information, structure information and physicochemical characteristics, is the key technology in protein-protein interface prediction. In this paper, we study the protein-protein interface prediction problem. We propose a novel method for identifying residues on interfaces from an input protein with both sequence and 3D structure information, based on hexagon structure similarity. Experiments show that our method achieves better results than some state-of-the-art methods for identifying protein-protein interface. Comparing to existing methods, our approach improves F-measure value by at least 0.03. On a common dataset consisting of 41 complexes, our method has overall precision and recall values of 63% and 57%. On Benchmark v4.0, our method has overall precision and recall values of 55% and 56%. On CAPRI targets, our method has overall precision and recall values of 52% and 55%. PMID:26936323

  9. Local backbone structure prediction of proteins.

    PubMed

    de Brevern, Alexandre G; Benros, Cristina; Gautier, Romain; Valadié, Héléne; Hazout, Serge; Etchebest, Catherine

    2004-01-01

    A statistical analysis of the PDB structures has led us to define a new set of small 3D structural prototypes called Protein Blocks (PBs). This structural alphabet includes 16 PBs, each one is defined by the (phi, psi) dihedral angles of 5 consecutive residues. The amino acid distributions observed in sequence windows encompassing these PBs are used to predict by a Bayesian approach the local 3D structure of proteins from the sole knowledge of their sequences. LocPred is a software which allows the users to submit a protein sequence and performs a prediction in terms of PBs. The prediction results are given both textually and graphically. PMID:15724288

  10. The effect of denaturants on protein structure.

    PubMed Central

    Dunbar, J.; Yennawar, H. P.; Banerjee, S.; Luo, J.; Farber, G. K.

    1997-01-01

    Virtually all studies of the protein-folding reaction add either heat, acid, or a chemical denaturant to an aqueous protein solution in order to perturb the protein structure. When chemical denaturants are used, very high concentrations are usually necessary to observe any change in protein structure. In a solution with such high denaturant concentrations, both the structure of the protein and the structure of the solvent around the protein can be altered. X-ray crystallography is the obvious experimental technique to probe both types of changes. In this paper, we report the crystal structures of dihydrofolate reductase with urea and of ribonuclease A with guanidinium chloride. These two classic denaturants have similar effects on the native structure of the protein. The most important change that occurs is a reduction in the overall thermal factor. These structures offer a molecular explanation for the reduction in mobility. Although the reduction is observed only with the native enzyme in the crystal, a similar decrease in mobility has also been observed in the unfolded state in solution (Makhatadze G, Privalov PL. 1992. Protein interactions with urea and guanidinium chloride: A calorimetric study. PMID:9260285

  11. Optimized Null Model for Protein Structure Networks

    PubMed Central

    Lappe, Michael; Pržulj, Nataša

    2009-01-01

    Much attention has recently been given to the statistical significance of topological features observed in biological networks. Here, we consider residue interaction graphs (RIGs) as network representations of protein structures with residues as nodes and inter-residue interactions as edges. Degree-preserving randomized models have been widely used for this purpose in biomolecular networks. However, such a single summary statistic of a network may not be detailed enough to capture the complex topological characteristics of protein structures and their network counterparts. Here, we investigate a variety of topological properties of RIGs to find a well fitting network null model for them. The RIGs are derived from a structurally diverse protein data set at various distance cut-offs and for different groups of interacting atoms. We compare the network structure of RIGs to several random graph models. We show that 3-dimensional geometric random graphs, that model spatial relationships between objects, provide the best fit to RIGs. We investigate the relationship between the strength of the fit and various protein structural features. We show that the fit depends on protein size, structural class, and thermostability, but not on quaternary structure. We apply our model to the identification of significantly over-represented structural building blocks, i.e., network motifs, in protein structure networks. As expected, choosing geometric graphs as a null model results in the most specific identification of motifs. Our geometric random graph model may facilitate further graph-based studies of protein conformation space and have important implications for protein structure comparison and prediction. The choice of a well-fitting null model is crucial for finding structural motifs that play an important role in protein folding, stability and function. To our knowledge, this is the first study that addresses the challenge of finding an optimized null model for RIGs, by

  12. PSSweb: protein structural statistics web server.

    PubMed

    Gaillard, Thomas; Stote, Roland H; Dejaegere, Annick

    2016-07-01

    With the increasing number of protein structures available, there is a need for tools capable of automating the comparison of ensembles of structures, a common requirement in structural biology and bioinformatics. PSSweb is a web server for protein structural statistics. It takes as input an ensemble of PDB files of protein structures, performs a multiple sequence alignment and computes structural statistics for each position of the alignment. Different optional functionalities are proposed: structure superposition, Cartesian coordinate statistics, dihedral angle calculation and statistics, and a cluster analysis based on dihedral angles. An interactive report is generated, containing a summary of the results, tables, figures and 3D visualization of superposed structures. The server is available at http://pssweb.org. PMID:27174930

  13. PSSweb: protein structural statistics web server

    PubMed Central

    Gaillard, Thomas; Stote, Roland H.; Dejaegere, Annick

    2016-01-01

    With the increasing number of protein structures available, there is a need for tools capable of automating the comparison of ensembles of structures, a common requirement in structural biology and bioinformatics. PSSweb is a web server for protein structural statistics. It takes as input an ensemble of PDB files of protein structures, performs a multiple sequence alignment and computes structural statistics for each position of the alignment. Different optional functionalities are proposed: structure superposition, Cartesian coordinate statistics, dihedral angle calculation and statistics, and a cluster analysis based on dihedral angles. An interactive report is generated, containing a summary of the results, tables, figures and 3D visualization of superposed structures. The server is available at http://pssweb.org. PMID:27174930

  14. Protein Structure Determination Using Protein Threading and Sparse NMR Data

    SciTech Connect

    Crawford, O.H.; Einstein, J.R.; Xu, D.; Xu, Y.

    1999-11-14

    It is well known that the NMR method for protein structure determination applies to small proteins and that its effectiveness decreases very rapidly as the molecular weight increases beyond about 30 kD. We have recently developed a method for protein structure determination that can fully utilize partial NMR data as calculation constraints. The core of the method is a threading algorithm that guarantees to find a globally optimal alignment between a query sequence and a template structure, under distance constraints specified by NMR/NOE data. Our preliminary tests have demonstrated that a small number of NMR/NOE distance restraints can significantly improve threading performance in both fold recognition and threading-alignment accuracy, and can possibly extend threading's scope of applicability from structural homologs to structural analogs. An accurate backbone structure generated by NMR-constrained threading can then provide a significant amount of structural information, equivalent to that provided by the NMR method with many NMR/NOE restraints; and hence can greatly reduce the amount of NMR data typically required for accurate structure determination. Our preliminary study suggests that a small number of NMR/NOE restraints may suffice to determine adequately the all-atom structure when those restraints are incorporated in a procedure combining threading, modeling of loops and sidechains, and molecular dynamics simulation. Potentially, this new technique can expand NMR's capability to larger proteins.

  15. Mapping membrane protein structure with fluorescence

    PubMed Central

    Taraska, Justin W.

    2012-01-01

    Membrane proteins regulate many cellular processes including signaling cascades, ion transport, membrane fusion, and cell-to-cell communications. Understanding the architecture and conformational fluctuations of these proteins is critical to understanding their regulation and functions. Fluorescence methods including intensity mapping, fluorescence resonance energy transfer, and photo-induced electron transfer, allow for targeted measurements of domains within membrane proteins. These methods can reveal how a protein is structured and how it transitions between different conformational states. Here, I will review recent work done using fluorescence to map the structures of membrane proteins, focusing on how each of these methods can be applied to understanding the dynamic nature of individual membrane proteins and protein complexes. PMID:22445227

  16. Structure based prediction of protein folding intermediates.

    PubMed

    Xie, D; Freire, E

    1994-09-01

    The complete unfolding of a protein involves the disruption of non-covalent intramolecular interactions within the protein and the subsequent hydration of the backbone and amino acid side-chains. The magnitude of the thermodynamic parameters associated with this process is known accurately for a growing number of globular proteins for which high-resolution structures are also available. The existence of this database of structural and thermodynamic information has facilitated the development of statistical procedures aimed at quantifying the relationships existing between protein structure and the thermodynamic parameters of folding/unfolding. Under some conditions proteins do not unfold completely, giving rise to states (commonly known as molten globules) in which the molecule retains some secondary structure and remains in a compact configuration after denaturation. This phenomenon is reflected in the thermodynamics of the process. Depending on the nature of the residual structure that exists after denaturation, the observed enthalpy, entropy and heat capacity changes will deviate in a particular and predictable way from the values expected for complete unfolding. For several proteins, these deviations have been shown to exhibit similar characteristics, suggesting that their equilibrium folding intermediates exhibit some common structural features. Employing empirically derived structure-energetic relationships, it is possible to identify in the native structure of the protein those regions with the higher probability of being structured in equilibrium partly folded states. In this work, a thermodynamic search algorithm aimed at identifying the structural determinants of the molten globule state has been applied to six globular proteins; alpha-lactalbumin, barnase, IIIGlc, interleukin-1 beta, phage T4 lysozyme and phage 434 repressor. Remarkably, the structural features of the predicted equilibrium intermediates coincide to a large extent with the known

  17. Homology-Based Modeling of Protein Structure

    NASA Astrophysics Data System (ADS)

    Xiang, Zhexin

    The human genome project has already discovered millions of proteins (http://www.swissprot.com). The potential of the genome project can only be fully realized once we can assign, understand, manipulate, and predict the function of these new proteins (Sanchez and Sali, 1997; Frishman et al., 2000; Domingues et al., 2000). Predicting protein function generally requires knowledge of protein three-dimensional structure (Blundell et al., 1978;Weber, 1990), which is ultimately determined by protein sequence (Anfinsen, 1973). Protein structure determination using experimental methods such as X-ray crystallography or NMR spectroscopy is very time consuming (Johnson et al. 1994). To date, fewer than 2% of the known proteins have had their structures solved experimentally. In 2004, more than half a million new proteins were sequenced that almost doubled the efforts in the previous year, but only 5300 structures were solved. Although the rate of experimental structure determination will continue to increase, the number of newly discovered sequences grows much faster than the number of structures solved (see Fig. 10.1).

  18. Protein structure prediction from sequence variation

    PubMed Central

    Marks, Debora S; Hopf, Thomas A; Sander, Chris

    2015-01-01

    Genomic sequences contain rich evolutionary information about functional constraints on macromolecules such as proteins. This information can be efficiently mined to detect evolutionary couplings between residues in proteins and address the long-standing challenge to compute protein three-dimensional structures from amino acid sequences. Substantial progress has recently been made on this problem owing to the explosive growth in available sequences and the application of global statistical methods. In addition to three-dimensional structure, the improved understanding of covariation may help identify functional residues involved in ligand binding, protein-complex formation and conformational changes. We expect computation of covariation patterns to complement experimental structural biology in elucidating the full spectrum of protein structures, their functional interactions and evolutionary dynamics. PMID:23138306

  19. Lessons from making the Structural Classification of Proteins (SCOP) and their implications for protein structure modelling

    PubMed Central

    Andreeva, Antonina

    2016-01-01

    The Structural Classification of Proteins (SCOP) database has facilitated the development of many tools and algorithms and it has been successfully used in protein structure prediction and large-scale genome annotations. During the development of SCOP, numerous exceptions were found to topological rules, along with complex evolutionary scenarios and peculiarities in proteins including the ability to fold into alternative structures. This article reviews cases of structural variations observed for individual proteins and among groups of homologues, knowledge of which is essential for protein structure modelling. PMID:27284063

  20. Lessons from making the Structural Classification of Proteins (SCOP) and their implications for protein structure modelling.

    PubMed

    Andreeva, Antonina

    2016-06-15

    The Structural Classification of Proteins (SCOP) database has facilitated the development of many tools and algorithms and it has been successfully used in protein structure prediction and large-scale genome annotations. During the development of SCOP, numerous exceptions were found to topological rules, along with complex evolutionary scenarios and peculiarities in proteins including the ability to fold into alternative structures. This article reviews cases of structural variations observed for individual proteins and among groups of homologues, knowledge of which is essential for protein structure modelling. PMID:27284063

  1. Modeling Protein Aggregate Assembly and Structure

    NASA Astrophysics Data System (ADS)

    Guo, Jun-tao; Hall, Carol K.; Xu, Ying; Wetzel, Ronald

    One might say that "protein science" got its start in the domestic arts, built around the abilities of proteins to aggregate in response to environmental stresses such as heating (boiled eggs), heating and cooling (gelatin), and pH (cheese). Characterization of proteins in the late nineteenth century likewise focused on the ability of proteins to precipitate in response to certain salts and to aggregate in response to heating. Investigations by Chick and Martin (Chick and Martin, 1910) showed that the inactivating response of proteins to heat or solvent treatment is a two-step process involving separate denaturation and precipitation steps. Monitoring the coagulation and flocculation responses of proteins to heat and other stresses remained a major approach to understanding protein structure for decades, with solubility, or susceptibility to aggregation, serving as a kind of benchmark against which results of other methods, such as viscosity, chemical susceptibility, immune activity, crystallizability, and susceptibility to proteolysis, were compared (Mirsky and Pauling, 1936;Wu, 1931). Toward the middle of the last century, protein aggregation studies were largely left behind, as improved methods allowed elucidation of the primary sequence of proteins, reversible unfolding studies, and ultimately high-resolution structures. Curiously, the field of protein science, and in particular protein folding, is now gravitating back to a closer look at protein aggregation and protein aggregates. Unfortunately, the means developed during the second half of the twentieth century for studying native, globular proteins have not proved immediately amenable to the study of aggregate structures. Great progress is being made, however, to modify classical methods, including NMR and X-ray diffraction, as well as to develop newer techniques, that together should continue to expand our picture of aggregate structure (Kheterpal and Wetzel, 2006; Wetzel, 1999).

  2. Structural plasticity of 4-α-helical bundles exemplified by the puzzle-like molecular assembly of the Rop protein.

    PubMed

    Amprazi, Maria; Kotsifaki, Dina; Providaki, Mary; Kapetaniou, Evangelia G; Fellas, Georgios; Kyriazidis, Ioannis; Pérez, Javier; Kokkinidis, Michael

    2014-07-29

    The dimeric Repressor of Primer (Rop) protein, a widely used model system for the study of coiled-coil 4-α-helical bundles, is characterized by a remarkable structural plasticity. Loop region mutations lead to a wide range of topologies, folding states, and altered physicochemical properties. A protein-folding study of Rop and several loop variants has identified specific residues and sequences that are linked to the observed structural plasticity. Apart from the native state, native-like and molten-globule states have been identified; these states are sensitive to reducing agents due to the formation of nonnative disulfide bridges. Pro residues in the loop are critical for the establishment of new topologies and molten globule states; their effects, however, can be in part compensated by Gly residues. The extreme plasticity in the assembly of 4-α-helical bundles reflects the capacity of the Rop sequence to combine a specific set of hydrophobic residues into strikingly different hydrophobic cores. These cores include highly hydrated ones that are consistent with the formation of interchain, nonnative disulfide bridges and the establishment of molten globules. Potential applications of this structural plasticity are among others in the engineering of bio-inspired materials. PMID:25024213

  3. Microsecond Rearrangements of Hydrophobic Clusters in an Initially Collapsed Globule Prime Structure Formation during the Folding of a Small Protein.

    PubMed

    Goluguri, Rama Reddy; Udgaonkar, Jayant B

    2016-07-31

    Determining how polypeptide chain collapse initiates structure formation during protein folding is a long standing goal. It has been challenging to characterize experimentally the dynamics of the polypeptide chain, which lead to the formation of a compact kinetic molten globule (MG) in about a millisecond. In this study, the sub-millisecond events that occur early during the folding of monellin from the guanidine hydrochloride-unfolded state have been characterized using multiple fluorescence and fluorescence resonance energy transfer probes. The kinetic MG is shown to form in a noncooperative manner from the unfolded (U) state as a result of at least three different processes happening during the first millisecond of folding. Initial chain compaction completes within the first 37μs, and further compaction occurs only after structure formation commences at a few milliseconds of folding. The transient nonnative and native-like hydrophobic clusters with side chains of certain residues buried form during the initial chain collapse and the nonnative clusters quickly disassemble. Subsequently, partial chain desolvation occurs, leading to the formation of a kinetic MG. The initial chain compaction and subsequent chain rearrangement appear to be barrierless processes. The two structural rearrangements within the collapsed globule appear to prime the protein for the actual folding transition. PMID:27370109

  4. Improvement of protein structure comparison using a structural alphabet.

    PubMed

    Joseph, Agnel Praveen; Srinivasan, N; de Brevern, Alexandre G

    2011-09-01

    The three dimensional structure of a protein provides major insights into its function. Protein structure comparison has implications in functional and evolutionary studies. A structural alphabet (SA) is a library of local protein structure prototypes that can abstract every part of protein main chain conformation. Protein Blocks (PBs) is a widely used SA, composed of 16 prototypes, each representing a pentapeptide backbone conformation defined in terms of dihedral angles. Through this description, the 3D structural information can be translated into a 1D sequence of PBs. In a previous study, we have used this approach to compare protein structures encoded in terms of PBs. A classical sequence alignment procedure based on dynamic programming was used, with a dedicated PB Substitution Matrix (SM). PB-based pairwise structural alignment method gave an excellent performance, when compared to other established methods for mining. In this study, we have (i) refined the SMs and (ii) improved the Protein Block Alignment methodology (named as iPBA). The SM was normalized in regards to sequence and structural similarity. Alignment of protein structures often involves similar structural regions separated by dissimilar stretches. A dynamic programming algorithm that weighs these local similar stretches has been designed. Amino acid substitutions scores were also coupled linearly with the PB substitutions. iPBA improves (i) the mining efficiency rate by 6.8% and (ii) more than 82% of the alignments have a better quality. A higher efficiency in aligning multi-domain proteins could be also demonstrated. The quality of alignment is better than DALI and MUSTANG in 81.3% of the cases. Thus our study has resulted in an impressive improvement in the quality of protein structural alignment. PMID:21569819

  5. Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes.

    PubMed

    Martin, Juliette; Regad, Leslie; Etchebest, Catherine; Camproux, Anne-Claude

    2008-11-15

    Interresidue protein contacts in proteins structures and at protein-protein interface are classically described by the amino acid types of interacting residues and the local structural context of the contact, if any, is described using secondary structures. In this study, we present an alternate analysis of interresidue contact using local structures defined by the structural alphabet introduced by Camproux et al. This structural alphabet allows to describe a 3D structure as a sequence of prototype fragments called structural letters, of 27 different types. Each residue can then be assigned to a particular local structure, even in loop regions. The analysis of interresidue contacts within protein structures defined using Voronoï tessellations reveals that pairwise contact specificity is greater in terms of structural letters than amino acids. Using a simple heuristic based on specificity score comparison, we find that 74% of the long-range contacts within protein structures are better described using structural letters than amino acid types. The investigation is extended to a set of protein-protein complexes, showing that the similar global rules apply as for intraprotein contacts, with 64% of the interprotein contacts best described by local structures. We then present an evaluation of pairing functions integrating structural letters to decoy scoring and show that some complexes could benefit from the use of structural letter-based pairing functions. PMID:18491388

  6. Embracing proteins: structural themes in aptamer-protein complexes.

    PubMed

    Gelinas, Amy D; Davies, Douglas R; Janjic, Nebojsa

    2016-02-01

    Understanding the structural rules that govern specific, high-affinity binding characteristic of aptamer-protein interactions is important in view of the increasing use of aptamers across many applications. From the modest number of 16 aptamer-protein structures currently available, trends are emerging. The flexible phosphodiester backbone allows folding into precise three-dimensional structures using known nucleic acid motifs as scaffolds that orient specific functional groups for target recognition. Still, completely novel motifs essential for structure and function are found in modified aptamers with diversity-enhancing side chains. Aptamers and antibodies, two classes of macromolecules used as affinity reagents with entirely different backbones and composition, recognize protein epitopes of similar size and with comparably high shape complementarity. PMID:26919170

  7. Principles for designing ideal protein structures

    PubMed Central

    Koga, Nobuyasu; Tatsumi-Koga, Rie; Liu, Gaohua; Xiao, Rong; Acton, Thomas B.; Montelione, Gaetano T.; Baker, David

    2013-01-01

    Unlike random heteropolymers, natural proteins fold into unique ordered structures. Understanding how these are encoded in amino-acid sequences is complicated by energetically unfavourable non-ideal features—for example kinked α-helices, bulged β-strands, strained loops and buried polar groups—that arise in proteins from evolutionary selection for biological function or from neutral drift. Here we describe an approach to designing ideal protein structures stabilized by completely consistent local and non-local interactions. The approach is based on a set of rules relating secondary structure patterns to protein tertiary motifs, which make possible the design of funnel-shaped protein folding energy landscapes leading into the target folded state. Guided by these rules, we designed sequences predicted to fold into ideal protein structures consisting of α-helices, β-strands and minimal loops. Designs for five different topologies were found to be monomeric and very stable and to adopt structures in solution nearly identical to the computational models. These results illuminate how the folding funnels of natural proteins arise and provide the foundation for engineering a new generation of functional proteins free from natural evolution. PMID:23135467

  8. Protein Structure Is Related to RNA Structural Reactivity In Vivo.

    PubMed

    Tang, Yin; Assmann, Sarah M; Bevilacqua, Philip C

    2016-02-27

    We assessed whether in vivo mRNA structural reactivity and the structure of the encoded protein are related. This is the first investigation of such a relationship that utilizes information on RNA structure obtained in living cells. Based on our recent genome-wide Structure-seq analysis in Arabidopsis thaliana, we report that, as a meta property, regions of individual mRNAs that code for protein domains generally have higher reactivity to DMS (dimethyl sulfate), a chemical that covalently modifies accessible As and Cs, than regions that encode protein domain junctions. This relationship is prominent for proteins annotated for catalytic activity and reversed in proteins annotated for binding and transcription regulatory activity. Upon analyzing intrinsically disordered proteins, we found a similar pattern for disordered regions as compared to ordered regions: regions of individual mRNAs that code for ordered regions have significantly higher DMS reactivity than regions that code for intrinsically disordered regions. Based on these effects, we hypothesize that the decreased DMS reactivity of RNA regions that encode protein domain junctions or intrinsically disordered regions may reflect increased RNA structure that may slow translation, allowing time for the nascent protein domain or ordered region of the protein to fold, thereby reducing protein misfolding. In addition, a drop in DMS reactivity was observed on portions of mRNA sequences that correspond to the C-termini of protein domains, suggesting ribosome protection at these mRNA regions. Structural relationships between mRNAs and their encoded proteins may have evolved to allow efficient and accurate protein folding. PMID:26598238

  9. Structural proteins of Herpesvirus saimiri.

    PubMed Central

    Keil, G; Fleckenstein, B; Bodemer, W

    1983-01-01

    Herpesvirus saimiri particles were purified from productively infected owl monkey kidney cell cultures, and the virion polypeptides were analyzed by polyacrylamide gel electrophoresis. A total of 21 predominant proteins were found in lysates of H. saimiri 11 particles by Coomassie blue staining or by [35S]methionine labeling and autoradiography; all proteins were between 160,000 and 12,000 daltons in size. They are most probably virion constituents, as most of them were precipitated by immune sera, and no dominant proteins of equivalent sizes were found in mock-infected cultures. Four glycoproteins (gp 155/160, gp 128, gp 84/90, gp 55) and three polypeptides that appeared not to be glycosylated (p71, p35, p28) were assigned to the envelope or matrix of virions, whereas at least four phosphoproteins (pp132, pp118, pp55, pp13) and ten polypeptides without apparent secondary modification (p155/160, p106, p96, p67, p53, p36, p32, p15, p14, p12) were found in the nucleocapsid fraction. Analysis of virion proteins from different H. saimiri strains did not reveal appreciable differences in the migration behavior of most polypeptides, including all glycoproteins; however, determination of a strain-specific size pattern was possible for three of four phosphoproteins. The overall similarity in protein architecture of H. saimiri strains obviously does not reflect the variability in biology, such as oncogenic properties. In comparison, DNA sequence divergences appear to remain a better taxonomic criterion for strain distinction. Images PMID:6312078

  10. Datamining protein structure databanks for crystallization patterns of proteins.

    PubMed

    Valafar, Homayoun; Prestegard, James H; Valafar, Faramarz

    2002-12-01

    A study of 345 protein structures selected among 1,500 structures determined by nuclear magnetic resonance (NMR) methods, revealed useful correlations between crystallization properties and several parameters for the studied proteins. NMR methods of structure determination do not require the growth of protein crystals, and hence allow comparison of properties of proteins that have or have not been the subject of crystallographic approaches. One- and two-dimensional statistical analyses of the data confirmed a hypothesized relation between the size of the molecule and its crystallization potential. Furthermore, two-dimensional Bayesian analysis revealed a significant relationship between relative ratio of different secondary structures and the likelihood of success for crystallization trials. The most immediate result is an apparent correlation of crystallization potential with protein size. Further analysis of the data revealed a relationship between the unstructured fraction of proteins and the success of its crystallization. Utilization of Bayesian analysis on the latter correlation resulted in a prediction performance of about 64%, whereas a two-dimensional Bayesian analysis succeeded with a performance of about 75%. PMID:12594078

  11. Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

    SciTech Connect

    Yu,P.

    2007-01-01

    The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities) in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1) using the newly advanced synchrotron technology (S-FTIR) as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2) revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3) prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4) obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

  12. Fast loop modeling for protein structures

    NASA Astrophysics Data System (ADS)

    Zhang, Jiong; Nguyen, Son; Shang, Yi; Xu, Dong; Kosztin, Ioan

    2015-03-01

    X-ray crystallography is the main method for determining 3D protein structures. In many cases, however, flexible loop regions of proteins cannot be resolved by this approach. This leads to incomplete structures in the protein data bank, preventing further computational study and analysis of these proteins. For instance, all-atom molecular dynamics (MD) simulation studies of structure-function relationship require complete protein structures. To address this shortcoming, we have developed and implemented an efficient computational method for building missing protein loops. The method is database driven and uses deep learning and multi-dimensional scaling algorithms. We have implemented the method as a simple stand-alone program, which can also be used as a plugin in existing molecular modeling software, e.g., VMD. The quality and stability of the generated structures are assessed and tested via energy scoring functions and by equilibrium MD simulations. The proposed method can also be used in template-based protein structure prediction. Work supported by the National Institutes of Health [R01 GM100701]. Computer time was provided by the University of Missouri Bioinformatics Consortium.

  13. Unlocking the eukaryotic membrane protein structural proteome

    PubMed Central

    Lee, John Kyongwon; Stroud, Robert Michael

    2012-01-01

    Summary Most of the 231 unique membrane protein structures (as of 3/2010) are of bacterial membrane proteins (MPs) expressed in bacteria, or eukaryotic MPs from natural sources. However eukaryotic membrane proteins, especially those with more than three membrane crossings rarely succumb to any suitable expression in bacterial cells. They typically require expression in eukaryotic cells that can provide appropriate endoplasmic reticulum, chaperones, targeting and post-translational processing. In evidence, only ~20 eukaryotic MP structures have resulted from heterologous expression. This is required for a general approach to target particular human or pathogen membrane proteins of importance to human health. The first of these appeared in 2005. Our review addresses the special issues that pertain to the expression of eukaryotic and human membrane proteins, and recent advances in the tool kit for crystallization and structure determination. PMID:20739007

  14. AMASS: a database for investigating protein structures

    PubMed Central

    Mielke, Clinton J.; Mandarino, Lawrence J.; Dinu, Valentin

    2014-01-01

    Motivation: Modern techniques have produced many sequence annotation databases and protein structure portals, but these Web resources are rarely integrated in ways that permit straightforward exploration of protein functional residues and their co-localization. Results: We have created the AMASS database, which maps 1D sequence annotation databases to 3D protein structures with an intuitive visualization interface. Our platform also provides an analysis service that screens mass spectrometry sequence data for post-translational modifications that reside in functionally relevant locations within protein structures. The system is built on the premise that functional residues such as active sites, cancer mutations and post-translational modifications within proteins may co-localize and share common functions. Availability and implementation: AMASS database is implemented with Biopython and Apache as a freely available Web server at amass-db.org. Contact: clinton.mielke@gmail.com PMID:24497503

  15. Protein structure database search and evolutionary classification.

    PubMed

    Yang, Jinn-Moon; Tung, Chi-Hua

    2006-01-01

    As more protein structures become available and structural genomics efforts provide structural models in a genome-wide strategy, there is a growing need for fast and accurate methods for discovering homologous proteins and evolutionary classifications of newly determined structures. We have developed 3D-BLAST, in part, to address these issues. 3D-BLAST is as fast as BLAST and calculates the statistical significance (E-value) of an alignment to indicate the reliability of the prediction. Using this method, we first identified 23 states of the structural alphabet that represent pattern profiles of the backbone fragments and then used them to represent protein structure databases as structural alphabet sequence databases (SADB). Our method enhanced BLAST as a search method, using a new structural alphabet substitution matrix (SASM) to find the longest common substructures with high-scoring structured segment pairs from an SADB database. Using personal computers with Intel Pentium4 (2.8 GHz) processors, our method searched more than 10 000 protein structures in 1.3 s and achieved a good agreement with search results from detailed structure alignment methods. [3D-BLAST is available at http://3d-blast.life.nctu.edu.tw]. PMID:16885238

  16. Strong improvement of interfacial properties can result from slight structural modifications of proteins: the case of native and dry-heated lysozyme.

    PubMed

    Desfougères, Yann; Saint-Jalmes, Arnaud; Salonen, Anniina; Vié, Véronique; Beaufils, Sylvie; Pezennec, Stéphane; Desbat, Bernard; Lechevalier, Valérie; Nau, Françoise

    2011-12-20

    Identification of the key physicochemical parameters of proteins that determine their interfacial properties is still incomplete and represents a real stake challenge, especially for food proteins. Many studies have thus consisted in comparing the interfacial behavior of different proteins, but it is difficult to draw clear conclusions when the molecules are completely different on several levels. Here the adsorption process of a model protein, the hen egg-white lysozyme, and the same protein that underwent a thermal treatment in the dry state, was characterized. The consequences of this treatment have been previously studied: net charge and hydrophobicity increase and lesser protein stability, but no secondary and tertiary structure modification (Desfougères, Y.; Jardin, J.; Lechevalier, V.; Pezennec, S.; Nau, F. Biomacromolecules 2011, 12, 156-166). The present study shows that these slight modifications dramatically increase the interfacial properties of the protein, since the adsorption to the air-water interface is much faster and more efficient (higher surface pressure). Moreover, a thick and strongly viscoelastic multilayer film is created, while native lysozyme adsorbs in a fragile monolayer film. Another striking result is that completely different behaviors were observed between two molecular species, i.e., native and native-like lysozyme, even though these species could not be distinguished by usual spectroscopic methods. This suggests that the air-water interface could be considered as a useful tool to reveal very subtle differences between protein molecules. PMID:22040020

  17. Proteins with Novel Structure, Function and Dynamics

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew

    2014-01-01

    Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

  18. Contemporary Methodology for Protein Structure Determination.

    ERIC Educational Resources Information Center

    Hunkapiller, Michael W.; And Others

    1984-01-01

    Describes the nature and capabilities of methods used to characterize protein and peptide structure, indicating that they have undergone changes which have improved the speed, reliability, and applicability of the process. Also indicates that high-performance liquid chromatography and gel electrophoresis have made purifying proteins and peptides a…

  19. PEGylated nanoparticles: protein corona and secondary structure

    NASA Astrophysics Data System (ADS)

    Runa, Sabiha; Hill, Alexandra; Cochran, Victoria L.; Payne, Christine K.

    2014-09-01

    Nanoparticles have important biological and biomedical applications ranging from drug and gene delivery to biosensing. In the presence of extracellular proteins, a "corona" of proteins adsorbs on the surface of the nanoparticles, altering their interaction with cells, including immune cells. Nanoparticles are often functionalized with polyethylene glycol (PEG) to reduce this non-specific adsorption of proteins. To understand the change in protein corona that occurs following PEGylation, we first quantified the adsorption of blood serum proteins on bare and PEGylated gold nanoparticles using gel electrophoresis. We find a threefold decrease in the amount of protein adsorbed on PEGylated gold nanoparticles compared to the bare gold nanoparticles, showing that PEG reduces, but does not prevent, corona formation. To determine if the secondary structure of corona proteins was altered upon adsorption onto the bare and PEGylated gold nanoparticles, we use CD spectroscopy to characterize the secondary structure of bovine serum albumin following incubation with the nanoparticles. Our results show no significant change in protein secondary structure following incubation with bare or PEGylated nanoparticles. Further examination of the secondary structure of bovine serum albumin, α2-macroglobulin, and transferrin in the presence of free PEG showed similar results. These findings provide important insights for the use of PEGylated gold nanoparticles under physiological conditions.

  20. Information-driven structural modelling of protein-protein interactions.

    PubMed

    Rodrigues, João P G L M; Karaca, Ezgi; Bonvin, Alexandre M J J

    2015-01-01

    Protein-protein docking aims at predicting the three-dimensional structure of a protein complex starting from the free forms of the individual partners. As assessed in the CAPRI community-wide experiment, the most successful docking algorithms combine pure laws of physics with information derived from various experimental or bioinformatics sources. Of these so-called "information-driven" approaches, HADDOCK stands out as one of the most successful representatives. In this chapter, we briefly summarize which experimental information can be used to drive the docking prediction in HADDOCK, and then focus on the docking protocol itself. We discuss and illustrate with a tutorial example a "classical" protein-protein docking prediction, as well as more recent developments for modelling multi-body systems and large conformational changes. PMID:25330973

  1. Well-ordered trimeric HIV-1 subtype B and C soluble spike mimetics generated by negative selection display native-like properties.

    PubMed

    Guenaga, Javier; de Val, Natalia; Tran, Karen; Feng, Yu; Satchwell, Karen; Ward, Andrew B; Wyatt, Richard T

    2015-01-01

    The structure of BG505 gp140 SOSIP, a soluble mimic of the native HIV-1 envelope glycoprotein (Env), marks the beginning of new era in Env structure-based immunogen design. Displaying a well-ordered quaternary structure, these subtype A-derived trimers display an excellent antigenic profile, discriminating recognition by broadly neutralizing antibodies (bNAbs) from non-broadly neutralizing antibodies (non-bNAbs), and provide a solid Env-based immunogenic platform starting point. Even with this important advance, obtaining homogeneous well-ordered soluble SOSIP trimers derived from other subtypes remains challenging. Here, we report the "rescue" of homogeneous well-ordered subtype B and C SOSIP trimers from a heterogeneous Env mixture using CD4 binding site-directed (CD4bs) non-bNAbs in a negative-selection purification process. These non-bNAbs recognize the primary receptor CD4bs only on disordered trimers but not on the native Env spike or well-ordered soluble trimers due to steric hindrance. Following negative selection to remove disordered oligomers, we demonstrated recovery of well-ordered, homogeneous trimers by electron microscopy (EM). We obtained 3D EM reconstructions of unliganded trimers, as well as in complex with sCD4, a panel of CD4bs-directed bNAbs, and the cleavage-dependent, trimer-specific bNAb, PGT151. Using bio-layer light interferometry (BLI) we demonstrated that the well-ordered trimers were efficiently recognized by bNAbs and poorly recognized by non-bNAbs, representing soluble mimics of the native viral spike. Biophysical characterization was consistent with the thermostability of a homogeneous species that could be further stabilized by specific bNAbs. This study revealed that Env trimers generate different frequencies of well-ordered versus disordered aberrant trimers even when they are genetically identical. By negatively selecting the native-like well-ordered trimers, we establish a new means to obtain soluble Env mimetics derived from

  2. Well-Ordered Trimeric HIV-1 Subtype B and C Soluble Spike Mimetics Generated by Negative Selection Display Native-like Properties

    PubMed Central

    Guenaga, Javier; de Val, Natalia; Tran, Karen; Feng, Yu; Satchwell, Karen; Ward, Andrew B.; Wyatt, Richard T.

    2015-01-01

    The structure of BG505 gp140 SOSIP, a soluble mimic of the native HIV-1 envelope glycoprotein (Env), marks the beginning of new era in Env structure-based immunogen design. Displaying a well-ordered quaternary structure, these subtype A-derived trimers display an excellent antigenic profile, discriminating recognition by broadly neutralizing antibodies (bNAbs) from non-broadly neutralizing antibodies (non-bNAbs), and provide a solid Env-based immunogenic platform starting point. Even with this important advance, obtaining homogeneous well-ordered soluble SOSIP trimers derived from other subtypes remains challenging. Here, we report the “rescue” of homogeneous well-ordered subtype B and C SOSIP trimers from a heterogeneous Env mixture using CD4 binding site-directed (CD4bs) non-bNAbs in a negative-selection purification process. These non-bNAbs recognize the primary receptor CD4bs only on disordered trimers but not on the native Env spike or well-ordered soluble trimers due to steric hindrance. Following negative selection to remove disordered oligomers, we demonstrated recovery of well-ordered, homogeneous trimers by electron microscopy (EM). We obtained 3D EM reconstructions of unliganded trimers, as well as in complex with sCD4, a panel of CD4bs-directed bNAbs, and the cleavage-dependent, trimer-specific bNAb, PGT151. Using bio-layer light interferometry (BLI) we demonstrated that the well-ordered trimers were efficiently recognized by bNAbs and poorly recognized by non-bNAbs, representing soluble mimics of the native viral spike. Biophysical characterization was consistent with the thermostability of a homogeneous species that could be further stabilized by specific bNAbs. This study revealed that Env trimers generate different frequencies of well-ordered versus disordered aberrant trimers even when they are genetically identical. By negatively selecting the native-like well-ordered trimers, we establish a new means to obtain soluble Env mimetics derived

  3. The cold denatured state of the C-terminal domain of protein L9 is compact and contains both native and non-native structure.

    PubMed

    Shan, Bing; McClendon, Sebastian; Rospigliosi, Carla; Eliezer, David; Raleigh, Daniel P

    2010-04-01

    Cold denaturation is a general property of globular proteins, and the process provides insight into the origins of the cooperativity of protein folding and the nature of partially folded states. Unfortunately, studies of protein cold denaturation have been hindered by the fact that the cold denatured state is normally difficult to access experimentally. Special conditions such as addition of high concentrations of denaturant, encapsulation into reverse micelles, the formation of emulsified solutions, high pressure, or extremes of pH have been applied, but these can perturb the unfolded state of proteins. The cold denatured state of the C-terminal domain of the ribosomal protein L9 can be populated under native-like conditions by taking advantage of a destabilizing point mutation which leads to cold denaturation at temperatures above 0 degrees C. This state is in slow exchange with the native state on the NMR time scale. Virtually complete backbone (15)N, (13)C, and (1)H as well as side-chain (13)C(beta) and (1)H(beta) chemical shift assignments were obtained for the cold denatured state at pH 5.7, 12 degrees C. Chemical shift analysis, backbone N-H residual dipolar couplings, amide proton NOEs, and R(2) relaxation rates all indicate that the cold denatured state of CTL9 (the C-terminal domain of the ribosomal protein L9) not only contains significant native-like secondary structure but also non-native structure. The regions corresponding to the two native alpha-helices show a strong tendency to populate helical Phi and Psi angles. The segment which connects alpha-helix 2 and beta-strand 2 (residues 107-124) in the native state exhibits a significant preference to form non-native helical structure in the cold denatured state. The structure observed in the cold denatured state of the I98A mutant is similar to that observed in the pH 3.8 unfolded state of wild type CTL9 at 25 degrees C, suggesting that it is a robust feature of the denatured state ensemble of this

  4. Exploring representations of protein structure for automated remote homology detection and mapping of protein structure space

    PubMed Central

    2014-01-01

    Background Due to rapid sequencing of genomes, there are now millions of deposited protein sequences with no known function. Fast sequence-based comparisons allow detecting close homologs for a protein of interest to transfer functional information from the homologs to the given protein. Sequence-based comparison cannot detect remote homologs, in which evolution has adjusted the sequence while largely preserving structure. Structure-based comparisons can detect remote homologs but most methods for doing so are too expensive to apply at a large scale over structural databases of proteins. Recently, fragment-based structural representations have been proposed that allow fast detection of remote homologs with reasonable accuracy. These representations have also been used to obtain linearly-reducible maps of protein structure space. It has been shown, as additionally supported from analysis in this paper that such maps preserve functional co-localization of the protein structure space. Methods Inspired by a recent application of the Latent Dirichlet Allocation (LDA) model for conducting structural comparisons of proteins, we propose higher-order LDA-obtained topic-based representations of protein structures to provide an alternative route for remote homology detection and organization of the protein structure space in few dimensions. Various techniques based on natural language processing are proposed and employed to aid the analysis of topics in the protein structure domain. Results We show that a topic-based representation is just as effective as a fragment-based one at automated detection of remote homologs and organization of protein structure space. We conduct a detailed analysis of the information content in the topic-based representation, showing that topics have semantic meaning. The fragment-based and topic-based representations are also shown to allow prediction of superfamily membership. Conclusions This work opens exciting venues in designing novel

  5. Structural Characteristics of Novel Protein Folds

    PubMed Central

    Fernandez-Fuentes, Narcis; Dybas, Joseph M.; Fiser, Andras

    2010-01-01

    Folds are the basic building blocks of protein structures. Understanding the emergence of novel protein folds is an important step towards understanding the rules governing the evolution of protein structure and function and for developing tools for protein structure modeling and design. We explored the frequency of occurrences of an exhaustively classified library of supersecondary structural elements (Smotifs), in protein structures, in order to identify features that would define a fold as novel compared to previously known structures. We found that a surprisingly small set of Smotifs is sufficient to describe all known folds. Furthermore, novel folds do not require novel Smotifs, but rather are a new combination of existing ones. Novel folds can be typified by the inclusion of a relatively higher number of rarely occurring Smotifs in their structures and, to a lesser extent, by a novel topological combination of commonly occurring Smotifs. When investigating the structural features of Smotifs, we found that the top 10% of most frequent ones have a higher fraction of internal contacts, while some of the most rare motifs are larger, and contain a longer loop region. PMID:20421995

  6. Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet.

    PubMed

    Tyagi, M; Sharma, P; Swamy, C S; Cadet, F; Srinivasan, N; de Brevern, A G; Offmann, B

    2006-07-01

    Encoding protein 3D structures into 1D string using short structural prototypes or structural alphabets opens a new front for structure comparison and analysis. Using the well-documented 16 motifs of Protein Blocks (PBs) as structural alphabet, we have developed a methodology to compare protein structures that are encoded as sequences of PBs by aligning them using dynamic programming which uses a substitution matrix for PBs. This methodology is implemented in the applications available in Protein Block Expert (PBE) server. PBE addresses common issues in the field of protein structure analysis such as comparison of proteins structures and identification of protein structures in structural databanks that resemble a given structure. PBE-T provides facility to transform any PDB file into sequences of PBs. PBE-ALIGNc performs comparison of two protein structures based on the alignment of their corresponding PB sequences. PBE-ALIGNm is a facility for mining SCOP database for similar structures based on the alignment of PBs. Besides, PBE provides an interface to a database (PBE-SAdb) of preprocessed PB sequences from SCOP culled at 95% and of all-against-all pairwise PB alignments at family and superfamily levels. PBE server is freely available at http://bioinformatics.univ-reunion.fr/PBE/. PMID:16844973

  7. Development of electron spin echo envelope modulation spectroscopy to probe the secondary structure of recombinant membrane proteins in a lipid bilayer.

    PubMed

    Zhang, Rongfu; Sahu, Indra D; Gibson, Kaylee R; Muhammad, Nefertiti B; Bali, Avnika P; Comer, Raven G; Liu, Lishan; Craig, Andrew F; Mccarrick, Robert M; Dabney-Smith, Carole; Sanders, Charles R; Lorigan, Gary A

    2015-11-01

    Membrane proteins conduct many important biological functions essential to the survival of organisms. However, due to their inherent hydrophobic nature, it is very difficult to obtain structural information on membrane-bound proteins using traditional biophysical techniques. We are developing a new approach to probe the secondary structure of membrane proteins using the pulsed EPR technique of Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy. This method has been successfully applied to model peptides made synthetically. However, in order for this ESEEM technique to be widely applicable to larger membrane protein systems with no size limitations, protein samples with deuterated residues need to be prepared via protein expression methods. For the first time, this study shows that the ESEEM approach can be used to probe the local secondary structure of a (2) H-labeled d8 -Val overexpressed membrane protein in a membrane mimetic environment. The membrane-bound human KCNE1 protein was used with a known solution NMR structure to demonstrate the applicability of this methodology. Three different α-helical regions of KCNE1 were probed: the extracellular domain (Val21), transmembrane domain (Val50), and cytoplasmic domain (Val95). These results indicated α-helical structures in all three segments, consistent with the micelle structure of KCNE1. Furthermore, KCNE1 was incorporated into a lipid bilayer and the secondary structure of the transmembrane domain (Val50) was shown to be α-helical in a more native-like environment. This study extends the application of this ESEEM approach to much larger membrane protein systems that are difficult to study with X-ray crystallography and/or NMR spectroscopy. PMID:26355804

  8. Low Charge and Reduced Mobility of Membrane Protein Complexes Has Implications for Calibration of Collision Cross Section Measurements.

    PubMed

    Allison, Timothy M; Landreh, Michael; Benesch, Justin L P; Robinson, Carol V

    2016-06-01

    Ion mobility mass spectrometry of integral membrane proteins provides valuable insights into their architecture and stability. Here we show that, due to their lower charge, the average mobility of native-like membrane protein ions is approximately 30% lower than that of soluble proteins of similar mass. This has implications for drift time measurements, made on traveling wave ion mobility mass spectrometers, which have to be calibrated to extract collision cross sections (Ω). Common calibration strategies employ unfolded or native-like soluble protein standards with masses and mobilities comparable to the protein of interest. We compare Ω values for membrane proteins, derived from standard calibration protocols using soluble proteins, to values measured using an RF-confined drift tube. Our results demonstrate that, while common calibration methods underestimate Ω for native-like or unfolded membrane protein complexes, higher mass soluble calibration standards consistently yield more accurate Ω values. These findings enable us to obtain directly structural information for highly charge-reduced complexes by traveling wave ion mobility mass spectrometry. PMID:27153188

  9. Protein Folding-How and Why: By Hydrogen Exchange, Fragment Separation, and Mass Spectrometry.

    PubMed

    Englander, S Walter; Mayne, Leland; Kan, Zhong-Yuan; Hu, Wenbing

    2016-07-01

    Advanced hydrogen exchange (HX) methodology can now determine the structure of protein folding intermediates and their progression in folding pathways. Key developments over time include the HX pulse labeling method with nuclear magnetic resonance analysis, the fragment separation method, the addition to it of mass spectrometric (MS) analysis, and recent improvements in the HX MS technique and data analysis. Also, the discovery of protein foldons and their role supplies an essential interpretive link. Recent work using HX pulse labeling with MS analysis finds that a number of proteins fold by stepping through a reproducible sequence of native-like intermediates in an ordered pathway. The stepwise nature of the pathway is dictated by the cooperative foldon unit construction of the protein. The pathway order is determined by a sequential stabilization principle; prior native-like structure guides the formation of adjacent native-like structure. This view does not match the funneled energy landscape paradigm of a very large number of folding tracks, which was framed before foldons were known and is more appropriate for the unguided residue-level search to surmount an initial kinetic barrier rather than for the overall unfolded-state to native-state folding pathway. PMID:27145881

  10. Protein folding: When ribosomes pick the structure

    NASA Astrophysics Data System (ADS)

    Sivertsson, Elin M.; Itzhaki, Laura S.

    2014-05-01

    Anfinsen's principle tells us that the folded structure of a protein is determined solely by its sequence. Now, it has been shown that the rate at which a polypeptide chain is synthesized in the cell can affect which of two alternative folded structures it adopts.

  11. Modification and optimization of the united-residue (UNRES) potential-energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins

    PubMed Central

    Liwo, Adam; Khalili, Mey; Czaplewski, Cezary; Kalinowski, Sebastian; Ołdziej, Stanisław; Wachucik, Katarzyna; Scheraga, Harold A.

    2011-01-01

    We report the modification and parameterization of the united-residue (UNRES) force field for energy-based protein-structure prediction and protein-folding simulations. We tested the approach on three training proteins separately: 1E0L (β), 1GAB (α), and 1E0G (α + β). Heretofore, the UNRES force field had been designed and parameterized to locate native-like structures of proteins as global minima of their effective potential-energy surfaces, which largely neglected the conformational entropy because decoys composed of only lowest-energy conformations were used to optimize the force field. Recently, we developed a mesoscopic dynamics procedure for UNRES, and applied it with success to simulate protein folding pathways. How ever, the force field turned out to be largely biased towards α-helical structures in canonical simulations because the conformational entropy had been neglected in the parameterization. We applied the hierarchical optimization method developed in our earlier work to optimize the force field, in which the conformational space of a training protein is divided into levels each corresponding to a certain degree of native-likeness. The levels are ordered according to increasing native-likeness; level 0 corresponds to structures with no native-like elements and the highest level corresponds to the fully native-like structures. The aim of optimization is to achieve the order of the free energies of levels, decreasing as their native-likeness increases. The procedure is iterative, and decoys of the training protein(s) generated with the energy-function parameters of the preceding iteration are used to optimize the force field in a current iteration. We applied the multiplexing replica exchange molecular dynamics (MREMD) method, recently implemented in UNRES, to generate decoys; with this modification, conformational entropy is taken into account. Moreover, we optimized the free-energy gaps between levels at temperatures corresponding to a

  12. Protein structural domains: definition and prediction.

    PubMed

    Ezkurdia, Iakes; Tress, Michael L

    2011-11-01

    Recognition and prediction of structural domains in proteins is an important part of structure and function prediction. This unit lists the range of tools available for domain prediction, and describes sequence and structural analysis tools that complement domain prediction methods. Also detailed are the basic domain prediction steps, along with suggested strategies for different protein sequences and potential pitfalls in domain boundary prediction. The difficult problem of domain orientation prediction is also discussed. All the resources necessary for domain boundary prediction are accessible via publicly available Web servers and databases and do not require computational expertise. PMID:22045561

  13. Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method

    SciTech Connect

    Haibo Cao

    2003-12-12

    In this work, they try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. They found a strong correlation between amino acid sequences and the corresponding native structure of the protein. Some applications of this correlation were discussed in this dissertation include the domain partition and a new structural threading method as well as the performance of this method in the CASP5 competition. In the first part, they give a brief introduction to the protein folding problem. Some essential knowledge and progress from other research groups was discussed. This part includes discussions of interactions among amino acids residues, lattice HP model, and the design ability principle. In the second part, they try to establish the correlation between amino acid sequence and the corresponding native structure of the protein. This correlation was observed in the eigenvector study of protein contact matrix. They believe the correlation is universal, thus it can be used in automatic partition of protein structures into folding domains. In the third part, they discuss a threading method based on the correlation between amino acid sequences and ominant eigenvector of the structure contact-matrix. A mathematically straightforward iteration scheme provides a self-consistent optimum global sequence-structure alignment. The computational efficiency of this method makes it possible to search whole protein structure databases for structural homology without relying on sequence similarity. The sensitivity and specificity of this method is discussed, along with a case of blind test prediction. In the appendix, they list the overall performance of this threading method in CASP5 blind test in comparison with other existing approaches.

