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Sample records for common structural motif

  1. Two common structural motifs for TCR recognition by staphylococcal enterotoxins.

    PubMed

    Rödström, Karin E J; Regenthal, Paulina; Bahl, Christopher; Ford, Alex; Baker, David; Lindkvist-Petersson, Karin

    2016-01-01

    Superantigens are toxins produced by Staphylococcus aureus, called staphylococcal enterotoxins (abbreviated SEA to SEU). They can cross-link the T cell receptor (TCR) and major histocompatibility complex class II, triggering a massive T cell activation and hence disease. Due to high stability and toxicity, superantigens are potential agents of bioterrorism. Hence, antagonists may not only be useful in the treatment of disease but also serve as countermeasures to biological warfare. Of particular interest are inhibitors against SEA and SEB. SEA is the main cause of food poisoning, while SEB is a common toxin manufactured as a biological weapon. Here, we present the crystal structures of SEA in complex with TCR and SEE in complex with the same TCR, complemented with computational alanine-scanning mutagenesis of SEA, SEB, SEC3, SEE, and SEH. We have identified two common areas that contribute to the general TCR binding for these superantigens. This paves the way for design of single antagonists directed towards multiple toxins. PMID:27180909

  2. Two common structural motifs for TCR recognition by staphylococcal enterotoxins

    PubMed Central

    Rödström, Karin E. J.; Regenthal, Paulina; Bahl, Christopher; Ford, Alex; Baker, David; Lindkvist-Petersson, Karin

    2016-01-01

    Superantigens are toxins produced by Staphylococcus aureus, called staphylococcal enterotoxins (abbreviated SEA to SEU). They can cross-link the T cell receptor (TCR) and major histocompatibility complex class II, triggering a massive T cell activation and hence disease. Due to high stability and toxicity, superantigens are potential agents of bioterrorism. Hence, antagonists may not only be useful in the treatment of disease but also serve as countermeasures to biological warfare. Of particular interest are inhibitors against SEA and SEB. SEA is the main cause of food poisoning, while SEB is a common toxin manufactured as a biological weapon. Here, we present the crystal structures of SEA in complex with TCR and SEE in complex with the same TCR, complemented with computational alanine-scanning mutagenesis of SEA, SEB, SEC3, SEE, and SEH. We have identified two common areas that contribute to the general TCR binding for these superantigens. This paves the way for design of single antagonists directed towards multiple toxins. PMID:27180909

  3. A Common Structural Motif in the Binding of Virulence Factors to Bacterial Secretion Chaperones

    SciTech Connect

    Lilic,M.; Vujanac, M.; Stebbins, C.

    2006-01-01

    Salmonella invasion protein A (SipA) is translocated into host cells by a type III secretion system (T3SS) and comprises two regions: one domain binds its cognate type III secretion chaperone, InvB, in the bacterium to facilitate translocation, while a second domain functions in the host cell, contributing to bacterial uptake by polymerizing actin. We present here the crystal structures of the SipA chaperone binding domain (CBD) alone and in complex with InvB. The SipA CBD is found to consist of a nonglobular polypeptide as well as a large globular domain, both of which are necessary for binding to InvB. We also identify a structural motif that may direct virulence factors to their cognate chaperones in a diverse range of pathogenic bacteria. Disruption of this structural motif leads to a destabilization of several chaperone-substrate complexes from different species, as well as an impairment of secretion in Salmonella.

  4. Secondary structure model of the Mason-Pfizer monkey virus 5' leader sequence: identification of a structural motif common to a variety of retroviruses.

    PubMed Central

    Harrison, G P; Hunter, E; Lever, A M

    1995-01-01

    A stable secondary structure model is presented for the region 3' of the primer-binding site to 130 bases into the gag sequence of the prototype type D retrovirus Mason-Pfizer monkey virus. Using biochemical probing of RNA from this region in association with free energy minimization, we have identified a stem-loop structure in the region, which from other studies has been shown to be important for genomic RNA encapsidation. The structure involves a highly stable stem of five G-C pairs terminating in a heptaloop. Comparison of the Mason-Pfizer monkey virus structure with one predicted for squirrel monkey retrovirus demonstrates an identical stem and a common ACC motif in the loop. Free energy studies of the secondary structure of the 5' regions of eight other retroviruses predict stem loops which have similar GAYC motifs. We believe this may represent a common structural and sequence motif which among other functions may be involved in genomic RNA packaging in these viruses. PMID:7884866

  5. A common structural motif incorporating a cystine knot and a triple-stranded beta-sheet in toxic and inhibitory polypeptides.

    PubMed Central

    Pallaghy, P. K.; Nielsen, K. J.; Craik, D. J.; Norton, R. S.

    1994-01-01

    A common structural motif consisting of a cystine knot and a small triple-stranded beta-sheet has been defined from comparison of the 3-dimensional structures of the polypeptides omega-conotoxin GVIA (Conus geographus), kalata BI (Oldenlandia affinis DC), and CMTI-I (Curcurbita maxima). These 3 polypeptides have diverse biological activities and negligible amino acid sequence identity, but each contains 3 disulfide bonds that give rise to a cystine knot. This knot consists of a ring formed by the first 2 bonds (1-4 and 2-5) and the intervening polypeptide backbone, through which the third disulfide (3-6) passes. The other component of this motif is a triple-stranded, anti-parallel beta-sheet containing a minimum of 10 residues, XXC2, XC5X, XXC6X (where the numbers on the half-cysteine residues refer to their positions in the disulfide pattern). The presence in these polypeptides of both the cysteine knot and antiparallel beta-sheet suggests that both structural features are required for the stability of the motif. This structural motif is also present in other protease inhibitors and a spider toxin. It appears to be one of the smallest stable globular domains found in proteins and is commonly used in toxins and inhibitors that act by blocking the function of larger protein receptors such as ion channels or proteases. PMID:7849598

  6. Structural alphabet motif discovery and a structural motif database.

    PubMed

    Ku, Shih-Yen; Hu, Yuh-Jyh

    2012-01-01

    This study proposes a general framework for structural motif discovery. The framework is based on a modular design in which the system components can be modified or replaced independently to increase its applicability to various studies. It is a two-stage approach that first converts protein 3D structures into structural alphabet sequences, and then applies a sequence motif-finding tool to these sequences to detect conserved motifs. We named the structural motif database we built the SA-Motifbase, which provides the structural information conserved at different hierarchical levels in SCOP. For each motif, SA-Motifbase presents its 3D view; alphabet letter preference; alphabet letter frequency distribution; and the significance. SA-Motifbase is available at http://bioinfo.cis.nctu.edu.tw/samotifbase/. PMID:22099701

  7. Cofunctional Subpathways Were Regulated by Transcription Factor with Common Motif, Common Family, or Common Tissue

    PubMed Central

    Su, Fei; Shang, Desi; Xu, Yanjun; Feng, Li; Yang, Haixiu; Liu, Baoquan; Su, Shengyang; Chen, Lina; Li, Xia

    2015-01-01

    Dissecting the characteristics of the transcription factor (TF) regulatory subpathway is helpful for understanding the TF underlying regulatory function in complex biological systems. To gain insight into the influence of TFs on their regulatory subpathways, we constructed a global TF-subpathways network (TSN) to analyze systematically the regulatory effect of common-motif, common-family, or common-tissue TFs on subpathways. We performed cluster analysis to show that the common-motif, common-family, or common-tissue TFs that regulated the same pathway classes tended to cluster together and contribute to the same biological function that led to disease initiation and progression. We analyzed the Jaccard coefficient to show that the functional consistency of subpathways regulated by the TF pairs with common motif, common family, or common tissue was significantly greater than the random TF pairs at the subpathway level, pathway level, and pathway class level. For example, HNF4A (hepatocyte nuclear factor 4, alpha) and NR1I3 (nuclear receptor subfamily 1, group I, member 3) were a pair of TFs with common motif, common family, and common tissue. They were involved in drug metabolism pathways and were liver-specific factors required for physiological transcription. In short, we inferred that the cofunctional subpathways were regulated by common-motif, common-family, or common-tissue TFs. PMID:26688819

  8. 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

  9. Discovering common stem–loop motifs in unaligned RNA sequences

    PubMed Central

    Gorodkin, Jan; Stricklin, Shawn L.; Stormo, Gary D.

    2001-01-01

    Post-transcriptional regulation of gene expression is often accomplished by proteins binding to specific sequence motifs in mRNA molecules, to affect their translation or stability. The motifs are often composed of a combination of sequence and structural constraints such that the overall structure is preserved even though much of the primary sequence is variable. While several methods exist to discover transcriptional regulatory sites in the DNA sequences of coregulated genes, the RNA motif discovery problem is much more difficult because of covariation in the positions. We describe the combined use of two approaches for RNA structure prediction, FOLDALIGN and COVE, that together can discover and model stem–loop RNA motifs in unaligned sequences, such as UTRs from post-transcriptionally coregulated genes. We evaluate the method on two datasets, one a section of rRNA genes with randomly truncated ends so that a global alignment is not possible, and the other a hyper-variable collection of IRE-like elements that were inserted into randomized UTR sequences. In both cases the combined method identified the motifs correctly, and in the rRNA example we show that it is capable of determining the structure, which includes bulge and internal loops as well as a variable length hairpin loop. Those automated results are quantitatively evaluated and found to agree closely with structures contained in curated databases, with correlation coefficients up to 0.9. A basic server, Stem–Loop Align SearcH (SLASH), which will perform stem–loop searches in unaligned RNA sequences, is available at http://www.bioinf.au.dk/slash/. PMID:11353083

  10. A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins

    PubMed Central

    Buchko, Garry W.; Niemann, George; Baker, Erin S.; Belov, Mikhail E.; Smith, Richard D.; Heffron, Fred; Adkins, Joshua N.; McDermott, Jason E.

    2012-01-01

    Many pathogenic Gram-negative bacteria use a type III secretion system (T3SS) to deliver effector proteins into the host cell where they reprogram host defenses and facilitate pathogenesis. The first 20–30 N-terminal residues usually contain the ‘secretion signal’ that targets effector proteins for translocation, however, a consensus sequence motif has never been discerned. Recent machine-learning approaches, such as support vector machine (SVM)-based Identification and Evaluation of Virulence Effectors (SIEVE), have improved the ability to identify effector proteins from genomics sequence information. While these methods all suggest that the T3SS secretion signal has a characteristic amino acid composition bias, it is still unclear if the amino acid pattern is important and if there are any unifying structural properties that direct recognition. To address these issues a peptide corresponding to the secretion signal for Salmonella enterica serovar Typhimurium effector SseJ was synthesized (residues 1–30, SseJ) along with scrambled peptides of the same amino acid composition that produced high (SseJ-H) and low (SseJ-L) SIEVE scores. The secretion properties of these three peptides were tested using a secretion signal–CyaA fusion assay and their structural properties probed using circular dichroism, nuclear magnetic resonance, and ion mobility spectrometry–mass spectrometry. The secretion predictions from SIEVE matched signal–CyaA fusion experimental results with J774 macrophages suggesting that the SseJ secretion signal has some sequence order dependence. The structural studies showed that the SseJ, SseJ-H, and SseJ-L peptides were intrinsically disordered in aqueous solution with a small predisposition to adopt nascent helical structure only in the presence of structure stabilizing agents such as 1,1,1,3,3,3-hexafluoroisopropanol. Intrinsic disorder may be a universal feature of effector secretion signals as similar conclusions were reached following

  11. Analyzing network reliability using structural motifs

    NASA Astrophysics Data System (ADS)

    Khorramzadeh, Yasamin; Youssef, Mina; Eubank, Stephen; Mowlaei, Shahir

    2015-04-01

    This paper uses the reliability polynomial, introduced by Moore and Shannon in 1956, to analyze the effect of network structure on diffusive dynamics such as the spread of infectious disease. We exhibit a representation for the reliability polynomial in terms of what we call structural motifs that is well suited for reasoning about the effect of a network's structural properties on diffusion across the network. We illustrate by deriving several general results relating graph structure to dynamical phenomena.