  14. Protein structure, spectral properties, and photobiological function of lumazine protein

    NASA Astrophysics Data System (ADS)

    Lee, John W.; Bradley, Elizabeth A.; O'Kane, Dennis J.

    1992-04-01

    Protein sequence analysis, nuclear magnetic resonance, and fluorescence dynamics have been applied in a determination of the interactions of the lumazine derivative with the amino acid residues in the proposed ligand binding site of lumazine protein. It is these interactions that `tune' the excited state properties of the bound lumazine so that it can perform its photobiological function as the emitter of bioluminescence in Photobacterium species. A three- way sequence alignment shows that lumazine protein is homologous with the yellow- fluorescent protein of Vibrio fischeri and the riboflavin synthase from Bacillus subtilis. This last enzyme is ubiquitous in procaryotes, and utilizes two of these same lumazines as substrates for the production of riboflavin. By analogy with riboflavin synthase, a short sequence in the lumazine protein has been suggested as the ligand binding site. In riboflavin synthase there is a second binding site, but this is absent in lumazine protein, thus negating any synthase activity for this protein. Hydrogen bonds to the residues in this binding domain and `freeze' the lumazine structure into the highly polar tautomer deduced from NMR evidence. This also accounts for the rigidity of binding shown by the 23 ns (2 degree(s)C) rotational correlation time of the bound ligand as well as the strong blue shift of the fluorescence maximum, from 490 nm free to 475 nm when bound.

  15. SCOP: a structural classification of proteins database.

    PubMed Central

    Hubbard, T J; Murzin, A G; Brenner, S E; Chothia, C

    1997-01-01

    The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known proteins structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and far evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database, so far. SCOP also provides for each structure links to atomic co-ordinates, images of the structures, interactive viewers, sequence data, data on any conformational changes related to function and literature references. The database is freely accessible on the World Wide Web (WWW) with an entry point at URL http://scop.mrc-lmb.cam.ac.uk/scop/ PMID:9016544

  16. Recurrent Structural Motifs in Non-Homologous Protein Structures

    PubMed Central

    Johansson, Maria U.; Zoete, Vincent; Guex, Nicolas

    2013-01-01

    We have extracted an extensive collection of recurrent structural motifs (RSMs), which consist of sequentially non-contiguous structural motifs (4–6 residues), each of which appears with very similar conformation in three or more mutually unrelated protein structures. We find that the proteins in our set are covered to a substantial extent by the recurrent non-contiguous structural motifs, especially the helix and strand regions. Computational alanine scanning calculations indicate that the average folding free energy changes upon alanine mutation for most types of non-alanine residues are higher for amino acids that are present in recurrent structural motifs than for amino acids that are not. The non-alanine amino acids that are most common in the recurrent structural motifs, i.e., phenylalanine, isoleucine, leucine, valine and tyrosine and the less abundant methionine and tryptophan, have the largest folding free energy changes. This indicates that the recurrent structural motifs, as we define them, describe recurrent structural patterns that are important for protein stability. In view of their properties, such structural motifs are potentially useful for inter-residue contact prediction and protein structure refinement. PMID:23574940

  17. Structure and Non-Structure of Centrosomal Proteins

    PubMed Central

    Bertero, Michela G.; Boutin, Maïlys; Guarín, Nayibe; Méndez-Giraldez, Raúl; Nuñez, Alfonso; Pedrero, Juan G.; Redondo, Pilar; Sanz, María; Speroni, Silvia; Teichert, Florian; Bruix, Marta; Carazo, José M.; Gonzalez, Cayetano; Reina, José; Valpuesta, José M.; Vernos, Isabelle; Zabala, Juan C.; Montoya, Guillermo; Coll, Miquel; Bastolla, Ugo; Serrano, Luis

    2013-01-01

    Here we perform a large-scale study of the structural properties and the expression of proteins that constitute the human Centrosome. Centrosomal proteins tend to be larger than generic human proteins (control set), since their genes contain in average more exons (20.3 versus 14.6). They are rich in predicted disordered regions, which cover 57% of their length, compared to 39% in the general human proteome. They also contain several regions that are dually predicted to be disordered and coiled-coil at the same time: 55 proteins (15%) contain disordered and coiled-coil fragments that cover more than 20% of their length. Helices prevail over strands in regions homologous to known structures (47% predicted helical residues against 17% predicted as strands), and even more in the whole centrosomal proteome (52% against 7%), while for control human proteins 34.5% of the residues are predicted as helical and 12.8% are predicted as strands. This difference is mainly due to residues predicted as disordered and helical (30% in centrosomal and 9.4% in control proteins), which may correspond to alpha-helix forming molecular recognition features (α-MoRFs). We performed expression assays for 120 full-length centrosomal proteins and 72 domain constructs that we have predicted to be globular. These full-length proteins are often insoluble: Only 39 out of 120 expressed proteins (32%) and 19 out of 72 domains (26%) were soluble. We built or retrieved structural models for 277 out of 361 human proteins whose centrosomal localization has been experimentally verified. We could not find any suitable structural template with more than 20% sequence identity for 84 centrosomal proteins (23%), for which around 74% of the residues are predicted to be disordered or coiled-coils. The three-dimensional models that we built are available at http://ub.cbm.uam.es/centrosome/models/index.php. PMID:23671615

  18. Deciphering Supramolecular Structures with Protein-Protein Interaction Network Modeling

    PubMed Central

    Tsuji, Toshiyuki; Yoda, Takao; Shirai, Tsuyoshi

    2015-01-01

    Many biological molecules are assembled into supramolecules that are essential to perform complicated functions in the cell. However, experimental information about the structures of supramolecules is not sufficient at this point. We developed a method of predicting and modeling the structures of supramolecules in a biological network by combining structural data of the Protein Data Bank (PDB) and interaction data in IntAct databases. Templates for binary complexes in IntAct were extracted from PDB. Modeling was attempted by assembling binary complexes with superposed shared subunits. A total of 3,197 models were constructed, and 1,306 (41% of the total) contained at least one subunit absent from experimental structures. The models also suggested 970 (25% of the total) experimentally undetected subunit interfaces, and 41 human disease-related amino acid variants were mapped onto these model-suggested interfaces. The models demonstrated that protein-protein interaction network modeling is useful to fill the information gap between biological networks and structures. PMID:26549015

  19. Protein structures by spallation neutron crystallography

    PubMed Central

    Langan, Paul; Fisher, Zoë; Kovalevsky, Andrii; Mustyakimov, Marat; Sutcliffe Valone, Amanda; Unkefer, Cliff; Waltman, Mary Jo; Coates, Leighton; Adams, Paul D.; Afonine, Pavel V.; Bennett, Brad; Dealwis, Chris; Schoenborn, Benno P.

    2008-01-01

    The Protein Crystallography Station at Los Alamos Neutron Science Center is a high-performance beamline that forms the core of a capability for neutron macromolecular structure and function determination. This capability also includes the Macromolecular Neutron Crystallography (MNC) consortium between Los Alamos (LANL) and Lawrence Berkeley National Laboratories for developing computational tools for neutron protein crystallography, a biological deuteration laboratory, the National Stable Isotope Production Facility, and an MNC drug design consortium between LANL and Case Western Reserve University. PMID:18421142

  20. Structure and Function of Lipopolysaccharide Binding Protein

    NASA Astrophysics Data System (ADS)

    Schumann, Ralf R.; Leong, Steven R.; Flaggs, Gail W.; Gray, Patrick W.; Wright, Samuel D.; Mathison, John C.; Tobias, Peter S.; Ulevitch, Richard J.

    1990-09-01

    The primary structure of lipopolysaccharide binding protein (LBP), a trace plasma protein that binds to the lipid A moiety of bacterial lipopolysaccharides (LPSs), was deduced by sequencing cloned complementary DNA. LBP shares sequence identity with another LPS binding protein found in granulocytes, bactericidal/permeability-increasing protein, and with cholesterol ester transport protein of the plasma. LBP may control the response to LPS under physiologic conditions by forming high-affinity complexes with LPS that bind to monocytes and macrophages, which then secrete tumor necrosis factor. The identification of this pathway for LPS-induced monocyte stimulation may aid in the development of treatments for diseases in which Gram-negative sepsis or endotoxemia are involved.

  1. Enzyme dehydration using Microglassification™ preserves the protein's structure and function.

    PubMed

    Aniket; Gaul, David A; Bitterfield, Deborah L; Su, Jonathan T; Li, Victoria M; Singh, Ishita; Morton, Jackson; Needham, David

    2015-02-01

    Controlled enzyme dehydration using a new processing technique of Microglassification™ has been investigated. Aqueous solution microdroplets of lysozyme, α-chymotrypsin, catalase, and horseradish peroxidase were dehydrated in n-pentanol, n-octanol, n-decanol, triacetin, or butyl lactate, and changes in their structure and function were analyzed upon rehydration. Water solubility and microdroplet dissolution rate in each solvent decreased in the order: butyl lactate > n-pentanol > triacetin > n-octanol > n-decanol. Enzymes Microglassified™ in n-pentanol retained higher activity (93%-98%) than n-octanol (78%-85%) or n-decanol (75%-89%), whereas those Microglassified™ in triacetin (36%-75%) and butyl lactate (48%-79%) retained markedly lower activity. FTIR spectroscopy analyses showed α-helix to β-sheet transformation for all enzymes upon Microglassification™, reflecting a loss of bound water in the dried state; however, the enzymes reverted to native-like conformation upon rehydration. Accelerated stressed-storage tests using Microglassified™ lysozyme showed a significant (p < 0.01) decrease in enzymatic activity from 46,560 ± 2736 to 31,060 ± 4327 units/mg after 3 months of incubation; however, it was comparable to the activity of the lyophilized formulation throughout the test period. These results establish Microglassification™ as a viable technique for enzyme preservation without affecting its structure or function. PMID:25557848

  2. Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry

    PubMed Central

    Hu, Wenbing; Walters, Benjamin T.; Kan, Zhong-Yuan; Mayne, Leland; Rosen, Laura E.; Marqusee, Susan; Englander, S. Walter

    2013-01-01

    The kinetic folding of ribonuclease H was studied by hydrogen exchange (HX) pulse labeling with analysis by an advanced fragment separation mass spectrometry technology. The results show that folding proceeds through distinct intermediates in a stepwise pathway that sequentially incorporates cooperative native-like structural elements to build the native protein. Each step is seen as a concerted transition of one or more segments from an HX-unprotected to an HX-protected state. Deconvolution of the data to near amino acid resolution shows that each step corresponds to the folding of a secondary structural element of the native protein, termed a “foldon.” Each folded segment is retained through subsequent steps of foldon addition, revealing a stepwise buildup of the native structure via a single dominant pathway. Analysis of the pertinent literature suggests that this model is consistent with experimental results for many proteins and some current theoretical results. Two biophysical principles appear to dictate this behavior. The principle of cooperativity determines the central role of native-like foldon units. An interaction principle termed “sequential stabilization” based on native-like interfoldon interactions orders the pathway. PMID:23603271

  3. Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry.

    PubMed

    Hu, Wenbing; Walters, Benjamin T; Kan, Zhong-Yuan; Mayne, Leland; Rosen, Laura E; Marqusee, Susan; Englander, S Walter

    2013-05-01

    The kinetic folding of ribonuclease H was studied by hydrogen exchange (HX) pulse labeling with analysis by an advanced fragment separation mass spectrometry technology. The results show that folding proceeds through distinct intermediates in a stepwise pathway that sequentially incorporates cooperative native-like structural elements to build the native protein. Each step is seen as a concerted transition of one or more segments from an HX-unprotected to an HX-protected state. Deconvolution of the data to near amino acid resolution shows that each step corresponds to the folding of a secondary structural element of the native protein, termed a "foldon." Each folded segment is retained through subsequent steps of foldon addition, revealing a stepwise buildup of the native structure via a single dominant pathway. Analysis of the pertinent literature suggests that this model is consistent with experimental results for many proteins and some current theoretical results. Two biophysical principles appear to dictate this behavior. The principle of cooperativity determines the central role of native-like foldon units. An interaction principle termed "sequential stabilization" based on native-like interfoldon interactions orders the pathway. PMID:23603271

  4. Atomic-level analysis of membrane-protein structure.

    PubMed

    Hendrickson, Wayne A

    2016-06-01

    Membrane proteins are substantially more challenging than natively soluble proteins as subjects for structural analysis. Thus, membrane proteins are greatly underrepresented in structural databases. Recently, focused consortium efforts and advances in methodology for protein production, crystallographic analysis and cryo-EM analysis have accelerated the pace of atomic-level structure determination of membrane proteins. PMID:27273628

  5. Structure of the Nitrosomonas Europaea Rh Protein

    SciTech Connect

    Li, X.; Jayachandran, S.; Nguyen, H.-H.T.; Chan, M.K.

    2009-06-01

    Amt/MEP/Rh proteins are a family of integral membrane proteins implicated in the transport of NH3, CH(2)NH2, and CO2. Whereas Amt/MEP proteins are agreed to transport ammonia (NH3/NH4+), the primary substrate for Rh proteins has been controversial. Initial studies suggested that Rh proteins also transport ammonia, but more recent evidence suggests that they transport CO2. Here we report the first structure of an Rh family member, the Rh protein from the chemolithoautotrophic ammonia-oxidizing bacterium Nitrosomonas europaea. This Rh protein exhibits a number of similarities to its Amt cousins, including a trimeric oligomeric state, a central pore with an unusual twin-His site in the middle, and a Phe residue that blocks the channel for small-molecule transport. However, there are some significant differences, the most notable being the presence of an additional cytoplasmic C-terminal alpha-helix, an increased number of internal proline residues along the transmembrane helices, and a specific set of residues that appear to link the C-terminal helix to Phe blockage. This latter linkage suggests a mechanism in which binding of a partner protein to the C terminus could regulate channel opening. Another difference is the absence of the extracellular pi-cation binding site conserved in Amt/Mep structures. Instead, CO2 pressurization experiments identify a CO2 binding site near the intracellular exit of the channel whose residues are highly conserved in all Rh proteins, except those belonging to the Rh30 subfamily. The implications of these findings on the functional role of the human Rh antigens are discussed.

  6. Membrane protein structure from rotational diffusion☆

    PubMed Central

    Das, Bibhuti B.; Park, Sang Ho; Opella, Stanley J.

    2014-01-01

    The motional averaging of powder pattern line shapes is one of the most fundamental aspects of sold-state NMR. Since membrane proteins in liquid crystalline phospholipid bilayers undergo fast rotational diffusion, all of the signals reflect the angles of the principal axes of their dipole–dipole and chemical shift tensors with respect to the axis defined by the bilayer normal. The frequency span and sign of the axially symmetric powder patterns that result from motional averaging about a common axis provide sufficient structural restraints for the calculation of the three-dimensional structure of a membrane protein in a phospholipid bilayer environment. The method is referred to as rotationally aligned (RA) solid-state NMR and demonstrated with results on full-length, unmodified membrane proteins with one, two, and seven trans-membrane helices. RA solid-state NMR is complementary to other solid-state NMR methods, in particular oriented sample (OS) solid-state NMR of stationary, aligned samples. Structural distortions of membrane proteins from the truncations of terminal residues and other sequence modifications, and the use of detergent micelles instead of phospholipid bilayers have also been demonstrated. Thus, it is highly advantageous to determine the structures of unmodified membrane proteins in liquid crystalline phospholipid bilayers under physiological conditions. RA solid-state NMR provides a general method for obtaining accurate and precise structures of membrane proteins under near-native conditions. This article is part of a Special Issue entitled: NMR Spectroscopy for Atomistic Views of Biomembranes and Cell Surfaces. PMID:24747039

  7. Utilization of Protein Crystal Structures in Industry

    NASA Astrophysics Data System (ADS)

    Ishikawa, Kohki

    In industry, protein crystallography is used in mainly two technologies. One is structure-based drug design, and the other is structure-based enzyme engineering. Some successful cases together with recent advances are presented in this article. The cases include the development of an anti-influenza drug, and the introduction of engineered acid phosphatase to the manufacturing process of nucleotides used as umami seasoning.

  8. Reconstruction of SAXS Profiles from Protein Structures

    PubMed Central

    Putnam, Daniel K.; Lowe, Edward W.

    2013-01-01

    Small angle X-ray scattering (SAXS) is used for low resolution structural characterization of proteins often in combination with other experimental techniques. After briefly reviewing the theory of SAXS we discuss computational methods based on 1) the Debye equation and 2) Spherical Harmonics to compute intensity profiles from a particular macromolecular structure. Further, we review how these formulas are parameterized for solvent density and hydration shell adjustment. Finally we introduce our solution to compute SAXS profiles utilizing GPU acceleration. PMID:24688746

  9. Structural mechanisms of nonplanar hemes in proteins

    SciTech Connect

    Shelnutt, J.A.

    1997-05-01

    The objective is to assess the occurrence of nonplanar distortions of hemes and other tetrapyrroles in proteins and to determine the biological function of these distortions. Recently, these distortions were found by us to be conserved among proteins belonging to a functional class. Conservation of the conformation of the heme indicates a possible functional role. Researchers have suggested possible mechanisms by which heme distortions might influence biological properties; however, no heme distortion has yet been shown conclusively to participate in a structural mechanism of hemoprotein function. The specific aims of the proposed work are: (1) to characterize and quantify the distortions of the hemes in all of the more than 300 hemoprotein X-ray crystal structures in terms of displacements along the lowest-frequency normal coordinates, (2) to determine the structural features of the protein component that generate and control these nonplanar distortions by using spectroscopic studies and molecular-mechanics calculations for the native proteins, their mutants and heme-peptide fragments, and model porphyrins, (3) to determine spectroscopic markers for the various types of distortion, and, finally, (4) to discover the functional significance of the nonplanar distortions by correlating function with porphyrin conformation for proteins and model porphyrins.

  10. Repeating covalent structure of streptococcal M protein.

    PubMed Central

    Beachey, E H; Seyer, J M; Kang, A H

    1978-01-01

    We have attempted to identify the covalent structure of the M protein molecule of group A streptococci that is responsible for inducing type-specific, protective immunity. M protein was extracted from type 24 streptococci, purified, and cleaved with cyanogen bromide. Seven cyanogen bromide peptides were purified and further characterized. Together, the peptides account for the entire amino acid content of the M protein molecule. Each of the purified peptides possessed the type-specific determinant that inhibits opsonic antibodies for group A streptococci. The primary structures of the amino-terminal regions of each of the purified peptides was studied by automated Edman degradation. The partial sequences of two of the peptides were found to be identical to each other and to that of the uncleaved M protein molecule through at least the first 27 residues. The amino-terminal sequences of the remaining five peptides were identical to each other through the twentieth residue but completely different from the amino-terminal region of the other two peptides. However, the type-specific immunoreactivity and the incomplete analysis of the primary structure of the seven peptides suggest that the antiphagocytic determinant resides in a repeating amino acid sequence in the M protein molecule. PMID:80011

  11. Protein crowding affects hydration structure and dynamics

    PubMed Central

    Harada, Ryuhei; Sugita, Yuji; Feig, Michael

    2012-01-01

    The effect of protein crowding on the structure and dynamics of water was examined from explicit solvent molecular dynamics simulations of a series of protein G and protein G/villin systems at different protein concentrations. Hydration structure was analyzed in terms of radial distribution functions, three-dimensional hydration sites, and preservation of tetrahedral coordination. Analysis of hydration dynamics focused on self-diffusion rates and dielectric constants as a function of crowding. The results show significant changes in both structure and dynamics of water under highly crowded conditions. The structure of water is altered mostly beyond the first solvation shell. Diffusion rates and dielectric constants are significantly reduced following linear trends as a function of crowding reflecting highly constrained water in crowded environments. The reduced dynamics of diffusion is expected to be strongly related to hydrodynamic properties of crowded cellular environments while the reduced dielectric constant under crowded conditions has implications for the stability of biomolecules in crowded environments. The results from this study suggest a prescription for modeling solvation in simulations of cellular environments. PMID:22352398

  12. A structural alphabet for local protein structures: improved prediction methods.

    PubMed

    Etchebest, Catherine; Benros, Cristina; Hazout, Serge; de Brevern, Alexandre G

    2005-06-01

    Three-dimensional protein structures can be described with a library of 3D fragments that define a structural alphabet. We have previously proposed such an alphabet, composed of 16 patterns of five consecutive amino acids, called Protein Blocks (PBs). These PBs have been used to describe protein backbones and to predict local structures from protein sequences. The Q16 prediction rate reaches 40.7% with an optimization procedure. This article examines two aspects of PBs. First, we determine the effect of the enlargement of databanks on their definition. The results show that the geometrical features of the different PBs are preserved (local RMSD value equal to 0.41 A on average) and sequence-structure specificities reinforced when databanks are enlarged. Second, we improve the methods for optimizing PB predictions from sequences, revisiting the optimization procedure and exploring different local prediction strategies. Use of a statistical optimization procedure for the sequence-local structure relation improves prediction accuracy by 8% (Q16 = 48.7%). Better recognition of repetitive structures occurs without losing the prediction efficiency of the other local folds. Adding secondary structure prediction improved the accuracy of Q16 by only 1%. An entropy index (Neq), strongly related to the RMSD value of the difference between predicted PBs and true local structures, is proposed to estimate prediction quality. The Neq is linearly correlated with the Q16 prediction rate distributions, computed for a large set of proteins. An "expected" prediction rate QE16 is deduced with a mean error of 5%. PMID:15822101

  13. Protein tertiary structure recognition using optimized Hamiltonians with local interactions.

    PubMed Central

    Goldstein, R A; Luthey-Schulten, Z A; Wolynes, P G

    1992-01-01

    Protein folding codes embodying local interactions including surface and secondary structure propensities and residue-residue contacts are optimized for a set of training proteins by using spin-glass theory. A screening method based on these codes correctly matches the structure of a set of test proteins with proteins of similar topology with 100% accuracy, even with limited sequence similarity between the test proteins and the structural homologs and the absence of any structurally similar proteins in the training set. PMID:1409599

  14. Structural mechanisms of chaperone mediated protein disaggregation

    PubMed Central

    Sousa, Rui

    2014-01-01

    The ClpB/Hsp104 and Hsp70 classes of molecular chaperones use ATP hydrolysis to dissociate protein aggregates and complexes, and to move proteins through membranes. ClpB/Hsp104 are members of the AAA+ family of proteins which form ring-shaped hexamers. Loops lining the pore in the ring engage substrate proteins as extended polypeptides. Interdomain rotations and conformational changes in these loops coupled to ATP hydrolysis unfold and pull proteins through the pore. This provides a mechanism that progressively disrupts local secondary and tertiary structure in substrates, allowing these chaperones to dissociate stable aggregates such as β-sheet rich prions or coiled coil SNARE complexes. While the ClpB/Hsp104 mechanism appears to embody a true power-stroke in which an ATP powered conformational change in one protein is directly coupled to movement or structural change in another, the mechanism of force generation by Hsp70s is distinct and less well understood. Both active power-stroke and purely passive mechanisms in which Hsp70 captures spontaneous fluctuations in a substrate have been proposed, while a third proposed mechanism—entropic pulling—may be able to generate forces larger than seen in ATP-driven molecular motors without the conformational coupling required for a power-stroke. The disaggregase activity of these chaperones is required for thermotolerance, but unrestrained protein complex/aggregate dissociation is potentially detrimental. Disaggregating chaperones are strongly auto-repressed, and are regulated by co-chaperones which recruit them to protein substrates and activate the disaggregases via mechanisms involving either sequential transfer of substrate from one chaperone to another and/or simultaneous interaction of substrate with multiple chaperones. By effectively subjecting substrates to multiple levels of selection by multiple chaperones, this may insure that these potent disaggregases are only activated in the appropriate context. PMID

  15. Structural neighboring property for identifying protein-protein binding sites

    PubMed Central

    2015-01-01

    Background The protein-protein interaction plays a key role in the control of many biological functions, such as drug design and functional analysis. Determination of binding sites is widely applied in molecular biology research. Therefore, many efficient methods have been developed for identifying binding sites. In this paper, we calculate structural neighboring property through Voronoi diagram. Using 6,438 complexes, we study local biases of structural neighboring property on interface. Results We propose a novel statistical method to extract interacting residues, and interacting patches can be clustered as predicted interface residues. In addition, structural neighboring property can be adopted to construct a new energy function, for evaluating docking solutions. It includes new statistical property as well as existing energy items. Comparing to existing methods, our approach improves overall Fnat value by at least 3%. On Benchmark v4.0, our method has average Irmsd value of 3.31Å and overall Fnat value of 63%, which improves upon Irmsd of 3.89 Å and Fnat of 49% for ZRANK, and Irmsd of 3.99Å and Fnat of 46% for ClusPro. On the CAPRI targets, our method has average Irmsd value of 3.46 Å and overall Fnat value of 45%, which improves upon Irmsd of 4.18 Å and Fnat of 40% for ZRANK, and Irmsd of 5.12 Å and Fnat of 32% for ClusPro. Conclusions Experiments show that our method achieves better results than some state-of-the-art methods for identifying protein-protein binding sites, with the prediction quality improved in terms of CAPRI evaluation criteria. PMID:26356630

  16. Solving coiled-coil protein structures

    DOE PAGESBeta

    Dauter, Zbigniew

    2015-02-26

    With the availability of more than 100,000 entries stored in the Protein Data Bank (PDB) that can be used as search models, molecular replacement (MR) is currently the most popular method of solving crystal structures of macromolecules. Significant methodological efforts have been directed in recent years towards making this approach more powerful and practical. This resulted in the creation of several computer programs, highly automated and user friendly, that are able to successfully solve many structures even by researchers who, although interested in structures of biomolecules, are not very experienced in crystallography.

  17. Simulations of kinetically irreversible protein aggregate structure.

    PubMed Central

    Patro, S Y; Przybycien, T M

    1994-01-01

    We have simulated the structure of kinetically irreversible protein aggregates in two-dimensional space using a lattice-based Monte-Carlo routine. Our model specifically accounts for the intermolecular interactions between hydrophobic and hydrophilic protein surfaces and a polar solvent. The simulations provide information about the aggregate density, the types of inter-monomer contacts and solvent content within the aggregates, the type and extent of solvent exposed perimeter, and the short- and long-range order all as a function of (i) the extent of monomer hydrophobic surface area and its distribution on the model protein surface and (ii) the magnitude of the hydrophobic-hydrophobic contact energy. An increase in the extent of monomer hydrophobic surface area resulted in increased aggregate densities with concomitant decreased system free energies. These effects are accompanied by increases in the number of hydrophobic-hydrophobic contacts and decreases in the solvent-exposed hydrophobic surface area of the aggregates. Grouping monomer hydrophobic surfaces in a single contiguous stretch resulted in lower aggregate densities and lower short range order. More favorable hydrophobic-hydrophobic contact energies produced structures with higher densities but the number of unfavorable protein-protein contacts was also observed to increase; greater configurational entropy produced the opposite effect. Properties predicted by our model are in good qualitative agreement with available experimental observations. Images FIGURE 6 FIGURE 13 PMID:8061184

  18. Exploiting Microbeams for Membrane Protein Structure Determination.

    PubMed

    Warren, Anna J; Axford, Danny; Paterson, Neil G; Owen, Robin L

    2016-01-01

    A reproducible, and sample independent means of predictably obtaining large, well-ordered crystals has proven elusive in macromolecular crystallography. In the structure determination pipeline, crystallisation often proves to be a rate-limiting step, and the process of obtaining even small or badly ordered crystals can prove time-consuming and laborious. This is particularly true in the field of membrane protein crystallography and this is reflected in the limited number of unique membrane protein structures deposited in the protein data bank (less than 650 by June 2016 - http://blanco.biomol.uci.edu/mpstruc ). Over recent years the requirement for, and time and cost associated with obtaining, large crystals has been partially alleviated through the development of beamline instrumentation allowing data collection, and structure solution, from ever-smaller crystals. Advances in several areas have led to a step change in what might be considered achievable during a synchrotron trip over the last decade. This chapter will briefly review the current status of the field, the tools available to ease data collection and processing, and give some examples of exploitation of these for membrane protein microfocus macromolecular crystallography. PMID:27553238

  19. Photoinduced structural changes to protein kinase A

    NASA Astrophysics Data System (ADS)

    Rozinek, Sarah C.; Thomas, Robert J.; Brancaleon, Lorenzo

    2014-03-01

    The importance of porphyrins in organisms is underscored by the ubiquitous biological and biochemical functions that are mediated by these compounds and by their potential biomedical and biotechnological applications. Protoporphyrin IX (PPIX) is the precursor to heme and has biomedical applications such as its use as a photosensitizer in phototherapy and photodetection of cancer. Among other applications, our group has demonstrated that low-irradiance exposure to laser irradiation of PPIX, Fe-PPIX, or meso-tetrakis (4-sulfonatophenyl) porphyrin (TSPP) non-covalently docked to a protein causes conformational changes in the polypeptide. Such approach can have remarkable consequences in the study of protein structure/function relationship and can be used to prompt non-native protein properties. Therefore we have investigated protein kinase A (PKA), a more relevant protein model towards the photo-treatment of cancer. PKA's enzymatic functions are regulated by the presence of cyclic adenosine monophosphate for intracellular signal transduction involved in, among other things, stimulation of transcription, tumorigenesis in Carney complex and migration of breast carcinoma cells. Since phosphorylation is a necessary step in some cancers and inflammatory diseases, inhibiting the protein kinase, and therefore phosphorylation, may serve to treat these diseases. Changes in absorption, steady-state fluorescence, and fluorescence lifetime indicate: 1) both TSPP and PPIX non-covalently bind to PKA where they maintain photoreactivity; 2) absorptive photoproduct formation occurs only when PKA is bound to TSPP and irradiated; and 3) PKA undergoes secondary structural changes after irradiation with either porphyrin bound. These photoinduced changes could affect the protein's enzymatic and signaling capabilities.

  20. Dynamic Structure in Artificial Protein Hydrogels

    NASA Astrophysics Data System (ADS)

    Kennedy, Scott B.; Hong, Mei; de Azevedo, Eduardo; Tirrell, David A.; Russell, Thomas P.

    2000-03-01

    Artificial proteins that form reversible hydrogels have been designed and synthesized using recombinant DNA methodologies. Proteins are designed such that two helical, leucine zipper domains flank a central, water soluble domain. Under proper conditions of concentration, pH, and temperature the helical domains aggregate as coiled coils and act as physical crosslinks. Small angle x-ray and neutron scattering have been used to elucidate the gel structure, and NMR and fluorescence exchange experiments have been used to probe the dynamics of the gel system.

  1. Electronic structure of bacterial surface protein layers

    SciTech Connect

    Maslyuk, Volodymyr V.; Mertig, Ingrid; Bredow, Thomas; Mertig, Michael; Vyalikh, Denis V.; Molodtsov, Serguei L.

    2008-01-15

    We report an approach for the calculation of the electronic density of states of the dried two-dimensional crystalline surface protein layer (S layer) of the bacterium Bacillus sphaericus NCTC 9602. The proposed model is based on the consideration of individual amino acids in the corresponding conformation of the peptide chain which additively contribute to the electronic structure of the entire protein complex. The derived results agree well with the experimental data obtained by means of photoemission (PE), resonant PE, and near-edge x-ray absorption spectroscopy.

  2. ADAR proteins: structure and catalytic mechanism.

    PubMed

    Goodman, Rena A; Macbeth, Mark R; Beal, Peter A

    2012-01-01

    Since the discovery of the adenosine deaminase (ADA) acting on RNA (ADAR) family of proteins in 1988 (Bass and Weintraub, Cell 55:1089-1098, 1988) (Wagner et al. Proc Natl Acad Sci U S A 86:2647-2651, 1989), we have learned much about their structure and catalytic mechanism. However, much about these enzymes is still unknown, particularly regarding the selective recognition and processing of specific adenosines within substrate RNAs. While a crystal structure of the catalytic domain of human ADAR2 has been solved, we still lack structural data for an ADAR catalytic domain bound to RNA, and we lack any structural data for other ADARs. However, by analyzing the structural data that is available along with similarities to other deaminases, mutagenesis and other biochemical experiments, we have been able to advance the understanding of how these fascinating enzymes function. PMID:21769729

  3. Visualizing chaperone-assisted protein folding.

    PubMed

    Horowitz, Scott; Salmon, Loïc; Koldewey, Philipp; Ahlstrom, Logan S; Martin, Raoul; Quan, Shu; Afonine, Pavel V; van den Bedem, Henry; Wang, Lili; Xu, Qingping; Trievel, Raymond C; Brooks, Charles L; Bardwell, James C A

    2016-07-01

    Challenges in determining the structures of heterogeneous and dynamic protein complexes have greatly hampered past efforts to obtain a mechanistic understanding of many important biological processes. One such process is chaperone-assisted protein folding. Obtaining structural ensembles of chaperone-substrate complexes would ultimately reveal how chaperones help proteins fold into their native state. To address this problem, we devised a new structural biology approach based on X-ray crystallography, termed residual electron and anomalous density (READ). READ enabled us to visualize even sparsely populated conformations of the substrate protein immunity protein 7 (Im7) in complex with the Escherichia coli chaperone Spy, and to capture a series of snapshots depicting the various folding states of Im7 bound to Spy. The ensemble shows that Spy-associated Im7 samples conformations ranging from unfolded to partially folded to native-like states and reveals how a substrate can explore its folding landscape while being bound to a chaperone. PMID:27239796

  4. Helical Membrane Protein Conformations and their Environment

    PubMed Central

    Cross, Timothy A.; Murray, Dylan T.; Watts, Anthony

    2013-01-01

    Evidence that membrane proteins respond conformationally and functionally to their environment is gaining pace. Structural models, by necessity, have been characterized in preparations where the protein has been removed from its native environment. Different structural methods have used various membrane mimetics that have recently included lipid bilayers as a more native-like environment. Structural tools applied to lipid bilayer-embedded integral proteins are informing us about important generic characteristics of how membrane proteins respond to the lipid environment as compared with their response to other non-lipid environments. Here, we review the current status of the field, with specific reference to observations of some well-studied α-helical membrane proteins, as a starting point to aid the development of possible generic principals for model refinement. PMID:23996195

  5. Accurate Prediction of Docked Protein Structure Similarity.

    PubMed

    Akbal-Delibas, Bahar; Pomplun, Marc; Haspel, Nurit

    2015-09-01

    One of the major challenges for protein-protein docking methods is to accurately discriminate nativelike structures. The protein docking community agrees on the existence of a relationship between various favorable intermolecular interactions (e.g. Van der Waals, electrostatic, desolvation forces, etc.) and the similarity of a conformation to its native structure. Different docking algorithms often formulate this relationship as a weighted sum of selected terms and calibrate their weights against specific training data to evaluate and rank candidate structures. However, the exact form of this relationship is unknown and the accuracy of such methods is impaired by the pervasiveness of false positives. Unlike the conventional scoring functions, we propose a novel machine learning approach that not only ranks the candidate structures relative to each other but also indicates how similar each candidate is to the native conformation. We trained the AccuRMSD neural network with an extensive dataset using the back-propagation learning algorithm. Our method achieved predicting RMSDs of unbound docked complexes with 0.4Å error margin. PMID:26335807

  6. NMR structural studies on antifreeze proteins.

    PubMed

    Sönnichsen, F D; Davies, P L; Sykes, B D

    1998-01-01

    Antifreeze proteins (AFPs) are a structurally diverse class of proteins that bind to ice and inhibit its growth in a noncolligative manner. This adsorption-inhibition mechanism operating at the ice surface results in a lowering of the (nonequilibrium) freezing point below the melting point. A lowering of approximately 1 degree C, which is sufficient to prevent fish from freezing in ice-laden seawater, requires millimolar AFP levels in the blood. The solubility of AFPs at these millimolar concentrations and the small size of the AFPs (typically 3-15 kDa) make them ideal subjects for NMR analysis. Although fish AFPs are naturally abundant, seasonal expression, restricted access to polar fishes, and difficulties in separating numerous similar isoforms have made protein expression the method of choice for producing AFPs for structural studies. Expression of recombinant AFPs has also facilitated NMR analysis by permitting isotopic labeling with 15N and 13C and has permitted mutations to be made to help with the interpretation of NMR data. NMR analysis has recently solved two AFP structures and provided valuable information about the disposition of ice-binding side chains in a third. The potential exists to solve other AFP structures, including the newly described insect AFPs, and to use solid-state NMR techniques to address fundamental questions about the nature of the interaction between AFPs and ice. PMID:9923697

  7. Residual structures in the unfolded state of starch-binding domain of glucoamylase revealed by near-UV circular dichroism and protein engineering techniques.

    PubMed

    Ota, Chiaki; Ikeguchi, Masamichi; Tanaka, Akiyoshi; Hamada, Daizo

    2016-10-01

    Protein folding is a thermodynamic process driven by energy gaps between the native and unfolded states. Although a wealth of information is available on the structure of folded species, there is a paucity of data on unfolded species. Here, we analyzed the structural properties of the unfolded state of the starch-binding domain of glucoamylase from Aspergillus niger (SBD) formed in the presence of guanidinium hydrochloride (GuHCl). Although far-UV CD and intrinsic tryptophan fluorescence spectra as well as small angle X-ray scattering suggested that SBD assumes highly unfolded structures in the presence of GuHCl, near-UV circular dichroism of wild-type SBD suggested the presence of residual structures in the unfolded state. Analyses of the unfolded states of tryptophan mutants (W543L, W563A, W590A and W615L) using Similarity Parameter, a modified version of root mean square deviation as a measure of similarity between two spectra, suggested that W543 and W563 have preferences to form native-like residual structures in the GuHCl-unfolded state. In contrast, W615 was entirely unstructured, while W590 tended to form non-native ordered structures in the unfolded state. These data and the amino acid sequence of SBD suggest that local structural propensities in the unfolded state can be determined by the probability of the presence of hydrophobic or charged residues nearby tryptophan residues. PMID:27164491

  8. Recognizing the fold of a protein structure.

    PubMed

    Harrison, Andrew; Pearl, Frances; Sillitoe, Ian; Slidel, Tim; Mott, Richard; Thornton, Janet; Orengo, Christine

    2003-09-22

    This paper reports a graph-theoretic program, GRATH, that rapidly, and accurately, matches a novel structure against a library of domain structures to find the most similar ones. GRATH generates distributions of scores by comparing the novel domain against the different types of folds that have been classified previously in the CATH database of structural domains. GRATH uses a measure of similarity that details the geometric information, number of secondary structures and number of residues within secondary structures, that any two protein structures share. Although GRATH builds on well established approaches for secondary structure comparison, a novel scoring scheme has been introduced to allow ranking of any matches identified by the algorithm. More importantly, we have benchmarked the algorithm using a large dataset of 1702 non-redundant structures from the CATH database which have already been classified into fold groups, with manual validation. This has facilitated introduction of further constraints, optimization of parameters and identification of reliable thresholds for fold identification. Following these benchmarking trials, the correct fold can be identified with the top score with a frequency of 90%. It is identified within the ten most likely assignments with a frequency of 98%. GRATH has been implemented to use via a server (http://www.biochem.ucl.ac.uk/cgi-bin/cath/Grath.pl). GRATH's speed and accuracy means that it can be used as a reliable front-end filter for the more accurate, but computationally expensive, residue based structure comparison algorithm SSAP, currently used to classify domain structures in the CATH database. With an increasing number of structures being solved by the structural genomics initiatives, the GRATH server also provides an essential resource for determining whether newly determined structures are related to any known structures from which functional properties may be inferred. PMID:14512345

  9. Foldons, Protein Structural Modules, and Exons

    NASA Astrophysics Data System (ADS)

    Panchenko, Anna R.; Luthey-Schulten, Zaida; Wolynes, Peter G.

    1996-03-01

    Foldons, which are kinetically competent, quasi-independently folding units of a protein, may be defined using energy landscape analysis. Foldons can be identified by maxima in a scan of the ratio of a contiguous segment's energetic stability gap to the energy variance of that segment's molten globule states, reflecting the requirement of minimal frustration. The predicted foldons are compared with the exons and structural modules for 16 of the 30 proteins studied. Statistical analysis indicates a strong correlation between the energetically determined foldons and Go's geometrically defined structural modules, but there are marked sequence-dependent effects. There is only a weak correlation of foldons to exons. For γ II-crystallin, myoglobin, barnase, α -lactalbumin, and cytochrome c the foldons and some noncontiguous clusters of foldons compare well with intermediates observed in experiment.

  10. Quantitation of the area of overlap between second-derivative amide I infrared spectra to determine the structural similarity of a protein in different states.

    PubMed

    Kendrick, B S; Dong, A; Allison, S D; Manning, M C; Carpenter, J F

    1996-02-01

    Maintaining a native-like structure of protein pharmaceuticals during lyophilization is an important aspect of formulation. Infrared spectroscopy can be used to evaluate the effectiveness of formulations in protecting the secondary structural integrity of proteins in the dried solid. This necessitates making quantitative comparisons of the overall similarity of infrared spectra in the conformationally sensitive amide I region. We initially used the correlation coefficient r, as defined by Prestrelski et al. (Biophys. J. 1993, 65, 661-671), for this quantitation. Occasionally, we noticed that the r value did not agree with a visual assessment of the spectral similarity. In some cases this was due to an offset in baselines, which led artifactually to an unreasonably low r value. Conversely, if the spectra were baseline corrected and there existed a large similarity between peak positions, but differences in relative peak heights, the r value would be unreasonably high. Our approach to avoiding these problems is to use area-normalized second-derivative spectra. We have found that quantitating the area of overlap between area-normalized spectra provides a reliable, objective method to compare overall spectral similarity. In the current report, we demonstrate this method with selected protein spectra, which were taken from experiments where unfolding was induced by lyophilization or guanidine hydrochloride, and artificial data sets. With this analysis, we document how problems associated with calculation of the correlation coefficient, r, are avoided. PMID:8683440

  11. Structural Determinants of Misfolding in Multidomain Proteins

    PubMed Central

    Tian, Pengfei; Best, Robert B.

    2016-01-01

    Recent single molecule experiments, using either atomic force microscopy (AFM) or Förster resonance energy transfer (FRET) have shown that multidomain proteins containing tandem repeats may form stable misfolded structures. Topology-based simulation models have been used successfully to generate models for these structures with domain-swapped features, fully consistent with the available data. However, it is also known that some multidomain protein folds exhibit no evidence for misfolding, even when adjacent domains have identical sequences. Here we pose the question: what factors influence the propensity of a given fold to undergo domain-swapped misfolding? Using a coarse-grained simulation model, we can reproduce the known propensities of multidomain proteins to form domain-swapped misfolds, where data is available. Contrary to what might be naively expected based on the previously described misfolding mechanism, we find that the extent of misfolding is not determined by the relative folding rates or barrier heights for forming the domains present in the initial intermediates leading to folded or misfolded structures. Instead, it appears that the propensity is more closely related to the relative stability of the domains present in folded and misfolded intermediates. We show that these findings can be rationalized if the folded and misfolded domains are part of the same folding funnel, with commitment to one structure or the other occurring only at a relatively late stage of folding. Nonetheless, the results are still fully consistent with the kinetic models previously proposed to explain misfolding, with a specific interpretation of the observed rate coefficients. Finally, we investigate the relation between interdomain linker length and misfolding, and propose a simple alchemical model to predict the propensity for domain-swapped misfolding of multidomain proteins. PMID:27163669

  12. Proton assisted recoupling and protein structure determination

    PubMed Central

    De Paëpe, Gaël; Lewandowski, Józef R.; Loquet, Antoine; Böckmann, Anja; Griffin, Robert G.

    2008-01-01

    We introduce a homonuclear version of third spin assisted recoupling, a second-order mechanism that can be used for polarization transfer between 13C or 15N spins in magic angle spinning (MAS) NMR experiments, particularly at high spinning frequencies employed in contemporary high field MAS experiments. The resulting sequence, which we refer to as proton assisted recoupling (PAR), relies on a cross-term between 1H–13C (or 1H–15N) couplings to mediate zero quantum 13C–13C (or 15N–15N recoupling). In particular, using average Hamiltonian theory we derive an effective Hamiltonian for PAR and show that the transfer is mediated by trilinear terms of the form C1±C2∓HZ for 13C–13C recoupling experiments (or N1±N2∓HZ for 15N–15N). We use analytical and numerical simulations to explain the structure of the PAR optimization maps and to delineate the PAR matching conditions. We also detail the PAR polarization transfer dependence with respect to the local molecular geometry and explain the observed reduction in dipolar truncation. Finally, we demonstrate the utility of PAR in structural studies of proteins with 13C–13C spectra of uniformly 13C, 15N labeled microcrystalline Crh, a 85 amino acid model protein that forms a domain swapped dimer (MW=2×10.4 kDa). The spectra, which were acquired at high MAS frequencies (ωr2π>20 kHz) and magnetic fields (750–900 MHz 1H frequencies) using moderate rf fields, exhibit numerous cross peaks corresponding to long (up to 6–7 Å) 13C–13C distances which are particularly useful in protein structure determination. Using results from PAR spectra we calculate the structure of the Crh protein. PMID:19123534

  13. Proton assisted recoupling and protein structure determination

    NASA Astrophysics Data System (ADS)

    de Paëpe, Gaël; Lewandowski, Józef R.; Loquet, Antoine; Böckmann, Anja; Griffin, Robert G.

    2008-12-01

    We introduce a homonuclear version of third spin assisted recoupling, a second-order mechanism that can be used for polarization transfer between 13C or 15N spins in magic angle spinning (MAS) NMR experiments, particularly at high spinning frequencies employed in contemporary high field MAS experiments. The resulting sequence, which we refer to as proton assisted recoupling (PAR), relies on a cross-term between 1H-13C (or 1H-15N) couplings to mediate zero quantum 13C-13C (or 15N-15N recoupling). In particular, using average Hamiltonian theory we derive an effective Hamiltonian for PAR and show that the transfer is mediated by trilinear terms of the form C1+/-C2-/+HZ for 13C-13C recoupling experiments (or N1+/-N2-/+HZ for 15N-15N). We use analytical and numerical simulations to explain the structure of the PAR optimization maps and to delineate the PAR matching conditions. We also detail the PAR polarization transfer dependence with respect to the local molecular geometry and explain the observed reduction in dipolar truncation. Finally, we demonstrate the utility of PAR in structural studies of proteins with 13C-13C spectra of uniformly 13C, 15N labeled microcrystalline Crh, a 85 amino acid model protein that forms a domain swapped dimer (MW=2×10.4 kDa). The spectra, which were acquired at high MAS frequencies (ωr2π>20 kHz) and magnetic fields (750-900 MHz 1H frequencies) using moderate rf fields, exhibit numerous cross peaks corresponding to long (up to 6-7 A˚) 13C-13C distances which are particularly useful in protein structure determination. Using results from PAR spectra we calculate the structure of the Crh protein.

  14. Structural Determinants of Misfolding in Multidomain Proteins.

    PubMed

    Tian, Pengfei; Best, Robert B

    2016-05-01

    Recent single molecule experiments, using either atomic force microscopy (AFM) or Förster resonance energy transfer (FRET) have shown that multidomain proteins containing tandem repeats may form stable misfolded structures. Topology-based simulation models have been used successfully to generate models for these structures with domain-swapped features, fully consistent with the available data. However, it is also known that some multidomain protein folds exhibit no evidence for misfolding, even when adjacent domains have identical sequences. Here we pose the question: what factors influence the propensity of a given fold to undergo domain-swapped misfolding? Using a coarse-grained simulation model, we can reproduce the known propensities of multidomain proteins to form domain-swapped misfolds, where data is available. Contrary to what might be naively expected based on the previously described misfolding mechanism, we find that the extent of misfolding is not determined by the relative folding rates or barrier heights for forming the domains present in the initial intermediates leading to folded or misfolded structures. Instead, it appears that the propensity is more closely related to the relative stability of the domains present in folded and misfolded intermediates. We show that these findings can be rationalized if the folded and misfolded domains are part of the same folding funnel, with commitment to one structure or the other occurring only at a relatively late stage of folding. Nonetheless, the results are still fully consistent with the kinetic models previously proposed to explain misfolding, with a specific interpretation of the observed rate coefficients. Finally, we investigate the relation between interdomain linker length and misfolding, and propose a simple alchemical model to predict the propensity for domain-swapped misfolding of multidomain proteins. PMID:27163669

  15. Membrane protein structure determination by electron crystallography

    PubMed Central

    Ubarretxena-Belandia, Iban; Stokes, David L.

    2012-01-01

    During the past year, electron crystallography of membrane proteins has provided structural insights into the mechanism of several different transporters and into their interactions with lipid molecules within the bilayer. From a technical perspective there have been important advances in high-throughput screening of crystallization trials and in automated imaging of membrane crystals with the electron microscope. There have also been key developments in software, and in molecular replacement and phase extension methods designed to facilitate the process of structure determination. PMID:22572457

  16. Protein Structure Prediction with Evolutionary Algorithms

    SciTech Connect

    Hart, W.E.; Krasnogor, N.; Pelta, D.A.; Smith, J.

    1999-02-08

    Evolutionary algorithms have been successfully applied to a variety of molecular structure prediction problems. In this paper we reconsider the design of genetic algorithms that have been applied to a simple protein structure prediction problem. Our analysis considers the impact of several algorithmic factors for this problem: the confirmational representation, the energy formulation and the way in which infeasible conformations are penalized, Further we empirically evaluated the impact of these factors on a small set of polymer sequences. Our analysis leads to specific recommendations for both GAs as well as other heuristic methods for solving PSP on the HP model.

  17. The unfolded state of the C-terminal domain of the ribosomal protein L9 contains both native and non-native structure.

    PubMed

    Shan, Bing; Eliezer, David; Raleigh, Daniel P

    2009-06-01

    Interest in the structural and dynamic properties of unfolded proteins has increased in recent years owing to continued interest in protein folding and misfolding. Knowledge of the unfolded state under native conditions is particularly important for obtaining a complete picture of the protein folding process. The C-terminal domain of protein L9 is a globular alpha, beta protein with an unusual mixed parallel and antiparallel beta-strand structure. The folding kinetics and equilibrium unfolding of CTL9 strongly depend on pH, and follow a simple two state model. Both the native and the unfolded state can be significantly populated at pH 3.8 in the absence of denaturant, allowing the native state and the unfolded state to be characterized under identical conditions. Backbone (15)N, (13)C, (1)H and side-chain (13)C(beta), (1)H(beta) chemical shifts, amide proton NOEs, and (15)N R(2) relaxation rates were obtained for the two conformational states at pH 3.8. All the data indicate that the pH 3.8 native state is well folded and is similar to the native state at neutral pH. There is significant residual structure in the pH 3.8 unfolded state. The regions corresponding to the two native state alpha-helices show strong preference to populate helical phi and psi angles. The segment that connects alpha-helix 2 and beta-strand 2 has a significant tendency to form non-native alpha-helical structure. Comparison with the pH 2.0 unfolded state and the urea unfolded state indicates that the tendency to adopt both native and non-native helical structure is stronger at pH 3.8, demonstrating that the unfolded state of CTL9 under native-like conditions is more structured. The implications for the folding of CTL9 are discussed. PMID:19301913

  18. How Closely Related Are Conformations of Protein Ions Sampled by IM-MS to Native Solution Structures?

    NASA Astrophysics Data System (ADS)

    Chen, Shu-Hua; Russell, David H.

    2015-09-01

    Here, we critically evaluate the effects of changes in the ion internal energy (Eint) on ion-neutral collision cross sections (CCS) of ions of two structurally diverse proteins, specifically the [M + 6H]6+ ion of ubiquitin (ubq6+), the [M + 5H]5+ ion of the intrinsically disordered protein (IDP) apo-metallothionein-2A (MT), and its partially- and fully-metalated isoform, the [CdiMT]5+ ion. The ion-neutral CCS for ions formed by "native-state" ESI show a strong dependence on Eint. Collisional activation is used to increase Eint prior to the ions entering and within the traveling wave (TW) ion mobility analyzer. Comparisons of experimental CCSs with those generated by molecular dynamics (MD) simulation for solution-phase ions and solvent-free ions as a function of temperature provide new insights about conformational preferences and retention of solution conformations. The Eint-dependent CCSs, which reveal increased conformational diversity of the ion population, are discussed in terms of folding/unfolding of solvent-free ions. For example, ubiquitin ions that have low internal energies retain native-like conformations, whereas ions that are heated by collisional activation possess higher internal energies and yield a broader range of CCS owing to increased conformational diversity due to losses of secondary and tertiary structures. In contrast, the CCS profile for the IDP apoMT is consistent with kinetic trapping of an ion population composed of a wide range of conformers, and as the Eint is increased, these structurally labile conformers unfold to an elongated conformation.

  19. How Closely Related Are Conformations of Protein Ions Sampled by IM-MS to Native Solution Structures?

    PubMed

    Chen, Shu-Hua; Russell, David H

    2015-09-01

    Here, we critically evaluate the effects of changes in the ion internal energy (E(int)) on ion-neutral collision cross sections (CCS) of ions of two structurally diverse proteins, specifically the [M + 6H](6+) ion of ubiquitin (ubq(6+)), the [M + 5H](5+) ion of the intrinsically disordered protein (IDP) apo-metallothionein-2A (MT), and its partially- and fully-metalated isoform, the [CdiMT](5+) ion. The ion-neutral CCS for ions formed by "native-state" ESI show a strong dependence on E(int). Collisional activation is used to increase E(int) prior to the ions entering and within the traveling wave (TW) ion mobility analyzer. Comparisons of experimental CCSs with those generated by molecular dynamics (MD) simulation for solution-phase ions and solvent-free ions as a function of temperature provide new insights about conformational preferences and retention of solution conformations. The E(int)-dependent CCSs, which reveal increased conformational diversity of the ion population, are discussed in terms of folding/unfolding of solvent-free ions. For example, ubiquitin ions that have low internal energies retain native-like conformations, whereas ions that are heated by collisional activation possess higher internal energies and yield a broader range of CCS owing to increased conformational diversity due to losses of secondary and tertiary structures. In contrast, the CCS profile for the IDP apoMT is consistent with kinetic trapping of an ion population composed of a wide range of conformers, and as the E(int) is increased, these structurally labile conformers unfold to an elongated conformation. PMID:26115967

  20. Comparison of Backbone Modification in Protein β-Sheets by α→γ Residue Replacement and α-Residue Methylation

    PubMed Central

    Lengyel, George A.; Reinert, Zachary E.; Griffith, Brian D.

    2014-01-01

    The mimicry of protein tertiary structure by oligomers with unnatural backbones is a significant contemporary research challenge. Among common elements of secondary structure found in natural proteins, sheets have proven the most difficult to address. Here, we report the systematic comparison of different strategies for peptide backbone modification in β-sheets with the goal of identifying the best method for replacing a multi-stranded sheet in a protein tertiary fold. The most effective sheet modifications examined lead to native-like tertiary folding behavior with thermodynamic fold stability comparable to the prototype protein on which the modified backbones are based. PMID:24909436

  1. Surface-Induced Dissociation Mass Spectra as a Tool for Distinguishing Different Structural Forms of Gas-Phase Multimeric Protein Complexes.

    PubMed

    Quintyn, Royston S; Zhou, Mowei; Yan, Jing; Wysocki, Vicki H

    2015-12-01

    One attractive feature of ion mobility mass spectrometry (IM-MS) lies in its ability to provide experimental collision cross section (CCS) measurements, which can be used to distinguish different conformations that a protein complex may adopt during its gas-phase unfolding. However, CCS values alone give no detailed information on subunit structure within the complex. Consequently, structural characterization typically requires molecular modeling, which can have uncertainties without experimental support. One method of obtaining direct experimental evidence on the structures of these intermediates is utilizing gas-phase activation techniques that can effectively dissociate the complexes into substructures while preserving the native topological information. The most commonly used activation method, collision-induced dissociation (CID) with low-mass target gases, typically leads to unfolding of monomers of a protein complex. Here, we describe a method that couples IM-MS and surface-induced dissociation (SID) to dissociate the source-activated precursors of three model protein complexes: C-reactive protein (CRP), transthyretin (TTR), and concanavalin A (Con A). The results of this study confirm that CID involves the unfolding of the protein complex via several intermediates. More importantly, our experiments also indicate that retention of similar CCS between different intermediates does not guarantee retention of structure. Although CID spectra (at a given collision energy) of source-activated, mass-selected precursors do not distinguish between native-like, collapsed, and expanded forms of a protein complex, dissociation patterns and/or average charge states of monomer products in SID of each of these forms are unique. PMID:26499904

  2. Are distance-dependent statistical potentials considering three interacting bodies superior to two-body statistical potentials for protein structure prediction?

    PubMed

    Ghomi, Hamed Tabatabaei; Thompson, Jared J; Lill, Markus A

    2014-10-01

    Distance-based statistical potentials have long been used to model condensed matter systems, e.g. as scoring functions in differentiating native-like protein structures from decoys. These scoring functions are based on the assumption that the total free energy of the protein can be calculated as the sum of pairwise free energy contributions derived from a statistical analysis of pair-distribution functions. However, this fundamental assumption has been challenged theoretically. In fact the free energy of a system with N particles is only exactly related to the N-body distribution function. Based on this argument coarse-grained multi-body statistical potentials have been developed to capture higher-order interactions. Having a coarse representation of the protein and using geometric contacts instead of pairwise interaction distances renders these models insufficient in modeling details of multi-body effects. In this study, we investigated if extending distance-dependent pairwise atomistic statistical potentials to corresponding interaction functions that are conditional on a third interacting body, defined as quasi-three-body statistical potentials, could model details of three-body interactions. We also tested if this approach could improve the predictive capabilities of statistical scoring functions for protein structure prediction. We analyzed the statistical dependency between two simultaneous pairwise interactions and showed that there is surprisingly little if any dependency of a third interacting site on pairwise atomistic statistical potentials. Also the protein structure prediction performance of these quasi-three-body potentials is comparable with their corresponding two-body counterparts. The scoring functions developed in this study showed better or comparable performances compared to some widely used scoring functions for protein structure prediction. PMID:25212727

  3. Quaternion maps of global protein structure.

    PubMed

    Hanson, Andrew J; Thakur, Sidharth

    2012-09-01

    The geometric structures of proteins are vital to the understanding of biochemical interactions. However, there is much yet to be understood about the spatial arrangements of the chains of amino acids making up any given protein. In particular, while conventional analysis tools like the Ramachandran plot supply some insight into the local relative orientation of pairs of amino acid residues, they provide little information about the global relative orientations of large groups of residues. We apply quaternion maps to families of coordinate frames defined naturally by amino acid residue structures as a way to expose global spatial relationships among residues within proteins. The resulting visualizations enable comparisons of absolute orientations as well as relative orientations, and thus generalize the framework of the Ramachandran plot. There are a variety of possible quaternion frames and visual representation strategies that can be chosen, and very complex quaternion maps can result. Just as Ramachandran plots are useful for addressing particular questions and not others, quaternion tools have characteristic domains of relevance. In particular, quaternion maps show great potential for answering specific questions about global residue alignment in crystallographic data and statistical orientation properties in Nuclear Magnetic Resonance (NMR) data that are very difficult to treat by other methods. PMID:23099777

  4. Structures of the agouti signaling protein.

    PubMed

    McNulty, Joseph C; Jackson, Pilgrim J; Thompson, Darren A; Chai, Biaoxin; Gantz, Ira; Barsh, Gregory S; Dawson, Philip E; Millhauser, Glenn L

    2005-03-01

    Expression of the agouti signaling protein (ASIP) during hair growth produces the red/yellow pigment pheomelanin. ASIP, and its neuropeptide homolog the agouti-related protein (AgRP) involved in energy balance, are novel, paracrine signaling molecules that act as inverse agonists at distinct subsets of melanocortin receptors. Ubiquitous ASIP expression in mice gives rise to a pleiotropic phenotype characterized by a uniform yellow coat color, obesity, overgrowth, and metabolic derangements similar to type II diabetes in humans. Here we report the synthesis and NMR structure of ASIP's active, cysteine-rich, C-terminal domain. ASIP adopts the inhibitor cystine knot fold and, along with AgRP, are the only known mammalian proteins in this structure class. Moreover, ASIP populates two distinct conformers resulting from a cis peptide bond at Pro102-Pro103 and a coexistence of cis/trans isomers of Ala104-Pro105. Pharmacologic studies of Pro-->Ala mutants demonstrate that the minor conformation with two cis peptide bonds is responsible for activity at all MCRs. The loop containing the heterogeneous Ala-Pro peptide bond is conserved in mammals, and suggests that ASIP is either trapped by evolution in this unusual configuration or possesses function outside of strict MCR antagonism. PMID:15701517

  5. DAPS: Database of Aligned Protein Structures

    DOE Data Explorer

    Mallick, Parag; Rice, Danny; Eisenberg, David

    DAPS is based on the FSSP, DSSP, PDB and CATH databases. There also exists a subset of DAPS known as DDAPS (also pronounced DAPS) - Database of Distant Aligned Protein Structures. It is a database of structures that have low sequence similarity but share a similar fold. There are a number of filters used to make the DDAPS list more useful. The algorithm requires that an FSSP file exists for one of the members of a pair and that the other member is listed in that FSSP file. It requires that each member of the pair be within the CATH database and share a common CAT classification. It also requires that the secondary structure can be determined by DSSP. How is DAPS constructed? We begin with the set of all chains from the current release of the PDB. An all on all search is done on the list to find pairs that have the same fold acoording to both the FSSP and CATH databases and clustered into groups by a representative structure (representative structures have less than 25% sequence identity to each other). For each protein pair, regions aligned by the DALI program are extracted from the corresponding FSSP file, or recomputed using DALI-lite. In domain DAPS, only regions that are called "domains" by CATH are included in the alignment. The amino acid type, secondary structure type, and solvent accessibility are extracted from the DSSP file and written pairwise into the database. DAPS is updated with updates of CATH.[Taken from http://nihserver.mbi.ucla.edu/DAPS/daps_help.html

  6. Structural characterization of soy protein nanoparticles from high shear microfluidization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soy protein nanoparticles were produced with a microfluidizer and characterized in terms of particle size, size distribution, morphology, rheological properties, and aggregate structure. Three stages of structure breakdown were observed when the soy protein dispersion was passed through the microflu...

  7. Structure prediction of magnetosome-associated proteins.

    PubMed

    Nudelman, Hila; Zarivach, Raz

    2014-01-01

    Magnetotactic bacteria (MTB) are Gram-negative bacteria that can navigate along geomagnetic fields. This ability is a result of a unique intracellular organelle, the magnetosome. These organelles are composed of membrane-enclosed magnetite (Fe3O4) or greigite (Fe3S4) crystals ordered into chains along the cell. Magnetosome formation, assembly, and magnetic nano-crystal biomineralization are controlled by magnetosome-associated proteins (MAPs). Most MAP-encoding genes are located in a conserved genomic region - the magnetosome island (MAI). The MAI appears to be conserved in all MTB that were analyzed so far, although the MAI size and organization differs between species. It was shown that MAI deletion leads to a non-magnetic phenotype, further highlighting its important role in magnetosome formation. Today, about 28 proteins are known to be involved in magnetosome formation, but the structures and functions of most MAPs are unknown. To reveal the structure-function relationship of MAPs we used bioinformatics tools in order to build homology models as a way to understand their possible role in magnetosome formation. Here we present a predicted 3D structural models' overview for all known Magnetospirillum gryphiswaldense strain MSR-1 MAPs. PMID:24523717

  8. An overview of the structures of protein-DNA complexes

    PubMed Central

    Luscombe, Nicholas M; Austin, Susan E; Berman , Helen M; Thornton, Janet M

    2000-01-01

    On the basis of a structural analysis of 240 protein-DNA complexes contained in the Protein Data Bank (PDB), we have classified the DNA-binding proteins involved into eight different structural/functional groups, which are further classified into 54 structural families. Here we present this classification and review the functions, structures and binding interactions of these protein-DNA complexes. PMID:11104519

  9. Structure based alignment and clustering of proteins (STRALCP)

    DOEpatents

    Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

    2013-06-18

    Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

  10. Membrane Protein Structure and Dynamics from NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Hong, Mei; Zhang, Yuan; Hu, Fanghao

    2012-05-01

    We review the current state of membrane protein structure determination using solid-state nuclear magnetic resonance (NMR) spectroscopy. Multidimensional magic-angle-spinning correlation NMR combined with oriented-sample experiments has made it possible to measure a full panel of structural constraints of membrane proteins directly in lipid bilayers. These constraints include torsion angles, interatomic distances, oligomeric structure, protein dynamics, ligand structure and dynamics, and protein orientation and depth of insertion in the lipid bilayer. Using solid-state NMR, researchers have studied potassium channels, proton channels, Ca2+ pumps, G protein-coupled receptors, bacterial outer membrane proteins, and viral fusion proteins to elucidate their mechanisms of action. Many of these membrane proteins have also been investigated in detergent micelles using solution NMR. Comparison of the solid-state and solution NMR structures provides important insights into the effects of the solubilizing environment on membrane protein structure and dynamics.

  11. Course 12: Proteins: Structural, Thermodynamic and Kinetic Aspects

    NASA Astrophysics Data System (ADS)

    Finkelstein, A. V.

    1 Introduction 2 Overview of protein architectures and discussion of physical background of their natural selection 2.1 Protein structures 2.2 Physical selection of protein structures 3 Thermodynamic aspects of protein folding 3.1 Reversible denaturation of protein structures 3.2 What do denatured proteins look like? 3.3 Why denaturation of a globular protein is the first-order phase transition 3.4 "Gap" in energy spectrum: The main characteristic that distinguishes protein chains from random polymers 4 Kinetic aspects of protein folding 4.1 Protein folding in vivo 4.2 Protein folding in vitro (in the test-tube) 4.3 Theory of protein folding rates and solution of the Levinthal paradox

  12. Structural investigation of protein kinase C inhibitors

    NASA Technical Reports Server (NTRS)

    Barak, D.; Shibata, M.; Rein, R.

    1991-01-01

    The phospholipid and Ca2+ dependent protein kinase (PKC) plays an essential role in a variety of cellular events. Inhibition of PKC was shown to arrest growth in tumor cell cultures making it a target for possible antitumor therapy. Calphostins are potent inhibitors of PKC with high affinity for the enzyme regulatory site. Structural characteristics of calphostins, which confer the inhibitory activity, are investigated by comparing their optimized structures with the existing models for PKC activation. The resulting model of inhibitory activity assumes interaction with two out of the three electrostatic interaction sites postulated for activators. The model shows two sites of hydrophobic interaction and enables the inhibitory activity of gossypol to be accounted for.

  13. Protein flexibility in the light of structural alphabets.

    PubMed

    Craveur, Pierrick; Joseph, Agnel P; Esque, Jeremy; Narwani, Tarun J; Noël, Floriane; Shinada, Nicolas; Goguet, Matthieu; Leonard, Sylvain; Poulain, Pierre; Bertrand, Olivier; Faure, Guilhem; Rebehmed, Joseph; Ghozlane, Amine; Swapna, Lakshmipuram S; Bhaskara, Ramachandra M; Barnoud, Jonathan; Téletchéa, Stéphane; Jallu, Vincent; Cerny, Jiri; Schneider, Bohdan; Etchebest, Catherine; Srinivasan, Narayanaswamy; Gelly, Jean-Christophe; de Brevern, Alexandre G

    2015-01-01

    Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e., the classical secondary structures. More precise and complete description of protein backbone conformation can be obtained using libraries of small protein fragments that are able to approximate every part of protein structures. These libraries, called structural alphabets (SAs), have been widely used in structure analysis field, from definition of ligand binding sites to superimposition of protein structures. SAs are also well suited to analyze the dynamics of protein structures. Here, we review innovative approaches that investigate protein flexibility based on SAs description. Coupled to various sources of experimental data (e.g., B-factor) and computational methodology (e.g., Molecular Dynamic simulation), SAs turn out to be powerful tools to analyze protein dynamics, e.g., to examine allosteric mechanisms in large set of structures in complexes, to identify order/disorder transition. SAs were also shown to be quite efficient to predict protein flexibility from amino-acid sequence. Finally, in this review, we exemplify the interest of SAs for studying flexibility with different cases of proteins implicated in pathologies and diseases. PMID:26075209

  14. Protein flexibility in the light of structural alphabets

    PubMed Central

    Craveur, Pierrick; Joseph, Agnel P.; Esque, Jeremy; Narwani, Tarun J.; Noël, Floriane; Shinada, Nicolas; Goguet, Matthieu; Leonard, Sylvain; Poulain, Pierre; Bertrand, Olivier; Faure, Guilhem; Rebehmed, Joseph; Ghozlane, Amine; Swapna, Lakshmipuram S.; Bhaskara, Ramachandra M.; Barnoud, Jonathan; Téletchéa, Stéphane; Jallu, Vincent; Cerny, Jiri; Schneider, Bohdan; Etchebest, Catherine; Srinivasan, Narayanaswamy; Gelly, Jean-Christophe; de Brevern, Alexandre G.

    2015-01-01

    Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e., the classical secondary structures. More precise and complete description of protein backbone conformation can be obtained using libraries of small protein fragments that are able to approximate every part of protein structures. These libraries, called structural alphabets (SAs), have been widely used in structure analysis field, from definition of ligand binding sites to superimposition of protein structures. SAs are also well suited to analyze the dynamics of protein structures. Here, we review innovative approaches that investigate protein flexibility based on SAs description. Coupled to various sources of experimental data (e.g., B-factor) and computational methodology (e.g., Molecular Dynamic simulation), SAs turn out to be powerful tools to analyze protein dynamics, e.g., to examine allosteric mechanisms in large set of structures in complexes, to identify order/disorder transition. SAs were also shown to be quite efficient to predict protein flexibility from amino-acid sequence. Finally, in this review, we exemplify the interest of SAs for studying flexibility with different cases of proteins implicated in pathologies and diseases. PMID:26075209

  15. The continuity of protein structure space is an intrinsic property of proteins

    PubMed Central

    Skolnick, Jeffrey; Arakaki, Adrian K.; Lee, Seung Yup; Brylinski, Michal

    2009-01-01

    The classical view of the space of protein structures is that it is populated by a discrete set of protein folds. For proteins up to 200 residues long, by using structural alignments and building upon ideas of the completeness and continuity of structure space, we show that nearly any structure is significantly related to any other using a transitive set of no more than 7 intermediate structurally related proteins. This result holds for all structures in the Protein Data Bank, even when structural relationships between evolutionary related proteins (as detected by threading or functional analyses) are excluded. A similar picture holds for an artificial library of compact, hydrogen-bonded, homopolypeptide structures. The 3 sets share the global connectivity features of random graphs, in which the local connectivity of each node (i.e., the number of neighboring structures per protein) is preserved. This high connectivity supports the continuous view of single-domain protein structure space. More importantly, these results do not depend on evolution, rather just on the physics of protein structures. The fact that evolutionary divergence need not be invoked to explain the continuous nature of protein structure space has implications for how the universe of protein structures might have originated, and how function should be transferred between proteins of similar structure. PMID:19805219

  16. Structure prediction of magnetosome-associated proteins

    PubMed Central

    Nudelman, Hila; Zarivach, Raz

    2014-01-01

    Magnetotactic bacteria (MTB) are Gram-negative bacteria that can navigate along geomagnetic fields. This ability is a result of a unique intracellular organelle, the magnetosome. These organelles are composed of membrane-enclosed magnetite (Fe3O4) or greigite (Fe3S4) crystals ordered into chains along the cell. Magnetosome formation, assembly, and magnetic nano-crystal biomineralization are controlled by magnetosome-associated proteins (MAPs). Most MAP-encoding genes are located in a conserved genomic region – the magnetosome island (MAI). The MAI appears to be conserved in all MTB that were analyzed so far, although the MAI size and organization differs between species. It was shown that MAI deletion leads to a non-magnetic phenotype, further highlighting its important role in magnetosome formation. Today, about 28 proteins are known to be involved in magnetosome formation, but the structures and functions of most MAPs are unknown. To reveal the structure–function relationship of MAPs we used bioinformatics tools in order to build homology models as a way to understand their possible role in magnetosome formation. Here we present a predicted 3D structural models’ overview for all known Magnetospirillum gryphiswaldense strain MSR-1 MAPs. PMID:24523717

  17. Structure-Based Druggability Assessment of the Mammalian Structural Proteome with Inclusion of Light Protein Flexibility

    PubMed Central

    Loving, Kathryn A.; Lin, Andy; Cheng, Alan C.

    2014-01-01

    Advances reported over the last few years and the increasing availability of protein crystal structure data have greatly improved structure-based druggability approaches. However, in practice, nearly all druggability estimation methods are applied to protein crystal structures as rigid proteins, with protein flexibility often not directly addressed. The inclusion of protein flexibility is important in correctly identifying the druggability of pockets that would be missed by methods based solely on the rigid crystal structure. These include cryptic pockets and flexible pockets often found at protein-protein interaction interfaces. Here, we apply an approach that uses protein modeling in concert with druggability estimation to account for light protein backbone movement and protein side-chain flexibility in protein binding sites. We assess the advantages and limitations of this approach on widely-used protein druggability sets. Applying the approach to all mammalian protein crystal structures in the PDB results in identification of 69 proteins with potential druggable cryptic pockets. PMID:25079060

  18. Novel protein folds and their nonsequential structural analogs

    PubMed Central

    Guerler, Aysam; Knapp, Ernst-Walter

    2008-01-01

    Newly determined protein structures are classified to belong to a new fold, if the structures are sufficiently dissimilar from all other so far known protein structures. To analyze structural similarities of proteins, structure alignment tools are used. We demonstrate that the usage of nonsequential structure alignment tools, which neglect the polypeptide chain connectivity, can yield structure alignments with significant similarities between proteins of known three-dimensional structure and newly determined protein structures that possess a new fold. The recently introduced protein structure alignment tool, GANGSTA, is specialized to perform nonsequential alignments with proper assignment of the secondary structure types by focusing on helices and strands only. In the new version, GANGSTA+, the underlying algorithms were completely redesigned, yielding enhanced quality of structure alignments, offering alignment against a larger database of protein structures, and being more efficient. We applied DaliLite, TM-align, and GANGSTA+ on three protein crystal structures considered to be novel folds. Applying GANGSTA+ to these novel folds, we find proteins in the ASTRAL40 database, which possess significant structural similarities, albeit the alignments are nonsequential and in some cases involve secondary structure elements aligned in reverse orientation. A web server is available at http://agknapp.chemie.fu-berlin.de/gplus for pairwise alignment, visualization, and database comparison. PMID:18583523

  19. Distributions of intramolecular distances in the reduced and denatured states of bovine pancreatic ribonuclease A. Folding initiation structures in the C-terminal portions of the reduced protein.

    PubMed

    Navon, A; Ittah, V; Landsman, P; Scheraga, H A; Haas, E

    2001-01-01

    The purpose of this investigation is to characterize the reduced state of RNase A (r-RNase A) in terms of (i) intramolecular distances, (ii) the sequence of formation of stable loops in the initial stages of folding, and (iii) the unfolding transitions induced by GdnHCl. This is accomplished by identifying specific subdomain structures and local and long-range interactions that direct the folding process of this protein and lead to the native fold and formation of the disulfide bonds. Eleven pairs of dispersed sites in the RNase A molecule were labeled with fluorescent donor and acceptor probes, and the distributions of intramolecular distances (IDDs) were determined by means of time-resolved dynamic nonradiative excitation energy transfer (TR-FRET) measurements. The mutants were designed to search for (a) a possible nonrandom fold of the backbone in the collapsed state and (b) possible loops stabilized by long-range interactions. It was found that, under folding conditions, (i) the labeled mutants of r-RNase A in refolding buffer (the R(N) state) exhibit features of specific (nonrandom) compact but very dispersed subdomain structures (indicated by short mean distances, broad IDDs, and a weak dependence of the mean distances on segment length), (ii) the backbone fold in the C-terminal beta-like portion of the molecule appears to adopt a native-like overall fold, (iii) the N-terminal alpha-like portion of the chain is separated from the C-terminal core by very large intramolecular distances, larger than those in the crystal structure, and (iv) perturbations by addition of GdnHCl reveal several conformational transitions in different sections of the chain. Addition of GdnHCl to the native disulfide-intact protein provided a reference state for the extent of expansion of intramolecular distances under denaturing conditions. In conclusion, r-RNase A under folding conditions (the R(N) state) is poised for the final folding step(s) with a native-like trace of the chain

  20. Structural determination of intact proteins using mass spectrometry

    DOEpatents

    Kruppa, Gary; Schoeniger, Joseph S.; Young, Malin M.

    2008-05-06

    The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.

  1. Membrane protein structures without crystals, by single particle electron cryomicroscopy

    PubMed Central

    Vinothkumar, Kutti R

    2015-01-01

    It is an exciting period in membrane protein structural biology with a number of medically important protein structures determined at a rapid pace. However, two major hurdles still remain in the structural biology of membrane proteins. One is the inability to obtain large amounts of protein for crystallization and the other is the failure to get well-diffracting crystals. With single particle electron cryomicroscopy, both these problems can be overcome and high-resolution structures of membrane proteins and other labile protein complexes can be obtained with very little protein and without the need for crystals. In this review, I highlight recent advances in electron microscopy, detectors and software, which have allowed determination of medium to high-resolution structures of membrane proteins and complexes that have been difficult to study by other structural biological techniques. PMID:26435463

  2. Protein folding, protein structure and the origin of life: Theoretical methods and solutions of dynamical problems

    NASA Technical Reports Server (NTRS)

    Weaver, D. L.

    1982-01-01

    Theoretical methods and solutions of the dynamics of protein folding, protein aggregation, protein structure, and the origin of life are discussed. The elements of a dynamic model representing the initial stages of protein folding are presented. The calculation and experimental determination of the model parameters are discussed. The use of computer simulation for modeling protein folding is considered.

  3. Visualizing and Clustering Protein Similarity Networks: Sequences, Structures, and Functions.

    PubMed

    Mai, Te-Lun; Hu, Geng-Ming; Chen, Chi-Ming

    2016-07-01

    Research in the recent decade has demonstrated the usefulness of protein network knowledge in furthering the study of molecular evolution of proteins, understanding the robustness of cells to perturbation, and annotating new protein functions. In this study, we aimed to provide a general clustering approach to visualize the sequence-structure-function relationship of protein networks, and investigate possible causes for inconsistency in the protein classifications based on sequences, structures, and functions. Such visualization of protein networks could facilitate our understanding of the overall relationship among proteins and help researchers comprehend various protein databases. As a demonstration, we clustered 1437 enzymes by their sequences and structures using the minimum span clustering (MSC) method. The general structure of this protein network was delineated at two clustering resolutions, and the second level MSC clustering was found to be highly similar to existing enzyme classifications. The clustering of these enzymes based on sequence, structure, and function information is consistent with each other. For proteases, the Jaccard's similarity coefficient is 0.86 between sequence and function classifications, 0.82 between sequence and structure classifications, and 0.78 between structure and function classifications. From our clustering results, we discussed possible examples of divergent evolution and convergent evolution of enzymes. Our clustering approach provides a panoramic view of the sequence-structure-function network of proteins, helps visualize the relation between related proteins intuitively, and is useful in predicting the structure and function of newly determined protein sequences. PMID:27267620

  4. The Intrinsic Geometric Structure of Protein-Protein Interaction Networks for Protein Interaction Prediction.

    PubMed

    Fang, Yi; Sun, Mengtian; Dai, Guoxian; Ramain, Karthik

    2016-01-01

    Recent developments in high-throughput technologies for measuring protein-protein interaction (PPI) have profoundly advanced our ability to systematically infer protein function and regulation. However, inherently high false positive and false negative rates in measurement have posed great challenges in computational approaches for the prediction of PPI. A good PPI predictor should be 1) resistant to high rate of missing and spurious PPIs, and 2) robust against incompleteness of observed PPI networks. To predict PPI in a network, we developed an intrinsic geometry structure (IGS) for network, which exploits the intrinsic and hidden relationship among proteins in network through a heat diffusion process. In this process, all explicit PPIs participate simultaneously to glue local infinitesimal and noisy experimental interaction data to generate a global macroscopic descriptions about relationships among proteins. The revealed implicit relationship can be interpreted as the probability of two proteins interacting with each other. The revealed relationship is intrinsic and robust against individual, local and explicit protein interactions in the original network. We apply our approach to publicly available PPI network data for the evaluation of the performance of PPI prediction. Experimental results indicate that, under different levels of the missing and spurious PPIs, IGS is able to robustly exploit the intrinsic and hidden relationship for PPI prediction with a higher sensitivity and specificity compared to that of recently proposed methods. PMID:26886733

  5. Fold assessment for comparative protein structure modeling.

    PubMed

    Melo, Francisco; Sali, Andrej

    2007-11-01

    Accurate and automated assessment of both geometrical errors and incompleteness of comparative protein structure models is necessary for an adequate use of the models. Here, we describe a composite score for discriminating between models with the correct and incorrect fold. To find an accurate composite score, we designed and applied a genetic algorithm method that searched for a most informative subset of 21 input model features as well as their optimized nonlinear transformation into the composite score. The 21 input features included various statistical potential scores, stereochemistry quality descriptors, sequence alignment scores, geometrical descriptors, and measures of protein packing. The optimized composite score was found to depend on (1) a statistical potential z-score for residue accessibilities and distances, (2) model compactness, and (3) percentage sequence identity of the alignment used to build the model. The accuracy of the composite score was compared with the accuracy of assessment by single and combined features as well as by other commonly used assessment methods. The testing set was representative of models produced by automated comparative modeling on a genomic scale. The composite score performed better than any other tested score in terms of the maximum correct classification rate (i.e., 3.3% false positives and 2.5% false negatives) as well as the sensitivity and specificity across the whole range of thresholds. The composite score was implemented in our program MODELLER-8 and was used to assess models in the MODBASE database that contains comparative models for domains in approximately 1.3 million protein sequences. PMID:17905832

  6. Graph Theory In Protein Sequence Clustering And Tertiary Structural Matching

    NASA Astrophysics Data System (ADS)

    Abdullah, Rosni; Rashid, Nur'Aini Abdul; Othman, Fazilah

    2008-01-01

    The principle of graph theory which has been widely used in computer networks is now being adopted for work in protein clustering, protein structural matching, and protein folding and modeling. In this work, we present two case studies on the use of graph theory for protein clustering and tertiary structural matching. In protein clustering, we extended a clustering algorithm based on a maximal clique while in the protein tertiary structural matching we explored the bipartite graph matching algorithm. The results obtained in both the case studies will be presented.

  7. Structural hot spots for the solubility of globular proteins.

    PubMed

    Ganesan, Ashok; Siekierska, Aleksandra; Beerten, Jacinte; Brams, Marijke; Van Durme, Joost; De Baets, Greet; Van der Kant, Rob; Gallardo, Rodrigo; Ramakers, Meine; Langenberg, Tobias; Wilkinson, Hannah; De Smet, Frederik; Ulens, Chris; Rousseau, Frederic; Schymkowitz, Joost

    2016-01-01

    Natural selection shapes protein solubility to physiological requirements and recombinant applications that require higher protein concentrations are often problematic. This raises the question whether the solubility of natural protein sequences can be improved. We here show an anti-correlation between the number of aggregation prone regions (APRs) in a protein sequence and its solubility, suggesting that mutational suppression of APRs provides a simple strategy to increase protein solubility. We show that mutations at specific positions within a protein structure can act as APR suppressors without affecting protein stability. These hot spots for protein solubility are both structure and sequence dependent but can be computationally predicted. We demonstrate this by reducing the aggregation of human α-galactosidase and protective antigen of Bacillus anthracis through mutation. Our results indicate that many proteins possess hot spots allowing to adapt protein solubility independently of structure and function. PMID:26905391

  8. Structural hot spots for the solubility of globular proteins

    PubMed Central

    Ganesan, Ashok; Siekierska, Aleksandra; Beerten, Jacinte; Brams, Marijke; Van Durme, Joost; De Baets, Greet; Van der Kant, Rob; Gallardo, Rodrigo; Ramakers, Meine; Langenberg, Tobias; Wilkinson, Hannah; De Smet, Frederik; Ulens, Chris; Rousseau, Frederic; Schymkowitz, Joost

    2016-01-01

    Natural selection shapes protein solubility to physiological requirements and recombinant applications that require higher protein concentrations are often problematic. This raises the question whether the solubility of natural protein sequences can be improved. We here show an anti-correlation between the number of aggregation prone regions (APRs) in a protein sequence and its solubility, suggesting that mutational suppression of APRs provides a simple strategy to increase protein solubility. We show that mutations at specific positions within a protein structure can act as APR suppressors without affecting protein stability. These hot spots for protein solubility are both structure and sequence dependent but can be computationally predicted. We demonstrate this by reducing the aggregation of human α-galactosidase and protective antigen of Bacillus anthracis through mutation. Our results indicate that many proteins possess hot spots allowing to adapt protein solubility independently of structure and function. PMID:26905391

  9. Connectivity independent protein-structure alignment: a hierarchical approach

    PubMed Central

    Kolbeck, Bjoern; May, Patrick; Schmidt-Goenner, Tobias; Steinke, Thomas; Knapp, Ernst-Walter

    2006-01-01

    Background Protein-structure alignment is a fundamental tool to study protein function, evolution and model building. In the last decade several methods for structure alignment were introduced, but most of them ignore that structurally similar proteins can share the same spatial arrangement of secondary structure elements (SSE) but differ in the underlying polypeptide chain connectivity (non-sequential SSE connectivity). Results We perform protein-structure alignment using a two-level hierarchical approach implemented in the program GANGSTA. On the first level, pair contacts and relative orientations between SSEs (i.e. α-helices and β-strands) are maximized with a genetic algorithm (GA). On the second level residue pair contacts from the best SSE alignments are optimized. We have tested the method on visually optimized structure alignments of protein pairs (pairwise mode) and for database scans. For a given protein structure, our method is able to detect significant structural similarity of functionally important folds with non-sequential SSE connectivity. The performance for structure alignments with strictly sequential SSE connectivity is comparable to that of other structure alignment methods. Conclusion As demonstrated for several applications, GANGSTA finds meaningful protein-structure alignments independent of the SSE connectivity. GANGSTA is able to detect structural similarity of protein folds that are assigned to different superfamilies but nevertheless possess similar structures and perform related functions, even if these proteins differ in SSE connectivity. PMID:17118190

  10. 3-Dimensional Protein Structure of Influenza

    NASA Technical Reports Server (NTRS)

    2004-01-01

    The loss of productivity due to flu is staggering. Costs range as much as $20 billio a year. High mutation rates of the flu virus have hindered development of new drugs or vaccines. The secret lies in a small molecule which is attached to the host cell's surface. Each flu virus, no matter what strain, must remove this small molecule to escape the host cell to spread infection. Using data from space and earth grown crystals, researchers from the Center of Macromolecular Crystallography (CMC) are desining drugs to bind with this protein's active site. This lock and key fit reduces the spread of flu in the body by blocking its escape route. In collaboration with its corporate partner, the CMC has refined drug structure in preparation for clinical trials. Tested and approved relief is expected to reach drugstores by year 2004.

  11. Ensemble-based evaluation for protein structure models

    PubMed Central

    Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

    2016-01-01

    Motivation: Comparing protein tertiary structures is a fundamental procedure in structural biology and protein bioinformatics. Structure comparison is important particularly for evaluating computational protein structure models. Most of the model structure evaluation methods perform rigid body superimposition of a structure model to its crystal structure and measure the difference of the corresponding residue or atom positions between them. However, these methods neglect intrinsic flexibility of proteins by treating the native structure as a rigid molecule. Because different parts of proteins have different levels of flexibility, for example, exposed loop regions are usually more flexible than the core region of a protein structure, disagreement of a model to the native needs to be evaluated differently depending on the flexibility of residues in a protein. Results: We propose a score named FlexScore for comparing protein structures that consider flexibility of each residue in the native state of proteins. Flexibility information may be extracted from experiments such as NMR or molecular dynamics simulation. FlexScore considers an ensemble of conformations of a protein described as a multivariate Gaussian distribution of atomic displacements and compares a query computational model with the ensemble. We compare FlexScore with other commonly used structure similarity scores over various examples. FlexScore agrees with experts’ intuitive assessment of computational models and provides information of practical usefulness of models. Availability and implementation: https://bitbucket.org/mjamroz/flexscore Contact: dkihara@purdue.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307633

  12. PSSARD: protein sequence-structure analysis relational database.

    PubMed

    Guruprasad, Kunchur; Srikanth, K; Babu, A V N

    2005-09-15

    We have implemented a relational database comprising a representative dataset of amino acid sequences and their associated secondary structure. The representative amino acid sequences were selected according to the PDB_SELECT program by choosing proteins corresponding to protein crystal structure data deposited in the protein data bank that share less than 25% overall pair-wise sequence identity. The secondary structure was extracted from the protein data bank website. The information content in the database includes the protein description, PDB code, crystal structure resolution, total number of amino acid residues in the protein chain, amino acid sequence, secondary structure conformation and its summary. The database is freely accessible from the website mentioned below and is useful to query on any of the above fields. The database is particularly useful to quickly retrieve amino acid sequences that are compatible to any super-secondary structure conformation from several proteins simultaneously. PMID:16054209

  13. Prediction of protein folding rates from simplified secondary structure alphabet.

    PubMed

    Huang, Jitao T; Wang, Titi; Huang, Shanran R; Li, Xin

    2015-10-21

    Protein folding is a very complicated and highly cooperative dynamic process. However, the folding kinetics is likely to depend more on a few key structural features. Here we find that secondary structures can determine folding rates of only large, multi-state folding proteins and fails to predict those for small, two-state proteins. The importance of secondary structures for protein folding is ordered as: extended β strand > α helix > bend > turn > undefined secondary structure>310 helix > isolated β strand > π helix. Only the first three secondary structures, extended β strand, α helix and bend, can achieve a good correlation with folding rates. This suggests that the rate-limiting step of protein folding would depend upon the formation of regular secondary structures and the buckling of chain. The reduced secondary structure alphabet provides a simplified description for the machine learning applications in protein design. PMID:26247139

  14. On lattice protein structure prediction revisited.

    PubMed

    Dotu, Ivan; Cebrián, Manuel; Van Hentenryck, Pascal; Clote, Peter

    2011-01-01

    Protein structure prediction is regarded as a highly challenging problem both for the biology and for the computational communities. In recent years, many approaches have been developed, moving to increasingly complex lattice models and off-lattice models. This paper presents a Large Neighborhood Search (LNS) to find the native state for the Hydrophobic-Polar (HP) model on the Face-Centered Cubic (FCC) lattice or, in other words, a self-avoiding walk on the FCC lattice having a maximum number of H-H contacts. The algorithm starts with a tabu-search algorithm, whose solution is then improved by a combination of constraint programming and LNS. The flexible framework of this hybrid algorithm allows an adaptation to the Miyazawa-Jernigan contact potential, in place of the HP model, thus suggesting its potential for tertiary structure prediction. Benchmarking statistics are given for our method against the hydrophobic core threading program HPstruct, an exact method which can be viewed as complementary to our method. PMID:21358007

  15. Protein Structure, Function Set for Explosive Increase in Understanding.

    ERIC Educational Resources Information Center

    Chemical and Engineering News, 1986

    1986-01-01

    Cites advances in x-ray diffraction, nuclear magnetic resonance, computer modeling, and display to guide the design and analysis of protein structures. Reviews recent advances in knowledge, synthesis techniques, and theory of proteins. (JM)

  16. Protein folding guides disulfide bond formation

    PubMed Central

    Qin, Meng; Wang, Wei; Thirumalai, D.

    2015-01-01

    The Anfinsen principle that the protein sequence uniquely determines its structure is based on experiments on oxidative refolding of a protein with disulfide bonds. The problem of how protein folding drives disulfide bond formation is poorly understood. Here, we have solved this long-standing problem by creating a general method for implementing the chemistry of disulfide bond formation and rupture in coarse-grained molecular simulations. As a case study, we investigate the oxidative folding of bovine pancreatic trypsin inhibitor (BPTI). After confirming the experimental findings that the multiple routes to the folded state contain a network of states dominated by native disulfides, we show that the entropically unfavorable native single disulfide [14–38] between Cys14 and Cys38 forms only after polypeptide chain collapse and complete structuring of the central core of the protein containing an antiparallel β-sheet. Subsequent assembly, resulting in native two-disulfide bonds and the folded state, involves substantial unfolding of the protein and transient population of nonnative structures. The rate of [14–38] formation increases as the β-sheet stability increases. The flux to the native state, through a network of kinetically connected native-like intermediates, changes dramatically by altering the redox conditions. Disulfide bond formation between Cys residues not present in the native state are relevant only on the time scale of collapse of BPTI. The finding that formation of specific collapsed native-like structures guides efficient folding is applicable to a broad class of single-domain proteins, including enzyme-catalyzed disulfide proteins. PMID:26297249

  17. Algorithms, applications, and challenges of protein structure alignment.

    PubMed

    Ma, Jianzhu; Wang, Sheng

    2014-01-01

    As a fundamental problem in computational structure biology, protein structure alignment has attracted the focus of the community for more than 20 years. While the pairwise structure alignment could be applied to measure the similarity between two proteins, which is a first step for homology search and fold space construction, the multiple structure alignment could be used to understand evolutionary conservation and divergence from a family of protein structures. Structure alignment is an NP-hard problem, which is only computationally tractable by using heuristics. Three levels of heuristics for pairwise structure alignment have been proposed, from the representations of protein structure, the perspectives of viewing protein as a rigid-body or flexible, to the scoring functions as well as the search algorithms for the alignment. For multiple structure alignment, the fourth level of heuristics is applied on how to merge all input structures to a multiple structure alignment. In this review, we first present a small survey of current methods for protein pairwise and multiple alignment, focusing on those that are publicly available as web servers. In more detail, we also discuss the advancements on the development of the new approaches to increase the pairwise alignment accuracy, to efficiently and reliably merge input structures to the multiple structure alignment. Finally, besides broadening the spectrum of the applications of structure alignment for protein template-based prediction, we also list several open problems that need to be solved in the future, such as the large complex alignment and the fast database search. PMID:24629187

  18. A hidden markov model derived structural alphabet for proteins.

    PubMed

    Camproux, A C; Gautier, R; Tufféry, P

    2004-06-01

    Understanding and predicting protein structures depends on the complexity and the accuracy of the models used to represent them. We have set up a hidden Markov model that discretizes protein backbone conformation as series of overlapping fragments (states) of four residues length. This approach learns simultaneously the geometry of the states and their connections. We obtain, using a statistical criterion, an optimal systematic decomposition of the conformational variability of the protein peptidic chain in 27 states with strong connection logic. This result is stable over different protein sets. Our model fits well the previous knowledge related to protein architecture organisation and seems able to grab some subtle details of protein organisation, such as helix sub-level organisation schemes. Taking into account the dependence between the states results in a description of local protein structure of low complexity. On an average, the model makes use of only 8.3 states among 27 to describe each position of a protein structure. Although we use short fragments, the learning process on entire protein conformations captures the logic of the assembly on a larger scale. Using such a model, the structure of proteins can be reconstructed with an average accuracy close to 1.1A root-mean-square deviation and for a complexity of only 3. Finally, we also observe that sequence specificity increases with the number of states of the structural alphabet. Such models can constitute a very relevant approach to the analysis of protein architecture in particular for protein structure prediction. PMID:15147844

  19. Implementation of a parallel protein structure alignment service on cloud.

    PubMed

    Hung, Che-Lun; Lin, Yaw-Ling

    2013-01-01

    Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform. PMID:23671842

  20. Implementation of a Parallel Protein Structure Alignment Service on Cloud

    PubMed Central

    Hung, Che-Lun; Lin, Yaw-Ling

    2013-01-01

    Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform. PMID:23671842

  1. Molten globules, entropy-driven conformational change and protein folding.

    PubMed

    Baldwin, Robert L; Rose, George D

    2013-02-01

    The exquisite side chain close-packing in the protein core and at binding interfaces has prompted a conviction that packing selectivity is the primary mechanism for molecular recognition in folding and/or binding reactions. Contrary to this view, molten globule proteins can adopt native topology and bind targets tightly and specifically in the absence of side chain close-packing. The molten globule is a highly dynamic form with native-like secondary structure and a loose protein core that admits solvent. The related (but still controversial) dry molten globule is an expanded form of the native protein with largely intact topology but a tighter protein core that excludes solvent. Neither form retains side chain close-packing, and therefore both structure and function must result from other factors, assuming that the reality of the dry molten globule is accepted. This simplifying realization calls for a re-evaluation of established models. PMID:23237704

  2. The Potato leafroll virus structural proteins manipulate overlapping, yet distinct protein interaction networks during infection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Potato leafroll virus (PLRV) produces a readthrough protein (RTP) via translational readthrough of the coat protein amber stop codon. The RTP functions as a structural component of the virion and as a non-incorporated protein in concert with numerous insect and plant proteins to regulate virus movem...

  3. The Alba protein family: Structure and function.

    PubMed

    Goyal, Manish; Banerjee, Chinmoy; Nag, Shiladitya; Bandyopadhyay, Uday

    2016-05-01

    Alba family proteins are small, basic, dimeric nucleic acid-binding proteins, which are widely distributed in archaea and a number of eukaryotes. This family of proteins bears the distinct features of regulation through acetylation/deacetylation, hence named as acetylation lowers binding affinity (Alba). Alba family proteins bind DNA cooperatively with no apparent sequence specificity. Besides DNA, Alba proteins also interact with diverse RNA species and associate with ribonucleo-protein complexes. Initially, Alba proteins were recognized as chromosomal proteins and supposed to be involved in the maintenance of chromatin architecture and transcription repression. However, recent studies have shown increasing evidence of functional plasticity among Alba family of proteins that widely range from genome packaging and organization, transcriptional and translational regulation, RNA metabolism, and development and differentiation processes. In recent years, Alba family proteins have attracted growing interest due to their widespread occurrence in large number of organisms. Presence in multiple copies, functional crosstalk, differential binding affinity, and posttranslational modifications are some of the key factors that might regulate the biological functions of Alba family proteins. In this review article, we present an overview of the Alba family proteins, their salient features and emphasize their functional role in different organisms reported so far. PMID:26900088

  4. Structure and Function of Microbial Metal-Reduction Proteins

    SciTech Connect

    Xu, Ying; Crawford, Oakly H.; Xu, Dong; Larimer, Frank W.; Uberbacher, Edward C.; Zhou, Jizhong

    2009-09-02

    In this project, we proposed (i) identification of metal-reduction genes, (ii) development of new threading techniques and (iii) fold recognition and structure prediction of metal-reduction proteins. However, due to the reduction of the budget, we revised our plan to focus on two specific aims of (i) developing a new threading-based protein structure prediction method, and (ii) developing an expert system for protein structure prediction.