  12. 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

  13. 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

  14. Structural motifs of pre-nucleation clusters.

    PubMed

    Zhang, Y; Türkmen, I R; Wassermann, B; Erko, A; Rühl, E

    2013-10-01

    Structural motifs of pre-nucleation clusters prepared in single, optically levitated supersaturated aqueous aerosol microparticles containing CaBr2 as a model system are reported. Cluster formation is identified by means of X-ray absorption in the Br K-edge regime. The salt concentration beyond the saturation point is varied by controlling the humidity in the ambient atmosphere surrounding the 15-30 μm microdroplets. This leads to the formation of metastable supersaturated liquid particles. Distinct spectral shifts in near-edge spectra as a function of salt concentration are observed, in which the energy position of the Br K-edge is red-shifted by up to 7.1 ± 0.4 eV if the dilute solution is compared to the solid. The K-edge positions of supersaturated solutions are found between these limits. The changes in electronic structure are rationalized in terms of the formation of pre-nucleation clusters. This assumption is verified by spectral simulations using first-principle density functional theory and molecular dynamics calculations, in which structural motifs are considered, explaining the experimental results. These consist of solvated CaBr2 moieties, rather than building blocks forming calcium bromide hexahydrates, the crystal system that is formed by drying aqueous CaBr2 solutions. PMID:24116574

  15. A relational extension of the notion of motifs: application to the common 3D protein substructures searching problem.

    PubMed

    Pisanti, Nadia; Soldano, Henry; Carpentier, Mathilde; Pothier, Joel

    2009-12-01

    The geometrical configurations of atoms in protein structures can be viewed as approximate relations among them. Then, finding similar common substructures within a set of protein structures belongs to a new class of problems that generalizes that of finding repeated motifs. The novelty lies in the addition of constraints on the motifs in terms of relations that must hold between pairs of positions of the motifs. We will hence denote them as relational motifs. For this class of problems, we present an algorithm that is a suitable extension of the KMR paradigm and, in particular, of the KMRC as it uses a degenerate alphabet. Our algorithm contains several improvements that become especially useful when-as it is required for relational motifs-the inference is made by partially overlapping shorter motifs, rather than concatenating them. The efficiency, correctness and completeness of the algorithm is ensured by several non-trivial properties that are proven in this paper. The algorithm has been applied in the important field of protein common 3D substructure searching. The methods implemented have been tested on several examples of protein families such as serine proteases, globins and cytochromes P450 additionally. The detected motifs have been compared to those found by multiple structural alignments methods. PMID:20047489

  16. Structural motifs and the stability of fullerenes

    SciTech Connect

    Austin, S.J.; Fowler, P.W.; Manolopoulos, D.E.; Orlandi, G.; Zerbetto, F.

    1995-05-18

    Full geometry optimization has been performed within the semiempirical QCFF/PI model for the 1812 fullerene structural isomers of C{sub 60} formed by 12 pentagons and 20 hexagons. All are local minima on the potential energy hypersurface. Correlations of total energy with many structural motifs yield highly scattered diagrams, but some exhibit linear trends. Penalty and merit functions can be assigned to certain motifs: inclusion of a fused pentagon pair entails an average penalty of 111 kJ mol{sup -1}; a generic hexagon triple costs 23 kJ mol{sup -1}; a triple (open or fused) comprising a pentagon between two hexagonal neighbors gives a stabilization of 19 kJ mol{sup -1}. These results can be understood in terms of the curved nature of fullerene molecules: pentagons should be isolated to avoid sharp local curvature, hexagon triples are costly because they enforce local planarity and hence imply high curvature in another part of the fullerene surface, but hexagon-pentagon-hexagon triples allow the surface to distribute steric strain by warping. The best linear fit is found for H, the second moment of the hexagon-neighbor-index signature, which fits the total energies with a standard deviation of only 53 kJ mol{sup -1} and must be minimized for stability; this index too can be interpreted in terms of curvature. 26 refs., 5 figs.

  17. A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins

    SciTech Connect

    Buchko, Garry W.; Niemann, George; Baker, Erin Shammel; Belov, Mikhail E.; Smith, Richard D.; Heffron, Fred; Adkins, Joshua N.; McDermott, Jason E.

    2010-11-08

    Many pathogenic Gram-negative bacteria use a type III secretion system (T3SS) to deliver effector proteins into the host cell where they reprogram host defenses and facilitate pathogenesis. While it has been determined that the first 20 - 30 N-terminal residues usually contain the ‘secretion signal’ that targets effector proteins for translocation, the molecular basis for recognition of this signal is not understood. Recent machine-learning approaches, such as SVM-based Identification and Evaluation of Virulence Effectors (SIEVE), have improved the ability to identify effector proteins from genomics sequence information. While these methods all suggest that the T3SS secretion signal has a characteristic amino acid composition bias, it is still unclear if the amino acid pattern is important and if there are any unifying structural properties that direct recognition. To address these issues a peptide corresponding to the secretion signal for Salmonella enterica serovar Typhimurium effector SseJ was synthesized (residues 1-30, SseJ) along with scrambled peptides of the same amino acid composition that produced high (SseJ-H) and low (SseJ-L) SIEVE scores. The secretion properties of these three peptides were tested using a secretion signal-CyaA fusion assay and their structures systematically probed using circular dichroism, nuclear magnetic resonance, and ion mobility spectrometry-mass spectrometry. The signal-CyaA fusion assay showed that the native and SseJ-H fusion constructs were secreted into J774 macrophage at similar levels via the SPI-2 secretion pathway while secretion of the SseJ-L fusion construct was substantially retarded, suggesting that the SseJ secretion signal was sequence order dependent. The structural studies showed that the SseJ, SseJ-H, and SseJ-L peptides were intrinsically disordered in aqueous solution with only a small predisposition to adopt nascent helical structure in the presence of the powerful structure stabilizing agent, 1

  18. Occurrence probability of structured motifs in random sequences.

    PubMed

    Robin, S; Daudin, J-J; Richard, H; Sagot, M-F; Schbath, S

    2002-01-01

    The problem of extracting from a set of nucleic acid sequences motifs which may have biological function is more and more important. In this paper, we are interested in particular motifs that may be implicated in the transcription process. These motifs, called structured motifs, are composed of two ordered parts separated by a variable distance and allowing for substitutions. In order to assess their statistical significance, we propose approximations of the probability of occurrences of such a structured motif in a given sequence. An application of our method to evaluate candidate promoters in E. coli and B. subtilis is presented. Simulations show the goodness of the approximations. PMID:12614545

  19. Structure and dynamics of LC8 complexes with KXTQT-motif peptides: swallow and dynein intermediate chain compete for a common site.

    PubMed

    Benison, Gregory; Karplus, P Andrew; Barbar, Elisar

    2007-08-10

    The dynein light chain LC8 is an integral subunit of the cytoplasmic dynein motor complex that binds directly to and promotes assembly of the dynein intermediate chain (IC). LC8 interacts also with a variety of putative dynein cargo molecules such as Bim, a proapoptotic Bcl2 family protein, which have the KXTQT recognition sequence and neuronal nitric oxide synthase (nNOS), which has the GIQVD fingerprint but shares the same binding grooves at the LC8 dimer interface. The work reported here investigates the interaction of LC8 with IC and a putative cargo, Swallow, which share the KXTQT recognition sequence, and addresses the apparent paradox of how LC8, as part of dynein, mediates binding to cargo. The structures of Drosophila LC8 bound to peptides from IC and Swallow solved by X-ray diffraction show that the IC and Swallow peptides bind in the same grooves at the dimer interface. Differences in flexibility between bound and free LC8 were evaluated from hydrogen isotope exchange experiments using heteronuclear NMR spectroscopy. Peptide binding causes an increase in protection from exchange primarily in residues that interact directly with the peptide, such as the beta-strand intertwined at the interface and the N-terminal end of helix alpha2. There is considerably more protection upon Swallow binding, consistent with tighter binding relative to IC. Comparison with the LC8/nNOS complex shows how both the GIQVD and KXTQT fingerprints are recognized in the same groove. The similar structures of LC8/IC and LC8/Swa and the tighter binding of Swallow call into question the role for LC8 as a cargo adaptor protein, and suggest that binding of LC8 to Swallow serves another function, possibly that of a dimerization engine, which is independent of its role in dynein. PMID:17570393

  20. Ballast: A Ball-based Algorithm for Structural Motifs

    PubMed Central

    He, Lu; Vandin, Fabio; Pandurangan, Gopal

    2013-01-01

    Abstract Structural motifs encapsulate local sequence-structure-function relationships characteristic of related proteins, enabling the prediction of functional characteristics of new proteins, providing molecular-level insights into how those functions are performed, and supporting the development of variants specifically maintaining or perturbing function in concert with other properties. Numerous computational methods have been developed to search through databases of structures for instances of specified motifs. However, it remains an open problem how best to leverage the local geometric and chemical constraints underlying structural motifs in order to develop motif-finding algorithms that are both theoretically and practically efficient. We present a simple, general, efficient approach, called Ballast (ball-based algorithm for structural motifs), to match given structural motifs to given structures. Ballast combines the best properties of previously developed methods, exploiting the composition and local geometry of a structural motif and its possible instances in order to effectively filter candidate matches. We show that on a wide range of motif-matching problems, Ballast efficiently and effectively finds good matches, and we provide theoretical insights into why it works well. By supporting generic measures of compositional and geometric similarity, Ballast provides a powerful substrate for the development of motif-matching algorithms. PMID:23383999

  1. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures.

    PubMed

    Sarver, Michael; Zirbel, Craig L; Stombaugh, Jesse; Mokdad, Ali; Leontis, Neocles B

    2008-01-01

    New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, "Find RNA 3D" (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs whose

  2. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures

    PubMed Central

    Sarver, Michael; Stombaugh, Jesse; Mokdad, Ali; Leontis, Neocles B.