  5. Protein Structure and Function Prediction Using I-TASSER

    PubMed Central

    Yang, Jianyi; Zhang, Yang

    2016-01-01

    I-TASSER is a hierarchical protocol for automated protein structure prediction and structure-based function annotation. Starting from the amino acid sequence of target proteins, I-TASSER first generates full-length atomic structural models from multiple threading alignments and iterative structural assembly simulations followed by atomic-level structure refinement. The biological functions of the protein, including ligand-binding sites, enzyme commission number, and gene ontology terms, are then inferred from known protein function databases based on sequence and structure profile comparisons. I-TASSER is freely available as both an on-line server and a stand-alone package. This unit describes how to use the I-TASSER protocol to generate structure and function prediction and how to interpret the prediction results, as well as alternative approaches for further improving the I-TASSER modeling quality for distant-homologous and multi-domain protein targets. PMID:26678386

  6. Protein structure prediction and analysis using the Robetta server

    PubMed Central

    Kim, David E.; Chivian, Dylan; Baker, David

    2004-01-01

    The Robetta server (http://robetta.bakerlab.org) provides automated tools for protein structure prediction and analysis. For structure prediction, sequences submitted to the server are parsed into putative domains and structural models are generated using either comparative modeling or de novo structure prediction methods. If a confident match to a protein of known structure is found using BLAST, PSI-BLAST, FFAS03 or 3D-Jury, it is used as a template for comparative modeling. If no match is found, structure predictions are made using the de novo Rosetta fragment insertion method. Experimental nuclear magnetic resonance (NMR) constraints data can also be submitted with a query sequence for RosettaNMR de novo structure determination. Other current capabilities include the prediction of the effects of mutations on protein–protein interactions using computational interface alanine scanning. The Rosetta protein design and protein–protein docking methodologies will soon be available through the server as well. PMID:15215442

  7. Structural Assessment of the Effects of Amino Acid Substitutions on Protein Stability and Protein-Protein Interaction

    PubMed Central

    Teng, Shaolei; Wang, Liangjiang; Srivastava, Anand K.; Schwartz, Charles E.; Alexov, Emil

    2012-01-01

    A structure-based approach is described for predicting the effects of amino acid substitutions on protein function. Structures were predicted using a homology modelling method. Folding and binding energy differences between wild-type and mutant structures were computed to quantitatively assess the effects of amino acid substitutions on protein stability and protein–protein interaction, respectively. We demonstrated that pathogenic mutations at the interaction interface could affect binding energy and destabilise protein complex, whereas mutations at the non-interface might reduce folding energy and destabilise monomer structure. The results suggest that the structure-based analysis can provide useful information for understanding the molecular mechanisms of diseases. PMID:21297231

  8. Structural evolution during protein denaturation as induced by different methods.

    PubMed

    Chodankar, S; Aswal, V K; Kohlbrecher, J; Vavrin, R; Wagh, A G

    2008-03-01

    Small-angle neutron scattering (SANS) and dynamic light scattering (DLS) have been used to study conformational changes in protein bovine serum albumin (BSA) due to perturbation in its native structure as induced by varying temperature and pressure, and in presence of protein denaturating agents urea and surfactant. BSA has prolate ellipsoidal shape at ambient temperature and we observe no effect of temperature on its structure up to a temperature of about 60 degrees C . At temperatures beyond 60 degrees C , protein denaturation leads to aggregation. The protein solution exhibits a fractal structure at temperatures above 64 degrees C , and its fractal dimension increases with temperature. This is an indication of aggregation followed by gelation that evolves with increasing temperature. It is known for some of the proteins (e.g., Staphylococcal Nuclease) that pressure of 200 MPa can unfold the protein, whereas BSA does not show any protein unfolding even up to the pressure of 450 MPa . In presence of urea, the BSA protein unfolds for urea concentrations greater than 4M and acquires a random coil configuration. We make use of the dilution method to show the reversibility of protein unfolding with urea. The addition of surfactant denaturates the protein by the formation of micellelike aggregates of surfactants along the unfolded polypeptide chains of the protein. We show such structure of the protein-surfactant complex can be stabilized at higher temperatures, which is not the case for pure protein. PMID:18517416

  9. Structural evolution during protein denaturation as induced by different methods

    NASA Astrophysics Data System (ADS)

    Chodankar, S.; Aswal, V. K.; Kohlbrecher, J.; Vavrin, R.; Wagh, A. G.

    2008-03-01

    Small-angle neutron scattering (SANS) and dynamic light scattering (DLS) have been used to study conformational changes in protein bovine serum albumin (BSA) due to perturbation in its native structure as induced by varying temperature and pressure, and in presence of protein denaturating agents urea and surfactant. BSA has prolate ellipsoidal shape at ambient temperature and we observe no effect of temperature on its structure up to a temperature of about 60°C . At temperatures beyond 60°C , protein denaturation leads to aggregation. The protein solution exhibits a fractal structure at temperatures above 64°C , and its fractal dimension increases with temperature. This is an indication of aggregation followed by gelation that evolves with increasing temperature. It is known for some of the proteins (e.g., Staphylococcal Nuclease) that pressure of 200MPa can unfold the protein, whereas BSA does not show any protein unfolding even up to the pressure of 450MPa . In presence of urea, the BSA protein unfolds for urea concentrations greater than 4M and acquires a random coil configuration. We make use of the dilution method to show the reversibility of protein unfolding with urea. The addition of surfactant denaturates the protein by the formation of micellelike aggregates of surfactants along the unfolded polypeptide chains of the protein. We show such structure of the protein-surfactant complex can be stabilized at higher temperatures, which is not the case for pure protein.

  10. Dissecting the relationship between protein structure and sequence variation

    NASA Astrophysics Data System (ADS)

    Shahmoradi, Amir; Wilke, Claus; Wilke Lab Team

    2015-03-01

    Over the past decade several independent works have shown that some structural properties of proteins are capable of predicting protein evolution. The strength and significance of these structure-sequence relations, however, appear to vary widely among different proteins, with absolute correlation strengths ranging from 0 . 1 to 0 . 8 . Here we present the results from a comprehensive search for the potential biophysical and structural determinants of protein evolution by studying more than 200 structural and evolutionary properties in a dataset of 209 monomeric enzymes. We discuss the main protein characteristics responsible for the general patterns of protein evolution, and identify sequence divergence as the main determinant of the strengths of virtually all structure-evolution relationships, explaining ~ 10 - 30 % of observed variation in sequence-structure relations. In addition to sequence divergence, we identify several protein structural properties that are moderately but significantly coupled with the strength of sequence-structure relations. In particular, proteins with more homogeneous back-bone hydrogen bond energies, large fractions of helical secondary structures and low fraction of beta sheets tend to have the strongest sequence-structure relation. BEACON-NSF center for the study of evolution in action.

  11. Expression strategies for structural studies of eukaryotic membrane proteins.

    PubMed

    Lyons, Joseph A; Shahsavar, Azadeh; Paulsen, Peter Aasted; Pedersen, Bjørn Panyella; Nissen, Poul

    2016-06-01

    Integral membrane proteins in eukaryotes are central to various cellular processes and key targets in structural biology, biotechnology and drug development. However, the number of available structures for eukaryotic membrane protein belies their physiological importance. Recently, the number of available eukaryotic membrane protein structures has been steadily increasing due to the development of novel strategies in construct design, expression and structure determination. Here, we examine the major expression systems exploited for eukaryotic membrane proteins. Additionally we strive to tabulate and describe the recent expression strategies in eukaryotic membrane protein structural biology. We find that a majority of targets have been expressed in advanced host systems and modified from their wild-type form with distinct focus on conformation and thermostabilisation. However, strategies for native protein purification should also be considered where possible, particularly in light of the recent advances in single particle cryo electron microscopy. PMID:27362979

  12. GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions

    PubMed Central

    2012-01-01

    Protein-protein interactions are a key component of life processes. The knowledge of the three-dimensional structure of these interactions is important for understanding protein function. Genome-Wide Docking Database (http://gwidd.bioinformatics.ku.edu) offers an extensive source of data for structural studies of protein-protein complexes on genome scale. The current release of the database combines the available experimental data on the structure and characteristics of protein interactions with structural modeling of protein complexes for 771 organisms spanned over the entire universe of life from viruses to humans. The interactions are stored in a relational database with user-friendly interface that includes various search options. The search results can be interactively previewed; the structures, downloaded, along with the interaction characteristics. PMID:23245398

  13. The unexpected structure of the designed protein Octarellin V.1 forms a challenge for protein structure prediction tools.

    PubMed

    Figueroa, Maximiliano; Sleutel, Mike; Vandevenne, Marylene; Parvizi, Gregory; Attout, Sophie; Jacquin, Olivier; Vandenameele, Julie; Fischer, Axel W; Damblon, Christian; Goormaghtigh, Erik; Valerio-Lepiniec, Marie; Urvoas, Agathe; Durand, Dominique; Pardon, Els; Steyaert, Jan; Minard, Philippe; Maes, Dominique; Meiler, Jens; Matagne, André; Martial, Joseph A; Van de Weerdt, Cécile

    2016-07-01

    Despite impressive successes in protein design, designing a well-folded protein of more 100 amino acids de novo remains a formidable challenge. Exploiting the promising biophysical features of the artificial protein Octarellin V, we improved this protein by directed evolution, thus creating a more stable and soluble protein: Octarellin V.1. Next, we obtained crystals of Octarellin V.1 in complex with crystallization chaperons and determined the tertiary structure. The experimental structure of Octarellin V.1 differs from its in silico design: the (αβα) sandwich architecture bears some resemblance to a Rossman-like fold instead of the intended TIM-barrel fold. This surprising result gave us a unique and attractive opportunity to test the state of the art in protein structure prediction, using this artificial protein free of any natural selection. We tested 13 automated webservers for protein structure prediction and found none of them to predict the actual structure. More than 50% of them predicted a TIM-barrel fold, i.e. the structure we set out to design more than 10years ago. In addition, local software runs that are human operated can sample a structure similar to the experimental one but fail in selecting it, suggesting that the scoring and ranking functions should be improved. We propose that artificial proteins could be used as tools to test the accuracy of protein structure prediction algorithms, because their lack of evolutionary pressure and unique sequences features. PMID:27181418

  14. A New Hidden Markov Model for Protein Quality Assessment Using Compatibility Between Protein Sequence and Structure

    PubMed Central

    He, Zhiquan; Ma, Wenji; Zhang, Jingfen; Xu, Dong

    2015-01-01

    Protein structure Quality Assessment (QA) is an essential component in protein structure prediction and analysis. The relationship between protein sequence and structure often serves as a basis for protein structure QA. In this work, we developed a new Hidden Markov Model (HMM) to assess the compatibility of protein sequence and structure for capturing their complex relationship. More specifically, the emission of the HMM consists of protein local structures in angular space, secondary structures, and sequence profiles. This model has two capabilities: (1) encoding local structure of each position by jointly considering sequence and structure information, and (2) assigning a global score to estimate the overall quality of a predicted structure, as well as local scores to assess the quality of specific regions of a structure, which provides useful guidance for targeted structure refinement. We compared the HMM model to state-of-art single structure quality assessment methods OPUSCA, DFIRE, GOAP, and RW in protein structure selection. Computational results showed our new score HMM.Z can achieve better overall selection performance on the benchmark datasets. PMID:26221066

  15. Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks.

    PubMed

    Agarwal, Garima; Mahajan, Swapnil; Srinivasan, Narayanaswamy; de Brevern, Alexandre G

    2011-01-01

    Structure comparison tools can be used to align related protein structures to identify structurally conserved and variable regions and to infer functional and evolutionary relationships. While the conserved regions often superimpose well, the variable regions appear non superimposable. Differences in homologous protein structures are thought to be due to evolutionary plasticity to accommodate diverged sequences during evolution. One of the kinds of differences between 3-D structures of homologous proteins is rigid body displacement. A glaring example is not well superimposed equivalent regions of homologous proteins corresponding to α-helical conformation with different spatial orientations. In a rigid body superimposition, these regions would appear variable although they may contain local similarity. Also, due to high spatial deviation in the variable region, one-to-one correspondence at the residue level cannot be determined accurately. Another kind of difference is conformational variability and the most common example is topologically equivalent loops of two homologues but with different conformations. In the current study, we present a refined view of the "structurally variable" regions which may contain local similarity obscured in global alignment of homologous protein structures. As structural alphabet is able to describe local structures of proteins precisely through Protein Blocks approach, conformational similarity has been identified in a substantial number of 'variable' regions in a large data set of protein structural alignments; optimal residue-residue equivalences could be achieved on the basis of Protein Blocks which led to improved local alignments. Also, through an example, we have demonstrated how the additional information on local backbone structures through protein blocks can aid in comparative modeling of a loop region. In addition, understanding on sequence-structure relationships can be enhanced through our approach. This has been

  16. Addressing the Role of Conformational Diversity in Protein Structure Prediction

    PubMed Central

    Parisi, Gustavo; Fornasari, Maria Silvina

    2016-01-01

    Computational modeling of tertiary structures has become of standard use to study proteins that lack experimental characterization. Unfortunately, 3D structure prediction methods and model quality assessment programs often overlook that an ensemble of conformers in equilibrium populates the native state of proteins. In this work we collected sets of publicly available protein models and the corresponding target structures experimentally solved and studied how they describe the conformational diversity of the protein. For each protein, we assessed the quality of the models against known conformers by several standard measures and identified those models ranked best. We found that model rankings are defined by both the selected target conformer and the similarity measure used. 70% of the proteins in our datasets show that different models are structurally closest to different conformers of the same protein target. We observed that model building protocols such as template-based or ab initio approaches describe in similar ways the conformational diversity of the protein, although for template-based methods this description may depend on the sequence similarity between target and template sequences. Taken together, our results support the idea that protein structure modeling could help to identify members of the native ensemble, highlight the importance of considering conformational diversity in protein 3D quality evaluations and endorse the study of the variability of the native structure for a meaningful biological analysis. PMID:27159429

  17. Addressing the Role of Conformational Diversity in Protein Structure Prediction.

    PubMed

    Palopoli, Nicolas; Monzon, Alexander Miguel; Parisi, Gustavo; Fornasari, Maria Silvina

    2016-01-01

    Computational modeling of tertiary structures has become of standard use to study proteins that lack experimental characterization. Unfortunately, 3D structure prediction methods and model quality assessment programs often overlook that an ensemble of conformers in equilibrium populates the native state of proteins. In this work we collected sets of publicly available protein models and the corresponding target structures experimentally solved and studied how they describe the conformational diversity of the protein. For each protein, we assessed the quality of the models against known conformers by several standard measures and identified those models ranked best. We found that model rankings are defined by both the selected target conformer and the similarity measure used. 70% of the proteins in our datasets show that different models are structurally closest to different conformers of the same protein target. We observed that model building protocols such as template-based or ab initio approaches describe in similar ways the conformational diversity of the protein, although for template-based methods this description may depend on the sequence similarity between target and template sequences. Taken together, our results support the idea that protein structure modeling could help to identify members of the native ensemble, highlight the importance of considering conformational diversity in protein 3D quality evaluations and endorse the study of the variability of the native structure for a meaningful biological analysis. PMID:27159429

  18. Structure determination of archaea-specific ribosomal protein L46a reveals a novel protein fold

    SciTech Connect

    Feng, Yingang; Song, Xiaxia; Lin, Jinzhong; Xuan, Jinsong; Cui, Qiu; Wang, Jinfeng

    2014-07-18

    Highlights: • The archaea-specific ribosomal protein L46a has no homology to known proteins. • Three dimensional structure and backbone dynamics of L46a were determined by NMR. • The structure of L46a represents a novel protein fold. • A potential rRNA-binding surface on L46a was identified. • The potential position of L46a on the ribosome was proposed. - Abstract: Three archaea-specific ribosomal proteins recently identified show no sequence homology with other known proteins. Here we determined the structure of L46a, the most conserved one among the three proteins, from Sulfolobus solfataricus P2 using NMR spectroscopy. The structure presents a twisted β-sheet formed by the N-terminal part and two helices at the C-terminus. The L46a structure has a positively charged surface which is conserved in the L46a protein family and is the potential rRNA-binding site. Searching homologous structures in Protein Data Bank revealed that the structure of L46a represents a novel protein fold. The backbone dynamics identified by NMR relaxation experiments reveal significant flexibility at the rRNA binding surface. The potential position of L46a on the ribosome was proposed by fitting the structure into a previous electron microscopy map of the ribosomal 50S subunit, which indicated that L46a contacts to domain I of 23S rRNA near a multifunctional ribosomal protein L7ae.

  19. PSI-2: Structural Genomics to Cover Protein Domain Family Space

    PubMed Central

    Dessailly, Benoît H.; Nair, Rajesh; Jaroszewski, Lukasz; Fajardo, J. Eduardo; Kouranov, Andrei; Lee, David; Fiser, Andras; Godzik, Adam; Rost, Burkhard; Orengo, Christine

    2010-01-01

    Summary One major objective of structural genomics efforts, including the NIH-funded Protein Structure Initiative (PSI), has been to increase the structural coverage of protein sequence space. Here, we present the target selection strategy used during the second phase of PSI (PSI-2). This strategy, jointly devised by the bioinformatics groups associated with the PSI-2 large-scale production centres, targets representatives from large, structurally uncharacterised protein domain families, and from structurally uncharacterised subfamilies in very large and diverse families with incomplete structural coverage. These very large families are extremely diverse both structurally and functionally, and are highly over-represented in known proteomes. On the basis of several metrics, we then discuss to what extent PSI-2, during its first three years, has increased the structural coverage of genomes, and contributed structural and functional novelty. Together, the results presented here suggest that PSI-2 is successfully meeting its objectives and provides useful insights into structural and functional space. PMID:19523904

  20. The Structure and Function of Non-Collagenous Bone Proteins

    NASA Technical Reports Server (NTRS)

    Hook, Magnus; McQuillan, David J.

    1997-01-01

    The research done under the cooperative research agreement for the project titled 'The structure and function of non-collagenous bone proteins' represented the first phase of an ongoing program to define the structural and functional relationships of the principal noncollagenous proteins in bone. An ultimate goal of this research is to enable design and execution of useful pharmacological compounds that will have a beneficial effect in treatment of osteoporosis, both land-based and induced by long-duration space travel. The goals of the now complete first phase were as follows: 1. Establish and/or develop powerful recombinant protein expression systems; 2. Develop and refine isolation and purification of recombinant proteins; 3. Express wild-type non-collagenous bone proteins; 4. Express site-specific mutant proteins and domains of wild-type proteins to enhance likelihood of crystal formation for subsequent solution of structure.

  1. Structure Determination of Membrane Proteins by Nuclear Magnetic Resonance Spectroscopy

    NASA Astrophysics Data System (ADS)

    Opella, Stanley J.

    2013-06-01

    Many biological membranes consist of 50% or more (by weight) membrane proteins, which constitute approximately one-third of all proteins expressed in biological organisms. Helical membrane proteins function as receptors, enzymes, and transporters, among other unique cellular roles. Additionally, most drugs have membrane proteins as their receptors, notably the superfamily of G protein-coupled receptors with seven transmembrane helices. Determining the structures of membrane proteins is a daunting task because of the effects of the membrane environment; specifically, it has been difficult to combine biologically compatible environments with the requirements for the established methods of structure determination. There is strong motivation to determine the structures in their native phospholipid bilayer environment so that perturbations from nonnatural lipids and phases do not have to be taken into account. At present, the only method that can work with proteins in liquid crystalline phospholipid bilayers is solid-state NMR spectroscopy.

  2. Comparison of protein structures using 3D profile alignment.

    PubMed

    Suyama, M; Matsuo, Y; Nishikawa, K

    1997-01-01

    A novel method for protein structure comparison using 3D profile alignment is presented. The 3D profile is a position-dependent scoring matrix derived from three-dimensional structures and is basically used to estimate sequence-structure compatibility for prediction of protein structure. Our idea is to compare two 3D profiles using a dynamic programming algorithm to obtain optimal alignment and a similarity score between them. When the 3D profile of hemoglobin was compared with each of the profiles in the library, which contained 325 profiles of representative structures, all the profiles of other globins were detected with relatively high scores, and proteins in the same structural class followed the globins. Exhaustive comparison of 3D profiles in the library was also performed to depict protein relatedness in the structure space. Using multidimensional scaling, a planar projection of points in the protein structure space revealed an overall grouping in terms of structural classes, i.e., all-alpha, all-beta, alpha/beta, and alpha+beta. These results differ in implication from those obtained by the conventional structure-structure comparison method. Differences are discussed with respect to the structural divergence of proteins in the course of molecular evolution. PMID:9071025

  3. The history of the CATH structural classification of protein domains

    PubMed Central

    Sillitoe, Ian; Dawson, Natalie; Thornton, Janet; Orengo, Christine

    2015-01-01

    This article presents a historical review of the protein structure classification database CATH. Together with the SCOP database, CATH remains comprehensive and reasonably up-to-date with the now more than 100,000 protein structures in the PDB. We review the expansion of the CATH and SCOP resources to capture predicted domain structures in the genome sequence data and to provide information on the likely functions of proteins mediated by their constituent domains. The establishment of comprehensive function annotation resources has also meant that domain families can be functionally annotated allowing insights into functional divergence and evolution within protein families. PMID:26253692

  4. Overview on the use of NMR to examine protein structure.

    PubMed

    Breukels, Vincent; Konijnenberg, Albert; Nabuurs, Sanne M; Doreleijers, Jurgen F; Kovalevskaya, Nadezda V; Vuister, Geerten W

    2011-04-01

    Any protein structure determination process contains several steps, starting from obtaining a suitable sample, then moving on to acquiring data and spectral assignment, and lastly to the final steps of structure determination and validation. This unit describes all of these steps, starting with the basic physical principles behind NMR and some of the most commonly measured and observed phenomena such as chemical shift, scalar and residual coupling, and the nuclear Overhauser effect. Then, in somewhat more detail, the process of spectral assignment and structure elucidation is explained. Furthermore, the use of NMR to study protein-ligand interaction, protein dynamics, or protein folding is described. PMID:21488042

  5. The history of the CATH structural classification of protein domains.

    PubMed

    Sillitoe, Ian; Dawson, Natalie; Thornton, Janet; Orengo, Christine

    2015-12-01

    This article presents a historical review of the protein structure classification database CATH. Together with the SCOP database, CATH remains comprehensive and reasonably up-to-date with the now more than 100,000 protein structures in the PDB. We review the expansion of the CATH and SCOP resources to capture predicted domain structures in the genome sequence data and to provide information on the likely functions of proteins mediated by their constituent domains. The establishment of comprehensive function annotation resources has also meant that domain families can be functionally annotated allowing insights into functional divergence and evolution within protein families. PMID:26253692

  6. Mixing and Matching Detergents for Membrane Protein NMR Structure Determination

    SciTech Connect

    Columbus, Linda; Lipfert, Jan; Jambunathan, Kalyani; Fox, Daniel A.; Sim, Adelene Y.L.; Doniach, Sebastian; Lesley, Scott A.

    2009-10-21

    One major obstacle to membrane protein structure determination is the selection of a detergent micelle that mimics the native lipid bilayer. Currently, detergents are selected by exhaustive screening because the effects of protein-detergent interactions on protein structure are poorly understood. In this study, the structure and dynamics of an integral membrane protein in different detergents is investigated by nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy and small-angle X-ray scattering (SAXS). The results suggest that matching of the micelle dimensions to the protein's hydrophobic surface avoids exchange processes that reduce the completeness of the NMR observations. Based on these dimensions, several mixed micelles were designed that improved the completeness of NMR observations. These findings provide a basis for the rational design of mixed micelles that may advance membrane protein structure determination by NMR.

  7. Design of structurally distinct proteins using strategies inspired by evolution.

    PubMed

    Jacobs, T M; Williams, B; Williams, T; Xu, X; Eletsky, A; Federizon, J F; Szyperski, T; Kuhlman, B

    2016-05-01

    Natural recombination combines pieces of preexisting proteins to create new tertiary structures and functions. We describe a computational protocol, called SEWING, which is inspired by this process and builds new proteins from connected or disconnected pieces of existing structures. Helical proteins designed with SEWING contain structural features absent from other de novo designed proteins and, in some cases, remain folded at more than 100°C. High-resolution structures of the designed proteins CA01 and DA05R1 were solved by x-ray crystallography (2.2 angstrom resolution) and nuclear magnetic resonance, respectively, and there was excellent agreement with the design models. This method provides a new strategy to rapidly create large numbers of diverse and designable protein scaffolds. PMID:27151863

  8. Computational design of proteins with novel structure and functions

    NASA Astrophysics Data System (ADS)

    Wei, Yang; Lu-Hua, Lai

    2016-01-01

    Computational design of proteins is a relatively new field, where scientists search the enormous sequence space for sequences that can fold into desired structure and perform desired functions. With the computational approach, proteins can be designed, for example, as regulators of biological processes, novel enzymes, or as biotherapeutics. These approaches not only provide valuable information for understanding of sequence-structure-function relations in proteins, but also hold promise for applications to protein engineering and biomedical research. In this review, we briefly introduce the rationale for computational protein design, then summarize the recent progress in this field, including de novo protein design, enzyme design, and design of protein-protein interactions. Challenges and future prospects of this field are also discussed. Project supported by the National Basic Research Program of China (Grant No. 2015CB910300), the National High Technology Research and Development Program of China (Grant No. 2012AA020308), and the National Natural Science Foundation of China (Grant No. 11021463).

  9. A threading approach to protein structure prediction: Studies on TNF-like molecules, Rev proteins, and protein kinases

    NASA Astrophysics Data System (ADS)

    Ihm, Yungok

    The main focus of this dissertation is the application of the threading approach to specific biological problems. The threading scheme developed in our group targets incorporating important structural features necessary for detecting structural similarity between the target sequence and the template structure. This enables us to use our threading method to solve problems for which sequence-based methods are not very much useful. We applied our threading method to predict the three-dimensional structures of lentivirus (EIAV, HIV-1, FIV, SIV) Rev proteins. Predicted structures of Rev proteins suggest that they share a structural similarity among themselves (four-helix bundle). Also, the threading approach has been utilized for screening for potential TNF-like molecules in Arabidopsis. The threading approach identified 35 potential TNF-like proteins in Arabidopsis, six of which are particularly interesting to be tested for the receptor kinase ligand activity. Threading method has also been used to identify potentially new protein kinases, which are not included in the protein kinase data base of C. elegans and Arabidopis. We identified eleven potentially new protein kinases and an additional protein worth investigating for protein kinase activity in C. elegans. Further, we identified ten potentially new protein kinases and additional four proteins worth investigating for the protein kinase activity in Arabidopsis.

  10. Tactile Teaching: Exploring Protein Structure/Function Using Physical Models

    ERIC Educational Resources Information Center

    Herman, Tim; Morris, Jennifer; Colton, Shannon; Batiza, Ann; Patrick, Michael; Franzen, Margaret; Goodsell, David S.

    2006-01-01

    The technology now exists to construct physical models of proteins based on atomic coordinates of solved structures. We review here our recent experiences in using physical models to teach concepts of protein structure and function at both the high school and the undergraduate levels. At the high school level, physical models are used in a…

  11. The Structural Characterization of Tumor Fusion Genes and Proteins.

    PubMed

    Wang, Dandan; Li, Daixi; Qin, Guangrong; Zhang, Wen; Ouyang, Jian; Zhang, Menghuan; Xie, Lu

    2015-01-01

    Chromosomal translocation, which generates fusion proteins in blood tumor or solid tumor, is considered as one of the major causes leading to cancer. Recent studies suggested that the disordered fragments in a fusion protein might contribute to its carcinogenicity. Here, we investigated the sequence feature near the breakpoints in the fusion partner genes, the structure features of breakpoints in fusion proteins, and the posttranslational modification preference in the fusion proteins. Results show that the breakpoints in the fusion partner genes have both sequence preference and structural preference. At the sequence level, nucleotide combination AG is preferred before the breakpoint and GG is preferred at the breakpoint. At the structural level, the breakpoints in the fusion proteins prefer to be located in the disordered regions. Further analysis suggests the phosphorylation sites at serine, threonine, and the methylation sites at arginine are enriched in disordered regions of the fusion proteins. Using EML4-ALK as an example, we further explained how the fusion protein leads to the protein disorder and contributes to its carcinogenicity. The sequence and structural features of the fusion proteins may help the scientific community to predict novel breakpoints in fusion genes and better understand the structure and function of fusion proteins. PMID:26347798

  12. The Structural Characterization of Tumor Fusion Genes and Proteins

    PubMed Central

    Wang, Dandan; Li, Daixi; Qin, Guangrong; Zhang, Wen; Ouyang, Jian; Zhang, Menghuan; Xie, Lu

    2015-01-01

    Chromosomal translocation, which generates fusion proteins in blood tumor or solid tumor, is considered as one of the major causes leading to cancer. Recent studies suggested that the disordered fragments in a fusion protein might contribute to its carcinogenicity. Here, we investigated the sequence feature near the breakpoints in the fusion partner genes, the structure features of breakpoints in fusion proteins, and the posttranslational modification preference in the fusion proteins. Results show that the breakpoints in the fusion partner genes have both sequence preference and structural preference. At the sequence level, nucleotide combination AG is preferred before the breakpoint and GG is preferred at the breakpoint. At the structural level, the breakpoints in the fusion proteins prefer to be located in the disordered regions. Further analysis suggests the phosphorylation sites at serine, threonine, and the methylation sites at arginine are enriched in disordered regions of the fusion proteins. Using EML4-ALK as an example, we further explained how the fusion protein leads to the protein disorder and contributes to its carcinogenicity. The sequence and structural features of the fusion proteins may help the scientific community to predict novel breakpoints in fusion genes and better understand the structure and function of fusion proteins. PMID:26347798

  13. In-Cell Protein Structures from 2D NMR Experiments.

    PubMed

    Müntener, Thomas; Häussinger, Daniel; Selenko, Philipp; Theillet, Francois-Xavier

    2016-07-21

    In-cell NMR spectroscopy provides atomic resolution insights into the structural properties of proteins in cells, but it is rarely used to solve entire protein structures de novo. Here, we introduce a paramagnetic lanthanide-tag to simultaneously measure protein pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs) to be used as input for structure calculation routines within the Rosetta program. We employ this approach to determine the structure of the protein G B1 domain (GB1) in intact Xenopus laevis oocytes from a single set of 2D in-cell NMR experiments. Specifically, we derive well-defined GB1 ensembles from low concentration in-cell NMR samples (∼50 μM) measured at moderate magnetic field strengths (600 MHz), thus offering an easily accessible alternative for determining intracellular protein structures. PMID:27379949

  14. Automating the determination of 3D protein structure

    SciTech Connect

    Rayl, K.D.

    1993-12-31

    The creation of an automated method for determining 3D protein structure would be invaluable to the field of biology and presents an interesting challenge to computer science. Unfortunately, given the current level of protein knowledge, a completely automated solution method is not yet feasible, therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the first step toward designing a program to determine protein conformation automatically.

  15. Cotranslational protein folding on the ribosome monitored in real time.

    PubMed

    Holtkamp, Wolf; Kokic, Goran; Jäger, Marcus; Mittelstaet, Joerg; Komar, Anton A; Rodnina, Marina V

    2015-11-27

    Protein domains can fold into stable tertiary structures while they are synthesized on the ribosome. We used a high-performance, reconstituted in vitro translation system to investigate the folding of a small five-helix protein domain-the N-terminal domain of Escherichia coli N5-glutamine methyltransferase HemK-in real time. Our observations show that cotranslational folding of the protein, which folds autonomously and rapidly in solution, proceeds through a compact, non-native conformation that forms within the peptide tunnel of the ribosome. The compact state rearranges into a native-like structure immediately after the full domain sequence has emerged from the ribosome. Both folding transitions are rate-limited by translation, allowing for quasi-equilibrium sampling of the conformational space restricted by the ribosome. Cotranslational folding may be typical of small, intrinsically rapidly folding protein domains. PMID:26612953

  16. A local average distance descriptor for flexible protein structure comparison

    PubMed Central

    2014-01-01

    Background Protein structures are flexible and often show conformational changes upon binding to other molecules to exert biological functions. As protein structures correlate with characteristic functions, structure comparison allows classification and prediction of proteins of undefined functions. However, most comparison methods treat proteins as rigid bodies and cannot retrieve similarities of proteins with large conformational changes effectively. Results In this paper, we propose a novel descriptor, local average distance (LAD), based on either the geodesic distances (GDs) or Euclidean distances (EDs) for pairwise flexible protein structure comparison. The proposed method was compared with 7 structural alignment methods and 7 shape descriptors on two datasets comprising hinge bending motions from the MolMovDB, and the results have shown that our method outperformed all other methods regarding retrieving similar structures in terms of precision-recall curve, retrieval success rate, R-precision, mean average precision and F1-measure. Conclusions Both ED- and GD-based LAD descriptors are effective to search deformed structures and overcome the problems of self-connection caused by a large bending motion. We have also demonstrated that the ED-based LAD is more robust than the GD-based descriptor. The proposed algorithm provides an alternative approach for blasting structure database, discovering previously unknown conformational relationships, and reorganizing protein structure classification. PMID:24694083

  17. Protein structure. Structure and activity of tryptophan-rich TSPO proteins.

    PubMed

    Guo, Youzhong; Kalathur, Ravi C; Liu, Qun; Kloss, Brian; Bruni, Renato; Ginter, Christopher; Kloppmann, Edda; Rost, Burkhard; Hendrickson, Wayne A

    2015-01-30

    Translocator proteins (TSPOs) bind steroids and porphyrins, and they are implicated in many human diseases, for which they serve as biomarkers and therapeutic targets. TSPOs have tryptophan-rich sequences that are highly conserved from bacteria to mammals. Here we report crystal structures for Bacillus cereus TSPO (BcTSPO) down to 1.7 Å resolution, including a complex with the benzodiazepine-like inhibitor PK11195. We also describe BcTSPO-mediated protoporphyrin IX (PpIX) reactions, including catalytic degradation to a previously undescribed heme derivative. We used structure-inspired mutations to investigate reaction mechanisms, and we showed that TSPOs from Xenopus and man have similar PpIX-directed activities. Although TSPOs have been regarded as transporters, the catalytic activity in PpIX degradation suggests physiological importance for TSPOs in protection against oxidative stress. PMID:25635100

  18. Protein structure. Crystal structures of translocator protein (TSPO) and mutant mimic of a human polymorphism.

    PubMed

    Li, Fei; Liu, Jian; Zheng, Yi; Garavito, R Michael; Ferguson-Miller, Shelagh

    2015-01-30

    The 18-kilodalton translocator protein (TSPO), proposed to be a key player in cholesterol transport into mitochondria, is highly expressed in steroidogenic tissues, metastatic cancer, and inflammatory and neurological diseases such as Alzheimer's and Parkinson's. TSPO ligands, including benzodiazepine drugs, are implicated in regulating apoptosis and are extensively used in diagnostic imaging. We report crystal structures (at 1.8, 2.4, and 2.5 angstrom resolution) of TSPO from Rhodobacter sphaeroides and a mutant that mimics the human Ala(147)→Thr(147) polymorphism associated with psychiatric disorders and reduced pregnenolone production. Crystals obtained in the lipidic cubic phase reveal the binding site of an endogenous porphyrin ligand and conformational effects of the mutation. The three crystal structures show the same tightly interacting dimer and provide insights into the controversial physiological role of TSPO and how the mutation affects cholesterol binding. PMID:25635101

  19. Advances in Protein NMR Impacting Drug Discovery Provided by the NIGMS Protein Structure Initiative

    PubMed Central

    Montelione, Gaetano T.; Szyperski, Thomas

    2014-01-01

    Rational drug design relies on three-dimensional structures of biological macromolecules, especially proteins. Structural genomics high-throughput (HTP) structure determination platforms established by the NIH Protein Structure Initiative are uniquely suited to provide these structures. NMR plays a critical role since (i) many important protein targets do not form single crystals required for X-ray diffraction and (ii) NMR can provide valuable structural and dynamic information on proteins and their drug complexes that cannot be obtained with X-ray crystallography. In this article, recent advances of NMR driven by structural genomics projects are reviewed. These advances promise that future pharmaceutical discovery and design of drugs can increasingly rely on protocols for rapid and accurate NMR structure determination. PMID:20443167

  20. Computational Methods for Domain Partitioning of Protein Structures

    NASA Astrophysics Data System (ADS)

    Veretnik, Stella; Shindyalov, Ilya

    Analysis of protein structures typically begins with decomposition of structure into more basic units, called "structural domains". The underlying goal is to reduce a complex protein structure to a set of simpler yet structurally meaningful units, each of which can be analyzed independently. Structural semi-independence of domains is their hallmark: domains often have compact structure and can fold or function independently. Domains can undergo so-called "domain shuffling"when they reappear in different combinations in different proteins thus implementing different biological functions (Doolittle, 1995). Proteins can then be conceived as being built of such basic blocks: some, especially small proteins, consist usually of just one domain, while other proteins possess a more complex architecture containing multiple domains. Therefore, the methods for partitioning a structure into domains are of critical importance: their outcome defines the set of basic units upon which structural classifications are built and evolutionary analysis is performed. This is especially true nowadays in the era of structural genomics. Today there are many methods that decompose the structure into domains: some of them are manual (i.e., based on human judgment), others are semiautomatic, and still others are completely automatic (based on algorithms implemented as software). Overall there is a high level of consistency and robustness in the process of partitioning a structure into domains (for ˜80% of proteins); at least for structures where domain location is obvious. The picture is less bright when we consider proteins with more complex architectures—neither human experts nor computational methods can reach consistent partitioning in many such cases. This is a rather accurate reflection of biological phenomena in general since domains are formed by different mechanisms, hence it is nearly impossible to come up with a set of well-defined rules that captures all of the observed cases.

  1. Supramolecular Structures with Blood Plasma Proteins, Sugars and Nanosilica

    NASA Astrophysics Data System (ADS)

    Turov, V. V.; Gun'ko, V. M.; Galagan, N. P.; Rugal, A. A.; Barvinchenko, V. M.; Gorbyk, P. P.

    Supramolecular structures with blood plasma proteins (albumin, immunoglobulin and fibrinogen (HPF)), protein/water/silica and protein/water/ silica/sugar (glucose, fructose and saccharose) were studied by NMR, adsorption, IR and UV spectroscopy methods. Hydration parameters, amounts of weakly and strongly bound waters and interfacial energy (γ S) were determined over a wide range of component concentrations. The γ S(C protein,C silica) graphs were used to estimate the energy of protein-protein, protein-surface and particle-particle interactions. It was shown that interfacial energy of self-association (γ as) of protein molecules depends on a type of proteins. A large fraction of water bound to proteins can be displaced by sugars, and the effect of disaccharide (saccharose) was greater than that of monosugars. Changes in the structural parameters of cavities in HPF molecules and complexes with HPF/silica nanoparticles filled by bound water were analysed using NMR-cryoporometry showing that interaction of proteins with silica leads to a significant decrease in the amounts of water bound to both protein and silica surfaces. Bionanocomposites with BSA/nanosilica/sugar can be used to influence states of living cells and tissues after cryopreservation or other treatments. It was shown that interaction of proteins with silica leads to strong decrease in the volume of all types of internal cavities filled by water.

  2. Methods for optimizing the structure alphabet sequences of proteins.

    PubMed

    Dong, Qi-wen; Wang, Xiao-long; Lin, Lei

    2007-11-01

    Protein structure prediction based on fragment assemble has made great progress in recent years. Local protein structure prediction is receiving increased attention. One essential step of local protein structure prediction method is that the three-dimensional conformations must be compressed into one-dimensional series of letters of a structural alphabet. The traditional method assigns each structure fragment the structure alphabet that has the best local structure similarity. However, such locally optimal structure alphabet sequence does not guarantee to produce the globally optimal structure. This study presents two efficient methods trying to find the optimal structure alphabet sequence, which can model the native structures as accuracy as possible. First, a 28-letter structure alphabet is derived by clustering fragment in Cartesian space with fragment length of seven residues. The average quantization error of the 28 letters is 0.82 A in term of root mean square deviation. Then, two efficient methods are presented to encode the protein structures into series of structure alphabet letters, that is, the greedy and dynamic programming algorithm. They are tested on PDB database using the structure alphabet developed in Cartesian coordinates space (our structure alphabet) and in torsion angles space (the PB structure alphabet), respectively. The experimental results show that these two methods can find the approximately optimal structure alphabet sequences by searching a small fraction of the modeling space. The traditional local-optimization method achieves 26.27 A root mean square deviations between the reconstructed structures and the native one, while the modeling accuracy is improved to 3.28 A by the greedy algorithm. The results are helpful for local protein structure prediction. PMID:17493604

  3. Structural basis of a rationally rewired protein-protein interface critical to bacterial signaling

    PubMed Central

    Podgornaia, Anna I.; Casino, Patricia; Marina, Alberto; Laub, Michael T.

    2013-01-01

    Summary Two-component signal transduction systems typically involve a sensor histidine kinase that specifically phosphorylates a single, cognate response regulator. This protein-protein interaction relies on molecular recognition via a small set of residues in each protein. To better understand how these residues determine the specificity of kinase-substrate interactions, we rationally rewired the interaction interface of a Thermotoga maritima two-component system, HK853-RR468, to match that found in a different two-component system, E. coli PhoR-PhoB. The rewired proteins interacted robustly with each other, but no longer interacted with the parent proteins. Analysis of the crystal structures of the wild-type and mutant protein complexes, along with a systematic mutagenesis study, reveals how individual mutations contribute to the rewiring of interaction specificity. Our approach and conclusions have implications for studies of other protein-protein interactions, protein evolution, and the design of novel protein interfaces. PMID:23954504

  4. Structural basis of a rationally rewired protein-protein interface critical to bacterial signaling.

    PubMed

    Podgornaia, Anna I; Casino, Patricia; Marina, Alberto; Laub, Michael T

    2013-09-01

    Two-component signal transduction systems typically involve a sensor histidine kinase that specifically phosphorylates a single, cognate response regulator. This protein-protein interaction relies on molecular recognition via a small set of residues in each protein. To better understand how these residues determine the specificity of kinase-substrate interactions, we rationally rewired the interaction interface of a Thermotoga maritima two-component system, HK853-RR468, to match that found in a different two-component system, Escherichia coli PhoR-PhoB. The rewired proteins interacted robustly with each other, but no longer interacted with the parent proteins. Analysis of the crystal structures of the wild-type and mutant protein complexes and a systematic mutagenesis study reveal how individual mutations contribute to the rewiring of interaction specificity. Our approach and conclusions have implications for studies of other protein-protein interactions and protein evolution and for the design of novel protein interfaces. PMID:23954504

  5. Macromolecular crowding increases structural content of folded proteins.

    PubMed

    Perham, Michael; Stagg, Loren; Wittung-Stafshede, Pernilla

    2007-10-30

    Here we show that increased amount of secondary structure is acquired in the folded states of two structurally-different proteins (alpha-helical VlsE and alpha/beta flavodoxin) in the presence of macromolecular crowding agents. The structural content of flavodoxin and VlsE is enhanced by 33% and 70%, respectively, in 400 mg/ml Ficoll 70 (pH 7, 20 degrees C) and correlates with higher protein-thermal stability. In the same Ficoll range, there are only small effects on the unfolded-state structures of the proteins. This is the first in vitro assessment of crowding effects on the native-state structures at physiological conditions. Our findings imply that for proteins with low intrinsic stability, the functional structures in vivo may differ from those observed in dilute buffers. PMID:17919600

  6. A sampling approach for protein backbone fragment conformations.

    PubMed

    Yu, J Y; Zhang, W

    2013-01-01

    In protein structure prediction, backbone fragment bias information can narrow down the conformational space of the whole polypeptide chain significantly. Unlike existing methods that use fragments as building blocks, the paper presents a probabilistic sampling approach for protein backbone torsion angles by modelling angular correlation of (phi, psi) with a directional statistics distribution. Given a protein sequence and secondary structure information, this method samples backbone fragments conformations by using a backtrack sampling algorithm for the hidden Markov model with multiple inputs and a single output. The proposed approach is applied to a fragment library, and some well-known structural motifs are sampled very well on the optimal path. Computational results show that the method can help to obtain native-like backbone fragments conformations. PMID:23777175

  7. Proteins: sequence to structure and function--current status.

    PubMed

    Shenoy, Sandhya R; Jayaram, B

    2010-11-01

    In an era that has been dominated by Structural Biology for the last 30-40 years, a dramatic change of focus towards sequence analysis has spurred the advent of the genome projects and the resultant diverging sequence/structure deficit. The central challenge of Computational Structural Biology is therefore to rationalize the mass of sequence information into biochemical and biophysical knowledge and to decipher the structural, functional and evolutionary clues encoded in the language of biological sequences. In investigating the meaning of sequences, two distinct analytical themes have emerged: in the first approach, pattern recognition techniques are used to detect similarity between sequences and hence to infer related structures and functions; in the second ab initio prediction methods are used to deduce 3D structure, and ultimately to infer function, directly from the linear sequence. In this article, we attempt to provide a critical assessment of what one may and may not expect from the biological sequences and to identify major issues yet to be resolved. The presentation is organized under several subtitles like protein sequences, pattern recognition techniques, protein tertiary structure prediction, membrane protein bioinformatics, human proteome, protein-protein interactions, metabolic networks, potential drug targets based on simple sequence properties, disordered proteins, the sequence-structure relationship and chemical logic of protein sequences. PMID:20887265

  8. Kinetics of protein adsorption on gold nanoparticle with variable protein structure and nanoparticle size.

    PubMed

    Khan, S; Gupta, A; Verma, N C; Nandi, C K

    2015-10-28

    The spontaneous protein adsorption on nanomaterial surfaces and the formation of a protein corona around nanoparticles are poorly understood physical phenomena, with high biological relevance. The complexity arises mainly due to the poor knowledge of the structural orientation of the adsorbed proteins onto the nanoparticle surface and difficulties in correlating the protein nanoparticle interaction to the protein corona in real time scale. Here, we provide quantitative insights into the kinetics, number, and binding orientation of a few common blood proteins when they interact with citrate and cetyltriethylammoniumbromide stabilized spherical gold nanoparticles with variable sizes. The kinetics of the protein adsorption was studied experimentally by monitoring the change in hydrodynamic diameter and zeta potential of the nanoparticle-protein complex. To understand the competitive binding of human serum albumin and hemoglobin, time dependent fluorescence quenching was studied using dual fluorophore tags. We have performed molecular docking of three different proteins--human serum albumin, bovine serum albumin, and hemoglobin--on different nanoparticle surfaces to elucidate the possible structural orientation of the adsorbed protein. Our data show that the growth kinetics of a protein corona is exclusively dependent on both protein structure and surface chemistry of the nanoparticles. The study quantitatively suggests that a general physical law of protein adsorption is unlikely to exist as the interaction is unique and specific for a given pair. PMID:26520545

  9. Exploring Protein Dynamics Space: The Dynasome as the Missing Link between Protein Structure and Function

    PubMed Central

    Hensen, Ulf; Meyer, Tim; Haas, Jürgen; Rex, René; Vriend, Gert; Grubmüller, Helmut

    2012-01-01

    Proteins are usually described and classified according to amino acid sequence, structure or function. Here, we develop a minimally biased scheme to compare and classify proteins according to their internal mobility patterns. This approach is based on the notion that proteins not only fold into recurring structural motifs but might also be carrying out only a limited set of recurring mobility motifs. The complete set of these patterns, which we tentatively call the dynasome, spans a multi-dimensional space with axes, the dynasome descriptors, characterizing different aspects of protein dynamics. The unique dynamic fingerprint of each protein is represented as a vector in the dynasome space. The difference between any two vectors, consequently, gives a reliable measure of the difference between the corresponding protein dynamics. We characterize the properties of the dynasome by comparing the dynamics fingerprints obtained from molecular dynamics simulations of 112 proteins but our approach is, in principle, not restricted to any specific source of data of protein dynamics. We conclude that: 1. the dynasome consists of a continuum of proteins, rather than well separated classes. 2. For the majority of proteins we observe strong correlations between structure and dynamics. 3. Proteins with similar function carry out similar dynamics, which suggests a new method to improve protein function annotation based on protein dynamics. PMID:22606222

  10. Synchrotron IR microspectroscopy for protein structure analysis: Potential and questions

    DOE PAGESBeta

    Yu, Peiqiang

    2006-01-01

    Synchrotron radiation-based Fourier transform infrared microspectroscopy (S-FTIR) has been developed as a rapid, direct, non-destructive, bioanalytical technique. This technique takes advantage of synchrotron light brightness and small effective source size and is capable of exploring the molecular chemical make-up within microstructures of a biological tissue without destruction of inherent structures at ultra-spatial resolutions within cellular dimension. To date there has been very little application of this advanced technique to the study of pure protein inherent structure at a cellular level in biological tissues. In this review, a novel approach was introduced to show the potential of the newly developed, advancedmore » synchrotron-based analytical technology, which can be used to localize relatively “pure“ protein in the plant tissues and relatively reveal protein inherent structure and protein molecular chemical make-up within intact tissue at cellular and subcellular levels. Several complex protein IR spectra data analytical techniques (Gaussian and Lorentzian multi-component peak modeling, univariate and multivariate analysis, principal component analysis (PCA), and hierarchical cluster analysis (CLA) are employed to relatively reveal features of protein inherent structure and distinguish protein inherent structure differences between varieties/species and treatments in plant tissues. By using a multi-peak modeling procedure, RELATIVE estimates (but not EXACT determinations) for protein secondary structure analysis can be made for comparison purpose. The issues of pro- and anti-multi-peaking modeling/fitting procedure for relative estimation of protein structure were discussed. By using the PCA and CLA analyses, the plant molecular structure can be qualitatively separate one group from another, statistically, even though the spectral assignments are not known. The synchrotron-based technology provides a new approach for protein structure research in

  11. Tuning structure of oppositely charged nanoparticle and protein complexes

    SciTech Connect

    Kumar, Sugam Aswal, V. K.; Callow, P.

    2014-04-24

    Small-angle neutron scattering (SANS) has been used to probe the structures of anionic silica nanoparticles (LS30) and cationic lyszyme protein (M.W. 14.7kD, I.P. ∼ 11.4) by tuning their interaction through the pH variation. The protein adsorption on nanoparticles is found to be increasing with pH and determined by the electrostatic attraction between two components as well as repulsion between protein molecules. We show the strong electrostatic attraction between nanoparticles and protein molecules leads to protein-mediated aggregation of nanoparticles which are characterized by fractal structures. At pH 5, the protein adsorption gives rise to nanoparticle aggregation having surface fractal morphology with close packing of nanoparticles. The surface fractals transform to open structures of mass fractal morphology at higher pH (7 and 9) on approaching isoelectric point (I.P.)

  12. Genome Pool Strategy for Structural Coverage of Protein Families

    SciTech Connect

    Jaroszewski, L.; Slabinski, L.; Wooley, J.; Deacon, A.M.; Lesley, S.A.; Wilson, I.A.; Godzik, A.

    2009-05-18

    Even closely homologous proteins often have different crystallization properties and propensities. This observation can be used to introduce an additional dimension into crystallization trials by simultaneous targeting multiple homologs in what we call a 'genome pool' strategy. We show that this strategy works because protein physicochemical properties correlated with crystallization success have a surprisingly broad distribution within most protein families. There are also easy and difficult families where this distribution is tilted in one direction. This leads to uneven structural coverage of protein families, with more easy ones solved. Increasing the size of the genome pool can improve chances of solving the difficult ones. In contrast, our analysis does not indicate that any specific genomes are easy or difficult. Finally, we show that the group of proteins with known 3D structures is systematically different from the general pool of known proteins and we assess the structural consequences of these differences.

  13. Structure Determination of Membrane Proteins by Nuclear Magnetic Resonance Spectroscopy

    PubMed Central

    Opella, Stanley J.

    2014-01-01

    Many biological membranes consist of 50% or more (by weight) membrane proteins, which constitute approximately one-third of all proteins expressed in biological organisms. Helical membrane proteins function as receptors, enzymes, and transporters, among other unique cellular roles. Additionally, most drugs have membrane proteins as their receptors, notably the superfamily of G protein–coupled receptors with seven transmembrane helices. Determining the structures of membrane proteins is a daunting task because of the effects of the membrane environment; specifically, it has been difficult to combine biologically compatible environments with the requirements for the established methods of structure determination. There is strong motivation to determine the structures in their native phospholipid bilayer environment so that perturbations from nonnatural lipids and phases do not have to be taken into account. At present, the only method that can work with proteins in liquid crystalline phospholipid bilayers is solid-state NMR spectroscopy. PMID:23577669

  14. [Structure, Immunogenicity and Clinical Value of Chlamydiaphage Capsid Protein 3].

    PubMed

    Yao, Weifeng; Li, Yiju; Yuan, Jing; Wang, Lei; Li, Qunyan; Song, Mengmeng; Lu, Guiling; Zhang, Litao

    2015-07-01

    We wished to assess the role of chlamydia micro virus capsid protein Vp3 in recombinant molecules, chart its molecular evolution, screen the wild-type strain, and reveal its value in clinical research. Using a protein BLAST multiple-alignment program, we compared various strains of Chlamydia micro virus capsid protein Vp3 sequences. Using a "distance tree" of those results, we created a phylogenetic tree. We applied the Karplus-Schulz method of flexible-region analyses for highly conserved alignments of amino-acid sequences. Gamier-Robson and Chou-Fasman methods were employed to analyze two-level structures of sequences. The Emini method was used for analyses of the accessibility of surface epitopes. Studies of hydrophilic proteins were undertaken using Kyte-Doolittle and Hopp-Woods methods. Analyses of antigen epitopes helped to reveal the antigen index using the Jameson-Wolf method. All sequences in the six strains of chlamydia micro virus capsid protein Vp3 were highly conserved, with the main differences being between Vp3 protein in Chp1 and the other five strains of the micro virus. The viral strain of Vp3 protein was based mainly on micro-alpha helix structures, and multiple epitopes were noted in highly conserved regions. Vp3 protein was highly conserved structurally, and was an important protein of the chlamydiaphage capsid. Vp3 protein has a complicated molecular structure, highly conserved regions with strong immunogenicity, and has considerable research value. PMID:26524915

  15. Structural and Energetic Characterization of the Ankyrin Repeat Protein Family

    PubMed Central

    Parra, R. Gonzalo; Espada, Rocío; Verstraete, Nina; Ferreiro, Diego U.

    2015-01-01

    Ankyrin repeat containing proteins are one of the most abundant solenoid folds. Usually implicated in specific protein-protein interactions, these proteins are readily amenable for design, with promising biotechnological and biomedical applications. Studying repeat protein families presents technical challenges due to the high sequence divergence among the repeating units. We developed and applied a systematic method to consistently identify and annotate the structural repetitions over the members of the complete Ankyrin Repeat Protein Family, with increased sensitivity over previous studies. We statistically characterized the number of repeats, the folding of the repeat-arrays, their structural variations, insertions and deletions. An energetic analysis of the local frustration patterns reveal the basic features underlying fold stability and its relation to the functional binding regions. We found a strong linear correlation between the conservation of the energetic features in the repeat arrays and their sequence variations, and discuss new insights into the organization and function of these ubiquitous proteins. PMID:26691182

  16. Structural Analysis of Protein-Protein Interactions in Type I Polyketide Synthases

    PubMed Central

    Xu, Wei; Qiao, Kangjian; Tang, Yi

    2013-01-01

    Polyketide synthases (PKSs) are responsible for synthesizing a myriad of natural products with agricultural, medicinal relevance. The PKSs consist of multiple functional domains of which each can catalyze a specified chemical reaction leading to the synthesis of polyketides. Biochemical studies showed that protein-substrate and protein-protein interactions play crucial roles in these complex regio-/stereo- selective biochemical processes. Recent developments on X-ray crystallography and protein NMR techniques have allowed us to understand the biosynthetic mechanism of these enzymes from their structures. These structural studies have facilitated the elucidation of sequence-function relationship of PKSs and will ultimately contribute to the prediction of product structure. This review will focus on the current knowledge of type I PKS structures and the protein-protein interactions in this system. PMID:23249187

  17. Multiple oligomeric structures of a bacterial small heat shock protein

    PubMed Central

    Mani, Nandini; Bhandari, Spraha; Moreno, Rodolfo; Hu, Liya; Prasad, B. V. Venkataram; Suguna, Kaza

    2016-01-01

    Small heat shock proteins are ubiquitous molecular chaperones that form the first line of defence against the detrimental effects of cellular stress. Under conditions of stress they undergo drastic conformational rearrangements in order to bind to misfolded substrate proteins and prevent cellular protein aggregation. Owing to the dynamic nature of small heat shock protein oligomers, elucidating the structural basis of chaperone action and oligomerization still remains a challenge. In order to understand the organization of sHSP oligomers, we have determined crystal structures of a small heat shock protein from Salmonella typhimurium in a dimeric form and two higher oligomeric forms: an 18-mer and a 24-mer. Though the core dimer structure is conserved in all the forms, structural heterogeneity arises due to variation in the terminal regions. PMID:27053150

  18. Revealing Higher Order Protein Structure Using Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Chait, Brian T.; Cadene, Martine; Olinares, Paul Dominic; Rout, Michael P.; Shi, Yi

    2016-04-01

    The development of rapid, sensitive, and accurate mass spectrometric methods for measuring peptides, proteins, and even intact protein assemblies has made mass spectrometry (MS) an extraordinarily enabling tool for structural biology. Here, we provide a personal perspective of the increasingly useful role that mass spectrometric techniques are exerting during the elucidation of higher order protein structures. Areas covered in this brief perspective include MS as an enabling tool for the high resolution structural biologist, for compositional analysis of endogenous protein complexes, for stoichiometry determination, as well as for integrated approaches for the structural elucidation of protein complexes. We conclude with a vision for the future role of MS-based techniques in the development of a multi-scale molecular microscope.

  19. Revealing Higher Order Protein Structure Using Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Chait, Brian T.; Cadene, Martine; Olinares, Paul Dominic; Rout, Michael P.; Shi, Yi

    2016-06-01

    The development of rapid, sensitive, and accurate mass spectrometric methods for measuring peptides, proteins, and even intact protein assemblies has made mass spectrometry (MS) an extraordinarily enabling tool for structural biology. Here, we provide a personal perspective of the increasingly useful role that mass spectrometric techniques are exerting during the elucidation of higher order protein structures. Areas covered in this brief perspective include MS as an enabling tool for the high resolution structural biologist, for compositional analysis of endogenous protein complexes, for stoichiometry determination, as well as for integrated approaches for the structural elucidation of protein complexes. We conclude with a vision for the future role of MS-based techniques in the development of a multi-scale molecular microscope.

  20. Revealing Higher Order Protein Structure Using Mass Spectrometry.

    PubMed

    Chait, Brian T; Cadene, Martine; Olinares, Paul Dominic; Rout, Michael P; Shi, Yi

    2016-06-01

    The development of rapid, sensitive, and accurate mass spectrometric methods for measuring peptides, proteins, and even intact protein assemblies has made mass spectrometry (MS) an extraordinarily enabling tool for structural biology. Here, we provide a personal perspective of the increasingly useful role that mass spectrometric techniques are exerting during the elucidation of higher order protein structures. Areas covered in this brief perspective include MS as an enabling tool for the high resolution structural biologist, for compositional analysis of endogenous protein complexes, for stoichiometry determination, as well as for integrated approaches for the structural elucidation of protein complexes. We conclude with a vision for the future role of MS-based techniques in the development of a multi-scale molecular microscope. Graphical Abstract ᅟ. PMID:27080007

  1. PDBparam: Online Resource for Computing Structural Parameters of Proteins

    PubMed Central

    Nagarajan, R.; Archana, A.; Thangakani, A. Mary; Jemimah, S.; Velmurugan, D.; Gromiha, M. Michael

    2016-01-01

    Understanding the structure–function relationship in proteins is a longstanding goal in molecular and computational biology. The development of structure-based parameters has helped to relate the structure with the function of a protein. Although several structural features have been reported in the literature, no single server can calculate a wide-ranging set of structure-based features from protein three-dimensional structures. In this work, we have developed a web-based tool, PDBparam, for computing more than 50 structure-based features for any given protein structure. These features are classified into four major categories: (i) interresidue interactions, which include short-, medium-, and long-range interactions, contact order, long-range order, total contact distance, contact number, and multiple contact index, (ii) secondary structure propensities such as α-helical propensity, β-sheet propensity, and propensity of amino acids to exist at various positions of α-helix and amino acid compositions in high B-value regions, (iii) physicochemical properties containing ionic interactions, hydrogen bond interactions, hydrophobic interactions, disulfide interactions, aromatic interactions, surrounding hydrophobicity, and buriedness, and (iv) identification of binding site residues in protein–protein, protein–nucleic acid, and protein–ligand complexes. The server can be freely accessed at http://www.iitm.ac.in/bioinfo/pdbparam/. We suggest the use of PDBparam as an effective tool for analyzing protein structures. PMID:27330281

  2. Bayesian inference of protein structure from chemical shift data

    PubMed Central

    Bratholm, Lars A.; Christensen, Anders S.; Hamelryck, Thomas

    2015-01-01

    Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model, and a bias is introduced which might result in incorrect structures. In the inferential structure determination framework, both the unknown structure and the disagreement between experimental and back-calculated data are formulated as a joint probability distribution, thus utilizing the full information content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term, the simulations suggests that sampling both the structure and the uncertainties in chemical shift prediction leads more accurate structures compared to conventional methods using empirical determined weights. The Cauchy distribution, using either sampled uncertainties or predetermined weights, did, however, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction. PMID:25825683

  3. Rotamer strain as a determinant of protein structural specificity.

    PubMed Central

    Lazar, G. A.; Johnson, E. C.; Desjarlais, J. R.; Handel, T. M.

    1999-01-01

    We present direct evidence for a change in protein structural specificity due to hydrophobic core packing. High resolution structural analysis of a designed core variant of ubiquitin reveals that the protein is in slow exchange between two conformations. Examination of side-chain rotamers indicates that this dynamic response and the lower stability of the protein are coupled to greater strain and mobility in the core. The results suggest that manipulating the level of side-chain strain may be one way of fine tuning the stability and specificity of proteins. PMID:10631975

  4. Fusion proteins as alternate crystallization paths to difficult structure problems

    NASA Technical Reports Server (NTRS)

    Carter, Daniel C.; Rueker, Florian; Ho, Joseph X.; Lim, Kap; Keeling, Kim; Gilliland, Gary; Ji, Xinhua

    1994-01-01

    The three-dimensional structure of a peptide fusion product with glutathione transferase from Schistosoma japonicum (SjGST) has been solved by crystallographic methods to 2.5 A resolution. Peptides or proteins can be fused to SjGST and expressed in a plasmid for rapid synthesis in Escherichia coli. Fusion proteins created by this commercial method can be purified rapidly by chromatography on immobilized glutathione. The potential utility of using SjGST fusion proteins as alternate paths to the crystallization and structure determination of proteins is demonstrated.

  5. Distant homology recognition using structural classification of proteins.

    PubMed

    Murzin, A G; Bateman, A

    1997-01-01

    Protein structure prediction is arguably the biggest unsolved problem of structural biology. The notion of the number of naturally occurring different protein folds being limited allows partial solution of this problem by the use of fold recognition methods, which "thread" the sequence in question through a library of known protein folds. The fold recognition methods were thought to be superior to the distant homology recognition methods when there is no significant sequence similarity to known structures. We show here that the Structural Classification of Proteins (SCOP) database, organizing all known protein folds according their structural and evolutionary relationships, can be effectively used to enhance the sensitivity of the distant homology recognition methods to rival the "threading" methods. In the CASP2 experiment, our approach correctly assigned into existing SCOP superfamilies all of the six "fold recognition" targets we attempted. For each of the six targets, we correctly predicted the homologous protein with a very similar structure; often, it was the most similar structure. We correctly predicted local alignments of the sequence features that we found to be characteristic for the protein superfamily containing a given target. Our global alignments, extended manually from these local alignments, also appeared to be rather accurate. PMID:9485501

  6. Kinetics of protein adsorption on gold nanoparticle with variable protein structure and nanoparticle size

    NASA Astrophysics Data System (ADS)

    Khan, S.; Gupta, A.; Verma, N. C.; Nandi, C. K.

    2015-10-01

    The spontaneous protein adsorption on nanomaterial surfaces and the formation of a protein corona around nanoparticles are poorly understood physical phenomena, with high biological relevance. The complexity arises mainly due to the poor knowledge of the structural orientation of the adsorbed proteins onto the nanoparticle surface and difficulties in correlating the protein nanoparticle interaction to the protein corona in real time scale. Here, we provide quantitative insights into the kinetics, number, and binding orientation of a few common blood proteins when they interact with citrate and cetyltriethylammoniumbromide stabilized spherical gold nanoparticles with variable sizes. The kinetics of the protein adsorption was studied experimentally by monitoring the change in hydrodynamic diameter and zeta potential of the nanoparticle-protein complex. To understand the competitive binding of human serum albumin and hemoglobin, time dependent fluorescence quenching was studied using dual fluorophore tags. We have performed molecular docking of three different proteins—human serum albumin, bovine serum albumin, and hemoglobin—on different nanoparticle surfaces to elucidate the possible structural orientation of the adsorbed protein. Our data show that the growth kinetics of a protein corona is exclusively dependent on both protein structure and surface chemistry of the nanoparticles. The study quantitatively suggests that a general physical law of protein adsorption is unlikely to exist as the interaction is unique and specific for a given pair.

  7. Conservation of protein structure over four billion years

    PubMed Central

    Ingles-Prieto, Alvaro; Ibarra-Molero, Beatriz; Delgado-Delgado, Asuncion; Perez-Jimenez, Raul; Fernandez, Julio M.; Gaucher, Eric A.; Sanchez-Ruiz, Jose M.; Gavira, Jose A.

    2013-01-01

    SUMMARY Little is known with certainty about the evolution of protein structures in general and the degree of protein structure conservation over planetary time scales in particular. Here we report the X-ray crystal structures of seven laboratory resurrections of Precambrian thioredoxins dating back up to ~4 billion years before present. Despite considerable sequence differences compared with extant enzymes, the ancestral proteins display the canonical thioredoxin fold while only small structural changes have occurred over 4 billion years. This remarkable degree of structure conservation since a time near the last common ancestor of life supports a punctuated-equilibrium model of structure evolution in which the generation of new folds occurs over comparatively short periods of time and is followed by long periods of structural stasis. PMID:23932589

  8. Conservation of protein structure over four billion years.

    PubMed

    Ingles-Prieto, Alvaro; Ibarra-Molero, Beatriz; Delgado-Delgado, Asuncion; Perez-Jimenez, Raul; Fernandez, Julio M; Gaucher, Eric A; Sanchez-Ruiz, Jose M; Gavira, Jose A

    2013-09-01

    Little is known about the evolution of protein structures and the degree of protein structure conservation over planetary time scales. Here, we report the X-ray crystal structures of seven laboratory resurrections of Precambrian thioredoxins dating up to approximately four billion years ago. Despite considerable sequence differences compared with extant enzymes, the ancestral proteins display the canonical thioredoxin fold, whereas only small structural changes have occurred over four billion years. This remarkable degree of structure conservation since a time near the last common ancestor of life supports a punctuated-equilibrium model of structure evolution in which the generation of new folds occurs over comparatively short periods and is followed by long periods of structural stasis. PMID:23932589

  9. Proteins comparison through probabilistic optimal structure local alignment

    PubMed Central

    Micale, Giovanni; Pulvirenti, Alfredo; Giugno, Rosalba; Ferro, Alfredo

    2014-01-01

    Multiple local structure comparison helps to identify common structural motifs or conserved binding sites in 3D structures in distantly related proteins. Since there is no best way to compare structures and evaluate the alignment, a wide variety of techniques and different similarity scoring schemes have been proposed. Existing algorithms usually compute the best superposition of two structures or attempt to solve it as an optimization problem in a simpler setting (e.g., considering contact maps or distance matrices). Here, we present PROPOSAL (PROteins comparison through Probabilistic Optimal Structure local ALignment), a stochastic algorithm based on iterative sampling for multiple local alignment of protein structures. Our method can efficiently find conserved motifs across a set of protein structures. Only the distances between all pairs of residues in the structures are computed. To show the accuracy and the effectiveness of PROPOSAL we tested it on a few families of protein structures. We also compared PROPOSAL with two state-of-the-art tools for pairwise local alignment on a dataset of manually annotated motifs. PROPOSAL is available as a Java 2D standalone application or a command line program at http://ferrolab.dmi.unict.it/proposal/proposal.html. PMID:25228906

  10. Structure characterization of protein fractions from lotus ( Nelumbo nucifera) seed

    NASA Astrophysics Data System (ADS)

    Zeng, Hong-Yan; Cai, Lian-Hui; Cai, Xi-Ling; Wang, Ya-Ju; Li, Yu-Qin

    2011-08-01

    Protein fractionation of lotus seed was carried out and the structures of the protein fractions were studied. Fourier transform infrared spectroscopy (FTIR) as well as ultraviolet visible spectroscopy (UV-vis) was used to investigate changes in molecular structures of the protein fractions. FTIR and UV-vis spectra showed the protein fractions had different protein molecular structures. FTIR spectra showed β-sheets and β-turns as the major secondary structures in the individual protein fractions, while the amounts of α-helix and random coil structures among the different fractions did not significantly change. The amounts of β-sheet structures of albumin and globulin were significantly higher than ones of prolamin and glutelin, implying albumin and globulin had high stabilities because of the high content in β-sheet structures. The observed similarity in the amounts of α-helix, random coil, β-sheet and β-turn structures shared by albumin and globulin indicated that their interior conformations were similar.

  11. Sequence and structural analysis of BTB domain proteins

    PubMed Central

    Stogios, Peter J; Downs, Gregory S; Jauhal, Jimmy JS; Nandra, Sukhjeen K; Privé, Gilbert G

    2005-01-01

    Background The BTB domain (also known as the POZ domain) is a versatile protein-protein interaction motif that participates in a wide range of cellular functions, including transcriptional regulation, cytoskeleton dynamics, ion channel assembly and gating, and targeting proteins for ubiquitination. Several BTB domain structures have been experimentally determined, revealing a highly conserved core structure. Results We surveyed the protein architecture, genomic distribution and sequence conservation of BTB domain proteins in 17 fully sequenced eukaryotes. The BTB domain is typically found as a single copy in proteins that contain only one or two other types of domain, and this defines the BTB-zinc finger (BTB-ZF), BTB-BACK-kelch (BBK), voltage-gated potassium channel T1 (T1-Kv), MATH-BTB, BTB-NPH3 and BTB-BACK-PHR (BBP) families of proteins, among others. In contrast, the Skp1 and ElonginC proteins consist almost exclusively of the core BTB fold. There are numerous lineage-specific expansions of BTB proteins, as seen by the relatively large number of BTB-ZF and BBK proteins in vertebrates, MATH-BTB proteins in Caenorhabditis elegans, and BTB-NPH3 proteins in Arabidopsis thaliana. Using the structural homology between Skp1 and the PLZF BTB homodimer, we present a model of a BTB-Cul3 SCF-like E3 ubiquitin ligase complex that shows that the BTB dimer or the T1 tetramer is compatible in this complex. Conclusion Despite widely divergent sequences, the BTB fold is structurally well conserved. The fold has adapted to several different modes of self-association and interactions with non-BTB proteins. PMID:16207353

  12. Structural study of surfactant-dependent interaction with protein

    SciTech Connect

    Mehan, Sumit; Aswal, Vinod K.; Kohlbrecher, Joachim

    2015-06-24

    Small-angle neutron scattering (SANS) has been used to study the complex structure of anionic BSA protein with three different (cationic DTAB, anionic SDS and non-ionic C12E10) surfactants. These systems form very different surfactant-dependent complexes. We show that the structure of protein-surfactant complex is initiated by the site-specific electrostatic interaction between the components, followed by the hydrophobic interaction at high surfactant concentrations. It is also found that hydrophobic interaction is preferred over the electrostatic interaction in deciding the resultant structure of protein-surfactant complexes.

  13. Accuracy of functional surfaces on comparatively modeled protein structures

    PubMed Central

    Zhao, Jieling; Dundas, Joe; Kachalo, Sema; Ouyang, Zheng; Liang, Jie

    2012-01-01

    Identification and characterization of protein functional surfaces are important for predicting protein function, understanding enzyme mechanism, and docking small compounds to proteins. As the rapid speed of accumulation of protein sequence information far exceeds that of structures, constructing accurate models of protein functional surfaces and identify their key elements become increasingly important. A promising approach is to build comparative models from sequences using known structural templates such as those obtained from structural genome projects. Here we assess how well this approach works in modeling binding surfaces. By systematically building three-dimensional comparative models of proteins using Modeller, we determine how well functional surfaces can be accurately reproduced. We use an alpha shape based pocket algorithm to compute all pockets on the modeled structures, and conduct a large-scale computation of similarity measurements (pocket RMSD and fraction of functional atoms captured) for 26,590 modeled enzyme protein structures. Overall, we find that when the sequence fragment of the binding surfaces has more than 45% identity to that of the tempalte protein, the modeled surfaces have on average an RMSD of 0.5 Å, and contain 48% or more of the binding surface atoms, with nearly all of the important atoms in the signatures of binding pockets captured. PMID:21541664

  14. NMR Structures of Membrane Proteins in Phospholipid Bilayers

    PubMed Central

    Radoicic, Jasmina; Lu, George J.; Opella, Stanley J.

    2014-01-01

    Membrane proteins have always presented technical challenges for structural studies because of their requirement for a lipid environment. Multiple approaches exist including X-ray crystallography and electron microscopy that can give significant insights into their structure and function. However, nuclear magnetic resonance (NMR) is unique in that it offers the possibility of determining the structures of unmodified membrane proteins in their native environment of phospholipid bilayers under physiological conditions. Furthermore, NMR enables the characterization of the structure and dynamics of backbone and side chain sites of the proteins alone and in complexes with both small molecules and other biopolymers. The learning curve has been steep for the field as most initial studies were performed under non-native environments using modified proteins until ultimately progress in both techniques and instrumentation led to the possibility of examining unmodified membrane proteins in phospholipid bilayers under physiological conditions. This review aims to provide an overview of the development and application of NMR to membrane proteins. It highlights some of the most significant structural milestones that have been reached by NMR spectroscopy of membrane proteins; especially those accomplished with the proteins in phospholipid bilayer environments where they function. PMID:25032938

  15. How Rab proteins determine Golgi structure.

    PubMed

    Liu, Shijie; Storrie, Brian

    2015-01-01

    Rab proteins, small GTPases, are key regulators of mammalian Golgi apparatus organization. Based on the effect of Rab activation state, Rab proteins fall into two functional classes. In Class1, inactivation induces Golgi ribbon fragmentation and/or redistribution of Golgi enzymes to the Endoplasmic Reticulum, while overexpression of wild type or activation has little, if any, effect on Golgi ribbon organization. In Class 2, the reverse is true. We give emphasis to Rab6, the most abundant Golgi-associated Rab protein. Rab6 depletion in HeLa cells causes an increase in Golgi cisternal number, longer, more continuous cisternae, and a pronounced accumulation of vesicles; the effect of Rab6 on Golgi ribbon organization is probably through regulation of vesicle transport. In effector studies, motor proteins and their regulators are found to be key Rab6 effectors. A related Rab, Rab41, affects Golgi ribbon organization in a contrasting manner. The balance between minus- and plus-end directed motor recruitment may well be the major Rab-dependent factor in Golgi ribbon organization. PMID:25708460

  16. A Dominant Factor for Structural Classification of Protein Crystals.

    PubMed

    Qi, Fei; Fudo, Satoshi; Neya, Saburo; Hoshino, Tyuji

    2015-08-24

    With the increasing number of solved protein crystal structures, much information on protein shape and atom geometry has become available. It is of great interest to know the structural diversity for a single kind of protein. Our preliminary study suggested that multiple crystal structures of a single kind of protein can be classified into several groups from the viewpoint of structural similarity. In order to broadly examine this finding, cluster analysis was applied to the crystal structures of hemoglobin (Hb), myoglobin (Mb), human serum albumin (HSA), hen egg-white lysozyme (HEWL), and human immunodeficiency virus type 1 protease (HIV-1 PR), downloaded from the Protein Data Bank (PDB). As a result of classification by cluster analysis, 146 crystal structures of Hb were separated into five groups. The crystal structures of Mb (n = 284), HEWL (n = 336), HSA (n = 63), and HIV-1 PR (n = 488) were separated into six, five, three, and six groups, respectively. It was found that a major factor causing these structural separations is the space group of crystals and that crystallizing agents have an influence on the crystal structures. Amino acid mutation is a minor factor for the separation because no obvious point mutation making a specific cluster group was observed for the five kinds of proteins. In the classification of Hb and Mb, the species of protein source such as humans, rabbits, and mice is another significant factor. When the difference in amino sequence is large among species, the species of protein source is the primary factor causing cluster separation in the classification of crystal structures. PMID:26230289

  17. Protein structure determination by exhaustive search of Protein Data Bank derived databases

    PubMed Central

    Stokes-Rees, Ian; Sliz, Piotr

    2010-01-01

    Parallel sequence and structure alignment tools have become ubiquitous and invaluable at all levels in the study of biological systems. We demonstrate the application and utility of this same parallel search paradigm to the process of protein structure determination, benefitting from the large and growing corpus of known structures. Such searches were previously computationally intractable. Through the method of Wide Search Molecular Replacement, developed here, they can be completed in a few hours with the aide of national-scale federated cyberinfrastructure. By dramatically expanding the range of models considered for structure determination, we show that small (less than 12% structural coverage) and low sequence identity (less than 20% identity) template structures can be identified through multidimensional template scoring metrics and used for structure determination. Many new macromolecular complexes can benefit significantly from such a technique due to the lack of known homologous protein folds or sequences. We demonstrate the effectiveness of the method by determining the structure of a full-length p97 homologue from Trichoplusia ni. Example cases with the MHC/T-cell receptor complex and the EmoB protein provide systematic estimates of minimum sequence identity, structure coverage, and structural similarity required for this method to succeed. We describe how this structure-search approach and other novel computationally intensive workflows are made tractable through integration with the US national computational cyberinfrastructure, allowing, for example, rapid processing of the entire Structural Classification of Proteins protein fragment database. PMID:21098306

  18. Protein structure determination by exhaustive search of Protein Data Bank derived databases.

    PubMed

    Stokes-Rees, Ian; Sliz, Piotr

    2010-12-14

    Parallel sequence and structure alignment tools have become ubiquitous and invaluable at all levels in the study of biological systems. We demonstrate the application and utility of this same parallel search paradigm to the process of protein structure determination, benefitting from the large and growing corpus of known structures. Such searches were previously computationally intractable. Through the method of Wide Search Molecular Replacement, developed here, they can be completed in a few hours with the aide of national-scale federated cyberinfrastructure. By dramatically expanding the range of models considered for structure determination, we show that small (less than 12% structural coverage) and low sequence identity (less than 20% identity) template structures can be identified through multidimensional template scoring metrics and used for structure determination. Many new macromolecular complexes can benefit significantly from such a technique due to the lack of known homologous protein folds or sequences. We demonstrate the effectiveness of the method by determining the structure of a full-length p97 homologue from Trichoplusia ni. Example cases with the MHC/T-cell receptor complex and the EmoB protein provide systematic estimates of minimum sequence identity, structure coverage, and structural similarity required for this method to succeed. We describe how this structure-search approach and other novel computationally intensive workflows are made tractable through integration with the US national computational cyberinfrastructure, allowing, for example, rapid processing of the entire Structural Classification of Proteins protein fragment database. PMID:21098306

  19. ArchDB 2014: structural classification of loops in proteins

    PubMed Central

    Bonet, Jaume; Planas-Iglesias, Joan; Garcia-Garcia, Javier; Marín-López, Manuel A.; Fernandez-Fuentes, Narcis; Oliva, Baldo

    2014-01-01

    The function of a protein is determined by its three-dimensional structure, which is formed by regular (i.e. β-strands and α-helices) and non-periodic structural units such as loops. Compared to regular structural elements, non-periodic, non-repetitive conformational units enclose a much higher degree of variability—raising difficulties in the identification of regularities, and yet represent an important part of the structure of a protein. Indeed, loops often play a pivotal role in the function of a protein and different aspects of protein folding and dynamics. Therefore, the structural classification of protein loops is an important subject with clear applications in homology modelling, protein structure prediction, protein design (e.g. enzyme design and catalytic loops) and function prediction. ArchDB, the database presented here (freely available at http://sbi.imim.es/archdb), represents such a resource and has been an important asset for the scientific community throughout the years. In this article, we present a completely reworked and updated version of ArchDB. The new version of ArchDB features a novel, fast and user-friendly web-based interface, and a novel graph-based, computationally efficient, clustering algorithm. The current version of ArchDB classifies 149,134 loops in 5739 classes and 9608 subclasses. PMID:24265221

  20. Structural changes in gluten protein structure after addition of emulsifier. A Raman spectroscopy study

    NASA Astrophysics Data System (ADS)

    Ferrer, Evelina G.; Gómez, Analía V.; Añón, María C.; Puppo, María C.

    2011-06-01

    Food protein product, gluten protein, was chemically modified by varying levels of sodium stearoyl lactylate (SSL); and the extent of modifications (secondary and tertiary structures) of this protein was analyzed by using Raman spectroscopy. Analysis of the Amide I band showed an increase in its intensity mainly after the addition of the 0.25% of SSL to wheat flour to produced modified gluten protein, pointing the formation of a more ordered structure. Side chain vibrations also confirmed the observed changes.

  1. Protein Structure and Stability in Neat Ionic Liquid

    NASA Astrophysics Data System (ADS)

    Bihari, Malvika; Russell, Thomas P.; Hoagland, David A.

    2010-03-01

    Ionic liquid (IL) as a medium for room temperature preservation of biomacromolecules has been proposed, and to investigate the possibility, we studied physicochemical and enzymatic properties of several proteins in the neat hydrophilic IL, ethylmethyl imidazolium ethyl sulfate [EMIM][EtSO4]. Molecular dissolution of α-chymotypsin, cytochrome-c and other proteins could be achieved with moderate heating (60C). Dynamic light scattering and dilute solution viscometry typically reveal protein size slightly larger than in buffer, suggesting different solvation or protein unfolding. Spectroscopic methods (UV-Vis, fluorescence, FTIR, CD) show largely unchanged secondary structure but significantly changed tertiary structure. IL-dissolved cytochrome-c has heightened peroxidase activity, supporting the same conclusions. Transfer of dissolved protein from IL to buffer and ensuing alterations to protein conformation/activity will be discussed.

  2. Biological Insights from Structures of Two-Component Proteins

    PubMed Central

    Gao, Rong; Stock, Ann M.

    2013-01-01

    Two-component signal transduction based on phosphotransfer from a histidine protein kinase to a response regulator protein is a prevalent strategy for coupling environmental stimuli to adaptive responses in bacteria. In both histidine kinases and response regulators, modular domains with conserved structures and biochemical activities adopt different conformational states in the presence of stimuli or upon phosphorylation, enabling a diverse array of regulatory mechanisms based on inhibitory and/or activating protein-protein interactions imparted by different domain arrangements. This review summarizes some of the recent structural work that has provided insight to the functioning of bacterial histidine kinases and response regulators. Particular emphasis is placed on identifying features that are expected to be conserved among different two-component proteins from those that are expected to differ, with the goal of defining the extent to which knowledge of previously characterized two-component proteins can be applied to newly discovered systems. PMID:19575571

  3. Drug leads for interactive protein targets with unknown structure.

    PubMed

    Fernández, Ariel; Scott, L Ridgway

    2016-04-01

    The disruption of protein-protein interfaces (PPIs) remains a challenge in drug discovery. The problem becomes daunting when the structure of the target protein is unknown and is even further complicated when the interface is susceptible to disruptive phosphorylation. Based solely on protein sequence and information about phosphorylation-susceptible sites within the PPI, a new technology has been developed to identify drug leads to inhibit protein associations. Here we reveal this technology and contrast it with current structure-based technologies for the generation of drug leads. The novel technology is illustrated by a patented invention to treat heart failure. The success of this technology shows that it is possible to generate drug leads in the absence of target structure. PMID:26484433

  4. A novel method to compare protein structures using local descriptors

    PubMed Central

    2011-01-01

    Background Protein structure comparison is one of the most widely performed tasks in bioinformatics. However, currently used methods have problems with the so-called "difficult similarities", including considerable shifts and distortions of structure, sequential swaps and circular permutations. There is a demand for efficient and automated systems capable of overcoming these difficulties, which may lead to the discovery of previously unknown structural relationships. Results We present a novel method for protein structure comparison based on the formalism of local descriptors of protein structure - DEscriptor Defined Alignment (DEDAL). Local similarities identified by pairs of similar descriptors are extended into global structural alignments. We demonstrate the method's capability by aligning structures in difficult benchmark sets: curated alignments in the SISYPHUS database, as well as SISY and RIPC sets, including non-sequential and non-rigid-body alignments. On the most difficult RIPC set of sequence alignment pairs the method achieves an accuracy of 77% (the second best method tested achieves 60% accuracy). Conclusions DEDAL is fast enough to be used in whole proteome applications, and by lowering the threshold of detectable structure similarity it may shed additional light on molecular evolution processes. It is well suited to improving automatic classification of structure domains, helping analyze protein fold space, or to improving protein classification schemes. DEDAL is available online at http://bioexploratorium.pl/EP/DEDAL. PMID:21849047

  5. MEGADOCK: an all-to-all protein-protein interaction prediction system using tertiary structure data.

    PubMed

    Ohue, Masahito; Matsuzaki, Yuri; Uchikoga, Nobuyuki; Ishida, Takashi; Akiyama, Yutaka

    2014-01-01

    The elucidation of protein-protein interaction (PPI) networks is important for understanding cellular structure and function and structure-based drug design. However, the development of an effective method to conduct exhaustive PPI screening represents a computational challenge. We have been investigating a protein docking approach based on shape complementarity and physicochemical properties. We describe here the development of the protein-protein docking software package "MEGADOCK" that samples an extremely large number of protein dockings at high speed. MEGADOCK reduces the calculation time required for docking by using several techniques such as a novel scoring function called the real Pairwise Shape Complementarity (rPSC) score. We showed that MEGADOCK is capable of exhaustive PPI screening by completing docking calculations 7.5 times faster than the conventional docking software, ZDOCK, while maintaining an acceptable level of accuracy. When MEGADOCK was applied to a subset of a general benchmark dataset to predict 120 relevant interacting pairs from 120 x 120 = 14,400 combinations of proteins, an F-measure value of 0.231 was obtained. Further, we showed that MEGADOCK can be applied to a large-scale protein-protein interaction-screening problem with accuracy better than random. When our approach is combined with parallel high-performance computing systems, it is now feasible to search and analyze protein-protein interactions while taking into account three-dimensional structures at the interactome scale. MEGADOCK is freely available at http://www.bi.cs.titech.ac.jp/megadock. PMID:23855673

  6. Bioinformatics and variability in drug response: a protein structural perspective

    PubMed Central

    Lahti, Jennifer L.; Tang, Grace W.; Capriotti, Emidio; Liu, Tianyun; Altman, Russ B.

    2012-01-01

    Marketed drugs frequently perform worse in clinical practice than in the clinical trials on which their approval is based. Many therapeutic compounds are ineffective for a large subpopulation of patients to whom they are prescribed; worse, a significant fraction of patients experience adverse effects more severe than anticipated. The unacceptable risk–benefit profile for many drugs mandates a paradigm shift towards personalized medicine. However, prior to adoption of patient-specific approaches, it is useful to understand the molecular details underlying variable drug response among diverse patient populations. Over the past decade, progress in structural genomics led to an explosion of available three-dimensional structures of drug target proteins while efforts in pharmacogenetics offered insights into polymorphisms correlated with differential therapeutic outcomes. Together these advances provide the opportunity to examine how altered protein structures arising from genetic differences affect protein–drug interactions and, ultimately, drug response. In this review, we first summarize structural characteristics of protein targets and common mechanisms of drug interactions. Next, we describe the impact of coding mutations on protein structures and drug response. Finally, we highlight tools for analysing protein structures and protein–drug interactions and discuss their application for understanding altered drug responses associated with protein structural variants. PMID:22552919

  7. Structural and functional properties of hemp seed protein products.

    PubMed

    Malomo, Sunday A; He, Rong; Aluko, Rotimi E

    2014-08-01

    The effects of pH and protein concentration on some structural and functional properties of hemp seed protein isolate (HPI, 84.15% protein content) and defatted hemp seed protein meal (HPM, 44.32% protein content) were determined. The HPI had minimum protein solubility (PS) at pH 4.0, which increased as pH was decreased or increased. In contrast, the HPM had minimum PS at pH 3.0, which increased at higher pH values. Gel electrophoresis showed that some of the high molecular weight proteins (>45 kDa) present in HPM were not well extracted by the alkali and were absent or present in low ratio in the HPI polypeptide profile. The amino acid composition showed that the isolation process increased the Arg/Lys ratio of HPI (5.52%) when compared to HPM (3.35%). Intrinsic fluorescence and circular dichroism data indicate that the HPI proteins had a well-defined structure at pH 3.0, which was lost as pH value increased. The differences in structural conformation of HPI at different pH values were reflected as better foaming capacity at pH 3.0 when compared to pH 5.0, 7.0, and 9.0. At 10 and 25 mg/mL protein concentrations, emulsions formed by the HPM had smaller oil droplet sizes (higher quality), when compared to the HPI-formed emulsions. In contrast at 50 mg/mL protein concentration, the HPI-formed emulsions had smaller oil droplet sizes (except at pH 3.0). We conclude that the functional properties of hemp seed protein products are dependent on structural conformations as well as protein concentration and pH. PMID:25048774

  8. Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction

    NASA Astrophysics Data System (ADS)

    Lipska, Agnieszka G.; Seidman, Steven R.; Sieradzan, Adam K.; Giełdoń, Artur; Liwo, Adam; Scheraga, Harold A.

    2016-05-01

    The folding of the N-terminal part of the B-domain of staphylococcal protein A (PDB ID: 1BDD, a 46-residue three-α-helix bundle) and the formin-binding protein 28 WW domain (PDB ID: 1E0L, a 37-residue three-stranded anti-parallel β protein) was studied by means of Langevin dynamics with the coarse-grained UNRES force field to assess the influence of hydrodynamic interactions on protein-folding pathways and kinetics. The unfolded, intermediate, and native-like structures were identified by cluster analysis, and multi-exponential functions were fitted to the time dependence of the fractions of native and intermediate structures, respectively, to determine bulk kinetics. It was found that introducing hydrodynamic interactions slows down both the formation of an intermediate state and the transition from the collapsed structures to the final native-like structures by creating multiple kinetic traps. Therefore, introducing hydrodynamic interactions considerably slows the folding, as opposed to the results obtained from earlier studies with the use of Gō-like models.

  9. Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction.

    PubMed

    Lipska, Agnieszka G; Seidman, Steven R; Sieradzan, Adam K; Giełdoń, Artur; Liwo, Adam; Scheraga, Harold A

    2016-05-14

    The folding of the N-terminal part of the B-domain of staphylococcal protein A (PDB ID: 1BDD, a 46-residue three-α-helix bundle) and the formin-binding protein 28 WW domain (PDB ID: 1E0L, a 37-residue three-stranded anti-parallel β protein) was studied by means of Langevin dynamics with the coarse-grained UNRES force field to assess the influence of hydrodynamic interactions on protein-folding pathways and kinetics. The unfolded, intermediate, and native-like structures were identified by cluster analysis, and multi-exponential functions were fitted to the time dependence of the fractions of native and intermediate structures, respectively, to determine bulk kinetics. It was found that introducing hydrodynamic interactions slows down both the formation of an intermediate state and the transition from the collapsed structures to the final native-like structures by creating multiple kinetic traps. Therefore, introducing hydrodynamic interactions considerably slows the folding, as opposed to the results obtained from earlier studies with the use of Gō-like models. PMID:27179474

  10. The Use of Experimental Structures to Model Protein Dynamics

    PubMed Central

    Katebi, Ataur R.; Sankar, Kannan; Jia, Kejue; Jernigan, Robert L.

    2014-01-01

    Summary The number of solved protein structures submitted in the Protein Data Bank (PDB) has increased dramatically in recent years. For some specific proteins, this number is very high – for example, there are over 550 solved structures for HIV-1 protease, one protein that is essential for the life cycle of human immunodeficiency virus (HIV) which causes acquired immunodeficiency syndrome (AIDS) in humans. The large number of structures for the same protein and its variants include a sample of different conformational states of the protein. A rich set of structures solved experimentally for the same protein has information buried within the dataset that can explain the functional dynamics and structural mechanism of the protein. To extract the dynamics information and functional mechanism from the experimental structures, this chapter focuses on two methods – Principal Component Analysis (PCA) and Elastic Network Models (ENM). PCA is a widely used statistical dimensionality reduction technique to classify and visualize high-dimensional data. On the other hand, ENMs are well-established simple biophysical method for modeling the functionally important global motions of proteins. This chapter covers the basics of these two. Moreover, an improved ENM version that utilizes the variations found within a given set of structures for a protein is described. As a practical example, we have extracted the functional dynamics and mechanism of HIV-1 protease dimeric structure by using a set of 329 PDB structures of this protein. We have described, step by step, how to select a set of protein structures, how to extract the needed information from the PDB files for PCA, how to extract the dynamics information using PCA, how to calculate ENM modes, how to measure the congruency between the dynamics computed from the principal components (PCs) and the ENM modes, and how to compute entropies using the PCs. We provide the computer programs or references to software tools to

  11. Potato leafroll virus structural proteins manipulate overlapping, yet distinct protein interaction networks during infection.

    PubMed

    DeBlasio, Stacy L; Johnson, Richard; Sweeney, Michelle M; Karasev, Alexander; Gray, Stewart M; MacCoss, Michael J; Cilia, Michelle

    2015-06-01

    Potato leafroll virus (PLRV) produces a readthrough protein (RTP) via translational readthrough of the coat protein amber stop codon. The RTP functions as a structural component of the virion and as a nonincorporated protein in concert with numerous insect and plant proteins to regulate virus movement/transmission and tissue tropism. Affinity purification coupled to quantitative MS was used to generate protein interaction networks for a PLRV mutant that is unable to produce the read through domain (RTD) and compared to the known wild-type PLRV protein interaction network. By quantifying differences in the protein interaction networks, we identified four distinct classes of PLRV-plant interactions: those plant and nonstructural viral proteins interacting with assembled coat protein (category I); plant proteins in complex with both coat protein and RTD (category II); plant proteins in complex with the RTD (category III); and plant proteins that had higher affinity for virions lacking the RTD (category IV). Proteins identified as interacting with the RTD are potential candidates for regulating viral processes that are mediated by the RTP such as phloem retention and systemic movement and can potentially be useful targets for the development of strategies to prevent infection and/or viral transmission of Luteoviridae species that infect important crop species. PMID:25787689

  12. Structural studies of human glioma pathogenesis-related protein 1

    SciTech Connect

    Asojo, Oluwatoyin A.; Koski, Raymond A.; Bonafé, Nathalie

    2011-10-01

    Structural analysis of a truncated soluble domain of human glioma pathogenesis-related protein 1, a membrane protein implicated in the proliferation of aggressive brain cancer, is presented. Human glioma pathogenesis-related protein 1 (GLIPR1) is a membrane protein that is highly upregulated in brain cancers but is barely detectable in normal brain tissue. GLIPR1 is composed of a signal peptide that directs its secretion, a conserved cysteine-rich CAP (cysteine-rich secretory proteins, antigen 5 and pathogenesis-related 1 proteins) domain and a transmembrane domain. GLIPR1 is currently being investigated as a candidate for prostate cancer gene therapy and for glioblastoma targeted therapy. Crystal structures of a truncated soluble domain of the human GLIPR1 protein (sGLIPR1) solved by molecular replacement using a truncated polyalanine search model of the CAP domain of stecrisp, a snake-venom cysteine-rich secretory protein (CRISP), are presented. The correct molecular-replacement solution could only be obtained by removing all loops from the search model. The native structure was refined to 1.85 Å resolution and that of a Zn{sup 2+} complex was refined to 2.2 Å resolution. The latter structure revealed that the putative binding cavity coordinates Zn{sup 2+} similarly to snake-venom CRISPs, which are involved in Zn{sup 2+}-dependent mechanisms of inflammatory modulation. Both sGLIPR1 structures have extensive flexible loop/turn regions and unique charge distributions that were not observed in any of the previously reported CAP protein structures. A model is also proposed for the structure of full-length membrane-bound GLIPR1.

  13. Vertebrate Membrane Proteins: Structure, Function, and Insights from Biophysical Approaches

    PubMed Central

    MÜLLER, DANIEL J.; WU, NAN; PALCZEWSKI, KRZYSZTOF

    2008-01-01

    Membrane proteins are key targets for pharmacological intervention because they are vital for cellular function. Here, we analyze recent progress made in the understanding of the structure and function of membrane proteins with a focus on rhodopsin and development of atomic force microscopy techniques to study biological membranes. Membrane proteins are compartmentalized to carry out extra- and intracellular processes. Biological membranes are densely populated with membrane proteins that occupy approximately 50% of their volume. In most cases membranes contain lipid rafts, protein patches, or paracrystalline formations that lack the higher-order symmetry that would allow them to be characterized by diffraction methods. Despite many technical difficulties, several crystal structures of membrane proteins that illustrate their internal structural organization have been determined. Moreover, high-resolution atomic force microscopy, near-field scanning optical microscopy, and other lower resolution techniques have been used to investigate these structures. Single-molecule force spectroscopy tracks interactions that stabilize membrane proteins and those that switch their functional state; this spectroscopy can be applied to locate a ligand-binding site. Recent development of this technique also reveals the energy landscape of a membrane protein, defining its folding, reaction pathways, and kinetics. Future development and application of novel approaches during the coming years should provide even greater insights to the understanding of biological membrane organization and function. PMID:18321962

  14. Crystal structures of fusion proteins with large-affinity tags.

    PubMed

    Smyth, Douglas R; Mrozkiewicz, Marek K; McGrath, William J; Listwan, Pawel; Kobe, Bostjan

    2003-07-01

    The fusion of a protein of interest to a large-affinity tag, such as the maltose-binding protein (MBP), thioredoxin (TRX), or glutathione-S-transferase (GST), can be advantageous in terms of increased expression, enhanced solubility, protection from proteolysis, improved folding, and protein purification via affinity chromatography. Unfortunately, crystal growth is hindered by the conformational heterogeneity induced by the fusion tag, requiring that the tag is removed by a potentially problematic cleavage step. The first three crystal structures of fusion proteins with large-affinity tags have been reported recently. All three structures used a novel strategy to rigidly fuse the protein of interest to MBP via a short three- to five-amino acid spacer. This strategy has the potential to aid structure determination of proteins that present particular experimental challenges and are not conducive to more conventional crystallization strategies (e.g., membrane proteins). Structural genomics initiatives may also benefit from this approach as a way to crystallize problematic proteins of significant interest. PMID:12824478

  15. Structural Similarity and Classification of Protein Interaction Interfaces

    PubMed Central

    Zhao, Nan; Pang, Bin; Shyu, Chi-Ren; Korkin, Dmitry

    2011-01-01

    Interactions between proteins play a key role in many cellular processes. Studying protein-protein interactions that share similar interaction interfaces may shed light on their evolution and could be helpful in elucidating the mechanisms behind stability and dynamics of the protein complexes. When two complexes share structurally similar subunits, the similarity of the interaction interfaces can be found through a structural superposition of the subunits. However, an accurate detection of similarity between the protein complexes containing subunits of unrelated structure remains an open problem. Here, we present an alignment-free machine learning approach to measure interface similarity. The approach relies on the feature-based representation of protein interfaces and does not depend on the superposition of the interacting subunit pairs. Specifically, we develop an SVM classifier of similar and dissimilar interfaces and derive a feature-based interface similarity measure. Next, the similarity measure is applied to a set of 2,806×2,806 binary complex pairs to build a hierarchical classification of protein-protein interactions. Finally, we explore case studies of similar interfaces from each level of the hierarchy, considering cases when the subunits forming interactions are either homologous or structurally unrelated. The analysis has suggested that the positions of charged residues in the homologous interfaces are not necessarily conserved and may exhibit more complex conservation patterns. PMID:21589874

  16. A physical approach to protein structure prediction: CASP4 results

    SciTech Connect

    Crivelli, Silvia; Eskow, Elizabeth; Bader, Brett; Lamberti, Vincent; Byrd, Richard; Schnabel, Robert; Head-Gordon, Teresa

    2001-02-27

    We describe our global optimization method called Stochastic Perturbation with Soft Constraints (SPSC), which uses information from known proteins to predict secondary structure, but not in the tertiary structure predictions or in generating the terms of the physics-based energy function. Our approach is also characterized by the use of an all atom energy function that includes a novel hydrophobic solvation function derived from experiments that shows promising ability for energy discrimination against misfolded structures. We present the results obtained using our SPSC method and energy function for blind prediction in the 4th Critical Assessment of Techniques for Protein Structure Prediction (CASP4) competition, and show that our approach is more effective on targets for which less information from known proteins is available. In fact our SPSC method produced the best prediction for one of the most difficult targets of the competition, a new fold protein of 240 amino acids.