    2010-01-01

    New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, “Find RNA 3D” (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs

  3. Coagulase and Efb of Staphylococcus aureus Have a Common Fibrinogen Binding Motif

    PubMed Central

    Ko, Ya-Ping; Kang, Mingsong; Ganesh, Vannakambadi K.; Ravirajan, Dharmanand; Li, Bin

    2016-01-01

    ABSTRACT Coagulase (Coa) and Efb, secreted Staphylococcus aureus proteins, are important virulence factors in staphylococcal infections. Coa interacts with fibrinogen (Fg) and induces the formation of fibrin(ogen) clots through activation of prothrombin. Efb attracts Fg to the bacterial surface and forms a shield to protect the bacteria from phagocytic clearance. This communication describes the use of an array of synthetic peptides to identify variants of a linear Fg binding motif present in Coa and Efb which are responsible for the Fg binding activities of these proteins. This motif represents the first Fg binding motif identified for any microbial protein. We initially located the Fg binding sites to Coa’s C-terminal disordered segment containing tandem repeats by using recombinant fragments of Coa in enzyme-linked immunosorbent assay-type binding experiments. Sequence analyses revealed that this Coa region contained shorter segments with sequences similar to the Fg binding segments in Efb. An alanine scanning approach allowed us to identify the residues in Coa and Efb that are critical for Fg binding and to define the Fg binding motifs in the two proteins. In these motifs, the residues required for Fg binding are largely conserved, and they therefore constitute variants of a common Fg binding motif which binds to Fg with high affinity. Defining a specific motif also allowed us to identify a functional Fg binding register for the Coa repeats that is different from the repeat unit previously proposed. PMID:26733070

  4. Mining tertiary structural motifs for assessment of designability.

    PubMed

    Zhang, Jian; Grigoryan, Gevorg

    2013-01-01

    The observation of a limited secondary-structural alphabet in native proteins, with significant sequence preferences, has profoundly influenced the fields of protein design and structure prediction (Simons, Kooperberg, Huang, & Baker, 1997; Verschueren et al., 2011). In the era of structural genomics, as the size of the structural dataset continues to grow rapidly, it is becoming possible to extend this analysis to tertiary structural motifs and their sequences. For a hypothetical tertiary motif, the rate of its utilization in natural proteins may be used to assess its designability-the ease with which the motif can be realized with natural amino acids. This requires a structural similarity search methodology, which rather than looking for global topological agreement (more appropriate for categorization of full proteins or domains), identifies detailed geometric matches. In this chapter, we introduce such a method, called MaDCaT, and demonstrate its use by assessing the designability landscapes of two tertiary structural motifs. We also show that such analysis can establish structure/sequence links by providing the sequence constraints necessary to encode designable motifs. As logical extension of their secondary-structure counterparts, tertiary structural preferences will likely prove extremely useful in de novo protein design and structure prediction. PMID:23422424

  5. A novel secondary structure based on fused five-membered rings motif

    PubMed Central

    Dhar, Jesmita; Kishore, Raghuvansh; Chakrabarti, Pinak

    2016-01-01

    An analysis of protein structures indicates the existence of a novel, fused five-membered rings motif, comprising of two residues (i and i + 1), stabilized by interresidue Ni+1–H∙∙∙Ni and intraresidue Ni+1–H∙∙∙O=Ci+1 hydrogen bonds. Fused-rings geometry is the common thread running through many commonly occurring motifs, such as β-turn, β-bulge, Asx-turn, Ser/Thr-turn, Schellman motif, and points to its structural robustness. A location close to the beginning of a β-strand is rather common for the motif. Devoid of side chain, Gly seems to be a key player in this motif, occurring at i, for which the backbone torsion angles cluster at ~(−90°, −10°) and (70°, 20°). The fused-rings structures, distant from each other in sequence, can hydrogen bond with each other, and the two segments aligned to each other in a parallel fashion, give rise to a novel secondary structure, topi, which is quite common in proteins, distinct from two major secondary structures, α-helix and β-sheet. Majority of the peptide segments making topi are identified as aggregation-prone and the residues tend to be conserved among homologous proteins. PMID:27511362

  6. Direct vs 2-stage approaches to structured motif finding

    PubMed Central

    2012-01-01

    Background The notion of DNA motif is a mathematical abstraction used to model regions of the DNA (known as Transcription Factor Binding Sites, or TFBSs) that are bound by a given Transcription Factor to regulate gene expression or repression. In turn, DNA structured motifs are a mathematical counterpart that models sets of TFBSs that work in concert in the gene regulations processes of higher eukaryotic organisms. Typically, a structured motif is composed of an ordered set of isolated (or simple) motifs, separated by a variable, but somewhat constrained number of “irrelevant” base-pairs. Discovering structured motifs in a set of DNA sequences is a computationally hard problem that has been addressed by a number of authors using either a direct approach, or via the preliminary identification and successive combination of simple motifs. Results We describe a computational tool, named SISMA, for the de-novo discovery of structured motifs in a set of DNA sequences. SISMA is an exact, enumerative algorithm, meaning that it finds all the motifs conforming to the specifications. It does so in two stages: first it discovers all the possible component simple motifs, then combines them in a way that respects the given constraints. We developed SISMA mainly with the aim of understanding the potential benefits of such a 2-stage approach w.r.t. direct methods. In fact, no 2-stage software was available for the general problem of structured motif discovery, but only a few tools that solved restricted versions of the problem. We evaluated SISMA against other published tools on a comprehensive benchmark made of both synthetic and real biological datasets. In a significant number of cases, SISMA outperformed the competitors, exhibiting a good performance also in most of the cases in which it was inferior. Conclusions A reflection on the results obtained lead us to conclude that a 2-stage approach can be implemented with many advantages over direct approaches. Some of these

  7. Functionally related transcripts have common RNA motifs for specific RNA-binding proteins in trypanosomes

    PubMed Central

    Noé, Griselda; De Gaudenzi, Javier G; Frasch, Alberto C

    2008-01-01

    Background Trypanosomes mostly control gene expression by post-transcriptional events such as modulation of mRNA stability and translational efficiency. These mechanisms involve RNA-binding proteins (RBPs), which associate with transcripts to form messenger ribonucleoprotein (mRNP) complexes. Results In this study, we report the identification of mRNA targets for Trypanosoma cruzi U-rich RBP 1 (TcUBP1) and T. cruzi RBP 3 (TcRBP3), two phylogenetically conserved proteins among Kinetoplastids. Co-immunoprecipitated RBP-associated RNAs were extracted from mRNP complexes and binding of RBPs to several targets was confirmed by independent experimental assays. Analysis of target transcript sequences allowed the identification of different signature RNA motifs for each protein. Cis-elements for RBP binding have a stem-loop structure of 30–35 bases and are more frequently represented in the 3'-untranslated region (UTR) of mRNAs. Insertion of the correctly folded RNA elements to a non-specific mRNA rendered it into a target transcript, whereas substitution of the RNA elements abolished RBP interaction. In addition, RBPs competed for RNA-binding sites in accordance with the distribution of different and overlapping motifs in the 3'-UTRs of common mRNAs. Conclusion Functionally related transcripts were preferentially associated with a given RBP; TcUBP1 targets were enriched in genes encoding proteins involved in metabolism, whereas ribosomal protein-encoding transcripts were the largest group within TcRBP3 targets. Together, these results suggest coordinated control of different mRNA subsets at the post-transcriptional level by specific RBPs. PMID:19063746

  8. A Common Molecular Motif Characterizes Extracellular Allosteric Enhancers of GPCR Aminergic Receptors and Suggests Enhancer Mechanism of Action

    PubMed Central

    Bernstein, Robert Root; Dillon, Patrick F

    2014-01-01

    Several classes of compounds that have no intrinsic activity on aminergic systems nonetheless enhance the potency of aminergic receptor ligands three-fold or more while significantly increasing their duration of activity, preventing tachyphylaxis and reversing fade. Enhancer compounds include ascorbic acid, ethylenediaminetetraacetic acid, cortico-steroids, opioid peptides, opiates and opiate antagonists. This paper provides the first review of aminergic enhancement, demonstrating that all enhancers have a common, inobvious molecular motif and work through a common mechanism that is manifested by three common characteristics. First, aminergic enhancers bind directly to the amines they enhance, suggesting that the common structural motif is reflected in common binding targets. Second, one common target is the first extracellular loop of aminergic receptors. Third, at least some enhancers are antiphosphodiesterases. These observations suggest that aminergic enhancers act on the extracellular surface of aminergic receptors to keep the receptor in its high affinity state, trapping the ligand inside the receptor. Enhancer binding produces allosteric modifications of the receptor structure that interfere with phosphorylation of the receptor, thereby inhibiting down-regulation of the receptor. The mechanism explains how enhancers potentiate aminergic activity and increase duration of activity and makes testable predictions about additional compounds that should act as aminergic enhancers. PMID:25174918

  9. Squash inhibitors: from structural motifs to macrocyclic knottins.

    PubMed

    Chiche, Laurent; Heitz, Annie; Gelly, Jean-Christophe; Gracy, Jérôme; Chau, Pham T T; Ha, Phan T; Hernandez, Jean-François; Le-Nguyen, Dung

    2004-10-01

    In this article, we will first introduce the squash inhibitor, a well established family of highly potent canonical serine proteinase inhibitors isolated from Cucurbitaceae. The squash inhibitors were among the first discovered proteins with the typical knottin fold shared by numerous peptides extracted from plants, animals and fungi. Knottins contain three knotted disulfide bridges, two of them arranged as a Cystine-Stabilized Beta-sheet motif. In contrast to cyclotides for which no natural linear homolog is known, most squash inhibitors are linear. However, Momordica cochinchinensis Trypsin Inhibitor-I and (MCoTI-I and -II), 34-residue squash inhibitors isolated from seeds of a common Cucurbitaceae from Vietnam, were recently shown to be macrocyclic. In these circular squash inhibitors, a short peptide linker connects residues that correspond to the N- and C-termini in homologous linear squash inhibitors. In this review we present the isolation, characterization, chemical synthesis, and activity of these macrocyclic knottins. The solution structure of MCoTI-II will be compared with topologically similar cyclotides, homologous linear squash inhibitors and other knottins, and potential applications of such scaffolds will be discussed. PMID:15551519

  10. Maximum likelihood density modification by pattern recognition of structural motifs

    DOEpatents

    Terwilliger, Thomas C.

    2004-04-13

    An electron density for a crystallographic structure having protein regions and solvent regions is improved by maximizing the log likelihood of a set of structures factors {F.sub.h } using a local log-likelihood function: (x)+p(.rho.(x).vertline.SOLV)p.sub.SOLV (x)+p(.rho.(x).vertline.H)p.sub.H (x)], where p.sub.PROT (x) is the probability that x is in the protein region, p(.rho.(x).vertline.PROT) is the conditional probability for .rho.(x) given that x is in the protein region, and p.sub.SOLV (x) and p(.rho.(x).vertline.SOLV) are the corresponding quantities for the solvent region, p.sub.H (x) refers to the probability that there is a structural motif at a known location, with a known orientation, in the vicinity of the point x; and p(.rho.(x).vertline.H) is the probability distribution for electron density at this point given that the structural motif actually is present. One appropriate structural motif is a helical structure within the crystallographic structure.

  11. Variable structure motifs for transcription factor binding sites

    PubMed Central

    2010-01-01

    Background Classically, models of DNA-transcription factor binding sites (TFBSs) have been based on relatively few known instances and have treated them as sites of fixed length using position weight matrices (PWMs). Various extensions to this model have been proposed, most of which take account of dependencies between the bases in the binding sites. However, some transcription factors are known to exhibit some flexibility and bind to DNA in more than one possible physical configuration. In some cases this variation is known to affect the function of binding sites. With the increasing volume of ChIP-seq data available it is now possible to investigate models that incorporate this flexibility. Previous work on variable length models has been constrained by: a focus on specific zinc finger proteins in yeast using restrictive models; a reliance on hand-crafted models for just one transcription factor at a time; and a lack of evaluation on realistically sized data sets. Results We re-analysed binding sites from the TRANSFAC database and found motivating examples where our new variable length model provides a better fit. We analysed several ChIP-seq data sets with a novel motif search algorithm and compared the results to one of the best standard PWM finders and a recently developed alternative method for finding motifs of variable structure. All the methods performed comparably in held-out cross validation tests. Known motifs of variable structure were recovered for p53, Stat5a and Stat5b. In addition our method recovered a novel generalised version of an existing PWM for Sp1 that allows for variable length binding. This motif improved classification performance. Conclusions We have presented a new gapped PWM model for variable length DNA binding sites that is not too restrictive nor over-parameterised. Our comparison with existing tools shows that on average it does not have better predictive accuracy than existing methods. However, it does provide more interpretable

  12. 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

  13. Nucleic Acid i-Motif Structures in Analytical Chemistry.

    PubMed

    Alba, Joan Josep; Sadurní, Anna; Gargallo, Raimundo

    2016-09-01

    Under the appropriate experimental conditions of pH and temperature, cytosine-rich segments in DNA or RNA sequences may produce a characteristic folded structure known as an i-motif. Besides its potential role in vivo, which is still under investigation, this structure has attracted increasing interest in other fields due to its sharp, fast and reversible pH-driven conformational changes. This "on/off" switch at molecular level is being used in nanotechnology and analytical chemistry to develop nanomachines and sensors, respectively. This paper presents a review of the latest applications of this structure in the field of chemical analysis. PMID:26939549

  14. Recognition of Conserved Amino Acid Motifs of Common Viruses and Its Role in Autoimmunity

    PubMed Central

    2005-01-01

    The triggers of autoimmune diseases such as multiple sclerosis (MS) remain elusive. Epidemiological studies suggest that common pathogens can exacerbate and also induce MS, but it has been difficult to pinpoint individual organisms. Here we demonstrate that in vivo clonally expanded CD4+ T cells isolated from the cerebrospinal fluid of a MS patient during disease exacerbation respond to a poly-arginine motif of the nonpathogenic and ubiquitous Torque Teno virus. These T cell clones also can be stimulated by arginine-enriched protein domains from other common viruses and recognize multiple autoantigens. Our data suggest that repeated infections with common pathogenic and even nonpathogenic viruses could expand T cells specific for conserved protein domains that are able to cross-react with tissue-derived and ubiquitous autoantigens. PMID:16362076

  15. Structure and ubiquitin binding of the ubiquitin-interacting motif

    SciTech Connect

    Fisher,R.; Wang, B.; Alam, S.; Higginson, D.; Robinson, H.; Sundquist, C.; Hill, C.

    2003-01-01

    Ubiquitylation is used to target proteins into a large number of different biological processes including proteasomal degradation, endocytosis, virus budding, and vacuolar protein sorting (Vps). Ubiquitylated proteins are typically recognized using one of several different conserved ubiquitin binding modules. Here, we report the crystal structure and ubiquitin binding properties of one such module, the ubiquitin-interacting motif (UIM). We found that UIM peptides from several proteins involved in endocytosis and vacuolar protein sorting including Hrs, Vps27p, Stam1, and Eps15 bound specifically, but with modest affinity (K{sub d} = 0.1-1 mM), to free ubiquitin. Full affinity ubiquitin binding required the presence of conserved acidic patches at the N and C terminus of the UIM, as well as highly conserved central alanine and serine residues. NMR chemical shift perturbation mapping experiments demonstrated that all of these UIM peptides bind to the I44 surface of ubiquitin. The 1.45 {angstrom} resolution crystal structure of the second yeast Vps27p UIM (Vps27p-2) revealed that the ubiquitin-interacting motif forms an amphipathic helix. Although Vps27p-2 is monomeric in solution, the motif unexpectedly crystallized as an antiparallel four-helix bundle, and the potential biological implications of UIM oligomerization are therefore discussed.

  16. Motif structure and cooperation in real-world complex networks

    NASA Astrophysics Data System (ADS)

    Salehi, Mostafa; Rabiee, Hamid R.; Jalili, Mahdi

    2010-12-01

    Networks of dynamical nodes serve as generic models for real-world systems in many branches of science ranging from mathematics to physics, technology, sociology and biology. Collective behavior of agents interacting over complex networks is important in many applications. The cooperation between selfish individuals is one of the most interesting collective phenomena. In this paper we address the interplay between the motifs’ cooperation properties and their abundance in a number of real-world networks including yeast protein-protein interaction, human brain, protein structure, email communication, dolphins’ social interaction, Zachary karate club and Net-science coauthorship networks. First, the amount of cooperativity for all possible undirected subgraphs with three to six nodes is calculated. To this end, the evolutionary dynamics of the Prisoner’s Dilemma game is considered and the cooperativity of each subgraph is calculated as the percentage of cooperating agents at the end of the simulation time. Then, the three- to six-node motifs are extracted for each network. The significance of the abundance of a motif, represented by a Z-value, is obtained by comparing them with some properly randomized versions of the original network. We found that there is always a group of motifs showing a significant inverse correlation between their cooperativity amount and Z-value, i.e. the more the Z-value the less the amount of cooperativity. This suggests that networks composed of well-structured units do not have good cooperativity properties.

  17. Spectral Barcoding of Quantum Dots: Deciphering Structural Motifs from the Excitonic Spectra

    SciTech Connect

    Mlinar, V.; Zunger, A.

    2009-01-01

    Self-assembled semiconductor quantum dots (QDs) show in high-resolution single-dot spectra a multitude of sharp lines, resembling a barcode, due to various neutral and charged exciton complexes. Here we propose the 'spectral barcoding' method that deciphers structural motifs of dots by using such barcode as input to an artificial-intelligence learning system. Thus, we invert the common practice of deducing spectra from structure by deducing structure from spectra. This approach (i) lays the foundation for building a much needed structure-spectra understanding for large nanostructures and (ii) can guide future design of desired optical features of QDs by controlling during growth only those structural motifs that decide given optical features.

  18. Composite motifs integrating multiple protein structures increase sensitivity for function prediction.

    PubMed

    Chen, Brian Y; Bryant, Drew H; Cruess, Amanda E; Bylund, Joseph H; Fofanov, Viacheslav Y; Kristensen, David M; Kimmel, Marek; Lichtarge, Olivier; Kavraki, Lydia E

    2007-01-01

    The study of disease often hinges on the biological function of proteins, but determining protein function is a difficult experimental process. To minimize duplicated effort, algorithms for function prediction seek characteristics indicative of possible protein function. One approach is to identify substructural matches of geometric and chemical similarity between motifs representing known active sites and target protein structures with unknown function. In earlier work, statistically significant matches of certain effective motifs have identified functionally related active sites. Effective motifs must be carefully designed to maintain similarity to functionally related sites (sensitivity) and avoid incidental similarities to functionally unrelated protein geometry (specificity). Existing motif design techniques use the geometry of a single protein structure. Poor selection of this structure can limit motif effectiveness if the selected functional site lacks similarity to functionally related sites. To address this problem, this paper presents composite motifs, which combine structures of functionally related active sites to potentially increase sensitivity. Our experimentation compares the effectiveness of composite motifs with simple motifs designed from single protein structures. On six distinct families of functionally related proteins, leave-one-out testing showed that composite motifs had sensitivity comparable to the most sensitive of all simple motifs and specificity comparable to the average simple motif. On our data set, we observed that composite motifs simultaneously capture variations in active site conformation, diminish the problem of selecting motif structures, and enable the fusion of protein structures from diverse data sources. PMID:17951837

  19. DNA nanotechnology based on i-motif structures.

    PubMed

    Dong, Yuanchen; Yang, Zhongqiang; Liu, Dongsheng

    2014-06-17

    CONSPECTUS: Most biological processes happen at the nanometer scale, and understanding the energy transformations and material transportation mechanisms within living organisms has proved challenging. To better understand the secrets of life, researchers have investigated artificial molecular motors and devices over the past decade because such systems can mimic certain biological processes. DNA nanotechnology based on i-motif structures is one system that has played an important role in these investigations. In this Account, we summarize recent advances in functional DNA nanotechnology based on i-motif structures. The i-motif is a DNA quadruplex that occurs as four stretches of cytosine repeat sequences form C·CH(+) base pairs, and their stabilization requires slightly acidic conditions. This unique property has produced the first DNA molecular motor driven by pH changes. The motor is reliable, and studies show that it is capable of millisecond running speeds, comparable to the speed of natural protein motors. With careful design, the output of these types of motors was combined to drive micrometer-sized cantilevers bend. Using established DNA nanostructure assembly and functionalization methods, researchers can easily integrate the motor within other DNA assembled structures and functional units, producing DNA molecular devices with new functions such as suprahydrophobic/suprahydrophilic smart surfaces that switch, intelligent nanopores triggered by pH changes, molecular logic gates, and DNA nanosprings. Recently, researchers have produced motors driven by light and electricity, which have allowed DNA motors to be integrated within silicon-based nanodevices. Moreover, some devices based on i-motif structures have proven useful for investigating processes within living cells. The pH-responsiveness of the i-motif structure also provides a way to control the stepwise assembly of DNA nanostructures. In addition, because of the stability of the i-motif, this

  20. ET-Motif: Solving the Exact (l, d)-Planted Motif Problem Using Error Tree Structure.

    PubMed

    Al-Okaily, Anas; Huang, Chun-Hsi

    2016-07-01

    Motif finding is an important and a challenging problem in many biological applications such as discovering promoters, enhancers, locus control regions, transcription factors, and more. The (l, d)-planted motif search, PMS, is one of several variations of the problem. In this problem, there are n given sequences over alphabets of size [Formula: see text], each of length m, and two given integers l and d. The problem is to find a motif m of length l, where in each sequence there is at least an l-mer at a Hamming distance of [Formula: see text] of m. In this article, we propose ET-Motif, an algorithm that can solve the PMS problem in [Formula: see text] time and [Formula: see text] space. The time bound can be further reduced by a factor of m with [Formula: see text] space. In case the suffix tree that is built for the input sequences is balanced, the problem can be solved in [Formula: see text] time and [Formula: see text] space. Similarly, the time bound can be reduced by a factor of m using [Formula: see text] space. Moreover, the variations of the problem, namely the edit distance PMS and edited PMS (Quorum), can be solved using ET-Motif with simple modifications but upper bands of space and time. For edit distance PMS, the time and space bounds will be increased by [Formula: see text], while for edited PMS the increase will be of [Formula: see text] in the time bound. PMID:27152692

  1. Crystal Structures of IAPP Amyloidogenic Segments Reveal a Novel Packing Motif of Out-of-Register Beta Sheets.

    PubMed

    Soriaga, Angela B; Sangwan, Smriti; Macdonald, Ramsay; Sawaya, Michael R; Eisenberg, David

    2016-07-01

    Structural studies of amyloidogenic segments by X-ray crystallography have revealed a novel packing motif, consisting of out-of-register β sheets, which may constitute one of the toxic species in aggregation related diseases. Here we sought to determine the presence of such a motif in islet amyloid polypeptide (IAPP), whose amyloidogenic properties are associated with type 2 diabetes. We determined four new crystal structures of segments within IAPP, all forming steric zippers. Most interestingly, one of the segments in the fibril core of IAPP forms an out-of-register steric zipper. Analysis of this structure reveals several commonalities with previously solved out-of-register fibrils. Our results provide additional evidence of out-of-register β sheets as a common structural motif in amyloid aggregates. PMID:26629790

  2. Junctions between i-motif tetramers in supramolecular structures

    PubMed Central

    Guittet, Eric; Renciuk, Daniel; Leroy, Jean-Louis

    2012-01-01

    The symmetry of i-motif tetramers gives to cytidine-rich oligonucleotides the capacity to associate into supramolecular structures (sms). In order to determine how the tetramers are linked together in such structures, we have measured by gel filtration chromatography and NMR the formation and dissociation kinetics of sms built by oligonucleotides containing two short C stretches separated by a non-cytidine-base. We show that a stretch of only two cytidines either at the 3′- or 5′-end is long enough to link the tetramers into sms. The analysis of the properties of sms formed by oligonucleotides differing by the length of the oligo-C stretches, the sequence orientation and the nature of the non-C base provides a model of the junction connecting the tetramers in sms. PMID:22362739

  3. Maximum-likelihood density modification using pattern recognition of structural motifs

    SciTech Connect

    Terwilliger, Thomas C.