  17. An object-oriented database for protein structure analysis.

    PubMed

    Gray, P M; Paton, N W; Kemp, G J; Fothergill, J E

    1990-03-01

    An object-oriented database system has been developed which is being used to store protein structure data. The database can be queried using the logic programming language Prolog or the query language Daplex. Queries retrieve information by navigating through a network of objects which represent the primary, secondary and tertiary structures of proteins. Routines written in both Prolog and Daplex can integrate complex calculations with the retrieval of data from the database, and can also be stored in the database for sharing among users. Thus object-oriented databases are better suited to prototyping applications and answering complex queries about protein structure than relational databases. This system has been used to find loops of varying length and anchor positions when modelling homologous protein structures. PMID:2188261

  18. Bovine parotid secretory protein: structure, expression and relatedness to other BPI (bactericidal/permeability-increasing protein)-like proteins.

    PubMed

    Wheeler, T T; Hood, K; Oden, K; McCracken, J; Morris, C A

    2003-08-01

    Members of the family of BPI (bactericidal/permeability-increasing protein)-like proteins are as yet incompletely characterized, particularly in cattle, where full-length sequence information is available for only three of the 13 family members known from other species. Structural bioinformatic analyses incorporating bovine homologues of several members of the BPI-like protein family, including two forms of bovine parotid secretory protein (PSP), showed that this family is also present in cattle. Expression analyses of several members of the BPI-like protein family in cattle, including PSP (Bsp30), von Ebner's minor salivary gland protein (VEMSGP) and lung-specific X protein (LUNX), showed a restricted pattern of expression, consistent with earlier hypotheses that these proteins function in the innate immune response to bacteria. The possible role of bovine PSP in susceptibility to pasture bloat in cattle is discussed. PMID:12887305

  19. Meeting Report: Structural Determination of Environmentally Responsive Proteins

    PubMed Central

    Reinlib, Leslie

    2005-01-01

    The three-dimensional structure of gene products continues to be a missing lynchpin between linear genome sequences and our understanding of the normal and abnormal function of proteins and pathways. Enhanced activity in this area is likely to lead to better understanding of how discrete changes in molecular patterns and conformation underlie functional changes in protein complexes and, with it, sensitivity of an individual to an exposure. The National Institute of Environmental Health Sciences convened a workshop of experts in structural determination and environmental health to solicit advice for future research in structural resolution relative to environmentally responsive proteins and pathways. The highest priorities recommended by the workshop were to support studies of structure, analysis, control, and design of conformational and functional states at molecular resolution for environmentally responsive molecules and complexes; promote understanding of dynamics, kinetics, and ligand responses; investigate the mechanisms and steps in posttranslational modifications, protein partnering, impact of genetic polymorphisms on structure/function, and ligand interactions; and encourage integrated experimental and computational approaches. The workshop participants also saw value in improving the throughput and purity of protein samples and macromolecular assemblies; developing optimal processes for design, production, and assembly of macromolecular complexes; encouraging studies on protein–protein and macromolecular interactions; and examining assemblies of individual proteins and their functions in pathways of interest for environmental health. PMID:16263521

  20. Defining and predicting structurally conserved regions in protein superfamilies

    PubMed Central

    Huang, Ivan K.; Grishin, Nick V.

    2013-01-01

    Motivation: The structures of homologous proteins are generally better conserved than their sequences. This phenomenon is demonstrated by the prevalence of structurally conserved regions (SCRs) even in highly divergent protein families. Defining SCRs requires the comparison of two or more homologous structures and is affected by their availability and divergence, and our ability to deduce structurally equivalent positions among them. In the absence of multiple homologous structures, it is necessary to predict SCRs of a protein using information from only a set of homologous sequences and (if available) a single structure. Accurate SCR predictions can benefit homology modelling and sequence alignment. Results: Using pairwise DaliLite alignments among a set of homologous structures, we devised a simple measure of structural conservation, termed structural conservation index (SCI). SCI was used to distinguish SCRs from non-SCRs. A database of SCRs was compiled from 386 SCOP superfamilies containing 6489 protein domains. Artificial neural networks were then trained to predict SCRs with various features deduced from a single structure and homologous sequences. Assessment of the predictions via a 5-fold cross-validation method revealed that predictions based on features derived from a single structure perform similarly to ones based on homologous sequences, while combining sequence and structural features was optimal in terms of accuracy (0.755) and Matthews correlation coefficient (0.476). These results suggest that even without information from multiple structures, it is still possible to effectively predict SCRs for a protein. Finally, inspection of the structures with the worst predictions pinpoints difficulties in SCR definitions. Availability: The SCR database and the prediction server can be found at http://prodata.swmed.edu/SCR. Contact: 91huangi@gmail.com or grishin@chop.swmed.edu Supplementary information: Supplementary data are available at Bioinformatics

  1. Structural protein 4.1 is located in mammalian centrosomes

    SciTech Connect

    Krauss, S.W.; Chasis, J.A.; Rogers, C.; Mohandas, N.; Krockmalnic, G.; Penman, S.

    1997-07-01

    Structural protein 4.1 was first characterized as an important 80-kDa protein in the mature red cell membrane skeleton. It is now known to be a member of a family of protein isoforms detected at diverse intracellular sites in many nucleated mammalian cells. We recently reported that protein 4.1 isoforms are present at interphase in nuclear matrix and are rearranged during the cell cycle. Here we report that protein 4.1 epitopes are present in centrosomes of human and murine cells and are detected by using affinity-purified antibodies specific for 80-kDa red cell 4.1 and for 4.1 peptides. Immunofluorescence, by both conventional and confocal microscopy, showed that protein 4.1 epitopes localized in the pericentriolar region. Protein 4.1 epitopes remained in centrosomes after extraction of cells with detergent, salt, and DNase. Higher resolution electron microscopy of detergent-extracted cell whole mounts showed centrosomal protein 4.1 epitopes distributed along centriolar cylinders and on pericentriolar fibers, at least some of which constitute the filamentous network surrounding each centriole. Double-label electron microscopy showed that protein 4.1 epitopes were predominantly localized in regions also occupied by epitopes for centrosome-specific autoimmune serum 5051 but were not found on microtubules. Our results suggest that protein 4.1 is an integral component of centrosome structure, in which it may play an important role in centrosome function during cell division and organization of cellular architecture.

  2. Overcoming bottlenecks in the membrane protein structural biology pipeline.

    PubMed

    Hardy, David; Bill, Roslyn M; Jawhari, Anass; Rothnie, Alice J

    2016-06-15

    Membrane proteins account for a third of the eukaryotic proteome, but are greatly under-represented in the Protein Data Bank. Unfortunately, recent technological advances in X-ray crystallography and EM cannot account for the poor solubility and stability of membrane protein samples. A limitation of conventional detergent-based methods is that detergent molecules destabilize membrane proteins, leading to their aggregation. The use of orthologues, mutants and fusion tags has helped improve protein stability, but at the expense of not working with the sequence of interest. Novel detergents such as glucose neopentyl glycol (GNG), maltose neopentyl glycol (MNG) and calixarene-based detergents can improve protein stability without compromising their solubilizing properties. Styrene maleic acid lipid particles (SMALPs) focus on retaining the native lipid bilayer of a membrane protein during purification and biophysical analysis. Overcoming bottlenecks in the membrane protein structural biology pipeline, primarily by maintaining protein stability, will facilitate the elucidation of many more membrane protein structures in the near future. PMID:27284049

  3. Illuminating structural proteins in viral "dark matter" with metaproteomics.

    PubMed

    Brum, Jennifer R; Ignacio-Espinoza, J Cesar; Kim, Eun-Hae; Trubl, Gareth; Jones, Robert M; Roux, Simon; VerBerkmoes, Nathan C; Rich, Virginia I; Sullivan, Matthew B

    2016-03-01

    Viruses are ecologically important, yet environmental virology is limited by dominance of unannotated genomic sequences representing taxonomic and functional "viral dark matter." Although recent analytical advances are rapidly improving taxonomic annotations, identifying functional dark matter remains problematic. Here, we apply paired metaproteomics and dsDNA-targeted metagenomics to identify 1,875 virion-associated proteins from the ocean. Over one-half of these proteins were newly functionally annotated and represent abundant and widespread viral metagenome-derived protein clusters (PCs). One primarily unannotated PC dominated the dataset, but structural modeling and genomic context identified this PC as a previously unidentified capsid protein from multiple uncultivated tailed virus families. Furthermore, four of the five most abundant PCs in the metaproteome represent capsid proteins containing the HK97-like protein fold previously found in many viruses that infect all three domains of life. The dominance of these proteins within our dataset, as well as their global distribution throughout the world's oceans and seas, supports prior hypotheses that this HK97-like protein fold is the most abundant biological structure on Earth. Together, these culture-independent analyses improve virion-associated protein annotations, facilitate the investigation of proteins within natural viral communities, and offer a high-throughput means of illuminating functional viral dark matter. PMID:26884177

  4. Illuminating structural proteins in viral "dark matter" with metaproteomics

    DOE PAGESBeta

    Brum, Jennifer R.; Ignacio-Espinoza, J. Cesar; Kim, Eun -Hae; Trubl, Gareth; Jones, Robert M.; Roux, Simon; Verberkmoes, Nathan C.; Rich, Virginia I.; Sullivan, Matthew B.

    2016-02-16

    Viruses are ecologically important, yet environmental virology is limited by dominance of unannotated genomic sequences representing taxonomic and functional "viral dark matter." Although recent analytical advances are rapidly improving taxonomic annotations, identifying functional darkmatter remains problematic. Here, we apply paired metaproteomics and dsDNA-targeted metagenomics to identify 1,875 virion-associated proteins from the ocean. Over one-half of these proteins were newly functionally annotated and represent abundant and widespread viral metagenome-derived protein clusters (PCs). One primarily unannotated PC dominated the dataset, but structural modeling and genomic context identified this PC as a previously unidentified capsid protein from multiple uncultivated tailed virus families. Furthermore,more » four of the five most abundant PCs in the metaproteome represent capsid proteins containing the HK97-like protein fold previously found in many viruses that infect all three domains of life. The dominance of these proteins within our dataset, as well as their global distribution throughout the world's oceans and seas, supports prior hypotheses that this HK97-like protein fold is the most abundant biological structure on Earth. Altogether, these culture-independent analyses improve virion-associated protein annotations, facilitate the investigation of proteins within natural viral communities, and offer a high-throughput means of illuminating functional viral dark matter.« less

  5. Protein short loop prediction in terms of a structural alphabet.

    PubMed

    Tyagi, Manoj; Bornot, Aurélie; Offmann, Bernard; de Brevern, Alexandre G

    2009-08-01

    Loops connect regular secondary structures. In many instances, they are known to play crucial biological roles. To bypass the limitation of secondary structure description, we previously defined a structural alphabet composed of 16 structural prototypes, called Protein Blocks (PBs). It leads to an accurate description of every region of 3D protein backbones and has been used in local structure prediction. In the present study, we used our structural alphabet to predict the loops connecting two repetitive structures. Thus, we showed interest to take into account the flanking regions, leading to prediction rate improvement up to 19.8%, but we also underline the sensitivity of such an approach. This research can be used to propose different structures for the loops and to probe and sample their flexibility. It is a useful tool for ab initio loop prediction and leads to insights into flexible docking approach. PMID:19625218

  6. Compact structure and proteins of pasta retard in vitro digestive evolution of branched starch molecular structure.

    PubMed

    Zou, Wei; Sissons, Mike; Warren, Frederick J; Gidley, Michael J; Gilbert, Robert G

    2016-11-01

    The roles that the compact structure and proteins in pasta play in retarding evolution of starch molecular structure during in vitro digestion are explored, using four types of cooked samples: whole pasta, pasta powder, semolina (with proteins) and extracted starch without proteins. These were subjected to in vitro digestion with porcine α-amylase, collecting samples at different times and characterizing the weight distribution of branched starch molecules using size-exclusion chromatography. Measurement of α-amylase activity showed that a protein (or proteins) from semolina or pasta powder interacted with α-amylase, causing reduced enzymatic activity and retarding digestion of branched starch molecules with hydrodynamic radius (Rh)<100nm; this protein(s) was susceptible to proteolysis. Thus the compact structure of pasta protects the starch and proteins in the interior of the whole pasta, reducing the enzymatic degradation of starch molecules, especially for molecules with Rh>100nm. PMID:27516291

  7. Conformational changes in redox pairs of protein structures

    PubMed Central

    Fan, Samuel W; George, Richard A; Haworth, Naomi L; Feng, Lina L; Liu, Jason Y; Wouters, Merridee A

    2009-01-01

    Disulfides are conventionally viewed as structurally stabilizing elements in proteins but emerging evidence suggests two disulfide subproteomes exist. One group mediates the well known role of structural stabilization. A second redox-active group are best known for their catalytic functions but are increasingly being recognized for their roles in regulation of protein function. Redox-active disulfides are, by their very nature, more susceptible to reduction than structural disulfides; and conversely, the Cys pairs that form them are more susceptible to oxidation. In this study, we searched for potentially redox-active Cys Pairs by scanning the Protein Data Bank for structures of proteins in alternate redox states. The PDB contains over 1134 unique redox pairs of proteins, many of which exhibit conformational differences between alternate redox states. Several classes of structural changes were observed, proteins that exhibit: disulfide oxidation following expulsion of metals such as zinc; major reorganisation of the polypeptide backbone in association with disulfide redox-activity; order/disorder transitions; and changes in quaternary structure. Based on evidence gathered supporting disulfide redox activity, we propose disulfides present in alternate redox states are likely to have physiologically relevant redox activity. PMID:19598234

  8. Generating folded protein structures with a lattice chain growth algorithm

    NASA Astrophysics Data System (ADS)

    Gan, Hin Hark; Tropsha, Alexander; Schlick, Tamar

    2000-10-01

    We present a new application of the chain growth algorithm to lattice generation of protein structure and thermodynamics. Given the difficulty of ab initio protein structure prediction, this approach provides an alternative to current folding algorithms. The chain growth algorithm, unlike Metropolis folding algorithms, generates independent protein structures to achieve rapid and efficient exploration of configurational space. It is a modified version of the Rosenbluth algorithm where the chain growth transition probability is a normalized Boltzmann factor; it was previously applied only to simple polymers and protein models with two residue types. The independent protein configurations, generated segment-by-segment on a refined cubic lattice, are based on a single interaction site for each amino acid and a statistical interaction energy derived by Miyazawa and Jernigan. We examine for several proteins the algorithm's ability to produce nativelike folds and its effectiveness for calculating protein thermodynamics. Thermal transition profiles associated with the internal energy, entropy, and radius of gyration show characteristic folding/unfolding transitions and provide evidence for unfolding via partially unfolded (molten-globule) states. From the configurational ensembles, the protein structures with the lowest distance root-mean-square deviations (dRMSD) vary between 2.2 to 3.8 Å, a range comparable to results of an exhaustive enumeration search. Though the ensemble-averaged dRMSD values are about 1.5 to 2 Å larger, the lowest dRMSD structures have similar overall folds to the native proteins. These results demonstrate that the chain growth algorithm is a viable alternative to protein simulations using the whole chain.

  9. A Historical Perspective and Overview of Protein Structure Prediction

    NASA Astrophysics Data System (ADS)

    Wooley, John C.; Ye, Yuzhen

    Carrying on many different biological functions, proteins are all composed of one or more polypeptide chains, each containing from several to hundreds or even thousands of the 20 amino acids. During the 1950s at the dawn of modern biochemistry, an essential question for biochemists was to understand the structure and function of these polypeptide chains. The sequences of protein, also referred to as their primary structures, determine the different chemical properties for different proteins, and thus continue to captivate much of the attention of biochemists. As an early step in characterizing protein chemistry, British biochemist Frederick Sanger designed an experimental method to identify the sequence of insulin (Sanger et al., 1955). He became the first person to obtain the primary structure of a protein and in 1958 won his first Nobel Price in Chemistry. This important progress in sequencing did not answer the question of whether a single (individual) protein has a distinctive shape in three dimensions (3D), and if so, what factors determine its 3D architecture. However, during the period when Sanger was studying the primary structure of proteins, American biochemist Christian Anfinsen observed that the active polypeptide chain of a model protein, bovine pancreatic ribonuclease (RNase), could fold spontaneously into a unique 3D structure, which was later called native conformation of the protein (Anfinsen et al., 1954). Anfinsen also studied the refolding of RNase enzyme and observed that an enzyme unfolded under extreme chemical environment could refold spontaneously back into its native conformation upon changing the environment back to natural conditions (Anfinsen et al., 1961). By 1962, Anfinsen had developed his theory of protein folding (which was summarized in his 1972 Nobel acceptance speech): "The native conformation is determined by the totality of interatomic interactions and hence, by the amino acid sequence, in a given environment."

  10. Sequence- and Temperature-Dependent Properties of Unfolded and Disordered Proteins from Atomistic Simulations.

    PubMed

    Zerze, Gül H; Best, Robert B; Mittal, Jeetain

    2015-11-19

    We use all-atom molecular simulation with explicit solvent to study the properties of selected intrinsically disordered proteins and unfolded states of foldable proteins, which include chain dimensions and shape, secondary structure propensity, solvent accessible surface area, and contact formation. We find that the qualitative scaling behavior of the chains matches expectations from theory under ambient conditions. In particular, unfolded globular proteins tend to be more collapsed under the same conditions than charged disordered sequences of the same length. However, inclusion of explicit solvent in addition naturally captures temperature-dependent solvation effects, which results in an initial collapse of the chains as temperature is increased, in qualitative agreement with experiment. There is a universal origin to the collapse, revealed in the change of hydration of individual residues as a function of temperature: namely, that the initial collapse is driven by unfavorable solvation free energy of individual residues, which in turn has a strong temperature dependence. We also observe that in unfolded globular proteins, increased temperature also initially favors formation of native-like (rather than non-native-like) structure. Our results help to establish how sequence encodes the degree of intrinsic disorder or order as well as its response to changes in environmental conditions. PMID:26498157

  11. CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

    PubMed Central

    Cui, Xuefeng; Lu, Zhiwu; Wang, Sheng; Jing-Yan Wang, Jim; Gao, Xin

    2016-01-01

    Motivation: Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment, threading and alignment-free methods, protein homology detection remains a challenging open problem. Recently, network methods that try to find transitive paths in the protein structure space demonstrate the importance of incorporating network information of the structure space. Yet, current methods merge the sequence space and the structure space into a single space, and thus introduce inconsistency in combining different sources of information. Method: We present a novel network-based protein homology detection method, CMsearch, based on cross-modal learning. Instead of exploring a single network built from the mixture of sequence and structure space information, CMsearch builds two separate networks to represent the sequence space and the structure space. It then learns sequence–structure correlation by simultaneously taking sequence information, structure information, sequence space information and structure space information into consideration. Results: We tested CMsearch on two challenging tasks, protein homology detection and protein structure prediction, by querying all 8332 PDB40 proteins. Our results demonstrate that CMsearch is insensitive to the similarity metrics used to define the sequence and the structure spaces. By using HMM–HMM alignment as the sequence similarity metric, CMsearch clearly outperforms state-of-the-art homology detection methods and the CASP-winning template-based protein structure prediction methods. Availability and implementation: Our program is freely available for download from http://sfb.kaust.edu.sa/Pages/Software.aspx. Contact: xin.gao@kaust.edu.sa Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307635

  12. PCI-SS: MISO dynamic nonlinear protein secondary structure prediction

    PubMed Central

    Green, James R; Korenberg, Michael J; Aboul-Magd, Mohammed O

    2009-01-01

    Background Since the function of a protein is largely dictated by its three dimensional configuration, determining a protein's structure is of fundamental importance to biology. Here we report on a novel approach to determining the one dimensional secondary structure of proteins (distinguishing α-helices, β-strands, and non-regular structures) from primary sequence data which makes use of Parallel Cascade Identification (PCI), a powerful technique from the field of nonlinear system identification. Results Using PSI-BLAST divergent evolutionary profiles as input data, dynamic nonlinear systems are built through a black-box approach to model the process of protein folding. Genetic algorithms (GAs) are applied in order to optimize the architectural parameters of the PCI models. The three-state prediction problem is broken down into a combination of three binary sub-problems and protein structure classifiers are built using 2 layers of PCI classifiers. Careful construction of the optimization, training, and test datasets ensures that no homology exists between any training and testing data. A detailed comparison between PCI and 9 contemporary methods is provided over a set of 125 new protein chains guaranteed to be dissimilar to all training data. Unlike other secondary structure prediction methods, here a web service is developed to provide both human- and machine-readable interfaces to PCI-based protein secondary structure prediction. This server, called PCI-SS, is available at . In addition to a dynamic PHP-generated web interface for humans, a Simple Object Access Protocol (SOAP) interface is added to permit invocation of the PCI-SS service remotely. This machine-readable interface facilitates incorporation of PCI-SS into multi-faceted systems biology analysis pipelines requiring protein secondary structure information, and greatly simplifies high-throughput analyses. XML is used to represent the input protein sequence data and also to encode the resulting

  13. First Crystal Structure for a Gold Carbene-Protein Adduct.

    PubMed

    Ferraro, Giarita; Gabbiani, Chiara; Merlino, Antonello

    2016-07-20

    The X-ray structure of the adduct formed in the reaction between the gold N-heterocyclic carbene compound Au(NHC)Cl (with NHC = 1-butyl-3-methyl-imidazole-2-ylidene) and the model protein thaumatin is reported here. The structure reveals binding of Au(NHC)(+) fragments to distinct protein sites. Notably, binding of the gold compound occurs at lysine side chains and at the N-terminal tail; the metal binds the protein after releasing Cl(-) ligand, but retaining NHC fragment. PMID:27364343

  14. Computing a new family of shape descriptors for protein structures.

    PubMed

    Røgen, Peter; Sinclair, Robert

    2003-01-01

    The large-scale 3D structure of a protein can be represented by the polygonal curve through the carbon alpha atoms of the protein backbone. We introduce an algorithm for computing the average number of times that a given configuration of crossings on such polygonal curves is seen, the average being taken over all directions in space. Hereby, we introduce a new family of global geometric measures of protein structures, which we compare with the so-called generalized Gauss integrals. PMID:14632419

  15. Artificial membranes for membrane protein purification, functionality and structure studies.

    PubMed

    Parmar, Mayuriben J; Lousa, Carine De Marcos; Muench, Stephen P; Goldman, Adrian; Postis, Vincent L G

    2016-06-15

    Membrane proteins represent one of the most important targets for pharmaceutical companies. Unfortunately, technical limitations have long been a major hindrance in our understanding of the function and structure of such proteins. Recent years have seen the refinement of classical approaches and the emergence of new technologies that have resulted in a significant step forward in the field of membrane protein research. This review summarizes some of the current techniques used for studying membrane proteins, with overall advantages and drawbacks for each method. PMID:27284055

  16. Persistent homology analysis of protein structure, flexibility and folding

    PubMed Central

    Xia, Kelin; Wei, Guo-Wei

    2014-01-01

    Proteins are the most important biomolecules for living organisms. The understanding of protein structure, function, dynamics and transport is one of most challenging tasks in biological science. In the present work, persistent homology is, for the first time, introduced for extracting molecular topological fingerprints (MTFs) based on the persistence of molecular topological invariants. MTFs are utilized for protein characterization, identification and classification. The method of slicing is proposed to track the geometric origin of protein topological invariants. Both all-atom and coarse-grained representations of MTFs are constructed. A new cutoff-like filtration is proposed to shed light on the optimal cutoff distance in elastic network models. Based on the correlation between protein compactness, rigidity and connectivity, we propose an accumulated bar length generated from persistent topological invariants for the quantitative modeling of protein flexibility. To this end, a correlation matrix based filtration is developed. This approach gives rise to an accurate prediction of the optimal characteristic distance used in protein B-factor analysis. Finally, MTFs are employed to characterize protein topological evolution during protein folding and quantitatively predict the protein folding stability. An excellent consistence between our persistent homology prediction and molecular dynamics simulation is found. This work reveals the topology-function relationship of proteins. PMID:24902720

  17. An Algebro-Topological Description of Protein Domain Structure

    PubMed Central

    Penner, Robert Clark; Knudsen, Michael; Wiuf, Carsten; Andersen, Jørgen Ellegaard

    2011-01-01

    The space of possible protein structures appears vast and continuous, and the relationship between primary, secondary and tertiary structure levels is complex. Protein structure comparison and classification is therefore a difficult but important task since structure is a determinant for molecular interaction and function. We introduce a novel mathematical abstraction based on geometric topology to describe protein domain structure. Using the locations of the backbone atoms and the hydrogen bonds, we build a combinatorial object – a so-called fatgraph. The description is discrete yet gives rise to a 2-dimensional mathematical surface. Thus, each protein domain corresponds to a particular mathematical surface with characteristic topological invariants, such as the genus (number of holes) and the number of boundary components. Both invariants are global fatgraph features reflecting the interconnectivity of the domain by hydrogen bonds. We introduce the notion of robust variables, that is variables that are robust towards minor changes in the structure/fatgraph, and show that the genus and the number of boundary components are robust. Further, we invesigate the distribution of different fatgraph variables and show how only four variables are capable of distinguishing different folds. We use local (secondary) and global (tertiary) fatgraph features to describe domain structures and illustrate that they are useful for classification of domains in CATH. In addition, we combine our method with two other methods thereby using primary, secondary, and tertiary structure information, and show that we can identify a large percentage of new and unclassified structures in CATH. PMID:21629687

  18. Impact of structure space continuity on protein fold classification

    PubMed Central

    Xu, Jinrui; Zhang, Jianzhi

    2016-01-01

    Protein structure classification hierarchically clusters domain structures based on structure and/or sequence similarities and plays important roles in the study of protein structure-function relationship and protein evolution. Among many classifications, SCOP and CATH are widely viewed as the gold standards. Fold classification is of special interest because this is the lowest level of classification that does not depend on protein sequence similarity. The current fold classifications such as those in SCOP and CATH are controversial because they implicitly assume that folds are discrete islands in the structure space, whereas increasing evidence suggests significant similarities among folds and supports a continuous fold space. Although this problem is widely recognized, its impact on fold classification has not been quantitatively evaluated. Here we develop a likelihood method to classify a domain into the existing folds of CATH or SCOP using both query-fold structure similarities and within-fold structure heterogeneities. The new classification differs from the original classification for 3.4–12% of domains, depending on factors such as the structure similarity score and original classification scheme used. Because these factors differ for different biological purposes, our results indicate that the importance of considering structure space continuity in fold classification depends on the specific question asked. PMID:27006112

  19. Proteins at flowing interfaces: From understanding structure to treating disease

    NASA Astrophysics Data System (ADS)

    Posada, David; Young, James; Hirsa, Amir

    2012-11-01

    The field of soft matter offers vast opportunities for scientific and technological developments, with many challenges that need to be addressed by various disciplines. Fluid dynamics has a tremendous potential for greater impact, from broadening fundamental understanding to treating disease. Here we demonstrate the use of fluid dynamics in two biotechnology problems involving proteins at the air/water interface: a) 2-Dimensional protein crystallization and b) amyloid fibril formation. Protein crystallization is usually the most challenging step in X-ray diffraction analysis of protein structure. Recently it was demonstrated that flow can induce 2-D protein crystallization at conditions under which quiescent systems do not form crystals. A different form of protein structuring, namely amyloid fibrillization, is also of interest due to its association with several neurodegenerative diseases such as Alzheimer's and Parkinson's disease. Protein denaturation, which is the root of the fibrillization process, is also a significant concern in biotherapeutics production. Both problems are studied by using shearing free-surface flows in simple geometries. The common finding is that flow can significantly enhance the growth of protein structures.

  20. Water Determines the Structure and Dynamics of Proteins.

    PubMed

    Bellissent-Funel, Marie-Claire; Hassanali, Ali; Havenith, Martina; Henchman, Richard; Pohl, Peter; Sterpone, Fabio; van der Spoel, David; Xu, Yao; Garcia, Angel E

    2016-07-13

    Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist. PMID:27186992

  1. Protein-Nanoparticle Interaction-Induced Changes in Protein Structure and Aggregation.

    PubMed

    Kim, Yuna; Ko, Sung Min; Nam, Jwa-Min

    2016-07-01

    Large surface area, small size, strong optical properties, controllable structural features, variety of bioconjugation chemistries, and biocompatibility make many different types of nanoparticles (NPs), such as gold NPs, useful for many biological applications, such as biosensing, cellular imaging, disease diagnostics, drug delivery, and therapeutics. Recently, interactions between proteins and NPs have been extensively studied to understand, control, and utilize the interactions involved in biomedical applications of NPs and several biological processes, such as protein aggregation, for many diseases, including Alzheimer's disease. These studies also offer fundamental knowledge on changes in protein structure, protein aggregation mechanisms, and ways to unravel the roles and fates of NPs within the human body. This review focuses on recent studies on the roles and uses of NPs in protein structural changes and aggregation processes. PMID:27062521

  2. Characterizing Protein Structure, Dynamics and Conformation in Lyophilized Solids

    PubMed Central

    Moorthy, Balakrishnan S.; Iyer, Lavanya K.; Topp, Elizabeth M.

    2015-01-01

    The long-term stability of protein therapeutics in the solid-state depends on the preservation of native structure during lyophilization and in the lyophilized powder. Proteins can reversibly or irreversibly unfold upon lyophilization, acquiring conformations susceptible to degradation during storage. Therefore, characterizing proteins in the dried state is crucial for the design of safe and efficacious formulations. This review summarizes the basic principles and applications of the analytical techniques that are commonly used to characterize protein structure, dynamics and conformation in lyophilized solids. The review also discusses the applications of recently developed mass spectrometry based methods (solid-state hydrogen deuterium exchange mass spectrometry (ssHDX-MS) and solid-state photolytic labeling mass spectrometry (ssPL-MS)) and their ability to study proteins in the solid-state at high resolution. PMID:26446463

  3. Automated High Throughput Protein Crystallization Screening at Nanoliter Scale and Protein Structural Study on Lactate Dehydrogenase

    SciTech Connect

    Fenglei Li

    2006-08-09

    The purposes of our research were: (1) To develop an economical, easy to use, automated, high throughput system for large scale protein crystallization screening. (2) To develop a new protein crystallization method with high screening efficiency, low protein consumption and complete compatibility with high throughput screening system. (3) To determine the structure of lactate dehydrogenase complexed with NADH by x-ray protein crystallography to study its inherent structural properties. Firstly, we demonstrated large scale protein crystallization screening can be performed in a high throughput manner with low cost, easy operation. The overall system integrates liquid dispensing, crystallization and detection and serves as a whole solution to protein crystallization screening. The system can dispense protein and multiple different precipitants in nanoliter scale and in parallel. A new detection scheme, native fluorescence, has been developed in this system to form a two-detector system with a visible light detector for detecting protein crystallization screening results. This detection scheme has capability of eliminating common false positives by distinguishing protein crystals from inorganic crystals in a high throughput and non-destructive manner. The entire system from liquid dispensing, crystallization to crystal detection is essentially parallel, high throughput and compatible with automation. The system was successfully demonstrated by lysozyme crystallization screening. Secondly, we developed a new crystallization method with high screening efficiency, low protein consumption and compatibility with automation and high throughput. In this crystallization method, a gas permeable membrane is employed to achieve the gentle evaporation required by protein crystallization. Protein consumption is significantly reduced to nanoliter scale for each condition and thus permits exploring more conditions in a phase diagram for given amount of protein. In addition

  4. Relationship between Molecular Structure Characteristics of Feed Proteins and Protein In vitro Digestibility and Solubility.

    PubMed

    Bai, Mingmei; Qin, Guixin; Sun, Zewei; Long, Guohui

    2016-08-01

    The nutritional value of feed proteins and their utilization by livestock are related not only to the chemical composition but also to the structure of feed proteins, but few studies thus far have investigated the relationship between the structure of feed proteins and their solubility as well as digestibility in monogastric animals. To address this question we analyzed soybean meal, fish meal, corn distiller's dried grains with solubles, corn gluten meal, and feather meal by Fourier transform infrared (FTIR) spectroscopy to determine the protein molecular spectral band characteristics for amides I and II as well as α-helices and β-sheets and their ratios. Protein solubility and in vitro digestibility were measured with the Kjeldahl method using 0.2% KOH solution and the pepsin-pancreatin two-step enzymatic method, respectively. We found that all measured spectral band intensities (height and area) of feed proteins were correlated with their the in vitro digestibility and solubility (p≤0.003); moreover, the relatively quantitative amounts of α-helices, random coils, and α-helix to β-sheet ratio in protein secondary structures were positively correlated with protein in vitro digestibility and solubility (p≤0.004). On the other hand, the percentage of β-sheet structures was negatively correlated with protein in vitro digestibility (p<0.001) and solubility (p = 0.002). These results demonstrate that the molecular structure characteristics of feed proteins are closely related to their in vitro digestibility at 28 h and solubility. Furthermore, the α-helix-to-β-sheet ratio can be used to predict the nutritional value of feed proteins. PMID:26954145

  5. Relationship between Molecular Structure Characteristics of Feed Proteins and Protein In vitro Digestibility and Solubility

    PubMed Central

    Bai, Mingmei; Qin, Guixin; Sun, Zewei; Long, Guohui

    2016-01-01

    The nutritional value of feed proteins and their utilization by livestock are related not only to the chemical composition but also to the structure of feed proteins, but few studies thus far have investigated the relationship between the structure of feed proteins and their solubility as well as digestibility in monogastric animals. To address this question we analyzed soybean meal, fish meal, corn distiller’s dried grains with solubles, corn gluten meal, and feather meal by Fourier transform infrared (FTIR) spectroscopy to determine the protein molecular spectral band characteristics for amides I and II as well as α-helices and β-sheets and their ratios. Protein solubility and in vitro digestibility were measured with the Kjeldahl method using 0.2% KOH solution and the pepsin-pancreatin two-step enzymatic method, respectively. We found that all measured spectral band intensities (height and area) of feed proteins were correlated with their the in vitro digestibility and solubility (p≤0.003); moreover, the relatively quantitative amounts of α-helices, random coils, and α-helix to β-sheet ratio in protein secondary structures were positively correlated with protein in vitro digestibility and solubility (p≤0.004). On the other hand, the percentage of β-sheet structures was negatively correlated with protein in vitro digestibility (p<0.001) and solubility (p = 0.002). These results demonstrate that the molecular structure characteristics of feed proteins are closely related to their in vitro digestibility at 28 h and solubility. Furthermore, the α-helix-to-β-sheet ratio can be used to predict the nutritional value of feed proteins. PMID:26954145

  6. New approach to protein fold recognition based on Delaunay tessellation of protein structure

    SciTech Connect

    Zheng, W.; Cho, S.J.; Vaisman, I.I.; Tropsha, A.

    1996-12-31

    We propose new algorithms for sequence-structure compatibility (fold recognition) searches in multidimensional sequence-structure space. Individual amino acid residues in protein structures are represented by their C{sup {alpha}} atoms; thus each protein is described as a collection of points in three-dimensional space. Delaunay tessellation of a protein generates an aggregate of space-filling, irregular tetrahedra, or Delaunay simplices. Statistical analysis of quadruplet residue compositions of all Delaunay simplices in a representative dataset of protein structures leads to a novel four body contact residue potential expressed as log likelihood factor q. The q factors are calculated for native 20 letter amino acid alphabet and several reduced alphabets. Two sequence structure compatibility functions are computed as (i) the sum of q factors for all Delaunay simplices in a given protein, or (ii) 3D-1D Delaunay tessellation profiles where the individual residue profile value is calculated as the sum of q factors for all simplices that share this vertex residue. Both threading functions have been implemented in structure-recognizes-sequence and sequence-recognizes-structure protocols for protein fold recognition. We find that both profile and total score based threading functions can distinguish both the native fold from incorrect folds for a sequence, and the native sequence from non-native sequences for a fold. 25 refs., 4 figs., 1 tab.

  7. Crystal structure of Homo sapiens protein LOC79017

    SciTech Connect

    Bae, Euiyoung; Bingman, Craig A.; Aceti, David J.; Phillips, Jr., George N.

    2010-02-08

    LOC79017 (MW 21.0 kDa, residues 1-188) was annotated as a hypothetical protein encoded by Homo sapiens chromosome 7 open reading frame 24. It was selected as a target by the Center for Eukaryotic Structural Genomics (CESG) because it did not share more than 30% sequence identity with any protein for which the three-dimensional structure is known. The biological function of the protein has not been established yet. Parts of LOC79017 were identified as members of uncharacterized Pfam families (residues 1-95 as PB006073 and residues 104-180 as PB031696). BLAST searches revealed homologues of LOC79017 in many eukaryotes, but none of them have been functionally characterized. Here, we report the crystal structure of H. sapiens protein LOC79017 (UniGene code Hs.530024, UniProt code O75223, CESG target number go.35223).

  8. Applications of graph theory in protein structure identification.

    PubMed

    Yan, Yan; Zhang, Shenggui; Wu, Fang-Xiang

    2011-01-01

    There is a growing interest in the identification of proteins on the proteome wide scale. Among different kinds of protein structure identification methods, graph-theoretic methods are very sharp ones. Due to their lower costs, higher effectiveness and many other advantages, they have drawn more and more researchers' attention nowadays. Specifically, graph-theoretic methods have been widely used in homology identification, side-chain cluster identification, peptide sequencing and so on. This paper reviews several methods in solving protein structure identification problems using graph theory. We mainly introduce classical methods and mathematical models including homology modeling based on clique finding, identification of side-chain clusters in protein structures upon graph spectrum, and de novo peptide sequencing via tandem mass spectrometry using the spectrum graph model. In addition, concluding remarks and future priorities of each method are given. PMID:22165974

  9. Linkers in the structural biology of protein–protein interactions

    PubMed Central

    Reddy Chichili, Vishnu Priyanka; Kumar, Veerendra; Sivaraman, J

    2013-01-01

    Linkers or spacers are short amino acid sequences created in nature to separate multiple domains in a single protein. Most of them are rigid and function to prohibit unwanted interactions between the discrete domains. However, Gly-rich linkers are flexible, connecting various domains in a single protein without interfering with the function of each domain. The advent of recombinant DNA technology made it possible to fuse two interacting partners with the introduction of artificial linkers. Often, independent proteins may not exist as stable or structured proteins until they interact with their binding partner, following which they gain stability and the essential structural elements. Gly-rich linkers have been proven useful for these types of unstable interactions, particularly where the interaction is weak and transient, by creating a covalent link between the proteins to form a stable protein–protein complex. Gly-rich linkers are also employed to form stable covalently linked dimers, and to connect two independent domains that create a ligand-binding site or recognition sequence. The lengths of linkers vary from 2 to 31 amino acids, optimized for each condition so that the linker does not impose any constraints on the conformation or interactions of the linked partners. Various structures of covalently linked protein complexes have been described using X-ray crystallography, nuclear magnetic resonance and cryo-electron microscopy techniques. In this review, we evaluate several structural studies where linkers have been used to improve protein quality, to produce stable protein–protein complexes, and to obtain protein dimers. PMID:23225024

  10. HMGA proteins as modulators of chromatin structure during transcriptional activation

    PubMed Central

    Ozturk, Nihan; Singh, Indrabahadur; Mehta, Aditi; Braun, Thomas; Barreto, Guillermo

    2013-01-01

    High mobility group (HMG) proteins are the most abundant non-histone chromatin associated proteins. HMG proteins bind to DNA and nucleosome and alter the structure of chromatin locally and globally. Accessibility to DNA within chromatin is a central factor that affects DNA-dependent nuclear processes, such as transcription, replication, recombination, and repair. HMG proteins associate with different multi-protein complexes to regulate these processes by mediating accessibility to DNA. HMG proteins can be subdivided into three families: HMGA, HMGB, and HMGN. In this review, we will focus on recent advances in understanding the function of HMGA family members, specifically their role in gene transcription regulation during development and cancer. PMID:25364713

  11. Protein structure prediction with local adjust tabu search algorithm

    PubMed Central

    2014-01-01

    Background Protein folding structure prediction is one of the most challenging problems in the bioinformatics domain. Because of the complexity of the realistic protein structure, the simplified structure model and the computational method should be adopted in the research. The AB off-lattice model is one of the simplification models, which only considers two classes of amino acids, hydrophobic (A) residues and hydrophilic (B) residues. Results The main work of this paper is to discuss how to optimize the lowest energy configurations in 2D off-lattice model and 3D off-lattice model by using Fibonacci sequences and real protein sequences. In order to avoid falling into local minimum and faster convergence to the global minimum, we introduce a novel method (SATS) to the protein structure problem, which combines simulated annealing algorithm and tabu search algorithm. Various strategies, such as the new encoding strategy, the adaptive neighborhood generation strategy and the local adjustment strategy, are adopted successfully for high-speed searching the optimal conformation corresponds to the lowest energy of the protein sequences. Experimental results show that some of the results obtained by the improved SATS are better than those reported in previous literatures, and we can sure that the lowest energy folding state for short Fibonacci sequences have been found. Conclusions Although the off-lattice models is not very realistic, they can reflect some important characteristics of the realistic protein. It can be found that 3D off-lattice model is more like native folding structure of the realistic protein than 2D off-lattice model. In addition, compared with some previous researches, the proposed hybrid algorithm can more effectively and more quickly search the spatial folding structure of a protein chain. PMID:25474708

  12. Identification of structural domains in proteins by a graph heuristic.

    PubMed

    Wernisch, L; Hunting, M; Wodak, S J

    1999-05-15

    A novel automatic procedure for identifying domains from protein atomic coordinates is presented. The procedure, termed STRUDL (STRUctural Domain Limits), does not take into account information on secondary structures and handles any number of domains made up of contiguous or non-contiguous chain segments. The core algorithm uses the Kernighan-Lin graph heuristic to partition the protein into residue sets which display minimum interactions between them. These interactions are deduced from the weighted Voronoi diagram. The generated partitions are accepted or rejected on the basis of optimized criteria, representing basic expected physical properties of structural domains. The graph heuristic approach is shown to be very effective, it approximates closely the exact solution provided by a branch and bound algorithm for a number of test proteins. In addition, the overall performance of STRUDL is assessed on a set of 787 representative proteins from the Protein Data Bank by comparison to domain definitions in the CATH protein classification. The domains assigned by STRUDL agree with the CATH assignments in at least 81% of the tested proteins. This result is comparable to that obtained previously using PUU (Holm and Sander, Proteins 1994;9:256-268), the only other available algorithm designed to identify domains with any number of non-contiguous chain segments. A detailed discussion of the structures for which our assignments differ from those in CATH brings to light some clear inconsistencies between the concept of structural domains based on minimizing inter-domain interactions and that of delimiting structural motifs that represent acceptable folding topologies or architectures. Considering both concepts as complementary and combining them in a layered approach might be the way forward. PMID:10328269

  13. Seeking significance in three-dimensional protein structure comparisons.

    PubMed

    Mizuguchi, K; Go, N

    1995-06-01

    What is the significance of three-dimensional structural similarity? This fundamental question still remains unanswered in spite of advances in automatic structure comparison methods that have been made in the last few years. The answer to this question will give us a much deeper insight into the principles of protein architecture. PMID:7583636

  14. Matt: local flexibility aids protein multiple structure alignment.

    PubMed

    Menke, Matthew; Berger, Bonnie; Cowen, Lenore

    2008-01-01

    Even when there is agreement on what measure a protein multiple structure alignment should be optimizing, finding the optimal alignment is computationally prohibitive. One approach used by many previous methods is aligned fragment pair chaining, where short structural fragments from all the proteins are aligned against each other optimally, and the final alignment chains these together in geometrically consistent ways. Ye and Godzik have recently suggested that adding geometric flexibility may help better model protein structures in a variety of contexts. We introduce the program Matt (Multiple Alignment with Translations and Twists), an aligned fragment pair chaining algorithm that, in intermediate steps, allows local flexibility between fragments: small translations and rotations are temporarily allowed to bring sets of aligned fragments closer, even if they are physically impossible under rigid body transformations. After a dynamic programming assembly guided by these "bent" alignments, geometric consistency is restored in the final step before the alignment is output. Matt is tested against other recent multiple protein structure alignment programs on the popular Homstrad and SABmark benchmark datasets. Matt's global performance is competitive with the other programs on Homstrad, but outperforms the other programs on SABmark, a benchmark of multiple structure alignments of proteins with more distant homology. On both datasets, Matt demonstrates an ability to better align the ends of alpha-helices and beta-strands, an important characteristic of any structure alignment program intended to help construct a structural template library for threading approaches to the inverse protein-folding problem. The related question of whether Matt alignments can be used to distinguish distantly homologous structure pairs from pairs of proteins that are not homologous is also considered. For this purpose, a p-value score based on the length of the common core and average root

  15. Higher order structure of proteins solubilized in AOT reverse micelles.

    PubMed

    Naoe, Kazumitsu; Noda, Kazuki; Kawagoe, Mikio; Imai, Masanao

    2004-11-15

    The higher order structure of proteins solubilized in an bis(2-ethylhexyl) sulfosuccinate sodium (AOT) reverse micellar system was investigated. From circular dichroic (CD) measurement, CD spectra of cytochrome c, which is solubilized at the interface of reverse micelles, markedly changed on going from buffer solution to the reverse micellar solution, and the ellipticity values in the far- and near-UV regions decreased with decreasing the water content (W0: molar ratio of water to AOT), indicating that the secondary and tertiary structures of cytochrome c changed with the water content. The ellipticity of ribonuclease A, which is solubilized in the center of micellar water pool, in the near-UV region was dependent on W0 and became minimum when W0 of ca. 8 while the ellipticity in the far-UV region was almost constant, indicating that the tertiary structure of ribonuclease A was affected by the water content, but the secondary structure was conserved. The degree of curvature of the micellar interface appears to influence the protein structure because the reverse micelle size is linearly proportional to the W0 value. As evidence of this, when the micelle size was comparable to the protein's dimensions, the structures were more affected by the water content. Judging from the dependence of the factor influencing the protein structure on the protein species, the location of solubilized protein in reverse micelles is significantly related to whether the protein structure in the system is affected by the micellar interface. In the cases of cytochrome c and lysozyme, the ellipticity against W0 was dependent on the AOT concentration. In contrast, ribonuclease A gave very similar ellipticity values whatever the AOT concentration. In the n-hexane micellar system, cytochrome c exhibited lower ellipticity values and ribonuclease A in the lower W0 range (W0protein and the micellar

  16. SCOPmap: Automated assignment of protein structures to evolutionary superfamilies

    PubMed Central

    Cheek, Sara; Qi, Yuan; Krishna, S Sri; Kinch, Lisa N; Grishin, Nick V

    2004-01-01

    Background Inference of remote homology between proteins is very challenging and remains a prerogative of an expert. Thus a significant drawback to the use of evolutionary-based protein structure classifications is the difficulty in assigning new proteins to unique positions in the classification scheme with automatic methods. To address this issue, we have developed an algorithm to map protein domains to an existing structural classification scheme and have applied it to the SCOP database. Results The general strategy employed by this algorithm is to combine the results of several existing sequence and structure comparison tools applied to a query protein of known structure in order to find the homologs already classified in SCOP database and thus determine classification assignments. The algorithm is able to map domains within newly solved structures to the appropriate SCOP superfamily level with ~95% accuracy. Examples of correctly mapped remote homologs are discussed. The algorithm is also capable of identifying potential evolutionary relationships not specified in the SCOP database, thus helping to make it better. The strategy of the mapping algorithm is not limited to SCOP and can be applied to any other evolutionary-based classification scheme as well. SCOPmap is available for download. Conclusion The SCOPmap program is useful for assigning domains in newly solved structures to appropriate superfamilies and for identifying evolutionary links between different superfamilies. PMID:15598351

  17. Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity

    PubMed Central

    2010-01-01

    Background Computational comparison of two protein structures is the starting point of many methods that build on existing knowledge, such as structure modeling (including modeling of protein complexes and conformational changes), molecular replacement, or annotation by structural similarity. In a commonly used strategy, significant effort is invested in matching two sets of atoms. In a complementary approach, a global descriptor is assigned to the overall structure, thus losing track of the substructures within. Results Using a small set of geometric features, we define a reduced representation of protein structure, together with an optimizing function for matching two representations, to provide a pre-filtering stage in a database search. We show that, in a straightforward implementation, the representation performs well in terms of resolution in the space of protein structures, and its ability to make new predictions. Conclusions Perhaps unexpectedly, a substantial discriminating power already exists at the level of main features of protein structure, such as directions of secondary structural elements, possibly constrained by their sequential order. This can be used toward efficient comparison of protein (sub)structures, allowing for various degrees of conformational flexibility within the compared pair, which in turn can be used for modeling by homology of protein structure and dynamics. PMID:20338066

  18. Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses.

    PubMed

    Sarti, Edoardo; Gladich, Ivan; Zamuner, Stefano; Correia, Bruno E; Laio, Alessandro

    2016-09-01

    The prediction of protein-protein interactions and their structural configuration remains a largely unsolved problem. Most of the algorithms aimed at finding the native conformation of a protein complex starting from the structure of its monomers are based on searching the structure corresponding to the global minimum of a suitable scoring function. However, protein complexes are often highly flexible, with mobile side chains and transient contacts due to thermal fluctuations. Flexibility can be neglected if one aims at finding quickly the approximate structure of the native complex, but may play a role in structure refinement, and in discriminating solutions characterized by similar scores. We here benchmark the capability of some state-of-the-art scoring functions (BACH-SixthSense, PIE/PISA and Rosetta) in discriminating finite-temperature ensembles of structures corresponding to the native state and to non-native configurations. We produce the ensembles by running thousands of molecular dynamics simulations in explicit solvent starting from poses generated by rigid docking and optimized in vacuum. We find that while Rosetta outperformed the other two scoring functions in scoring the structures in vacuum, BACH-SixthSense and PIE/PISA perform better in distinguishing near-native ensembles of structures generated by molecular dynamics in explicit solvent. Proteins 2016; 84:1312-1320. © 2016 Wiley Periodicals, Inc. PMID:27253756

  19. A Fourier analysis of symmetry in protein structure.

    PubMed

    Taylor, William R; Heringa, Jaap; Baud, Franck; Flores, Tomas P

    2002-02-01

    The score matrix from a structure comparison program (SAP) was used to search for repeated structures using a Fourier analysis. When tested with artificial data, a simple Fourier transform of the smoothed matrix provided a clear signal of the repeat periodicity that could be used to extract the repeating units with the SAP program. The strength of the Fourier signal was calibrated against the signal from model proteins. The most useful of these was the novel random-walk approach employed to generate realistic 'fake' structures. On the basis of these it was possible to conclude that only a small proportion of protein structures have an unexpected degree of symmetry. Artificially generated 'ideal' folds provided an upper limit on the strength of signal that could be expected from a 'perfectly' repeating compact structure. Unexpectedly, some of the very regular beta-propellor folds attained the same strength but the majority of symmetric structures lay below this region. When native proteins were ranked by the power of their spectrum a wide variety of fold types were seen to score highly. In the betaalpha class, these included the globular betaalpha proteins and the more repetitive leucine-rich betaalpha folds. In the all-beta class; beta-propellors, beta-prisms and beta-helices were found as well as the more globular gamma-crystalin domains. When this ranked list was filtered to remove proteins that contained detectable internal sequence similarity (using the program REPRO), the list became exclusively composed of just globular betaalpha class proteins and in the top 50 re-ranked proteins, only a single 4-fold propellor structure remained. PMID:11917144

  20. NMR structure of hypothetical protein MG354 from Mycoplasmagenitalium

    SciTech Connect

    Pelton, Jeffrey G.; Shi, Jianxia; Yokotoa, Hisao; Kim, Rosalind; Wemmer, David E.

    2005-04-12

    Mycoplasma genitalium (Mg) and M. pneumoniae (Mp) are human pathogens with two of the smallest genomes sequenced to date ({approx} 480 and 680 genes, respectively). The Berkeley Structural Genomics Center is determining representative structures for gene products in these organisms, helping to understand the set of protein folds needed to sustain this minimal organism. The protein coded by gene MG354 (gi3844938) from M. genitalium has a relatively unique sequence, related only to MPN530 from M. pneumoniae (68% identity, coverage 99%) and MGA{_}0870 from the avian pathogen M. gallisepticum (23% identity, coverage 94%), has no homologue with a determined structure, and no functional annotations.

  1. High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography

    PubMed Central

    Boutet, Sébastien; Lomb, Lukas; Williams, Garth J.; Barends, Thomas R. M.; Aquila, Andrew; Doak, R. Bruce; Weierstall, Uwe; DePonte, Daniel P.; Steinbrener, Jan; Shoeman, Robert L.; Messerschmidt, Marc; Barty, Anton; White, Thomas A.; Kassemeyer, Stephan; Kirian, Richard A.; Seibert, M. Marvin; Montanez, Paul A.; Kenney, Chris; Herbst, Ryan; Hart, Philip; Pines, Jack; Haller, Gunther; Gruner, Sol M.; Philipp, Hugh T.; Tate, Mark W.; Hromalik, Marianne; Koerner, Lucas J.; van Bakel, Niels; Morse, John; Ghonsalves, Wilfred; Arnlund, David; Bogan, Michael J.; Caleman, Carl; Fromme, Raimund; Hampton, Christina Y.; Hunter, Mark S.; Johansson, Linda C.; Katona, Gergely; Kupitz, Christopher; Liang, Mengning; Martin, Andrew V.; Nass, Karol; Redecke, Lars; Stellato, Francesco; Timneanu, Nicusor; Wang, Dingjie; Zatsepin, Nadia A.; Schafer, Donald; Defever, James; Neutze, Richard; Fromme, Petra; Spence, John C. H.; Chapman, Henry N.; Schlichting, Ilme

    2013-01-01

    Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules. PMID:22653729

  2. Dynamic insight into protein structure utilizing red edge excitation shift.

    PubMed

    Chattopadhyay, Amitabha; Haldar, Sourav

    2014-01-21

    Proteins are considered the workhorses in the cellular machinery. They are often organized in a highly ordered conformation in the crowded cellular environment. These conformations display characteristic dynamics over a range of time scales. An emerging consensus is that protein function is critically dependent on its dynamics. The subtle interplay between structure and dynamics is a hallmark of protein organization and is essential for its function. Depending on the environmental context, proteins can adopt a range of conformations such as native, molten globule, unfolded (denatured), and misfolded states. Although protein crystallography is a well established technique, it is not always possible to characterize various protein conformations by X-ray crystallography due to transient nature of these states. Even in cases where structural characterization is possible, the information obtained lacks dynamic component, which is needed to understand protein function. In this overall scenario, approaches that reveal information on protein dynamics are much appreciated. Dynamics of confined water has interesting implications in protein folding. Interfacial hydration combines the motion of water molecules with the slow moving protein molecules. The red edge excitation shift (REES) approach becomes relevant in this context. REES is defined as the shift in the wavelength of maximum fluorescence emission toward higher wavelengths, caused by a shift in the excitation wavelength toward the red edge of absorption spectrum. REES arises due to slow rates (relative to fluorescence lifetime) of solvent relaxation (reorientation) around an excited state fluorophore in organized assemblies such as proteins. Consequently, REES depends on the environment-induced motional restriction imposed on the solvent molecules in the immediate vicinity of the fluorophore. In the case of a protein, the confined water in the protein creates a dipolar field that acts as the solvent for a fluorophore

  3. Protein secondary structure classification revisited: processing DSSP information with PSSC.

    PubMed

    Zacharias, Jan; Knapp, Ernst-Walter

    2014-07-28

    A first step toward three-dimensional protein structure description is the characterization of secondary structure. The most widely used program for secondary structure assignment remains DSSP, introduced in 1983, with currently more than 400 citations per year. DSSP output is in a one-letter representation, where much of the information on DSSP's internal description is lost. Recently it became evident that DSSP overlooks most π-helical structures, which are more prevalent and important than anticipated before. We introduce an alternative concept, representing the internal structure characterization of DSSP as an eight-character string that is human-interpretable and easy to parse by software. We demonstrate how our protein secondary structure characterization (PSSC) code allows for inspection of complicated structural features. It recognizes ten times more π-helical residues than does the standard DSSP. The plausibility of introduced changes in interpreting DSSP information is demonstrated by better clustering of secondary structures in (φ, ψ) dihedral angle space. With a sliding sequence window (SSW), helical assignments with PSSC remain invariant compared with an assignment based on the complete structure. In contrast, assignment with DSSP can be changed by residues in the neighborhood that are in fact not interacting with the residue under consideration. We demonstrate how one can easily define new secondary structure classification schemes with PSSC and perform the classifications. Our approach works without changing the DSSP source code and allows for more detailed protein characterization. PMID:24866861

  4. Develop Infrared Structural Biology for Probing Structural Dynamics of Protein Functions

    NASA Astrophysics Data System (ADS)

    Xie, Aihua; Kang, Zhouyang; Causey, Oliver; Liu, Charle

    2015-03-01

    Protein functions are carried out through a series of structural transitions. Lack of knowledge on functionally important structural motions of proteins impedes our understanding of protein functions. Infrared structural biology is an emerging technology with powerful applications for protein structural dynamics. One key element of infrared structural biology is the development of vibrational structural marker (VSM) database library that translates infrared spectroscopic signals into specific structural information. We report the development of VSM for probing the type, geometry and strength of hydrogen bonding interactions of buried COO- side chains of Asp and Glu in proteins. Quantum theory based first principle computational studies combined with bioinformatic hydrogen bond analysis are employed in this study. We will discuss the applications of VSM in mechanistic studies of protein functions. Infrared structural biology is expected to emerge as a powerful technique for elucidating the functional mechanism of a broad range of proteins, including water soluble and membrane proteins. This work is supported by OCAST HR10-078 and NSF DBI1338097.

  5. A structural-alphabet-based strategy for finding structural motifs across protein families.

    PubMed

    Wu, Chih Yuan; Chen, Yao Chi; Lim, Carmay

    2010-08-01

    Proteins with insignificant sequence and overall structure similarity may still share locally conserved contiguous structural segments; i.e. structural/3D motifs. Most methods for finding 3D motifs require a known motif to search for other similar structures or functionally/structurally crucial residues. Here, without requiring a query motif or essential residues, a fully automated method for discovering 3D motifs of various sizes across protein families with different folds based on a 16-letter structural alphabet is presented. It was applied to structurally non-redundant proteins bound to DNA, RNA, obligate/non-obligate proteins as well as free DNA-binding proteins (DBPs) and proteins with known structures but unknown function. Its usefulness was illustrated by analyzing the 3D motifs found in DBPs. A non-specific motif was found with a 'corner' architecture that confers a stable scaffold and enables diverse interactions, making it suitable for binding not only DNA but also RNA and proteins. Furthermore, DNA-specific motifs present 'only' in DBPs were discovered. The motifs found can provide useful guidelines in detecting binding sites and computational protein redesign. PMID:20525797

  6. A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications.

    PubMed

    Tyagi, Manoj; Gowri, Venkataraman S; Srinivasan, Narayanaswamy; de Brevern, Alexandre G; Offmann, Bernard

    2006-10-01

    Analysis of protein structures based on backbone structural patterns known as structural alphabets have been shown to be very useful. Among them, a set of 16 pentapeptide structural motifs known as protein blocks (PBs) has been identified and upon which backbone model of most protein structures can be built. PBs allows simplification of 3D space onto 1D space in the form of sequence of PBs. Here, for the first time, substitution probabilities of PBs in a large number of aligned homologous protein structures have been studied and are expressed as a simplified 16 x 16 substitution matrix. The matrix was validated by benchmarking how well it can align sequences of PBs rather like amino acid alignment to identify structurally equivalent regions in closely or distantly related proteins using dynamic programming approach. The alignment results obtained are very comparable to well established structure comparison methods like DALI and STAMP. Other interesting applications of the matrix have been investigated. We first show that, in variable regions between two superimposed homologous proteins, one can distinguish between local conformational differences and rigid-body displacement of a conserved motif by comparing the PBs and their substitution scores. Second, we demonstrate, with the example of aspartic proteinases, that PBs can be efficiently used to detect the lobe/domain flexibility in the multidomain proteins. Lastly, using protein kinase as an example, we identify regions of conformational variations and rigid body movements in the enzyme as it is changed to the active state from an inactive state. PMID:16894618

  7. Structural insights into protein-metal ion partnerships.

    PubMed

    Barondeau, David P; Getzoff, Elizabeth D

    2004-12-01

    New metalloprotein structures continue to provide discoveries regarding protein-metal ion partnerships. Many recent structures reveal metal ion sites that control or are controlled by protein conformational change, including modulation by alternative splice variants and striking conformational changes. Only a few novel catalytic metal centers have been revealed recently, such as the surprising Ni-hook superoxide dismutase catalytic site and the cubane-like Mn(3)CaO(4) photosynthetic oxygen-evolving center. However, important new variations on old heme themes, breakthroughs in the fields of metal ion regulation and metallochaperones, and captivating insights into partnerships between proteins and minerals have also been described. Very high resolution metal site structures and metalloprotein design will be increasingly important in order to leverage the wealth of native metalloprotein structures into a deep understanding of metal ion site specificity and activity. PMID:15582401

  8. Integrating Mass Spectrometry of Intact Protein Complexes into Structural Proteomics

    PubMed Central

    Hyung, Suk-Joon; Ruotolo, Brandon T.

    2013-01-01

    Summary Mass spectrometry analysis of intact protein complexes has emerged as an established technology for assessing the composition and connectivity within dynamic, heterogeneous multiprotein complexes at low concentrations and in the context of mixtures. As this technology continues to move forward, one of the main challenges is to integrate the information content of such intact protein complex measurements with other mass spectrometry approaches in structural biology. Methods such as H/D exchange, oxidative foot-printing, chemical cross-linking, affinity purification, and ion mobility separation add complementary information that allows access to every level of protein structure and organization. Here, we survey the structural information that can be retrieved by such experiments, demonstrate the applicability of integrative mass spectrometry approaches in structural proteomics, and look to the future to explore upcoming innovations in this rapidly-advancing area. PMID:22611037

  9. Giant protein kinases: domain interactions and structural basis of autoregulation.

    PubMed Central

    Kobe, B; Heierhorst, J; Feil, S C; Parker, M W; Benian, G M; Weiss, K R; Kemp, B E

    1996-01-01

    The myosin-associated giant protein kinases twitchin and titin are composed predominantly of fibronectin- and immunoglobulin-like modules. We report the crystal structures of two autoinhibited twitchin kinase fragments, one from Aplysia and a larger fragment from Caenorhabditis elegans containing an additional C-terminal immunoglobulin-like domain. The structure of the longer fragment shows that the immunoglobulin domain contacts the protein kinase domain on the opposite side from the catalytic cleft, laterally exposing potential myosin binding residues. Together, the structures reveal the cooperative interactions between the autoregulatory region and the residues from the catalytic domain involved in protein substrate binding, ATP binding, catalysis and the activation loop, and explain the differences between the observed autoinhibitory mechanism and the one found in the structure of calmodulin-dependent kinase I. Images PMID:9003756

  10. WeFold: A Coopetition for Protein Structure Prediction

    PubMed Central

    Khoury, George A.; Liwo, Adam; Khatib, Firas; Zhou, Hongyi; Chopra, Gaurav; Bacardit, Jaume; Bortot, Leandro O.; Faccioli, Rodrigo A.; Deng, Xin; He, Yi; Krupa, Pawel; Li, Jilong; Mozolewska, Magdalena A.; Sieradzan, Adam K.; Smadbeck, James; Wirecki, Tomasz; Cooper, Seth; Flatten, Jeff; Xu, Kefan; Baker, David; Cheng, Jianlin; Delbem, Alexandre C. B.; Floudas, Christodoulos A.; Keasar, Chen; Levitt, Michael; Popović, Zoran; Scheraga, Harold A.; Skolnick, Jeffrey; Crivelli, Silvia N.; Players, Foldit

    2014-01-01

    The protein structure prediction problem continues to elude scientists. Despite the introduction of many methods, only modest gains were made over the last decade for certain classes of prediction targets. To address this challenge, a social-media based worldwide collaborative effort, named WeFold, was undertaken by thirteen labs. During the collaboration, the labs were simultaneously competing with each other. Here, we present the first attempt at “coopetition” in scientific research applied to the protein structure prediction and refinement problems. The coopetition was possible by allowing the participating labs to contribute different components of their protein structure prediction pipelines and create new hybrid pipelines that they tested during CASP10. This manuscript describes both successes and areas needing improvement as identified throughout the first WeFold experiment and discusses the efforts that are underway to advance this initiative. A footprint of all contributions and structures are publicly accessible at http://www.wefold.org. PMID:24677212

  11. WeFold: a coopetition for protein structure prediction.

    PubMed

    Khoury, George A; Liwo, Adam; Khatib, Firas; Zhou, Hongyi; Chopra, Gaurav; Bacardit, Jaume; Bortot, Leandro O; Faccioli, Rodrigo A; Deng, Xin; He, Yi; Krupa, Pawel; Li, Jilong; Mozolewska, Magdalena A; Sieradzan, Adam K; Smadbeck, James; Wirecki, Tomasz; Cooper, Seth; Flatten, Jeff; Xu, Kefan; Baker, David; Cheng, Jianlin; Delbem, Alexandre C B; Floudas, Christodoulos A; Keasar, Chen; Levitt, Michael; Popović, Zoran; Scheraga, Harold A; Skolnick, Jeffrey; Crivelli, Silvia N

    2014-09-01

    The protein structure prediction problem continues to elude scientists. Despite the introduction of many methods, only modest gains were made over the last decade for certain classes of prediction targets. To address this challenge, a social-media based worldwide collaborative effort, named WeFold, was undertaken by 13 labs. During the collaboration, the laboratories were simultaneously competing with each other. Here, we present the first attempt at "coopetition" in scientific research applied to the protein structure prediction and refinement problems. The coopetition was possible by allowing the participating labs to contribute different components of their protein structure prediction pipelines and create new hybrid pipelines that they tested during CASP10. This manuscript describes both successes and areas needing improvement as identified throughout the first WeFold experiment and discusses the efforts that are underway to advance this initiative. A footprint of all contributions and structures are publicly accessible at http://www.wefold.org. PMID:24677212

  12. pyDockSAXS: protein-protein complex structure by SAXS and computational docking.

    PubMed

    Jiménez-García, Brian; Pons, Carles; Svergun, Dmitri I; Bernadó, Pau; Fernández-Recio, Juan

    2015-07-01

    Structural characterization of protein-protein interactions at molecular level is essential to understand biological processes and identify new therapeutic opportunities. However, atomic resolution structural techniques cannot keep pace with current advances in interactomics. Low-resolution structural techniques, such as small-angle X-ray scattering (SAXS), can be applied at larger scale, but they miss atomic details. For efficient application to protein-protein complexes, low-resolution information can be combined with theoretical methods that provide energetic description and atomic details of the interactions. Here we present the pyDockSAXS web server (http://life.bsc.es/pid/pydocksaxs) that provides an automatic pipeline for modeling the structure of a protein-protein complex from SAXS data. The method uses FTDOCK to generate rigid-body docking models that are subsequently evaluated by a combination of pyDock energy-based scoring function and their capacity to describe SAXS data. The only required input files are structural models for the interacting partners and a SAXS curve. The server automatically provides a series of structural models for the complex, sorted by the pyDockSAXS scoring function. The user can also upload a previously computed set of docking poses, which opens the possibility to filter the docking solutions by potential interface residues or symmetry restraints. The server is freely available to all users without restriction. PMID:25897115

  13. Novel bioresorbabale composite fiber structures loaded with proteins for tissue regeneration applications: microstructure and protein release.

    PubMed

    Levy, Yair; Zilberman, Meital

    2006-12-15

    Novel bioresorbable core/shell composite fiber structures loaded with proteins were developed and studied. These unique polymeric structures are designed to combine good mechanical properties with a desired controlled protein-release profile, to serve as scaffolds for tissue regeneration applications. Core/shell fiber structures were formed by "coating" poly(L-lactic acid) fibers with protein-containing poly(DL-lactic-co-glycolic acid) porous structures. Shell preparation (coating) was performed by the freeze-drying of water in oil emulsions. The present study focused on the effect of the emulsion's formulation on the porous shell structure and on the resulting cumulative protein release from the composite fibers for 90 days. Horseradish peroxidase (HRP) was used as the protein source. The release profiles usually exhibited an initial burst effect, accompanied by a decrease in release rate with time, as is typical for diffusion-controlled systems. The HRP content and the emulsion's organic:aqueous phase ratio exhibited significant effects on both the shell microstructure and the HRP release profile from the composite fibers, whereas the polymer content of the emulsion's organic phase only affected these fiber characteristics in certain cases. Proper selection of the emulsion's parameters can yield core/shell fiber structures with the desired protein release behavior and other useful physical properties. PMID:16883584

  14. Protein 3D Structure Computed from Evolutionary Sequence Variation

    PubMed Central

    Sheridan, Robert; Hopf, Thomas A.; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris

    2011-01-01

    The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing. In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy. We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues., including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7–4.8 Å Cα-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org). This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein

  15. Fluorinated proteins: from design and synthesis to structure and stability.

    PubMed

    Marsh, E Neil G

    2014-10-21

    recent detailed thermodynamic and structural studies in our laboratory have uncovered the basis for the remarkably general ability of fluorinated side chains to stabilize protein structure. Crystal structures of α4H and its fluorinated analogues show that the fluorinated residues fit into the hydrophobic core with remarkably little perturbation to the structure. This is explained by the fact that fluorinated side chains, although larger, very closely preserve the shape of the hydrophobic amino acids they replace. Thus, an increase in buried hydrophobic surface area in the folded state is responsible for the additional thermodynamic stability of the fluorinated protein. Measurements of ΔG°, ΔH°, ΔS°, and ΔCp° for unfolding demonstrate that the "fluorous" stabilization of these protein arises from the hydrophobic effect in the same way that hydrophobic partitioning stabilizes natural proteins. PMID:24883933

  16. The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from streptococcus pyogenes.

    SciTech Connect

    Chang, C.; Coggill, P.; Bateman, A.; Finn, R.; Cymborowski, M.; Otwinowski, Z.; Minor, W.; Volkart, L.; Joachimiak, A.; Wellcome Trust Sanger Inst.; Univ. of Virginia; UT Southwestern Medical Center

    2009-12-17

    Many Gram-positive lactic acid bacteria (LAB) produce anti-bacterial peptides and small proteins called bacteriocins, which enable them to compete against other bacteria in the environment. These peptides fall structurally into three different classes, I, II, III, with class IIa being pediocin-like single entities and class IIb being two-peptide bacteriocins. Self-protective cognate immunity proteins are usually co-transcribed with these toxins. Several examples of cognates for IIa have already been solved structurally. Streptococcus pyogenes, closely related to LAB, is one of the most common human pathogens, so knowledge of how it competes against other LAB species is likely to prove invaluable. We have solved the crystal structure of the gene-product of locus Spy-2152 from S. pyogenes, (PDB: 2fu2), and found it to comprise an anti-parallel four-helix bundle that is structurally similar to other bacteriocin immunity proteins. Sequence analyses indicate this protein to be a possible immunity protein protective against class IIa or IIb bacteriocins. However, given that S. pyogenes appears to lack any IIa pediocin-like proteins but does possess class IIb bacteriocins, we suggest this protein confers immunity to IIb-like peptides. Combined structural, genomic and proteomic analyses have allowed the identification and in silico characterization of a new putative immunity protein from S. pyogenes, possibly the first structure of an immunity protein protective against potential class IIb two-peptide bacteriocins. We have named the two pairs of putative bacteriocins found in S. pyogenes pyogenecin 1, 2, 3 and 4.

  17. Protein Structure Refinement Using 13Cα Chemical Shift Tensors

    PubMed Central

    Wylie, Benjamin J.; Schwieters, Charles D.; Oldfield, Eric; Rienstra, Chad M.

    2009-01-01

    We have obtained the 13Cα chemical shift tensors for each amino acid in the protein GB1. We then developed a CST force field and incorporated this into the Xplor-NIH structure determination program. GB1 structures obtained by using CST restraints had improved precision over those obtained in the absence of CST restraints, and were also more accurate. When combined with isotropic chemical shifts, distance and vector angle restraints, the root-mean squared error with respect to existing x-ray structures was better than ~1.0 Å. These results are of broad general interest since they show that chemical shift tensors can be used in protein structure refinement, improving both structural accuracy and precision, opening up the way to accurate de novo structure determination. PMID:19123862

  18. Rotational order–disorder structure of fluorescent protein FP480

    SciTech Connect

    Pletnev, Sergei; Morozova, Kateryna S.; Verkhusha, Vladislav V.; Dauter, Zbigniew

    2009-09-01

    An analysis of the rotational order–disorder structure of fluorescent protein FP480 is presented. In the last decade, advances in instrumentation and software development have made crystallography a powerful tool in structural biology. Using this method, structural information can now be acquired from pathological crystals that would have been abandoned in earlier times. In this paper, the order–disorder (OD) structure of fluorescent protein FP480 is discussed. The structure is composed of tetramers with 222 symmetry incorporated into the lattice in two different ways, namely rotated 90° with respect to each other around the crystal c axis, with tetramer axes coincident with crystallographic twofold axes. The random distribution of alternatively oriented tetramers in the crystal creates a rotational OD structure with statistically averaged I422 symmetry, although the presence of very weak and diffuse additional reflections suggests that the randomness is only approximate.

  19. Redundancy-weighting for better inference of protein structural features

    PubMed Central

    Yanover, Chen; Vanetik, Natalia; Levitt, Michael; Kolodny, Rachel; Keasar, Chen

    2014-01-01

    Motivation: Structural knowledge, extracted from the Protein Data Bank (PDB), underlies numerous potential functions and prediction methods. The PDB, however, is highly biased: many proteins have more than one entry, while entire protein families are represented by a single structure, or even not at all. The standard solution to this problem is to limit the studies to non-redundant subsets of the PDB. While alleviating biases, this solution hides the many-to-many relations between sequences and structures. That is, non-redundant datasets conceal the diversity of sequences that share the same fold and the existence of multiple conformations for the same protein. A particularly disturbing aspect of non-redundant subsets is that they hardly benefit from the rapid pace of protein structure determination, as most newly solved structures fall within existing families. Results: In this study we explore the concept of redundancy-weighted datasets, originally suggested by Miyazawa and Jernigan. Redundancy-weighted datasets include all available structures and associate them (or features thereof) with weights that are inversely proportional to the number of their homologs. Here, we provide the first systematic comparison of redundancy-weighted datasets with non-redundant ones. We test three weighting schemes and show that the distributions of structural features that they produce are smoother (having higher entropy) compared with the distributions inferred from non-redundant datasets. We further show that these smoothed distributions are both more robust and more correct than their non-redundant counterparts. We suggest that the better distributions, inferred using redundancy-weighting, may improve the accuracy of knowledge-based potentials and increase the power of protein structure prediction methods. Consequently, they may enhance model-driven molecular biology. Contact: cheny@il.ibm.com or chen.keasar@gmail.com PMID:24771517

  20. Refolding and purification of recombinant L-asparaginase from inclusion bodies of E. coli into active tetrameric protein.

    PubMed

    Upadhyay, Arun K; Singh, Anupam; Mukherjee, K J; Panda, Amulya K

    2014-01-01

    A tetrameric protein of therapeutic importance, Escherichia coli L-asparaginase-II was expressed in Escherichia coli as inclusion bodies (IBs). Asparaginase IBs were solubilized using low concentration of urea and refolded into active tetrameric protein using pulsatile dilution method. Refolded asparaginase was purified in two steps by ion-exchange and gel filtration chromatographic techniques. The recovery of bioactive asparaginase from IBs was around 50%. The melting temperature (Tm) of the purified asparaginase was found to be 64°C. The specific activity of refolded, purified asparaginase was found to be comparable to the commercial asparaginase (190 IU/mg). Enzymatic activity of the refolded asparaginase was high even at four molar urea solutions, where the IB aggregates are completely solubilized. From the comparison of chemical denaturation data and activity at different concentrations of guanidine hydrochloride, it was observed that dissociation of monomeric units precedes the complete loss of helical secondary structures. Protection of the existing native-like protein structure during solubilization of IB aggregates with 4 M urea improved the propensity of monomer units to form oligomeric structure. Our mild solubilization technique retaining native-like structures, improved recovery of asparaginase in bioactive tetrameric form. PMID:25309524

  1. Refolding and purification of recombinant L-asparaginase from inclusion bodies of E. coli into active tetrameric protein

    PubMed Central

    Upadhyay, Arun K.; Singh, Anupam; Mukherjee, K. J.; Panda, Amulya K.

    2014-01-01

    A tetrameric protein of therapeutic importance, Escherichia coli L-asparaginase-II was expressed in Escherichia coli as inclusion bodies (IBs). Asparaginase IBs were solubilized using low concentration of urea and refolded into active tetrameric protein using pulsatile dilution method. Refolded asparaginase was purified in two steps by ion-exchange and gel filtration chromatographic techniques. The recovery of bioactive asparaginase from IBs was around 50%. The melting temperature (Tm) of the purified asparaginase was found to be 64°C. The specific activity of refolded, purified asparaginase was found to be comparable to the commercial asparaginase (190 IU/mg). Enzymatic activity of the refolded asparaginase was high even at four molar urea solutions, where the IB aggregates are completely solubilized. From the comparison of chemical denaturation data and activity at different concentrations of guanidine hydrochloride, it was observed that dissociation of monomeric units precedes the complete loss of helical secondary structures. Protection of the existing native-like protein structure during solubilization of IB aggregates with 4 M urea improved the propensity of monomer units to form oligomeric structure. Our mild solubilization technique retaining native-like structures, improved recovery of asparaginase in bioactive tetrameric form. PMID:25309524

  2. RBO Aleph: leveraging novel information sources for protein structure prediction

    PubMed Central

    Mabrouk, Mahmoud; Putz, Ines; Werner, Tim; Schneider, Michael; Neeb, Moritz; Bartels, Philipp; Brock, Oliver

    2015-01-01

    RBO Aleph is a novel protein structure prediction web server for template-based modeling, protein contact prediction and ab initio structure prediction. The server has a strong emphasis on modeling difficult protein targets for which templates cannot be detected. RBO Aleph's unique features are (i) the use of combined evolutionary and physicochemical information to perform residue–residue contact prediction and (ii) leveraging this contact information effectively in conformational space search. RBO Aleph emerged as one of the leading approaches to ab initio protein structure prediction and contact prediction during the most recent Critical Assessment of Protein Structure Prediction experiment (CASP11, 2014). In addition to RBO Aleph's main focus on ab initio modeling, the server also provides state-of-the-art template-based modeling services. Based on template availability, RBO Aleph switches automatically between template-based modeling and ab initio prediction based on the target protein sequence, facilitating use especially for non-expert users. The RBO Aleph web server offers a range of tools for visualization and data analysis, such as the visualization of predicted models, predicted contacts and the estimated prediction error along the model's backbone. The server is accessible at http://compbio.robotics.tu-berlin.de/rbo_aleph/. PMID:25897112

  3. RBO Aleph: leveraging novel information sources for protein structure prediction.

    PubMed

    Mabrouk, Mahmoud; Putz, Ines; Werner, Tim; Schneider, Michael; Neeb, Moritz; Bartels, Philipp; Brock, Oliver

    2015-07-01

    RBO Aleph is a novel protein structure prediction web server for template-based modeling, protein contact prediction and ab initio structure prediction. The server has a strong emphasis on modeling difficult protein targets for which templates cannot be detected. RBO Aleph's unique features are (i) the use of combined evolutionary and physicochemical information to perform residue-residue contact prediction and (ii) leveraging this contact information effectively in conformational space search. RBO Aleph emerged as one of the leading approaches to ab initio protein structure prediction and contact prediction during the most recent Critical Assessment of Protein Structure Prediction experiment (CASP11, 2014). In addition to RBO Aleph's main focus on ab initio modeling, the server also provides state-of-the-art template-based modeling services. Based on template availability, RBO Aleph switches automatically between template-based modeling and ab initio prediction based on the target protein sequence, facilitating use especially for non-expert users. The RBO Aleph web server offers a range of tools for visualization and data analysis, such as the visualization of predicted models, predicted contacts and the estimated prediction error along the model's backbone. The server is accessible at http://compbio.robotics.tu-berlin.de/rbo_aleph/. PMID:25897112

  4. Structural domains and main-chain flexibility in prion proteins.

    PubMed

    Blinov, N; Berjanskii, M; Wishart, D S; Stepanova, M

    2009-02-24

    In this study we describe a novel approach to define structural domains and to characterize the local flexibility in both human and chicken prion proteins. The approach we use is based on a comprehensive theory of collective dynamics in proteins that was recently developed. This method determines the essential collective coordinates, which can be found from molecular dynamics trajectories via principal component analysis. Under this particular framework, we are able to identify the domains where atoms move coherently while at the same time to determine the local main-chain flexibility for each residue. We have verified this approach by comparing our results for the predicted dynamic domain systems with the computed main-chain flexibility profiles and the NMR-derived random coil indexes for human and chicken prion proteins. The three sets of data show excellent agreement. Additionally, we demonstrate that the dynamic domains calculated in this fashion provide a highly sensitive measure of protein collective structure and dynamics. Furthermore, such an analysis is capable of revealing structural and dynamic properties of proteins that are inaccessible to the conventional assessment of secondary structure. Using the collective dynamic simulation approach described here along with a high-temperature simulations of unfolding of human prion protein, we have explored whether locations of relatively low stability could be identified where the unfolding process could potentially be facilitated. According to our analysis, the locations of relatively low stability may be associated with the beta-sheet formed by strands S1 and S2 and the adjacent loops, whereas helix HC appears to be a relatively stable part of the protein. We suggest that this kind of structural analysis may provide a useful background for a more quantitative assessment of potential routes of spontaneous misfolding in prion proteins. PMID:19178154

  5. The Challenge of Producing Ubiquitinated Proteins for Structural Studies

    PubMed Central

    Faggiano, Serena; Pastore, Annalisa

    2014-01-01

    Protein ubiquitination is an important post-translational modification involved in several essential signalling pathways. It has different effects on the target protein substrate, i.e., it can trigger the degradation of the protein in the proteasome, change the interactions of the modified protein with its partners, or affect its localization and activity. In order to understand the molecular mechanisms underlying the consequences of protein ubiquitination, scientists have to face the challenging task of producing ubiquitinated proteins for structural characterization with X-ray crystallography and/or nuclear magnetic resonance (NMR) spectroscopy. These techniques require milligrams of homogeneous samples of high purity. The strategies proposed so far for the production of ubiquitinated proteins can be divided into two groups, i.e., chemical (or non-enzymatic) and enzymatic methodologies. In this review, we summarize the still very sparse examples available in the literature that describe successful production of ubiquitinated proteins amenable for biochemical and structural studies, and discuss advantages and disadvantages of the techniques proposed. We also give a perspective of the direction in which the field might evolve. PMID:24926903

  6. Linking structural features of protein complexes and biological function.

    PubMed

    Sowmya, Gopichandran; Breen, Edmond J; Ranganathan, Shoba

    2015-09-01

    Protein-protein interaction (PPI) establishes the central basis for complex cellular networks in a biological cell. Association of proteins with other proteins occurs at varying affinities, yet with a high degree of specificity. PPIs lead to diverse functionality such as catalysis, regulation, signaling, immunity, and inhibition, playing a crucial role in functional genomics. The molecular principle of such interactions is often elusive in nature. Therefore, a comprehensive analysis of known protein complexes from the Protein Data Bank (PDB) is essential for the characterization of structural interface features to determine structure-function relationship. Thus, we analyzed a nonredundant dataset of 278 heterodimer protein complexes, categorized into major functional classes, for distinguishing features. Interestingly, our analysis has identified five key features (interface area, interface polar residue abundance, hydrogen bonds, solvation free energy gain from interface formation, and binding energy) that are discriminatory among the functional classes using Kruskal-Wallis rank sum test. Significant correlations between these PPI interface features amongst functional categories are also documented. Salt bridges correlate with interface area in regulator-inhibitors (r = 0.75). These representative features have implications for the prediction of potential function of novel protein complexes. The results provide molecular insights for better understanding of PPIs and their relation to biological functions. PMID:26131659

  7. Structural Insights into KCTD Protein Assembly and Cullin3 Recognition.

    PubMed

    Ji, Alan X; Chu, Anh; Nielsen, Tine Kragh; Benlekbir, Samir; Rubinstein, John L; Privé, Gilbert G

    2016-01-16

    Cullin3 (Cul3)-based ubiquitin E3 ligase complexes catalyze the transfer of ubiquitin from an E2 enzyme to target substrate proteins. In these assemblies, the C-terminal region of Cul3 binds Rbx1/E2-ubiquitin, while the N-terminal region interacts with various BTB (bric-à-brac, tramtrack, broad complex) domain proteins that serve as substrate adaptors. Previous crystal structures of the homodimeric BTB proteins KLHL3, KLHL11 and SPOP in complex with the N-terminal domain of Cul3 revealed the features required for Cul3 recognition in these proteins. A second class of BTB-domain-containing proteins, the KCTD proteins, is also Cul3 substrate adaptors, but these do not share many of the previously identified determinants for Cul3 binding. We report the pentameric crystal structures of the KCTD1 and KCTD9 BTB domains and identify plasticity in the KCTD1 rings. We find that the KCTD proteins 5, 6, 9 and 17 bind to Cul3 with high affinity, while the KCTD proteins 1 and 16 do not have detectable binding. Finally, we confirm the 5:5 assembly of KCTD9/Cul3 complexes by cryo-electron microscopy and provide a molecular rationale for BTB-mediated Cul3 binding specificity in the KCTD family. PMID:26334369

  8. 3D structures of membrane proteins from genomic sequencing

    PubMed Central

    Hopf, Thomas A.; Colwell, Lucy J.; Sheridan, Robert; Rost, Burkhard; Sander, Chris; Marks, Debora S.

    2012-01-01

    Summary We show that amino acid co-variation in proteins, extracted from the evolutionary sequence record, can be used to fold transmembrane proteins. We use this technique to predict previously unknown, 3D structures for 11 transmembrane proteins (with up to 14 helices) from their sequences alone. The prediction method (EVfold_membrane), applies a maximum entropy approach to infer evolutionary co-variation in pairs of sequence positions within a protein family and then generates all-atom models with the derived pairwise distance constraints. We benchmark the approach with blinded, de novo computation of known transmembrane protein structures from 23 families, demonstrating unprecedented accuracy of the method for large transmembrane proteins. We show how the method can predict oligomerization, functional sites, and conformational changes in transmembrane proteins. With the rapid rise in large-scale sequencing, more accurate and more comprehensive information on evolutionary constraints can be decoded from genetic variation, greatly expanding the repertoire of transmembrane proteins amenable to modelling by this method. PMID:22579045

  9. Protein-associated water and secondary structure effect removal of blood proteins from metallic substrates.

    PubMed

    Anand, Gaurav; Zhang, Fuming; Linhardt, Robert J; Belfort, Georges

    2011-03-01

    Removing adsorbed protein from metals has significant health and industrial consequences. There are numerous protein-adsorption studies using model self-assembled monolayers or polymeric substrates but hardly any high-resolution measurements of adsorption and removal of proteins on industrially relevant transition metals. Surgeons and ship owners desire clean metal surfaces to reduce transmission of disease via surgical instruments and minimize surface fouling (to reduce friction and corrosion), respectively. A major finding of this work is that, besides hydrophobic interaction adhesion energy, water content in an adsorbed protein layer and secondary structure of proteins determined the access and hence ability to remove adsorbed proteins from metal surfaces with a strong alkaline-surfactant solution (NaOH and 5 mg/mL SDS in PBS at pH 11). This is demonstrated with three blood proteins (bovine serum albumin, immunoglobulin, and fibrinogen) and four transition metal substrates and stainless steel (platinum (Pt), gold (Au), tungsten (W), titanium (Ti), and 316 grade stainless steel (SS)). All the metallic substrates were checked for chemical contaminations like carbon and sulfur and were characterized using X-ray photoelectron spectroscopy (XPS). While Pt and Au surfaces were oxide-free (fairly inert elements), W, Ti, and SS substrates were associated with native oxide. Difference measurements between a quartz crystal microbalance with dissipation (QCM-D) and surface plasmon resonance spectroscopy (SPR) provided a measure of the water content in the protein-adsorbed layers. Hydrophobic adhesion forces, obtained with atomic force microscopy, between the proteins and the metals correlated with the amount of the adsorbed protein-water complex. Thus, the amount of protein adsorbed decreased with Pt, Au, W, Ti and SS, in this order. Neither sessile contact angle nor surface roughness of the metal substrates was useful as predictors here. All three globular proteins

  10. A photon-free approach to transmembrane protein structure determination.

    PubMed

    Soto, Cinque S; Hannigan, Brett T; DeGrado, William F

    2011-12-01

    The structures of membrane proteins are generally solved using samples dissolved in micelles, bicelles, or occasionally phospholipid bilayers using X-ray diffraction or magnetic resonance. Because these are less than perfect mimics of true biological membranes, the structures are often confirmed by evaluating the effects of mutations on the properties of the protein in their native cellular environments. Low-resolution structures are also sometimes generated from the results of site-directed mutagenesis when other structural data are incomplete or not available. Here, we describe a rapid and automated approach to determine structures from data on site-directed mutants for the special case of homo-oligomeric helical bundles. The method uses as input an experimental profile of the effects of mutations on some property of the protein. This profile is then interpreted by assuming that positions that have large effects on structure/function when mutated project toward the center of the oligomeric bundle. Model bundles are generated, and correlation analysis is used to score which structures have inter-subunit C(β) distances between adjoining monomers that best correlate with the experimental profile. These structures are then clustered and refined using energy-based minimization methods. For a set of 10 homo-oligomeric TM protein structures ranging from dimers to pentamers, we show that our method predicts structures to within 1-2 Å backbone RMSD relative to X-ray and NMR structures. This level of agreement approaches the precision of NMR structures solved in different membrane mimetics. PMID:22024595

  11. Synergistic effect of temperature, protein and salt concentration on structures and interactions among lysozyme proteins

    NASA Astrophysics Data System (ADS)

    Kundu, Sarathi; Aswal, V. K.; Kohlbrecher, Joachim

    2016-07-01

    Synergistic effect of temperature, protein and salt concentration on structures and interactions among lysozyme proteins in solution has been studied using small angle neutron scattering technique. Scattering study shows that for a particular protein concentration, with increasing temperature, short-range attraction decreases but long-range repulsion becomes system specific. In absence of salt, lower value of attractive interaction is obtained, however, in presence of salt it becomes higher and decreases with increasing temperature. For specific condition, weak long range attraction and intermediate range repulsion exists. At higher temperature (90 °C), fractal structure develops and the corresponding fractal dimension depends upon the experimental conditions.

  12. Data mining of metal ion environments present in protein structures.

    PubMed

    Zheng, Heping; Chruszcz, Maksymilian; Lasota, Piotr; Lebioda, Lukasz; Minor, Wladek

    2008-09-01

    Analysis of metal-protein interaction distances, coordination numbers, B-factors (displacement parameters), and occupancies of metal-binding sites in protein structures determined by X-ray crystallography and deposited in the PDB shows many unusual values and unexpected correlations. By measuring the frequency of each amino acid in metal ion-binding sites, the positive or negative preferences of each residue for each type of cation were identified. Our approach may be used for fast identification of metal-binding structural motifs that cannot be identified on the basis of sequence similarity alone. The analysis compares data derived separately from high and medium-resolution structures from the PDB with those from very high-resolution small-molecule structures in the Cambridge Structural Database (CSD). For high-resolution protein structures, the distribution of metal-protein or metal-water interaction distances agrees quite well with data from CSD, but the distribution is unrealistically wide for medium (2.0-2.5A) resolution data. Our analysis of cation B-factors versus average B-factors of atoms in the cation environment reveals substantial numbers of structures contain either an incorrect metal ion assignment or an unusual coordination pattern. Correlation between data resolution and completeness of the metal coordination spheres is also found. PMID:18614239

  13. Protein structure prediction enhanced with evolutionary diversity : SPEED.

    SciTech Connect

    DeBartolo, J.; Hocky, G.; Wilde, M.; Xu, J.; Freed, K. F.; Sosnick, T. R.; Univ. of Chicago; Toyota Technological Inst. at Chicago

    2010-03-01

    For naturally occurring proteins, similar sequence implies similar structure. Consequently, multiple sequence alignments (MSAs) often are used in template-based modeling of protein structure and have been incorporated into fragment-based assembly methods. Our previous homology-free structure prediction study introduced an algorithm that mimics the folding pathway by coupling the formation of secondary and tertiary structure. Moves in the Monte Carlo procedure involve only a change in a single pair of {phi},{psi} backbone dihedral angles that are obtained from a Protein Data Bank-based distribution appropriate for each amino acid, conditional on the type and conformation of the flanking residues. We improve this method by using MSAs to enrich the sampling distribution, but in a manner that does not require structural knowledge of any protein sequence (i.e., not homologous fragment insertion). In combination with other tools, including clustering and refinement, the accuracies of the predicted secondary and tertiary structures are substantially improved and a global and position-resolved measure of confidence is introduced for the accuracy of the predictions. Performance of the method in the Critical Assessment of Structure Prediction (CASP8) is discussed.

  14. Enhanced protein fold recognition using a structural alphabet.

    PubMed

    Deschavanne, Patrick; Tufféry, Pierre

    2009-07-01

    Fold recognition from sequence can be an important step in protein structure and function prediction. Many methods have tackled this goal. Most of them, based on sequence alignment, fail for sequences of low similarity. Alignment-free approaches can provide an efficient alternative. For such approaches, the identification of efficient fold discriminatory features is critical. We propose a new fold recognition approach that relies on the encoding of the local structure of proteins using a Hidden Markov Model Structural Alphabet. This encoding provides a 1D description of the conformation of complete proteins structures, including loops. At the fold level, compared with the classical secondary structure helix, strand, and coil states, such encoding is expected to provide the means of a better discrimination between loop conformations, hence providing better fold identification. Compared with previous related approaches, this supplement of information results in significant improvement. When combining this information with supplementary information of secondary structure and residue burial, we obtain a fold recognition accuracy of 78% for 27 protein families, that is, 8% higher than the best available method so far, and of 68% for 60 families. Corresponding scores at the class level are of 92% and 90% indicating that mispredictions are mostly within structural classes. PMID:19089985

  15. Data mining of metal ion environments present in protein structures

    PubMed Central

    Zheng, Heping; Chruszcz, Maksymilian; Lasota, Piotr; Lebioda, Lukasz; Minor, Wladek

    2010-01-01

    Analysis of metal-protein interaction distances, coordination numbers, B-factors (displacement parameters), and occupancies of metal binding sites in protein structures determined by X-ray crystallography and deposited in the PDB shows many unusual values and unexpected correlations. By measuring the frequency of each amino acid in metal ion binding sites, the positive or negative preferences of each residue for each type of cation were identified. Our approach may be used for fast identification of metal-binding structural motifs that cannot be identified on the basis of sequence similarity alone. The analysis compares data derived separately from high and medium resolution structures from the PDB with those from very high resolution small-molecule structures in the Cambridge Structural Database (CSD). For high resolution protein structures, the distribution of metal-protein or metal-water interaction distances agrees quite well with data from CSD, but the distribution is unrealistically wide for medium (2.0 – 2.5 Å) resolution data. Our analysis of cation B-factors versus average B-factors of atoms in the cation environment reveals substantial numbers of structures contain either an incorrect metal ion assignment or an unusual coordination pattern. Correlation between data resolution and completeness of the metal coordination spheres is also found. PMID:18614239

  16. Scoring docking conformations using predicted protein interfaces

    PubMed Central

    2014-01-01

    Background Since proteins function by interacting with other molecules, analysis of protein-protein interactions is essential for comprehending biological processes. Whereas understanding of atomic interactions within a complex is especially useful for drug design, limitations of experimental techniques have restricted their practical use. Despite progress in docking predictions, there is still room for improvement. In this study, we contribute to this topic by proposing T-PioDock, a framework for detection of a native-like docked complex 3D structure. T-PioDock supports the identification of near-native conformations from 3D models that docking software produced by scoring those models using binding interfaces predicted by the interface predictor, Template based Protein Interface Prediction (T-PIP). Results First, exhaustive evaluation of interface predictors demonstrates that T-PIP, whose predictions are customised to target complexity, is a state-of-the-art method. Second, comparative study between T-PioDock and other state-of-the-art scoring methods establishes T-PioDock as the best performing approach. Moreover, there is good correlation between T-PioDock performance and quality of docking models, which suggests that progress in docking will lead to even better results at recognising near-native conformations. Conclusion Accurate identification of near-native conformations remains a challenging task. Although availability of 3D complexes will benefit from template-based methods such as T-PioDock, we have identified specific limitations which need to be addressed. First, docking software are still not able to produce native like models for every target. Second, current interface predictors do not explicitly consider pairwise residue interactions between proteins and their interacting partners which leaves ambiguity when assessing quality of complex conformations. PMID:24906633

  17. Backbone Solution Structures of Proteins Using Residual Dipolar Couplings: Application to a Novel Structural Genomics Target

    PubMed Central

    Valafar, H.; Mayer, K. L.; Bougault, C. M.; LeBlond, P. D.; Jenney, F. E.; Brereton, P. S.; Adams, M.W.W.; Prestegard, J.H.

    2006-01-01

    Structural genomics (or proteomics) activities are critically dependent on the availability of high-throughput structure determination methodology. Development of such methodology has been a particular challenge for NMR based structure determination because of the demands for isotopic labeling of proteins and the requirements for very long data acquisition times. We present here a methodology that gains efficiency from a focus on determination of backbone structures of proteins as opposed to full structures with all side chains in place. This focus is appropriate given the presumption that many protein structures in the future will be built using computational methods that start from representative fold family structures and replace as many as 70% of the side chains in the course of structure determination. The methodology we present is based primarily on residual dipolar couplings (RDCs), readily accessible NMR observables that constrain the orientation of backbone fragments irrespective of separation in space. A new software tool is described for the assembly of backbone fragments under RDC constraints and an application to a structural genomics target is presented. The target is an 8.7 kDa protein from Pyrococcus furiosus, PF1061, that was previously not well annotated, and had a nearest structurally characterized neighbor with only 33% sequence identity. The structure produced shows structural similarity to this sequence homologue, but also shows similarity to other proteins that suggests a functional role in sulfur transfer. Given the backbone structure and a possible functional link this should be an ideal target for development of modeling methods. PMID:15704012

  18. Structural studies of human glioma pathogenesis-related protein 1

    PubMed Central

    Asojo, Oluwatoyin A.; Koski, Raymond A.; Bonafé, Nathalie

    2011-01-01

    Human glioma pathogenesis-related protein 1 (GLIPR1) is a membrane protein that is highly upregulated in brain cancers but is barely detectable in normal brain tissue. GLIPR1 is composed of a signal peptide that directs its secretion, a conserved cysteine-rich CAP (cysteine-rich secretory proteins, antigen 5 and pathogenesis-related 1 proteins) domain and a transmembrane domain. GLIPR1 is currently being investigated as a candidate for prostate cancer gene therapy and for glioblastoma targeted therapy. Crystal structures of a truncated soluble domain of the human GLIPR1 protein (sGLIPR1) solved by molecular replacement using a truncated polyalanine search model of the CAP domain of stecrisp, a snake-venom cysteine-rich secretory protein (CRISP), are presented. The correct molecular-replacement solution could only be obtained by removing all loops from the search model. The native structure was refined to 1.85 Å resolution and that of a Zn2+ complex was refined to 2.2 Å resolution. The latter structure revealed that the putative binding cavity coordinates Zn2+ similarly to snake-venom CRISPs, which are involved in Zn2+-dependent mechanisms of inflammatory modulation. Both sGLIPR1 structures have extensive flexible loop/turn regions and unique charge distributions that were not observed in any of the previously reported CAP protein structures. A model is also proposed for the structure of full-length membrane-bound GLIPR1. PMID:21931216

  19. MALISAM: a database of structurally analogous motifs in proteins.

    PubMed

    Cheng, Hua; Kim, Bong-Hyun; Grishin, Nick V

    2008-01-01

    MALISAM (manual alignments for structurally analogous motifs) represents the first database containing pairs of structural analogs and their alignments. To find reliable analogs, we developed an approach based on three ideas. First, an insertion together with a part of the evolutionary core of one domain family (a hybrid motif) is analogous to a similar motif contained within the core of another domain family. Second, a motif at an interface, formed by secondary structural elements (SSEs) contributed by two or more domains or subunits contacting along that interface, is analogous to a similar motif present in the core of a single domain. Third, an artificial protein obtained through selection from random peptides or in sequence design experiments not biased by sequences of a particular homologous family, is analogous to a structurally similar natural protein. Each analogous pair is superimposed and aligned manually, as well as by several commonly used programs. Applications of this database may range from protein evolution studies, e.g. development of remote homology inference tools and discriminators between homologs and analogs, to protein-folding research, since in the absence of evolutionary reasons, similarity between proteins is caused by structural and folding constraints. The database is publicly available at http://prodata.swmed.edu/malisam. PMID:17855399

  20. From protein structure to function via single crystal optical spectroscopy

    PubMed Central

    Ronda, Luca; Bruno, Stefano; Bettati, Stefano; Storici, Paola; Mozzarelli, Andrea

    2015-01-01

    The more than 100,000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic “artifacts,” including conformational selection, crystallization conditions and radiation damages, may affect the quality and the interpretation of the electron density maps, thus limiting the relevance of structure determinations. Moreover, for most of these structures, no functional data have been obtained in the crystalline state, thus posing serious questions on their validity in infereing protein mechanisms. In order to solve these issues, spectroscopic methods have been applied for the determination of equilibrium and kinetic properties of proteins in the crystalline state. These methods are UV-vis spectrophotometry, spectrofluorimetry, IR, EPR, Raman, and resonance Raman spectroscopy. Some of these approaches have been implemented with on-line instruments at X-ray synchrotron beamlines. Here, we provide an overview of investigations predominantly carried out in our laboratory by single crystal polarized absorption UV-vis microspectrophotometry, the most applied technique for the functional characterization of proteins in the crystalline state. Studies on hemoglobins, pyridoxal 5′-phosphate dependent enzymes and green fluorescent protein in the crystalline state have addressed key biological issues, leading to either straightforward structure-function correlations or limitations to structure-based mechanisms. PMID:25988179

  1. A challenging interpretation of a hexagonally layered protein structure

    SciTech Connect

    Thompson, Michael C.; Yeates, Todd O.