    2001-12-01

    A likelihood-based density-modification method is extended to include pattern recognition of structural motifs. The likelihood-based approach to density modification [Terwilliger (2000 ▶), Acta Cryst. D56, 965–972] is extended to include the recognition of patterns of electron density. Once a region of electron density in a map is recognized as corresponding to a known structural element, the likelihood of the map is reformulated to include a term that reflects how closely the map agrees with the expected density for that structural element. This likelihood is combined with other aspects of the likelihood of the map, including the presence of a flat solvent region and the electron-density distribution in the protein region. This likelihood-based pattern-recognition approach was tested using the recognition of helical segments in a largely helical protein. The pattern-recognition method yields a substantial phase improvement over both conventional and likelihood-based solvent-flattening and histogram-matching methods. The method can potentially be used to recognize any common structural motif and incorporate prior knowledge about that motif into density modification.

  4. Automated protein motif generation in the structure-based protein function prediction tool ProMOL.

    PubMed

    Osipovitch, Mikhail; Lambrecht, Mitchell; Baker, Cameron; Madha, Shariq; Mills, Jeffrey L; Craig, Paul A; Bernstein, Herbert J

    2015-12-01

    ProMOL, a plugin for the PyMOL molecular graphics system, is a structure-based protein function prediction tool. ProMOL includes a set of routines for building motif templates that are used for screening query structures for enzyme active sites. Previously, each motif template was generated manually and required supervision in the optimization of parameters for sensitivity and selectivity. We developed an algorithm and workflow for the automation of motif building and testing routines in ProMOL. The algorithm uses a set of empirically derived parameters for optimization and requires little user intervention. The automated motif generation algorithm was first tested in a performance comparison with a set of manually generated motifs based on identical active sites from the same 112 PDB entries. The two sets of motifs were equally effective in identifying alignments with homologs and in rejecting alignments with unrelated structures. A second set of 296 active site motifs were generated automatically, based on Catalytic Site Atlas entries with literature citations, as an expansion of the library of existing manually generated motif templates. The new motif templates exhibited comparable performance to the existing ones in terms of hit rates against native structures, homologs with the same EC and Pfam designations, and randomly selected unrelated structures with a different EC designation at the first EC digit, as well as in terms of RMSD values obtained from local structural alignments of motifs and query structures. This research is supported by NIH grant GM078077. PMID:26573864

  5. Plasticity of the RNA Kink Turn Structural Motif

    SciTech Connect

    Antonioli, A.; Cochrane, J; Lipchock, S; Strobel, S

    2010-01-01

    The kink turn (K-turn) is an RNA structural motif found in many biologically significant RNAs. While most examples of the K-turn have a similar fold, the crystal structure of the Azoarcus group I intron revealed a novel RNA conformation, a reverse kink turn bent in the direction opposite that of a consensus K-turn. The reverse K-turn is bent toward the major grooves rather than the minor grooves of the flanking helices, yet the sequence differs from the K-turn consensus by only a single nucleotide. Here we demonstrate that the reverse bend direction is not solely defined by internal sequence elements, but is instead affected by structural elements external to the K-turn. It bends toward the major groove under the direction of a tetraloop-tetraloop receptor. The ability of one sequence to form two distinct structures demonstrates the inherent plasticity of the K-turn sequence. Such plasticity suggests that the K-turn is not a primary element in RNA folding, but instead is shaped by other structural elements within the RNA or ribonucleoprotein assembly.

  6. Peptoid nanosheets exhibit a new secondary-structure motif

    NASA Astrophysics Data System (ADS)

    Mannige, Ranjan V.; Haxton, Thomas K.; Proulx, Caroline; Robertson, Ellen J.; Battigelli, Alessia; Butterfoss, Glenn L.; Zuckermann, Ronald N.; Whitelam, Stephen

    2015-10-01

    A promising route to the synthesis of protein-mimetic materials that are capable of complex functions, such as molecular recognition and catalysis, is provided by sequence-defined peptoid polymers--structural relatives of biologically occurring polypeptides. Peptoids, which are relatively non-toxic and resistant to degradation, can fold into defined structures through a combination of sequence-dependent interactions. However, the range of possible structures that are accessible to peptoids and other biological mimetics is unknown, and our ability to design protein-like architectures from these polymer classes is limited. Here we use molecular-dynamics simulations, together with scattering and microscopy data, to determine the atomic-resolution structure of the recently discovered peptoid nanosheet, an ordered supramolecular assembly that extends macroscopically in only two dimensions. Our simulations show that nanosheets are structurally and dynamically heterogeneous, can be formed only from peptoids of certain lengths, and are potentially porous to water and ions. Moreover, their formation is enabled by the peptoids' adoption of a secondary structure that is not seen in the natural world. This structure, a zigzag pattern that we call a Σ(`sigma')-strand, results from the ability of adjacent backbone monomers to adopt opposed rotational states, thereby allowing the backbone to remain linear and untwisted. Linear backbones tiled in a brick-like way form an extended two-dimensional nanostructure, the Σ-sheet. The binary rotational-state motif of the Σ-strand is not seen in regular protein structures, which are usually built from one type of rotational state. We also show that the concept of building regular structures from multiple rotational states can be generalized beyond the peptoid nanosheet system.

  7. Sulfur-induced structural motifs on copper and gold surfaces

    NASA Astrophysics Data System (ADS)

    Walen, Holly

    The interaction of sulfur with copper and gold surfaces plays a fundamental role in important phenomena that include coarsening of surface nanostructures, and self-assembly of alkanethiols. Here, we identify and analyze unique sulfur-induced structural motifs observed on the low-index surfaces of these two metals. We seek out these structures in an effort to better understand the fundamental interactions between these metals and sulfur that lends to the stability and favorability of metal-sulfur complexes vs. chemisorbed atomic sulfur. We choose very specific conditions: very low temperature (5 K), and very low sulfur coverage (≤ 0.1 monolayer). In this region of temperature-coverage space, which has not been examined previously for these adsorbate-metal systems, the effects of individual interactions between metals and sulfur are most apparent and can be assessed extensively with the aid of theory and modeling. Furthermore, at this temperature diffusion is minimal and relatively-mobile species can be isolated, and at low coverage the structures observed are not consumed by an extended reconstruction. The primary experimental technique is scanning tunneling microscopy (STM). The experimental observations presented here---made under identical conditions---together with extensive DFT analyses, allow comparisons and insights into factors that favor the existence of metal-sulfur complexes, vs. chemisorbed atomic sulfur, on metal terraces. We believe this data will be instrumental in better understanding the complex phenomena occurring between the surfaces of coinage metals and sulfur.

  8. Gentamicin Binds to the Megalin Receptor as a Competitive Inhibitor Using the Common Ligand Binding Motif of Complement Type Repeats

    PubMed Central

    Dagil, Robert; O'Shea, Charlotte; Nykjær, Anders; Bonvin, Alexandre M. J. J.; Kragelund, Birthe B.

    2013-01-01

    Gentamicin is an aminoglycoside widely used in treatments of, in particular, enterococcal, mycobacterial, and severe Gram-negative bacterial infections. Large doses of gentamicin cause nephrotoxicity and ototoxicity, entering the cell via the receptor megalin. Until now, no structural information has been available to describe the interaction with gentamicin in atomic detail, and neither have any three-dimensional structures of domains from the human megalin receptor been solved. To address this gap in our knowledge, we have solved the NMR structure of the 10th complement type repeat of human megalin and investigated its interaction with gentamicin. Using NMR titration data in HADDOCK, we have generated a three-dimensional model describing the complex between megalin and gentamicin. Gentamicin binds to megalin with low affinity and exploits the common ligand binding motif previously described (Jensen, G. A., Andersen, O. M., Bonvin, A. M., Bjerrum-Bohr, I., Etzerodt, M., Thogersen, H. C., O'Shea, C., Poulsen, F. M., and Kragelund, B. B. (2006) J. Mol. Biol. 362, 700–716) utilizing the indole side chain of Trp-1126 and the negatively charged residues Asp-1129, Asp-1131, and Asp-1133. Binding to megalin is highly similar to gentamicin binding to calreticulin. We discuss the impact of this novel insight for the future structure-based design of gentamicin antagonists. PMID:23275343

  9. Conserved rhodopsin intradiscal structural motifs mediate stabilization: effects of zinc.

    PubMed

    Gleim, Scott; Stojanovic, Aleksandar; Arehart, Eric; Byington, Daniel; Hwa, John

    2009-03-01

    Retinitis pigmentosa (RP), a neurodegenerative disorder, can arise from single point mutations in rhodopsin, leading to a cascade of protein instability, misfolding, aggregation, rod cell death, retinal degeneration, and ultimately blindness. Divalent cations, such as zinc and copper, have allosteric effects on misfolded aggregates of comparable neurodegenerative disorders including Alzheimer disease, prion diseases, and ALS. We report that two structurally conserved low-affinity zinc coordination motifs, located among a cluster of RP mutations in the intradiscal loop region, mediate dose-dependent rhodopsin destabilization. Disruption of native interactions involving histidines 100 and 195, through site-directed mutagenesis or exogenous zinc coordination, results in significant loss of receptor stability. Furthermore, chelation with EDTA stabilizes the structure of both wild-type rhodopsin and the most prevalent rhodopsin RP mutation, P(23)H. These interactions suggest that homeostatic regulation of trace metal concentrations in the rod outer segment of the retina may be important both physiologically and for an important cluster of RP mutations. Furthermore, with a growing awareness of allosteric zinc binding domains on a diverse range of GPCRs, such principles may apply to many other receptors and their associated diseases. PMID:19206210

  10. Conserved rhodopsin intradiscal structural motifs mediate stabilization; effects of zinc†

    PubMed Central

    Gleim, Scott; Stojanovic, Aleksandar; Arehart, Eric; Byington, Daniel; Hwa, John

    2009-01-01

    Retinitis pigmentosa (RP), a neurodegenerative disorder, can arise from single point mutations in rhodopsin, leading to a cascade of protein instability, misfolding, aggregation, rod cell death, retinal degeneration, and ultimately blindness. Divalent cations, such as zinc and copper, have allosteric effects on misfolded aggregates of comparable neurodegenerative disorders including Alzheimer disease, prion diseases, and ALS. We report that two structurally conserved low-affinity zinc coordination motifs, located among a cluster of RP mutations in the intradiscal loop region, mediate dose-dependent rhodopsin destabilization. Disruption of native interactions involving histidines 100 and 195, through site-directed mutagenesis or exogenous zinc coordination, results in significant loss of receptor stability. Furthermore, chelation with EDTA stabilizes the structure of both wild type rhodopsin and the most prevalent rhodopsin RP mutation, P23H. These interactions suggest that homeostatic regulation of trace metal concentrations in the rod outer segment of the retina may be important both physiologically and for an important cluster of RP mutations. Furthermore, with a growing awareness of allosteric zinc binding domains on a diverse range of GPCRs, such principles may apply to many other receptors and their associated diseases. PMID:19206210

  11. Construction of a Three-Dimensional Motif Dictionary for Protein Structural Data Mining

    NASA Astrophysics Data System (ADS)

    Hiroaki, Kato; Tadokoro, Tetsuo; Miyata, Hiroyuki; Chikamatsu, Shin-Ichi; Takahashi, Yoshimasa; Abe, Hidetsugu

    With the rapidly increasing number of proteins of which three-dimensional (3D) structures are known, the protein structure database is one of the key elements in many attempts being made to derive the knowledge of structure-function relationships of proteins. In this work, the authors have developed a software tool to assist in constructing the 3D protein motif dictionary that is closely related to the PROSITE sequence motif database. In the PROSITE, a structural feature called motif is described by a sequence pattern of amino acid residues with the regular expression defined in the database. The present system allows us to automatically find the related sites for all the 3D protein structures taken from a protein structure database such as the Protein Data Bank (PDB), and to make a dictionary of the 3D motifs related to the PROSITE sequence motif patterns. A computational trial was carried out for a subset of the PDB's structure data file. The structural feature analysis resulted with the tool showed that there are many different 3D motif patterns but having a particular PROSITE sequence pattern. For this reason, the authors also tried to classify the 3D motif patterns into several groups on the basis of distance similarity matrix, and to determine a representative pattern for each group in preparing the dictionary. The usefulness of the additional approach for preparing the 3D motif dictionary is also discussed with an illustrative example.

  12. Construction of DNA logic gates utilizing a H+/Ag+ induced i-motif structure.

    PubMed

    Shi, Yunhua; Sun, Hongxia; Xiang, Junfeng; Chen, Hongbo; Yang, Qianfan; Guan, Aijiao; Li, Qian; Yu, Lijia; Tang, Yalin

    2014-12-18

    A simple technology to construct diverse DNA logic gates (OR and INHIBIT) has been designed utilizing a H(+) and/or Ag(+) induced i-motif structure. The logic gates are easily controlled and also show a real time response towards inputs. The research provides a new insight for designing DNA logic gates using an i-motif DNA structure. PMID:25349963

  13. Phosphatidylinositol transfer proteins: sequence motifs in structural and evolutionary analyses

    PubMed Central

    Wyckoff, Gerald J.; Solidar, Ada; Yoden, Marilyn D.

    2016-01-01

    Phosphatidylinositol transfer proteins (PITP) are a family of monomeric proteins that bind and transfer phosphatidylinositol and phosphatidylcholine between membrane compartments. They are required for production of inositol and diacylglycerol second messengers, and are found in most metazoan organisms. While PITPs are known to carry out crucial cell-signaling roles in many organisms, the structure, function and evolution of the majority of family members remains unexplored; primarily because the ubiquity and diversity of the family thwarts traditional methods of global alignment. To surmount this obstacle, we instead took a novel approach, using MEME and a parsimony-based analysis to create a cladogram of conserved sequence motifs in 56 PITP family proteins from 26 species. In keeping with previous functional annotations, three clades were supported within our evolutionary analysis; two classes of soluble proteins and a class of membrane-associated proteins. By, focusing on conserved regions, the analysis allowed for in depth queries regarding possible functional roles of PITP proteins in both intra- and extra- cellular signaling.

  14. Distance-based identification of structure motifs in proteins using constrained frequent subgraph mining.

    PubMed

    Huan, Jun; Bandyopadhyay, Deepak; Prins, Jan; Snoeyink, Jack; Tropsha, Alexander; Wang, Wei

    2006-01-01

    Structure motifs are amino acid packing patterns that occur frequently within a set of protein structures. We define a labeled graph representation of protein structure in which vertices correspond to amino acid residues and edges connect pairs of residues and are labeled by (1) the Euclidian distance between the C(alpha) atoms of the two residues and (2) a boolean indicating whether the two residues are in physical/chemical contact. Using this representation, a structure motif corresponds to a labeled clique that occurs frequently among the graphs representing the protein structures. The pairwise distance constraints on each edge in a clique serve to limit the variation in geometry among different occurrences of a structure motif. We present an efficient constrained subgraph mining algorithm to discover structure motifs in this setting. Compared with contact graph representations, the number of spurious structure motifs is greatly reduced. Using this algorithm, structure motifs were located for several SCOP families including the Eukaryotic Serine Proteases, Nuclear Binding Domains, Papain-like Cysteine Proteases, and FAD/NAD-linked Reductases. For each family, we typically obtain a handful of motifs within seconds of processing time. The occurrences of these motifs throughout the PDB were strongly associated with the original SCOP family, as measured using a hyper-geometric distribution. The motifs were found to cover functionally important sites like the catalytic triad for Serine Proteases and co-factor binding sites for Nuclear Binding Domains. The fact that many motifs are highly family-specific can be used to classify new proteins or to provide functional annotation in Structural Genomics Projects. PMID:17369641

  15. GENOMIC ANALYSIS OF CANCER TISSUE REVEALS THAT SOMATIC MUTATIONS COMMONLY OCCUR IN A SPECIFIC MOTIF

    PubMed Central

    Makridakis, Nick M; Ferraz, Lúcio Fábio Caldas; Reichardt, Juergen KV

    2009-01-01

    Somatic mutations are hallmarks of cancer progression. We sequenced 26 matched human prostate tumor and constitutional DNA samples for somatic alterations in the SRD5A2, HPRT, and HSD3B2 genes, and identified 71 nucleotide substitutions. 79% (56/71) of these substitutions occur within a WKVnRRRnVWK sequence (THEMIS motif; W= A/T, K= G/T, V= G/A/C, R= purine (A/G) and n= any nucleotide), with one mismatch allowed. Literature searches identified this motif with one mismatch allowed in 66% (37/ 56) of the somatic prostate cancer mutations and in 74% (90/ 122) of the somatic breast cancer mutations found in all human genes analyzed. We also found the THEMIS motif with one allowed mismatch in 88% (23/26) of the ras1 gene somatic mutations formed in the SENCAR (SENsitive to skin CARcinogenesis) mouse model, after induction of error-prone DNA repair following mutagenic treatment. The high prevalence of the motif in each of the above mentioned cases cannot be explained by chance (p < 0.046). We further identified 27 somatic mutations in the error-prone DNA polymerase genes pol η, pol κ and pol β in these prostate cancer patients. The data suggest that most somatic nucleotide substitutions in human cancer may occur in sites that conform to the THEMIS motif. These mutations may be caused by “mutator” mutations in error-prone DNA polymerase genes. PMID:18623241

  16. O-xylosylation in a recombinant protein is directed at a common motif on glycine-serine linkers.

    PubMed

    Spencer, David; Novarra, Shabazz; Zhu, Liang; Mugabe, Sheila; Thisted, Thomas; Baca, Manuel; Depaz, Roberto; Barton, Christopher

    2013-11-01

    Glycine-serine (GS) linkers are commonly used in recombinant proteins to connect domains. Here, we report the posttranslational O-glycosylation of a GS linker in a novel fusion protein. The structure of the O-glycan moiety is a xylose-based core substituted with hexose and sulfated hexauronic acid residues. The total level of O-xylosylation was approximately 30% in the material expressed in HEK-293 cell lines. There was an approximate 10-fold reduction in O-xylosylation levels when the material was expressed in Chinese hamster ovary cell lines. Similar O-glycan structures have been reported for human urinary thrombomodulin and represent the initial building block for proteoglycans such as chondroitin sulfate and heparin. The sites of attachment, determined by electron transfer dissociation mass spectrometry, were localized to serine in the linker regions of the recombinant fusion protein. This attachment could be attributed, in part, to the inherent xylosyltransferase motif present in GS linkers. Elimination of the O-glycan moiety was achieved with modified linkers containing only glycine residues. The aggregation and fragmentation behavior of the GGG construct were comparable to the GSG-linked material during thermal stress. The O-xylosylation reported has implications for the manufacturing consistency of recombinant proteins containing GS linkers. PMID:24105735

  17. Leucine-rich Repeats of Bacterial Surface Proteins Serve as Common Pattern Recognition Motifs of Human Scavenger Receptor gp340*

    PubMed Central

    Loimaranta, Vuokko; Hytönen, Jukka; Pulliainen, Arto T.; Sharma, Ashu; Tenovuo, Jorma; Strömberg, Nicklas; Finne, Jukka

    2009-01-01

    Scavenger receptors are innate immune molecules recognizing and inducing the clearance of non-host as well as modified host molecules. To recognize a wide pattern of invading microbes, many scavenger receptors bind to common pathogen-associated molecular patterns, such as lipopolysaccharides and lipoteichoic acids. Similarly, the gp340/DMBT1 protein, a member of the human scavenger receptor cysteine-rich protein family, displays a wide ligand repertoire. The peptide motif VEVLXXXXW derived from its scavenger receptor cysteine-rich domains is involved in some of these interactions, but most of the recognition mechanisms are unknown. In this study, we used mass spectrometry sequencing, gene inactivation, and recombinant proteins to identify Streptococcus pyogenes protein Spy0843 as a recognition receptor of gp340. Antibodies against Spy0843 are shown to protect against S. pyogenes infection, but no function or host receptor have been identified for the protein. Spy0843 belongs to the leucine-rich repeat (Lrr) family of eukaryotic and prokaryotic proteins. Experiments with truncated forms of the recombinant proteins confirmed that the Lrr region is needed in the binding of Spy0843 to gp340. The same motif of two other Lrr proteins, LrrG from the Gram-positive S. agalactiae and BspA from the Gram-negative Tannerella forsythia, also mediated binding to gp340. Moreover, inhibition of Spy0843 binding occurred with peptides containing the VEVLXXXXW motif, but also peptides devoid of the XXXXW motif inhibited binding of Lrr proteins. These results thus suggest that the conserved Lrr motif in bacterial proteins serves as a novel pattern recognition motif for unique core peptides of human scavenger receptor gp340. PMID:19465482