    2014-01-01

    The authors describe the structure determination of a hexagonally layered protein structure that suffered from a complicated combination of translational non-crystallographic symmetry and hemihedral twinning. This case serves as a reminder that broken crystallographic symmetry resulting from doubling of a unit-cell axis often requires a new choice of origin. The carboxysome is a giant protein complex that acts as a metabolic organelle in cyanobacteria and some chemoautotrophs. Its outer structure is formed by the assembly of thousands of copies of hexameric shell protein subunits into a molecular layer. The structure determination of a CcmK1 shell protein mutant (L11K) from the β-carboxysome of the cyanobacterium Synechocystis PCC6803 led to challenges in structure determination. Twinning, noncrystallographic symmetry and packing of hexameric units in a special arrangement led to initial difficulties in space-group assignment. The correct space group was clarified after initial model refinement revealed additional symmetry. This study provides an instructive example in which broken symmetry requires a new choice of unit-cell origin in order to identify the highest symmetry space group. An additional observation related to the packing arrangement of molecules in this crystal suggests that these hexameric shell proteins might have lower internal symmetry than previously believed.

  2. RepeatsDB: a database of tandem repeat protein structures

    PubMed Central

    Di Domenico, Tomás; Potenza, Emilio; Walsh, Ian; Gonzalo Parra, R.; Giollo, Manuel; Minervini, Giovanni; Piovesan, Damiano; Ihsan, Awais; Ferrari, Carlo; Kajava, Andrey V.; Tosatto, Silvio C.E.

    2014-01-01

    RepeatsDB (http://repeatsdb.bio.unipd.it/) is a database of annotated tandem repeat protein structures. Tandem repeats pose a difficult problem for the analysis of protein structures, as the underlying sequence can be highly degenerate. Several repeat types haven been studied over the years, but their annotation was done in a case-by-case basis, thus making large-scale analysis difficult. We developed RepeatsDB to fill this gap. Using state-of-the-art repeat detection methods and manual curation, we systematically annotated the Protein Data Bank, predicting 10 745 repeat structures. In all, 2797 structures were classified according to a recently proposed classification schema, which was expanded to accommodate new findings. In addition, detailed annotations were performed in a subset of 321 proteins. These annotations feature information on start and end positions for the repeat regions and units. RepeatsDB is an ongoing effort to systematically classify and annotate structural protein repeats in a consistent way. It provides users with the possibility to access and download high-quality datasets either interactively or programmatically through web services. PMID:24311564

  3. Structure of apo acyl carrier protein and a proposal to engineer protein crystallization through metal ions

    SciTech Connect

    Qiu, Xiayang; Janson, Cheryl A.

    2010-11-16

    A topic of current interest is engineering surface mutations in order to improve the success rate of protein crystallization. This report explores the possibility of using metal-ion-mediated crystal-packing interactions to facilitate rational design. Escherichia coli apo acyl carrier protein was chosen as a test case because of its high content of negatively charged carboxylates suitable for metal binding with moderate affinity. The protein was successfully crystallized in the presence of zinc ions. The crystal structure was determined to 1.1 {angstrom} resolution with MAD phasing using anomalous signals from the co-crystallized Zn{sup 2+} ions. The case study suggested an integrated strategy for crystallization and structure solution of proteins via engineering surface Asp and Glu mutants, crystallizing them in the presence of metal ions such as Zn{sup 2+} and solving the structures using anomalous signals.

  4. Structure of YqgQ Protein from Bacillus subtilis, a Conserved Hypothetical Protein

    SciTech Connect

    Lakshminarasimhan, D.; Eswaramoorthy, S; Burley, S; Swaminathan, S

    2010-01-01

    The crystal structure of the hypothetical protein YqgQ from Bacillus subtilis has been determined to 2.1 {angstrom} resolution. The crystals belonged to space group P2{sub 1}, with unit-cell parameters a = 51.85, b = 41.25, c = 55.18 {angstrom}, {beta} = 113.4{sup o}, and contained three protein molecules in the asymmetric unit. The structure was determined by the single-wavelength anomalous dispersion method using selenium-labeled protein and was refined to a final R factor of 24.7% (R{sub free} = 28.0%). The protein molecule mainly comprises a three-helical bundle. Its putative function is inferred to be single-stranded nucleic acid binding based on sequence and structural homology.

  5. The first crystal structure of an archaeal helical repeat protein

    PubMed Central

    Yoneda, Kazunari; Sakuraba, Haruhiko; Tsuge, Hideaki; Katunuma, Nobuhiko; Kuramitsu, Seiki; Kawabata, Takeshi; Ohshima, Toshihisa

    2005-01-01

    The crystal structure of ST1625p, a protein encoded by a hypothetical open reading frame ST1625 in the genome of the hyperthermophilic archaeon Sulfolobus tokodaii, was determined at 2.2 Å resolution. The only sequence similarity exhibited by the amino-acid sequence of ST1625p was a 33% identity with the sequence of SSO0983p from S. solfataricus. The 19 kDa monomeric protein was observed to consist of a right-handed superhelix assembled from a tandem repeat of ten α-­helices. A structural homology search using the DALI and MATRAS algorithms indicates that this protein can be classified as a helical repeat protein. PMID:16511116

  6. Folding and Stabilization of Native-Sequence-Reversed Proteins.

    PubMed

    Zhang, Yuanzhao; Weber, Jeffrey K; Zhou, Ruhong

    2016-01-01

    Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we investigate how the reverse-sequences of native proteins might fold by examining a series of small proteins of increasing structural complexity (α-helix, β-hairpin, α-helix bundle, and α/β-protein). Employing a tandem protein structure prediction algorithmic and molecular dynamics simulation approach, we find that the ability of reverse sequences to adopt native-like folds is strongly influenced by protein size and the flexibility of the native hydrophobic core. For β-hairpins with reverse-sequences that fail to fold, we employ a simple mutational strategy for guiding stable hairpin formation that involves the insertion of amino acids into the β-turn region. This systematic look at reverse sequence duality sheds new light on the problem of protein sequence-structure mapping and may serve to inspire new protein design and protein structure prediction protocols. PMID:27113844

  7. Folding and Stabilization of Native-Sequence-Reversed Proteins

    PubMed Central

    Zhang, Yuanzhao; Weber, Jeffrey K; Zhou, Ruhong

    2016-01-01

    Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we investigate how the reverse-sequences of native proteins might fold by examining a series of small proteins of increasing structural complexity (α-helix, β-hairpin, α-helix bundle, and α/β-protein). Employing a tandem protein structure prediction algorithmic and molecular dynamics simulation approach, we find that the ability of reverse sequences to adopt native-like folds is strongly influenced by protein size and the flexibility of the native hydrophobic core. For β-hairpins with reverse-sequences that fail to fold, we employ a simple mutational strategy for guiding stable hairpin formation that involves the insertion of amino acids into the β-turn region. This systematic look at reverse sequence duality sheds new light on the problem of protein sequence-structure mapping and may serve to inspire new protein design and protein structure prediction protocols. PMID:27113844

  8. Ion mobility mass spectrometry of peptide, protein, and protein complex ions using a radio-frequency confining drift cell.

    PubMed

    Allen, Samuel J; Giles, Kevin; Gilbert, Tony; Bush, Matthew F

    2016-02-01

    Ion mobility mass spectrometry experiments enable the characterization of mass, assembly, and shape of biological molecules and assemblies. Here, a new radio-frequency confining drift cell is characterized and used to measure the mobilities of peptide, protein, and protein complex ions. The new drift cell replaced the traveling-wave ion mobility cell in a Waters Synapt G2 HDMS. Methods for operating the drift cell and determining collision cross section values using this experimental set up are presented within the context of the original instrument control software. Collision cross sections for 349 cations and anions are reported, 155 of which are for ions that have not been characterized previously using ion mobility. The values for the remaining ions are similar to those determined using a previous radio-frequency confining drift cell and drift tubes without radial confinement. Using this device under 2 Torr of helium gas and an optimized drift voltage, denatured and native-like ions exhibited average apparent resolving powers of 14.2 and 16.5, respectively. For ions with high mobility, which are also low in mass, the apparent resolving power is limited by contributions from ion gating. In contrast, the arrival-time distributions of low-mobility, native-like ions are not well explained using only contributions from ion gating and diffusion. For those species, the widths of arrival-time distributions are most consistent with the presence of multiple structures in the gas phase. PMID:26739109

  9. Structural Assembly of Multidomain Proteins and Protein Complexes Guided by the Overall Rotational Diffusion Tensor

    PubMed Central

    Ryabov, Yaroslav; Fushman, David

    2008-01-01

    We present a simple and robust approach that uses the overall rotational diffusion tensor as a structural constraint for domain positioning in multidomain proteins and protein-protein complexes. This method offers the possibility to use NMR relaxation data for detailed structure characterization of such systems provided the structures of individual domains are available. The proposed approach extends the concept of using long-range information contained in the overall rotational diffusion tensor. In contrast to the existing approaches, we use both the principal axes and principal values of protein’s rotational diffusion tensor to determine not only the orientation but also the relative positioning of the individual domains in a protein. This is achieved by finding the domain arrangement in a molecule that provides the best possible agreement with all components of the overall rotational diffusion tensor derived from experimental data. The accuracy of the proposed approach is demonstrated for two protein systems with known domain arrangement and parameters of the overall tumbling: the HIV-1 protease homodimer and Maltose Binding Protein. The accuracy of the method and its sensitivity to domain positioning is also tested using computer-generated data for three protein complexes, for which the experimental diffusion tensors are not available. In addition, the proposed method is applied here to determine, for the first time, the structure of both open and closed conformations of Lys48-linked di-ubiquitin chain, where domain motions render impossible accurate structure determination by other methods. The proposed method opens new avenues for improving structure characterization of proteins in solution. PMID:17550252

  10. The correlation of fragmentation and structure of a protein

    SciTech Connect

    Wu, Qinyuan; Cheng, Xueheng; Van Orden, S.

    1995-12-31

    Characterization of proteins of similar structures is important to understanding the biological function of the proteins and the processes with which they are involved. Cytochrome c variants typically have similar sequences, and have similar conformations in solution with almost identical absorption spectra and redox potentials. The authors chose cytochrome c`s from bovine, tuna, rabbit and horse as a model system in studying large biomolecules using MS{sup n} of multiply charged ions generated from electrospray ionization (ESI).

  11. Modeling Structural and Genomic Constraints in the Evolution of Proteins

    NASA Astrophysics Data System (ADS)

    Bastolla, Ugo; Porto, Markus

    Macromolecules influence the phenotype of the organism where they are expressed through their function, and in particular through their interactions. Nevertheless, it is very difficult to computationally predict protein function and interactions. Moreover, only a few residues take part in them. For these reasons, models of molecular evolution usually represent folded macromolecules such as RNA or proteins and identify the function of the molecule with the folded structure, whose stability determines the modeled fitness.

  12. From Ramachandran Maps to Tertiary Structures of Proteins.

    PubMed

    DasGupta, Debarati; Kaushik, Rahul; Jayaram, B

    2015-08-27

    Sequence to structure of proteins is an unsolved problem. A possible coarse grained resolution to this entails specification of all the torsional (Φ, Ψ) angles along the backbone of the polypeptide chain. The Ramachandran map quite elegantly depicts the allowed conformational (Φ, Ψ) space of proteins which is still very large for the purposes of accurate structure generation. We have divided the allowed (Φ, Ψ) space in Ramachandran maps into 27 distinct conformations sufficient to regenerate a structure to within 5 Å from the native, at least for small proteins, thus reducing the structure prediction problem to a specification of an alphanumeric string, i.e., the amino acid sequence together with one of the 27 conformations preferred by each amino acid residue. This still theoretically results in 27(n) conformations for a protein comprising "n" amino acids. We then investigated the spatial correlations at the two-residue (dipeptide) and three-residue (tripeptide) levels in what may be described as higher order Ramachandran maps, with the premise that the allowed conformational space starts to shrink as we introduce neighborhood effects. We found, for instance, for a tripeptide which potentially can exist in any of the 27(3) "allowed" conformations, three-fourths of these conformations are redundant to the 95% confidence level, suggesting sequence context dependent preferred conformations. We then created a look-up table of preferred conformations at the tripeptide level and correlated them with energetically favorable conformations. We found in particular that Boltzmann probabilities calculated from van der Waals energies for each conformation of tripeptides correlate well with the observed populations in the structural database (the average correlation coefficient is ∼0.8). An alpha-numeric string and hence the tertiary structure can be generated for any sequence from the look-up table within minutes on a single processor and to a higher level of accuracy

  13. Structural Conservation of the Myoviridae Phage Tail Sheath Protein Fold

    SciTech Connect

    Aksyuk, Anastasia A.; Kurochkina, Lidia P.; Fokine, Andrei; Forouhar, Farhad; Mesyanzhinov, Vadim V.; Tong, Liang; Rossmann, Michael G.

    2012-02-21

    Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 {angstrom} diameter icosahedral head and a 2000 {angstrom}-long contractile tail. The structure of the whole virus was previously reported, showing that its tail organization in the extended state is similar to the well-studied Myovirus bacteriophage T4 tail. The crystal structure of a tail sheath protein fragment of phiKZ was determined to 2.4 {angstrom} resolution. Furthermore, crystal structures of two prophage tail sheath proteins were determined to 1.9 and 3.3 {angstrom} resolution. Despite low sequence identity between these proteins, all of these structures have a similar fold. The crystal structure of the phiKZ tail sheath protein has been fitted into cryo-electron-microscopy reconstructions of the extended tail sheath and of a polysheath. The structural rearrangement of the phiKZ tail sheath contraction was found to be similar to that of phage T4.

  14. Systematic spatial mapping of proteins at exocytic and endocytic structures

    PubMed Central

    Larson, Ben T.; Sochacki, Kem A.; Kindem, Jonathan M.; Taraska, Justin W.

    2014-01-01

    Vesicular secretion (exocytosis) involves the release and then compensatory recycling of vesicle components through endocytosis. This fundamental cellular process is controlled by the coordinated assembly and interactions of dozens of proteins at the plasma membrane. Understanding the molecular composition of individual exocytic and endocytic structures and their organization across the plasma membrane is critical to understanding the behavior and regulation of these two cellular processes. Here we develop a high-resolution and high-throughput fluorescence imaging–based approach for the unbiased mapping of 78 proteins at single exocytic vesicles and endocytic structures in neuroendocrine PC12 cells. This analysis uses two-color single-frame images to provide a systems-level map of the steady-state distributions of proteins at individual exocytic and endocytic structures in the cell. Along with this quantitative map, we find that both calcium-regulated exocytic vesicles (dense core vesicles) and endocytic structures (clathrin-coated structures) and the proteins associated with these structures exhibit a random spatial distribution in unstimulated neuroendocrine PC12 cells. This approach is broadly applicable for quantitatively mapping the molecular composition and spatial organization of discrete cellular processes with central molecular hubs. PMID:24807904

  15. 3-D lookup: Fast protein structure database searches

    SciTech Connect

    Holm. L.; Sander, C.

    1995-12-31

    There are far fewer classes of three-dimensional protein folds than sequence families but the problem of detecting three-dimensional similarities is NP-complete. We present a novel heuristic for identifying 3-D similarities between a query structure and the database of known protein structures. Many methods for structure alignment use a bottom-up approach, identifying first local matches and then solving a combinatorial problem in building up larger clusters of matching substructures. Here the top-down approach is to start with the global comparison and select a rough superimposition using a fast 3-D lookup of secondary structure motifs. The superimposition is then extended to an alignment of C{sup {alpha}} atoms by an iterative dynamic programming step. An all-against-all comparison of 385-representative proteins (150,000 pair comparisons) took 1 day of computer time on a single R8000 processor. In other words, one query structure is scanned against the database in a matter of minutes. The method is rated at 90% reliability at capturing statistically significant similarities. It is useful as a rapid preprocessor to a comprehensive protein structure database search system.

  16. Structure and Protein-Protein Interaction Studies on Chlamydia trachomatis Protein CT670 (YscO Homolog)

    SciTech Connect

    Lorenzini, Emily; Singer, Alexander; Singh, Bhag; Lam, Robert; Skarina, Tatiana; Chirgadze, Nickolay Y.; Savchenko, Alexei; Gupta, Radhey S.

    2010-07-28

    Comparative genomic studies have identified many proteins that are found only in various Chlamydiae species and exhibit no significant sequence similarity to any protein in organisms that do not belong to this group. The CT670 protein of Chlamydia trachomatis is one of the proteins whose genes are in one of the type III secretion gene clusters but whose cellular functions are not known. CT670 shares several characteristics with the YscO protein of Yersinia pestis, including the neighboring genes, size, charge, and secondary structure, but the structures and/or functions of these proteins remain to be determined. Although a BLAST search with CT670 did not identify YscO as a related protein, our analysis indicated that these two proteins exhibit significant sequence similarity. In this paper, we report that the CT670 crystal, solved at a resolution of 2 {angstrom}, consists of a single coiled coil containing just two long helices. Gel filtration and analytical ultracentrifugation studies showed that in solution CT670 exists in both monomeric and dimeric forms and that the monomer predominates at lower protein concentrations. We examined the interaction of CT670 with many type III secretion system-related proteins (viz., CT091, CT665, CT666, CT667, CT668, CT669, CT671, CT672, and CT673) by performing bacterial two-hybrid assays. In these experiments, CT670 was found to interact only with the CT671 protein (YscP homolog), whose gene is immediately downstream of ct670. A specific interaction between CT670 and CT671 was also observed when affinity chromatography pull-down experiments were performed. These results suggest that CT670 and CT671 are putative homologs of the YcoO and YscP proteins, respectively, and that they likely form a chaperone-effector pair.

  17. Protein structure prediction: assembly of secondary structure elements by basin-hopping.

    PubMed

    Hoffmann, Falk; Vancea, Ioan; Kamat, Sanjay G; Strodel, Birgit

    2014-10-20

    The prediction of protein tertiary structure from primary structure remains a challenging task. One possible approach to this problem is the application of basin-hopping global optimization combined with an all-atom force field. In this work, the efficiency of basin-hopping is improved by introducing an approach that derives tertiary structures from the secondary structure assignments of individual residues. This approach is termed secondary-to-tertiary basin-hopping and benchmarked for three miniproteins: trpzip, trp-cage and ER-10. For each of the three miniproteins, the secondary-to-tertiary basin-hopping approach successfully and reliably predicts their three-dimensional structure. When it is applied to larger proteins, correctly folded structures are obtained. It can be concluded that the assembly of secondary structure elements using basin-hopping is a promising tool for de novo protein structure prediction. PMID:25056272

  18. Protein-protein complex structure predictions by multimeric threading and template recombination

    PubMed Central

    Mukherjee, Srayanta; Zhang, Yang

    2011-01-01

    Summary The number of protein-protein complex structures is nearly 6-times smaller than that of tertiary structures in PDB which limits the power of homology-based approaches to complex structure modeling. We present a new threading-recombination approach, COTH, to boost the protein complex structure library by combining tertiary structure templates with complex alignments. The query sequences are first aligned to complex templates using a modified dynamic programming algorithm, guided by ab initio binding-site predictions. The monomer alignments are then shifted to the multimeric template framework by structural alignments. COTH was tested on 500 non-homologous dimeric proteins, which can successfully detect correct templates for half of the cases after homologous templates are excluded, which significantly outperforms conventional homology modeling algorithms. It also shows a higher accuracy in interface modeling than rigid-body docking of unbound structures from ZDOCK although with lower coverage. These data demonstrate new avenues to model complex structures from non-homologous templates. PMID:21742262

  19. Contingency Table Browser - prediction of early stage protein structure.

    PubMed

    Kalinowska, Barbara; Krzykalski, Artur; Roterman, Irena

    2015-01-01

    The Early Stage (ES) intermediate represents the starting structure in protein folding simulations based on the Fuzzy Oil Drop (FOD) model. The accuracy of FOD predictions is greatly dependent on the accuracy of the chosen intermediate. A suitable intermediate can be constructed using the sequence-structure relationship information contained in the so-called contingency table - this table expresses the likelihood of encountering various structural motifs for each tetrapeptide fragment in the amino acid sequence. The limited accuracy with which such structures could previously be predicted provided the motivation for a more indepth study of the contingency table itself. The Contingency Table Browser is a tool which can visualize, search and analyze the table. Our work presents possible applications of Contingency Table Browser, among them - analysis of specific protein sequences from the point of view of their structural ambiguity. PMID:26664034

  20. Structural Basis of Protein Oxidation Resistance: A Lysozyme Study

    PubMed Central

    Girod, Marion; Enjalbert, Quentin; Brunet, Claire; Antoine, Rodolphe; Lemoine, Jérôme; Lukac, Iva; Radman, Miroslav; Krisko, Anita; Dugourd, Philippe

    2014-01-01

    Accumulation of oxidative damage in proteins correlates with aging since it can cause irreversible and progressive degeneration of almost all cellular functions. Apparently, native protein structures have evolved intrinsic resistance to oxidation since perfectly folded proteins are, by large most robust. Here we explore the structural basis of protein resistance to radiation-induced oxidation using chicken egg white lysozyme in the native and misfolded form. We study the differential resistance to oxidative damage of six different parts of native and misfolded lysozyme by a targeted tandem/mass spectrometry approach of its tryptic fragments. The decay of the amount of each lysozyme fragment with increasing radiation dose is found to be a two steps process, characterized by a double exponential evolution of their amounts: the first one can be largely attributed to oxidation of specific amino acids, while the second one corresponds to further degradation of the protein. By correlating these results to the structural parameters computed from molecular dynamics (MD) simulations, we find the protein parts with increased root-mean-square deviation (RMSD) to be more susceptible to modifications. In addition, involvement of amino acid side-chains in hydrogen bonds has a protective effect against oxidation Increased exposure to solvent of individual amino acid side chains correlates with high susceptibility to oxidative and other modifications like side chain fragmentation. Generally, while none of the structural parameters alone can account for the fate of peptides during radiation, together they provide an insight into the relationship between protein structure and susceptibility to oxidation. PMID:24999730

  1. On Ramachandran angles, closed strings and knots in protein structure

    NASA Astrophysics Data System (ADS)

    Chen, Si; Niemi, Antti J.

    2016-08-01

    The Ramachandran angles (φ,\\psi ) of a protein backbone form the vertices of a piecewise geodesic curve on the surface of a torus. When the ends of the curve are connected to each other similarly, by a geodesic, the result is a closed string that in general wraps around the torus a number of times both in the meridional and the longitudinal directions. The two wrapping numbers are global characteristics of the protein structure. A statistical analysis of the wrapping numbers in terms of crystallographic x-ray structures in the protein data bank (PDB) reveals that proteins have no net chirality in the ϕ direction but in the ψ direction, proteins prefer to display chirality. A comparison between the wrapping numbers and the concept of folding index discloses a non-linearity in their relationship. Thus these three integer valued invariants can be used in tandem, to scrutinize and classify the global loop structure of individual PDB proteins, in terms of the overall fold topology.

  2. Protein secondary structural types are differentially coded on messenger RNA.

    PubMed Central

    Thanaraj, T. A.; Argos, P.

    1996-01-01

    Tricodon regions on messenger RNAs corresponding to a set of proteins from Escherichia coli were scrutinized for their translation speed. The fractional frequency values of the individual codons as they occur in mRNAs of highly expressed genes from Escherichia coli were taken as an indicative measure of the translation speed. The tricodons were classified by the sum of the frequency values of the constituent codons. Examination of the conformation of the encoded amino acid residues in the corresponding protein tertiary structures revealed a correlation between codon usage in mRNA and topological features of the encoded proteins. Alpha helices on proteins tend to be preferentially coded by translationally fast mRNA regions while the slow segments often code for beta strands and coil regions. Fast regions correspondingly avoid coding for beta strands and coil regions while the slow regions similarly move away from encoding alpha helices. Structural and mechanistic aspects of the ribosome peptide channel support the relevance of sequence fragment translation and subsequent conformation. A discussion is presented relating the observation to the reported kinetic data on the formation and stabilization of protein secondary structural types during protein folding. The observed absence of such strong positive selection for codons in non-highly expressed genes is compatible with existing theories that mutation pressure may well dominate codon selection in non-highly expressed genes. PMID:8897597

  3. Cavities and Atomic Packing in Protein Structures and Interfaces

    PubMed Central

    Sonavane, Shrihari; Chakrabarti, Pinak

    2008-01-01

    A comparative analysis of cavities enclosed in a tertiary structure of proteins and interfaces formed by the interaction of two protein subunits in obligate and non-obligate categories (represented by homodimeric molecules and heterocomplexes, respectively) is presented. The total volume of cavities increases with the size of the protein (or the interface), though the exact relationship may vary in different cases. Likewise, for individual cavities also there is quantitative dependence of the volume on the number of atoms (or residues) lining the cavity. The larger cavities tend to be less spherical, solvated, and the interfaces are enriched in these. On average 15 Å3 of cavity volume is found to accommodate single water, with another 40–45 Å3 needed for each additional solvent molecule. Polar atoms/residues have a higher propensity to line solvated cavities. Relative to the frequency of occurrence in the whole structure (or interface), residues in β-strands are found more often lining the cavities, and those in turn and loop the least. Any depression in one chain not complemented by a protrusion in the other results in a cavity in the protein–protein interface. Through the use of the Voronoi volume, the packing of residues involved in protein–protein interaction has been compared to that in the protein interior. For a comparable number of atoms the interface has about twice the number of cavities relative to the tertiary structure. PMID:19005575

  4. RNA structures regulating ribosomal protein biosynthesis in bacilli.

    PubMed

    Deiorio-Haggar, Kaila; Anthony, Jon; Meyer, Michelle M

    2013-07-01

    In Bacilli, there are three experimentally validated ribosomal-protein autogenous regulatory RNAs that are not shared with E. coli. Each of these RNAs forms a unique secondary structure that interacts with a ribosomal protein encoded by a downstream gene, namely S4, S15, and L20. Only one of these RNAs that interacts with L20 is currently found in the RNA Families Database. We created, or modified, existing structural alignments for these three RNAs and used them to perform homology searches. We have determined that each structure exhibits a narrow phylogenetic distribution, mostly relegated to the Firmicute class Bacilli. This work, in conjunction with other similar work, demonstrates that there are most likely many non-homologous RNA regulatory elements regulating ribosomal protein biosynthesis that still await discovery and characterization in other bacterial species. PMID:23611891

  5. RNA structures regulating ribosomal protein biosynthesis in bacilli

    PubMed Central

    Deiorio-Haggar, Kaila; Anthony, Jon; Meyer, Michelle M.

    2013-01-01

    In Bacilli, there are three experimentally validated ribosomal-protein autogenous regulatory RNAs that are not shared with E. coli. Each of these RNAs forms a unique secondary structure that interacts with a ribosomal protein encoded by a downstream gene, namely S4, S15, and L20. Only one of these RNAs that interacts with L20 is currently found in the RNA Families Database. We created, or modified, existing structural alignments for these three RNAs and used them to perform homology searches. We have determined that each structure exhibits a narrow phylogenetic distribution, mostly relegated to the Firmicute class Bacilli. This work, in conjunction with other similar work, demonstrates that there are most likely many non-homologous RNA regulatory elements regulating ribosomal protein biosynthesis that still await discovery and characterization in other bacterial species. PMID:23611891

  6. LINC complex proteins in cardiac structure, function, and disease

    PubMed Central

    Stroud, Matthew J; Banerjee, Indroneal; Lowe, Jennifer; Chen, Ju

    2014-01-01

    The LINC (LInker of Nucleoskeleton and Cytoskeleton) complex, composed of proteins within the inner and the outer nuclear membranes, connects the nuclear lamina to the cytoskeleton. The importance of this complex has been highlighted by the discovery of mutations in genes encoding LINC complex proteins, which are causative for skeletal or cardiac myopathies. Herein, this review summarizes structure, function, and interactions of major components of the LINC complex, highlights how mutations in these proteins may lead to cardiac disease, and outlines future challenges in the field. PMID:24481844

  7. Crystal Structure of Human Retinoblastoma Binding Protein 9

    SciTech Connect

    Vorobiev, S.; Su, M; Seetharaman, J; Huang, Y; Chen, C; Maglaqui, M; Janjua, H; Montelione, G; Tong, L; et. al.

    2009-01-01

    As a step towards better integrating protein three-dimensional (3D) structural information in cancer systems biology, the Northeast Structural Genomics Consortium (NESG) (www.nesg.org) has constructed a Human Cancer Pathway Protein Interaction Network (HCPIN) by analysis of several classical cancer-associated signaling pathways and their physical protein-protein interactions. Many well-known cancer-associated proteins play central roles as hubs or bottlenecks in the HCPIN (http://nmr.cabm.rutgers.edu/hcpin). NESG has selected more than 1000 human proteins and protein domains from the HCPIN for sample production and 3D structure determination. The long-range goal of this effort is to provide a comprehensive 3D structure-function database for human cancer-associated proteins and protein complexes, in the context of their interaction networks. Human retinoblastoma binding protein 9 (RBBP9) is one of the HCPIN proteins targeted by NESG. RBBP9 was initially identified as the product of a new gene, Bog (for B5T over-expressed gene), in several transformed rat liver epithelial cell lines resistant to the growth-inhibitory effect of TGF-1 as well as in primary human liver tumors. RBBP9 contains the retinoblastoma (Rb) binding motif LxCxE in its sequence, and was shown to interact with Rb by yeast two-hybrid and coimmunoprecipitation experiments. Mutation of the Leu residue in this motif to Gln blocked the binding to Rb. RBBP9 can displace E2F1 from E2F1-Rb complexes, and over expression of RBBP9 overcomes TGF-1 induced growth arrest and results in transformation of rat liver epithelial cells leading to hepatoblastoma-like tumors in nude mice. RBBP9 may also play a role in cellular responses to chronic low dose radiation. A close homolog of RBBP9, sharing 93% amino acid sequence identity and also known as RBBP10, interacts with a protein with sua5-yciO-yrdC domains.

  8. A protein structural classes prediction method based on predicted secondary structure and PSI-BLAST profile.

    PubMed

    Ding, Shuyan; Li, Yan; Shi, Zhuoxing; Yan, Shoujiang

    2014-02-01

    Knowledge of protein secondary structural classes plays an important role in understanding protein folding patterns. In this paper, 25 features based on position-specific scoring matrices are selected to reflect evolutionary information. In combination with other 11 rational features based on predicted protein secondary structure sequences proposed by the previous researchers, a 36-dimensional representation feature vector is presented to predict protein secondary structural classes for low-similarity sequences. ASTRALtraining dataset is used to train and design our method, other three low-similarity datasets ASTRALtest, 25PDB and 1189 are used to test the proposed method. Comparisons with other methods show that our method is effective to predict protein secondary structural classes. Stand alone version of the proposed method (PSSS-PSSM) is written in MATLAB language and it can be downloaded from http://letsgob.com/bioinfo_PSSS_PSSM/. PMID:24067326

  9. Analyzing Large Protein Complexes by Structural Mass Spectrometry

    PubMed Central

    Kirshenbaum, Noam; Michaelevski, Izhak; Sharon, Michal

    2010-01-01

    Living cells control and regulate their biological processes through the coordinated action of a large number of proteins that assemble themselves into an array of dynamic, multi-protein complexes1. To gain a mechanistic understanding of the various cellular processes, it is crucial to determine the structure of such protein complexes, and reveal how their structural organization dictates their function. Many aspects of multi-protein complexes are, however, difficult to characterize, due to their heterogeneous nature, asymmetric structure, and dynamics. Therefore, new approaches are required for the study of the tertiary levels of protein organization. One of the emerging structural biology tools for analyzing macromolecular complexes is mass spectrometry (MS)2-5. This method yields information on the complex protein composition, subunit stoichiometry, and structural topology. The power of MS derives from its high sensitivity and, as a consequence, low sample requirement, which enables examination of protein complexes expressed at endogenous levels. Another advantage is the speed of analysis, which allows monitoring of reactions in real time. Moreover, the technique can simultaneously measure the characteristics of separate populations co-existing in a mixture. Here, we describe a detailed protocol for the application of structural MS to the analysis of large protein assemblies. The procedure begins with the preparation of gold-coated capillaries for nanoflow electrospray ionization (nESI). It then continues with sample preparation, emphasizing the buffer conditions which should be compatible with nESI on the one hand, and enable to maintain complexes intact on the other. We then explain, step-by-step, how to optimize the experimental conditions for high mass measurements and acquire MS and tandem MS spectra. Finally, we chart the data processing and analyses that follow. Rather than attempting to characterize every aspect of protein assemblies, this protocol

  10. Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields.

    PubMed

    Wang, Sheng; Peng, Jian; Ma, Jianzhu; Xu, Jinbo

    2016-01-01

    Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF) and shallow neural networks. DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy, ~85% SOV score, and ~72% Q8 accuracy, respectively, on the CASP and CAMEO test proteins, greatly outperforming currently popular predictors. As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions, and solvent accessibility. PMID:26752681

  11. Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields

    PubMed Central

    Wang, Sheng; Peng, Jian; Ma, Jianzhu; Xu, Jinbo

    2016-01-01

    Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF) and shallow neural networks. DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy, ~85% SOV score, and ~72% Q8 accuracy, respectively, on the CASP and CAMEO test proteins, greatly outperforming currently popular predictors. As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions, and solvent accessibility. PMID:26752681

  12. Functional and Structural Analysis of the Conserved EFhd2 Protein

    PubMed Central

    Acosta, Yancy Ferrer; Rodríguez Cruz, Eva N.; Vaquer, Ana del C.; Vega, Irving E.

    2013-01-01

    EFhd2 is a novel protein conserved from C. elegans to H. sapiens. This novel protein was originally identified in cells of the immune and central nervous systems. However, it is most abundant in the central nervous system, where it has been found associated with pathological forms of the microtubule-associated protein tau. The physiological or pathological roles of EFhd2 are poorly understood. In this study, a functional and structural analysis was carried to characterize the molecular requirements for EFhd2’s calcium binding activity. The results showed that mutations of a conserved aspartate on either EF-hand motif disrupted the calcium binding activity, indicating that these motifs work in pair as a functional calcium binding domain. Furthermore, characterization of an identified single-nucleotide polymorphisms (SNP) that introduced a missense mutation indicates the importance of a conserved phenylalanine on EFhd2 calcium binding activity. Structural analysis revealed that EFhd2 is predominantly composed of alpha helix and random coil structures and that this novel protein is thermostable. EFhd2’s thermo stability depends on its N-terminus. In the absence of the N-terminus, calcium binding restored EFhd2’s thermal stability. Overall, these studies contribute to our understanding on EFhd2 functional and structural properties, and introduce it into the family of canonical EF-hand domain containing proteins. PMID:22973849

  13. Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields

    NASA Astrophysics Data System (ADS)

    Wang, Sheng; Peng, Jian; Ma, Jianzhu; Xu, Jinbo

    2016-01-01

    Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF) and shallow neural networks. DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy, ~85% SOV score, and ~72% Q8 accuracy, respectively, on the CASP and CAMEO test proteins, greatly outperforming currently popular predictors. As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions, and solvent accessibility.

  14. How round is a protein? Exploring protein structures for globularity using conformal mapping

    PubMed Central

    Hass, Joel; Koehl, Patrice

    2014-01-01

    We present a new algorithm that automatically computes a measure of the geometric difference between the surface of a protein and a round sphere. The algorithm takes as input two triangulated genus zero surfaces representing the protein and the round sphere, respectively, and constructs a discrete conformal map f between these surfaces. The conformal map is chosen to minimize a symmetric elastic energy ES(f) that measures the distance of f from an isometry. We illustrate our approach on a set of basic sample problems and then on a dataset of diverse protein structures. We show first that ES(f) is able to quantify the roundness of the Platonic solids and that for these surfaces it replicates well traditional measures of roundness such as the sphericity. We then demonstrate that the symmetric elastic energy ES(f) captures both global and local differences between two surfaces, showing that our method identifies the presence of protruding regions in protein structures and quantifies how these regions make the shape of a protein deviate from globularity. Based on these results, we show that ES(f) serves as a probe of the limits of the application of conformal mapping to parametrize protein shapes. We identify limitations of the method and discuss its extension to achieving automatic registration of protein structures based on their surface geometry. PMID:25988167

  15. Protein Structure Refinement of CASP Target Proteins Using GNEIMO Torsional Dynamics Method

    PubMed Central

    2015-01-01

    A longstanding challenge in using computational methods for protein structure prediction is the refinement of low-resolution structural models derived from comparative modeling methods into highly accurate atomistic models useful for detailed structural studies. Previously, we have developed and demonstrated the utility of the internal coordinate molecular dynamics (MD) technique, generalized Newton–Euler inverse mass operator (GNEIMO), for refinement of small proteins. Using GNEIMO, the high-frequency degrees of freedom are frozen and the protein is modeled as a collection of rigid clusters connected by torsional hinges. This physical model allows larger integration time steps and focuses the conformational search in the low frequency torsional degrees of freedom. Here, we have applied GNEIMO with temperature replica exchange to refine low-resolution protein models of 30 proteins taken from the continuous assessment of structure prediction (CASP) competition. We have shown that GNEIMO torsional MD method leads to refinement of up to 1.3 Å in the root-mean-square deviation in coordinates for 30 CASP target proteins without using any experimental data as restraints in performing the GNEIMO simulations. This is in contrast with the unconstrained all-atom Cartesian MD method performed under the same conditions, where refinement requires the use of restraints during the simulations. PMID:24397429

  16. Structure and expression of a novel compact myelin protein – Small VCP-interacting protein (SVIP)

    SciTech Connect

    Wu, Jiawen; Peng, Dungeng; Voehler, Markus; Sanders, Charles R.; Li, Jun

    2013-10-11

    Highlights: •SVIP (small p97/VCP-interacting protein) co-localizes with myelin basic protein (MBP) in compact myelin. •We determined that SVIP is an intrinsically disordered protein (IDP). •The helical content of SVIP increases dramatically during its interaction with negatively charged lipid membrane. •This study provides structural insight into interactions between SVIP and myelin membranes. -- Abstract: SVIP (small p97/VCP-interacting protein) was initially identified as one of many cofactors regulating the valosin containing protein (VCP), an AAA+ ATPase involved in endoplasmic-reticulum-associated protein degradation (ERAD). Our previous study showed that SVIP is expressed exclusively in the nervous system. In the present study, SVIP and VCP were seen to be co-localized in neuronal cell bodies. Interestingly, we also observed that SVIP co-localizes with myelin basic protein (MBP) in compact myelin, where VCP was absent. Furthermore, using nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopic measurements, we determined that SVIP is an intrinsically disordered protein (IDP). However, upon binding to the surface of membranes containing a net negative charge, the helical content of SVIP increases dramatically. These findings provide structural insight into interactions between SVIP and myelin membranes.

  17. mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet.

    PubMed

    Léonard, Sylvain; Joseph, Agnel Praveen; Srinivasan, Narayanaswamy; Gelly, Jean-Christophe; de Brevern, Alexandre G

    2014-04-01

    The increasing number of available protein structures requires efficient tools for multiple structure comparison. Indeed, multiple structural alignments are essential for the analysis of function, evolution and architecture of protein structures. For this purpose, we proposed a new web server called multiple Protein Block Alignment (mulPBA). This server implements a method based on a structural alphabet to describe the backbone conformation of a protein chain in terms of dihedral angles. This 'sequence-like' representation enables the use of powerful sequence alignment methods for primary structure comparison, followed by an iterative refinement of the structural superposition. This approach yields alignments superior to most of the rigid-body alignment methods and highly comparable with the flexible structure comparison approaches. We implement this method in a web server designed to do multiple structure superimpositions from a set of structures given by the user. Outputs are given as both sequence alignment and superposed 3D structures visualized directly by static images generated by PyMol or through a Jmol applet allowing dynamic interaction. Multiple global quality measures are given. Relatedness between structures is indicated by a distance dendogram. Superimposed structures in PDB format can be also downloaded, and the results are quickly obtained. mulPBA server can be accessed at www.dsimb.inserm.fr/dsimb_tools/mulpba/ . PMID:23659291

  18. Structure of the signal transduction protein TRAP (target of RNAIII-activating protein)

    PubMed Central

    Henrick, Kim; Hirshberg, Miriam

    2012-01-01

    The crystal structure of the signal transduction protein TRAP is reported at 1.85 Å resolution. The structure of TRAP consists of a central eight-stranded β-­barrel flanked asymmetrically by helices and is monomeric both in solution and in the crystal structure. A formate ion was found bound to TRAP identically in all four molecules in the asymmetric unit. PMID:22750855

  19. Structures and Mechanisms of Viral Membrane Fusion Proteins

    PubMed Central

    White, Judith M.; Delos, Sue E.; Brecher, Matthew; Schornberg, Kathryn

    2009-01-01

    Recent work has identified three distinct classes of viral membrane fusion proteins based on structural criteria. In addition, there are at least four distinct mechanisms by which viral fusion proteins can be triggered to undergo fusion-inducing conformational changes. Viral fusion proteins also contain different types of fusion peptides and vary in their reliance on accessory proteins. These differing features combine to yield a rich diversity of fusion proteins. Yet despite this staggering diversity, all characterized viral fusion proteins convert from a fusion-competent state (dimers or trimers, depending on the class) to a membrane-embedded homotrimeric prehairpin, and then to a trimer-of-hairpins that brings the fusion peptide, attached to the target membrane, and the transmembrane domain, attached to the viral membrane, into close proximity thereby facilitating the union of viral and target membranes. During these conformational conversions, the fusion proteins induce membranes to progress through stages of close apposition, hemifusion, and then the formation of small, and finally large, fusion pores. Clearly, highly divergent proteins have converged on the same overall strategy to mediate fusion, an essential step in the life cycle of every enveloped virus. PMID:18568847

  20. Sequential protein unfolding through a carbon nanotube pore

    NASA Astrophysics Data System (ADS)

    Xu, Zhonghe; Zhang, Shuang; Weber, Jeffrey K.; Luan, Binquan; Zhou, Ruhong; Li, Jingyuan

    2016-06-01

    An assortment of biological processes, like protein degradation and the transport of proteins across membranes, depend on protein unfolding events mediated by nanopore interfaces. In this work, we exploit fully atomistic simulations of an artificial, CNT-based nanopore to investigate the nature of ubiquitin unfolding. With one end of the protein subjected to an external force, we observe non-canonical unfolding behaviour as ubiquitin is pulled through the pore opening. Secondary structural elements are sequentially detached from the protein and threaded into the nanotube, interestingly, the remaining part maintains native-like characteristics. The constraints of the nanopore interface thus facilitate the formation of stable ``unfoldon'' motifs above the nanotube aperture that can exist in the absence of specific native contacts with the other secondary structure. Destruction of these unfoldons gives rise to distinct force peaks in our simulations, providing us with a sensitive probe for studying the kinetics of serial unfolding events. Our detailed analysis of nanopore-mediated protein unfolding events not only provides insight into how related processes might proceed in the cell, but also serves to deepen our understanding of structural arrangements which form the basis for protein conformational stability.An assortment of biological processes, like protein degradation and the transport of proteins across membranes, depend on protein unfolding events mediated by nanopore interfaces. In this work, we exploit fully atomistic simulations of an artificial, CNT-based nanopore to investigate the nature of ubiquitin unfolding. With one end of the protein subjected to an external force, we observe non-canonical unfolding behaviour as ubiquitin is pulled through the pore opening. Secondary structural elements are sequentially detached from the protein and threaded into the nanotube, interestingly, the remaining part maintains native-like characteristics. The constraints of

  1. Analysis of interactions between ribosomal proteins and RNA structural motifs

    PubMed Central

    2010-01-01

    Background One important goal of structural bioinformatics is to recognize and predict the interactions between protein binding sites and RNA. Recently, a comprehensive analysis of ribosomal proteins and their interactions with rRNA has been done. Interesting results emerged from the comparison of r-proteins within the small subunit in T. thermophilus and E. coli, supporting the idea of a core made by both RNA and proteins, conserved by evolution. Recent work showed also that ribosomal RNA is modularly composed. Motifs are generally single-stranded sequences of consecutive nucleotides (ssRNA) with characteristic folding. The role of these motifs in protein-RNA interactions has been so far only sparsely investigated. Results This work explores the role of RNA structural motifs in the interaction of proteins with ribosomal RNA (rRNA). We analyze composition, local geometries and conformation of interface regions involving motifs such as tetraloops, kink turns and single extruded nucleotides. We construct an interaction map of protein binding sites that allows us to identify the common types of shared 3-D physicochemical binding patterns for tetraloops. Furthermore, we investigate the protein binding pockets that accommodate single extruded nucleotides either involved in kink-turns or in arbitrary RNA strands. This analysis reveals a new structural motif, called tripod. It corresponds to small pockets consisting of three aminoacids arranged at the vertices of an almost equilateral triangle. We developed a search procedure for the recognition of tripods, based on an empirical tripod fingerprint. Conclusion A comparative analysis with the overall RNA surface and interfaces shows that contact surfaces involving RNA motifs have distinctive features that may be useful for the recognition and prediction of interactions. PMID:20122215

  2. The Semantics of the Modular Architecture of Protein Structures.

    PubMed

    Hleap, Jose Sergio; Blouin, Christian

    2016-01-01

    Protein structures can be conceptualized as context-aware self-organizing systems. One of its emerging properties is a modular architecture. Such modular architecture has been identified as domains and defined as its units of evolution and function. However, this modular architecture is not exclusively defined by domains. Also, the definition of a domain is an ongoing debate. Here we propose differentiating structural, evolutionary and functional domains as distinct concepts. Defining domains or modules is confounded by diverse definitions of the concept, and also by other elements inherent to protein structures. An apparent hierarchy in protein structure architecture is one of these elements, where lower level interactions may create noise for the definition of higher levels. Diverse modularity-molding factors such as folding, function, and selection, can have a misleading effect when trying to define a given type of module. It is thus important to keep in mind this complexity when defining modularity in protein structures and interpreting the outcome modularity inference approaches. PMID:26412786

  3. Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures

    PubMed Central

    Sharma, Anuj; Manolakos, Elias S.

    2015-01-01

    Fast increasing computational demand for all-to-all protein structures comparison (PSC) is a result of three confounding factors: rapidly expanding structural proteomics databases, high computational complexity of pairwise protein comparison algorithms, and the trend in the domain towards using multiple criteria for protein structures comparison (MCPSC) and combining results. We have developed a software framework that exploits many-core and multicore CPUs to implement efficient parallel MCPSC in modern processors based on three popular PSC methods, namely, TMalign, CE, and USM. We evaluate and compare the performance and efficiency of the two parallel MCPSC implementations using Intel's experimental many-core Single-Chip Cloud Computer (SCC) as well as Intel's Core i7 multicore processor. We show that the 48-core SCC is more efficient than the latest generation Core i7, achieving a speedup factor of 42 (efficiency of 0.9), making many-core processors an exciting emerging technology for large-scale structural proteomics. We compare and contrast the performance of the two processors on several datasets and also show that MCPSC outperforms its component methods in grouping related domains, achieving a high F-measure of 0.91 on the benchmark CK34 dataset. The software implementation for protein structure comparison using the three methods and combined MCPSC, along with the developed underlying rckskel algorithmic skeletons library, is available via GitHub. PMID:26605332

  4. Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures.

    PubMed

    Sharma, Anuj; Manolakos, Elias S

    2015-01-01

    Fast increasing computational demand for all-to-all protein structures comparison (PSC) is a result of three confounding factors: rapidly expanding structural proteomics databases, high computational complexity of pairwise protein comparison algorithms, and the trend in the domain towards using multiple criteria for protein structures comparison (MCPSC) and combining results. We have developed a software framework that exploits many-core and multicore CPUs to implement efficient parallel MCPSC in modern processors based on three popular PSC methods, namely, TMalign, CE, and USM. We evaluate and compare the performance and efficiency of the two parallel MCPSC implementations using Intel's experimental many-core Single-Chip Cloud Computer (SCC) as well as Intel's Core i7 multicore processor. We show that the 48-core SCC is more efficient than the latest generation Core i7, achieving a speedup factor of 42 (efficiency of 0.9), making many-core processors an exciting emerging technology for large-scale structural proteomics. We compare and contrast the performance of the two processors on several datasets and also show that MCPSC outperforms its component methods in grouping related domains, achieving a high F-measure of 0.91 on the benchmark CK34 dataset. The software implementation for protein