  18. Stabilization of i-motif structures by 2'-β-fluorination of DNA.

    PubMed

    Assi, Hala Abou; Harkness, Robert W; Martin-Pintado, Nerea; Wilds, Christopher J; Campos-Olivas, Ramón; Mittermaier, Anthony K; González, Carlos; Damha, Masad J

    2016-06-20

    i-Motifs are four-stranded DNA structures consisting of two parallel DNA duplexes held together by hemi-protonated and intercalated cytosine base pairs (C:CH(+)). They have attracted considerable research interest for their potential role in gene regulation and their use as pH responsive switches and building blocks in macromolecular assemblies. At neutral and basic pH values, the cytosine bases deprotonate and the structure unfolds into single strands. To avoid this limitation and expand the range of environmental conditions supporting i-motif folding, we replaced the sugar in DNA by 2-deoxy-2-fluoroarabinose. We demonstrate that such a modification significantly stabilizes i-motif formation over a wide pH range, including pH 7. Nuclear magnetic resonance experiments reveal that 2-deoxy-2-fluoroarabinose adopts a C2'-endo conformation, instead of the C3'-endo conformation usually found in unmodified i-motifs. Nevertheless, this substitution does not alter the overall i-motif structure. This conformational change, together with the changes in charge distribution in the sugar caused by the electronegative fluorine atoms, leads to a number of favorable sequential and inter-strand electrostatic interactions. The availability of folded i-motifs at neutral pH will aid investigations into the biological function of i-motifs in vitro, and will expand i-motif applications in nanotechnology. PMID:27166371

  19. Stabilization of i-motif structures by 2′-β-fluorination of DNA

    PubMed Central

    Assi, Hala Abou; Harkness, Robert W.; Martin-Pintado, Nerea; Wilds, Christopher J.; Campos-Olivas, Ramón; Mittermaier, Anthony K.; González, Carlos; Damha, Masad J.

    2016-01-01

    i-Motifs are four-stranded DNA structures consisting of two parallel DNA duplexes held together by hemi-protonated and intercalated cytosine base pairs (C:CH+). They have attracted considerable research interest for their potential role in gene regulation and their use as pH responsive switches and building blocks in macromolecular assemblies. At neutral and basic pH values, the cytosine bases deprotonate and the structure unfolds into single strands. To avoid this limitation and expand the range of environmental conditions supporting i-motif folding, we replaced the sugar in DNA by 2-deoxy-2-fluoroarabinose. We demonstrate that such a modification significantly stabilizes i-motif formation over a wide pH range, including pH 7. Nuclear magnetic resonance experiments reveal that 2-deoxy-2-fluoroarabinose adopts a C2′-endo conformation, instead of the C3′-endo conformation usually found in unmodified i-motifs. Nevertheless, this substitution does not alter the overall i-motif structure. This conformational change, together with the changes in charge distribution in the sugar caused by the electronegative fluorine atoms, leads to a number of favorable sequential and inter-strand electrostatic interactions. The availability of folded i-motifs at neutral pH will aid investigations into the biological function of i-motifs in vitro, and will expand i-motif applications in nanotechnology. PMID:27166371

  20. Maximum-likelihood density modification using pattern recognition of structural motifs

    PubMed Central

    Terwilliger, Thomas C.

    2001-01-01

    The likelihood-based approach to density modification [Terwilliger (2000 ▶), Acta Cryst. D56, 965–972] is extended to include the recognition of patterns of electron density. Once a region of electron density in a map is recognized as corresponding to a known structural element, the likelihood of the map is reformulated to include a term that reflects how closely the map agrees with the expected density for that structural element. This likelihood is combined with other aspects of the likelihood of the map, including the presence of a flat solvent region and the electron-density distribution in the protein region. This likelihood-based pattern-recognition approach was tested using the recognition of helical segments in a largely helical protein. The pattern-recognition method yields a substantial phase improvement over both conventional and likelihood-based solvent-flattening and histogram-matching methods. The method can potentially be used to recognize any common structural motif and incorporate prior knowledge about that motif into density modification. PMID:11717487

  1. Excluded volume effects on the kinetic assembling of a structural motif for RNA catalysis

    NASA Astrophysics Data System (ADS)

    Fernández, Ariel

    1991-09-01

    We establish the role of excluded volume effects on the loss of conformational entropy due to pseudoknot formation in RNA. This pseudoknot appears to be the structural motif responsible for shaping the splicing site of certain noncoding RNA transcriptional products. Focusing on the illustrative example of the YC4 intron, we show that the emergence of this motif is kinetically driven and prevails over competing catalytically inert secondary structure due to excluded volume effects which favor the correlation of interacting intramolecular loops.

  2. Pressure-dependent formation of i-motif and G-quadruplex DNA structures.

    PubMed

    Takahashi, S; Sugimoto, N

    2015-12-14

    Pressure is an important physical stimulus that can influence the fate of cells by causing structural changes in biomolecules such as DNA. We investigated the effect of high pressure on the folding of duplex, DNA i-motif, and G-quadruplex (G4) structures; the non-canonical structures may be modulators of expression of genes involved in cancer progression. The i-motif structure was stabilized by high pressure, whereas the G4 structure was destabilized. The melting temperature of an intramolecular i-motif formed by 5'-dCGG(CCT)10CGG-3' increased from 38.8 °C at atmospheric pressure to 61.5 °C at 400 MPa. This effect was also observed in the presence of 40 wt% ethylene glycol, a crowding agent. In the presence of 40 wt% ethylene glycol, the G4 structure was less destabilized than in the absence of the crowding agent. P-T stability diagrams of duplex DNA with a telomeric sequence indicated that the duplex is more stable than G4 and i-motif structures under low pressure, but the i-motif dominates the structural composition under high pressure. Under crowding conditions, the P-T diagrams indicated that the duplex does not form under high pressure, and i-motif and G4 structures dominate. Our findings imply that temperature regulates the formation of the duplex structure, whereas pressure triggers the formation of non-canonical DNA structures like i-motif and G4. These results suggest that pressure impacts the function of nucleic acids by stabilizing non-canonical structures; this may be relevant to deep sea organisms and during evolution under prebiotic conditions. PMID:26387909

  3. Juvenile hormone binding protein and transferrin from Galleria mellonella share a similar structural motif.

    PubMed

    Krzyzanowska, D; Ozyhar, A; Lalik, A; Parkitna, J M; Szkudlarek, J; Waśniowska, K; Lisowska, E; Kochman, M

    2001-07-01

    It has been previously suggested that juvenile hormone binding protein(s) (JHBP) belongs to a new class of proteins. In the search for other protein(s) that may contain structural motifs similar to those found in JHBP, hemolymph from Galleria mellonella (Lepidoptera) was chromatographed over a Sephadex G-200 column and resulting fractions were subjected to SDS-PAGE, transferred onto nitrocellulose membrane and scanned with a monoclonal antibody, mAb 104, against hemolymph JHBP. Two proteins yielded a positive reaction with mAb 104, one corresponding to JHBP and the second corresponding to a transferrin, as judged from N-terminal amino acid sequencing staining. Transferrin was purified to about 80% homogeneity using a two-step procedure including Sephadex G-200 gel filtration and HPLC MonoQ column chromatography. Panning of a random peptide display library and analysis with immobilized synthetic peptides were applied for finding a common epitope present in JHBP and the transferrin molecule. The postulated epitope motif recognized by mAb 104 in the JHBP sequence is RDTKAVN, and is localized at position 82-88. PMID:11530933

  4. Structural Implications of Homopyrimidine Base Pairs in the Parallel-Stranded d(YGA) Motif.

    PubMed

    Tripathi, Shailesh; Paukstelis, Paul J

    2016-06-16

    DNA can adopt many other structures beyond the canonical B-form double helix. These alternative DNA structures have become increasingly significant as new biological roles are found for them. Additionally, there has been a growing interest in using non-canonical base pairs to provide structural diversity for designing DNA architectures for nanotechnology applications. We recently described the crystal structure of d(ACTCGGATGAT), which forms a tetraplex through parallel-stranded homo-base pairs and nucleobase intercalation. The homoduplex region contains a d(YGA⋅YGA) motif observed in crystal and solution structures. Here, we examine the structural implications of the homopyrimidine base pair within this motif. We determined crystal structures of two variants that differ from the original structure in the homopyrimidine base pairs and number of d(YGA) motifs. Our results show that the intercalation-locked tetraplex motif is predictable in these different sequence contexts and that substituting C⋅C base pairs for T⋅T base pairs introduces asymmetry to the homoduplex. These results have important implications for utilizing d(YGA) motifs in DNA crystal design and could provide a basis for understanding how local structures could be associated with repeat expansions. PMID:26629965

  5. Structural characterization of a capping protein interaction motif defines a family of actin filament regulators

    PubMed Central

    Hernandez-Valladares, Maria; Kim, Taekyung; Kannan, Balakrishnan; Tung, Alvin; Aguda, Adeleke H; Larsson, Mårten; Cooper, John A; Robinson, Robert C

    2011-01-01

    Capping protein (CP) regulates actin dynamics by binding the barbed ends of actin filaments. Removal of CP may be one means to harness actin polymerization for processes such as cell movement and endocytosis. Here we structurally and biochemically investigated a CP interaction (CPI) motif present in the otherwise unrelated proteins CARMIL and CD2AP. The CPI motif wraps around the stalk of the mushroom-shaped CP at a site distant from the actin-binding interface, which lies on the top of the mushroom cap. We propose that the CPI motif may act as an allosteric modulator, restricting CP to a low-affinity, filament-binding conformation. Structure-based sequence alignments extend the CPI motif–containing family to include CIN85, CKIP-1, CapZIP and a relatively uncharacterized protein, WASHCAP (FAM21). Peptides comprising these CPI motifs are able to inhibit CP and to uncap CP-bound actin filaments. PMID:20357771

  6. FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web.

    PubMed

    Shapiro, Jessica; Brutlag, Douglas

    2004-07-01

    The FoldMiner web server (http://foldminer.stanford.edu/) provides remote access to methods for protein structure alignment and unsupervised motif discovery. FoldMiner is unique among such algorithms in that it improves both the motif definition and the sensitivity of a structural similarity search by combining the search and motif discovery methods and using information from each process to enhance the other. In a typical run, a query structure is aligned to all structures in one of several databases of single domain targets in order to identify its structural neighbors and to discover a motif that is the basis for the similarity among the query and statistically significant targets. This process is fully automated, but options for manual refinement of the results are available as well. The server uses the Chime plugin and customized controls to allow for visualization of the motif and of structural superpositions. In addition, we provide an interface to the LOCK 2 algorithm for rapid alignments of a query structure to smaller numbers of user-specified targets. PMID:15215444

  7. An approach to delineate primers for a group of poorly conserved sequences incorporating the common motif region.

    PubMed

    Sahu, Mousumi; Sahu, Jagajjit; Sahoo, Smita; Dehury, Budheswar; Sarma, Kishore; Sarmah, Ranjan; Sen, Priyabrata; Modi, Mahendra Kumar; Barooah, Madhumita

    2012-01-01

    Glutathione synthetase (gshB) has previously been reported to confer tolerance to acidic soil condition in Rhizobium species. Cloning the gene coding for this enzyme necessitates the designing of proper primer sets which in turn depends on the identification of high quality sequence similarity in multiple global alignments. In this experiment, a group of homologous gene sequences related to gshB gene (accession no: gi-86355669:327589-328536) of Rhizobium etli CFN 42, were extracted from NCBI nucleotide sequence databases using BLASTN and were analyzed for designing degenerate primers. However, the T-coffee multiple global alignment results did not show any block of conserved region for the above sequence set to design the primers. Therefore, we attempted to identify the location of common motif region based on multiple local alignments employing the MEME algorithm supported with MAST and Primer3. The results revealed some common motif regions that enabled us to design the primer sets for related gshB gene sequences. The result will be validated in wet lab. PMID:22419837

  8. The ARTT motif and a unified structural understanding of substraterecognition in ADP ribosylating bacterial toxins and eukaryotic ADPribosyltransferases

    SciTech Connect

    Han, S.; Tainer, J.A.

    2001-08-01

    ADP-ribosylation is a widely occurring and biologically critical covalent chemical modification process in pathogenic mechanisms, intracellular signaling systems, DNA repair, and cell division. The reaction is catalyzed by ADP-ribosyltransferases, which transfer the ADP-ribose moiety of NAD to a target protein with nicotinamide release. A family of bacterial toxins and eukaryotic enzymes has been termed the mono-ADP-ribosyltransferases, in distinction to the poly-ADP-ribosyltransferases, which catalyze the addition of multiple ADP-ribose groups to the carboxyl terminus of eukaryotic nucleoproteins. Despite the limited primary sequence homology among the different ADP-ribosyltransferases, a central cleft bearing NAD-binding pocket formed by the two perpendicular b-sheet core has been remarkably conserved between bacterial toxins and eukaryotic mono- and poly-ADP-ribosyltransferases. The majority of bacterial toxins and eukaryotic mono-ADP-ribosyltransferases are characterized by conserved His and catalytic Glu residues. In contrast, Diphtheria toxin, Pseudomonas exotoxin A, and eukaryotic poly-ADP-ribosyltransferases are characterized by conserved Arg and catalytic Glu residues. The NAD-binding core of a binary toxin and a C3-like toxin family identified an ARTT motif (ADP-ribosylating turn-turn motif) that is implicated in substrate specificity and recognition by structural and mutagenic studies. Here we apply structure-based sequence alignment and comparative structural analyses of all known structures of ADP-ribosyltransfeases to suggest that this ARTT motif is functionally important in many ADP-ribosylating enzymes that bear a NAD binding cleft as characterized by conserved Arg and catalytic Glu residues. Overall, structure-based sequence analysis reveals common core structures and conserved active sites of ADP-ribosyltransferases to support similar NAD binding mechanisms but differing mechanisms of target protein binding via sequence variations within the ARTT

  9. Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements

    NASA Astrophysics Data System (ADS)

    Fernandez-Chamorro, Javier; Lozano, Gloria; Garcia-Martin, Juan Antonio; Ramajo, Jorge; Dotu, Ivan; Clote, Peter; Martinez-Salas, Encarnacion

    2016-04-01

    The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translation. A conserved motif is the pyrimidine-tract located upstream of the functional initiation codon in type I and II picornavirus IRES. By computationally designing synthetic RNAs to fold into a structure that sequesters the polypyrimidine tract in a hairpin, we establish a correlation between predicted inaccessibility of the pyrimidine tract and IRES activity, as determined in both in vitro and in vivo systems. Our data supports the hypothesis that structural sequestration of the pyrimidine-tract within a stable hairpin inactivates IRES activity, since the stronger the stability of the hairpin the higher the inhibition of protein synthesis. Destabilization of the stem-loop immediately upstream of the pyrimidine-tract also decreases IRES activity. Our work introduces a hybrid computational/experimental method to determine the importance of structural motifs for biological function. Specifically, we show the feasibility of using the software RNAiFold to design synthetic RNAs with particular sequence and structural motifs that permit subsequent experimental determination of the importance of such motifs for biological function.

  10. Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements

    PubMed Central

    Fernandez-Chamorro, Javier; Lozano, Gloria; Garcia-Martin, Juan Antonio; Ramajo, Jorge; Dotu, Ivan; Clote, Peter; Martinez-Salas, Encarnacion

    2016-01-01

    The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translation. A conserved motif is the pyrimidine-tract located upstream of the functional initiation codon in type I and II picornavirus IRES. By computationally designing synthetic RNAs to fold into a structure that sequesters the polypyrimidine tract in a hairpin, we establish a correlation between predicted inaccessibility of the pyrimidine tract and IRES activity, as determined in both in vitro and in vivo systems. Our data supports the hypothesis that structural sequestration of the pyrimidine-tract within a stable hairpin inactivates IRES activity, since the stronger the stability of the hairpin the higher the inhibition of protein synthesis. Destabilization of the stem-loop immediately upstream of the pyrimidine-tract also decreases IRES activity. Our work introduces a hybrid computational/experimental method to determine the importance of structural motifs for biological function. Specifically, we show the feasibility of using the software RNAiFold to design synthetic RNAs with particular sequence and structural motifs that permit subsequent experimental determination of the importance of such motifs for biological function. PMID:27053355

  11. A structure-based flexible search method for motifs in RNA.

    PubMed

    Veksler-Lublinsky, Isana; Ziv-Ukelson, Michal; Barash, Danny; Kedem, Klara

    2007-09-01

    The discovery of non-coding RNA (ncRNA) motifs and their role in regulating gene expression has recently attracted considerable attention. The goal is to discover these motifs in a sequence database. Current RNA motif search methods start from the primary sequence and only then take into account secondary structure considerations. One can think of developing a flexible structure-based motif search method that will filter datasets based on secondary structure first, while allowing extensive primary sequence factors and additional factors such as potential pseudoknots as constraints. Since different motifs vary in structure rigidity and in local sequence constraints, there is a need for algorithms and tools that can be fine-tuned according to the searched RNA motif, but differ in their approach from the RNAMotif descriptor language. We present an RNA motif search tool called STRMS (Structural RNA Motif Search), which takes as input the secondary structure of the query, including local sequence and structure constraints, and a target sequence database. It reports all occurrences of the query in the target, ranked by their similarity to the query, and produces an html file that displays graphical images of the predicted structures for both the query and the candidate hits. Our tool is flexible and takes into account a large number of sequence options and existence of potential pseudoknots as dictated by specific queries. Our approach combines pre-folding and an O(m n) RNA pattern matching algorithm based on subtree homeomorphism for ordered, rooted trees. An O(n(2) log n) extension is described that allows the search engine to take into account the pseudoknots typical to riboswitches. We employed STRMS in search for both new and known RNA motifs (riboswitches and tRNAs) in large target databases. Our results point to a number of additional purine bacterial riboswitch candidates in newly sequenced bacteria, and demonstrate high sensitivity on known riboswitches and t

  12. CHEM-PATH-TRACKER: An automated tool to analyze chemical motifs in molecular structures.

    PubMed

    Ribeiro, João V; Cerqueira, N M F S A; Fernandes, Pedro A; Ramos, Maria J

    2014-07-01

    In this article, we propose a method for locating functionally relevant chemical motifs in protein structures. The chemical motifs can be a small group of residues or structure protein fragments with highly conserved properties that have important biological functions. However, the detection of chemical motifs is rather difficult because they often consist of a set of amino acid residues separated by long, variable regions, and they only come together to form a functional group when the protein is folded into its three-dimensional structure. Furthermore, the assemblage of these residues is often dependent on non-covalent interactions among the constituent amino acids that are difficult to detect or visualize. To simplify the analysis of these chemical motifs and give access to a generalized use for all users, we developed chem-path-tracker. This software is a VMD plug-in that allows the user to highlight and reveal potential chemical motifs requiring only a few selections. The analysis is based on atoms/residues pair distances applying a modified version of Dijkstra's algorithm, and it makes possible to monitor the distances of a large pathway, even during a molecular dynamics simulation. This tool turned out to be very useful, fast, and user-friendly in the performed tests. The chem-path-tracker package is distributed as an independent platform and can be found at http://www.fc.up.pt/PortoBioComp/database/doku.php?id=chem-path-tracker. PMID:24775806

  13. Exploration of tetrahedral structures in silicate cathodes using a motif-network scheme

    SciTech Connect

    Zhao, Xin; Wu, Shunqing; Lv, Xiaobao; Nguyen, Manh Cuong; Wang, Cai -Zhuang; Lin, Zijing; Zhu, Zi -Zhong; Ho, Kai -Ming

    2015-10-26

    Using a motif-network search scheme, we studied the tetrahedral structures of the dilithium/disodium transition metal orthosilicates A2MSiO4 with A = Li or Na and M = Mn, Fe or Co. In addition to finding all previously reported structures, we discovered many other different tetrahedral-network-based crystal structures which are highly degenerate in energy. In addition, these structures can be classified into structures with 1D, 2D and 3D M-Si-O frameworks. A clear trend of the structural preference in different systems was revealed and possible indicators that affect the structure stabilities were introduced. For the case of Na systems which have been much less investigated in the literature relative to the Li systems, we predicted their ground state structures and found evidence for the existence of new structural motifs.

  14. Exploration of tetrahedral structures in silicate cathodes using a motif-network scheme

    DOE PAGESBeta

    Zhao, Xin; Wu, Shunqing; Lv, Xiaobao; Nguyen, Manh Cuong; Wang, Cai -Zhuang; Lin, Zijing; Zhu, Zi -Zhong; Ho, Kai -Ming

    2015-10-26

    Using a motif-network search scheme, we studied the tetrahedral structures of the dilithium/disodium transition metal orthosilicates A2MSiO4 with A = Li or Na and M = Mn, Fe or Co. In addition to finding all previously reported structures, we discovered many other different tetrahedral-network-based crystal structures which are highly degenerate in energy. In addition, these structures can be classified into structures with 1D, 2D and 3D M-Si-O frameworks. A clear trend of the structural preference in different systems was revealed and possible indicators that affect the structure stabilities were introduced. For the case of Na systems which have been muchmore » less investigated in the literature relative to the Li systems, we predicted their ground state structures and found evidence for the existence of new structural motifs.« less

  15. Exploration of tetrahedral structures in silicate cathodes using a motif-network scheme

    PubMed Central

    Zhao, Xin; Wu, Shunqing; Lv, Xiaobao; Nguyen, Manh Cuong; Wang, Cai-Zhuang; Lin, Zijing; Zhu, Zi-Zhong; Ho, Kai-Ming

    2015-01-01

    Using a motif-network search scheme, we studied the tetrahedral structures of the dilithium/disodium transition metal orthosilicates A2MSiO4 with A = Li or Na and M = Mn, Fe or Co. In addition to finding all previously reported structures, we discovered many other different tetrahedral-network-based crystal structures which are highly degenerate in energy. These structures can be classified into structures with 1D, 2D and 3D M-Si-O frameworks. A clear trend of the structural preference in different systems was revealed and possible indicators that affect the structure stabilities were introduced. For the case of Na systems which have been much less investigated in the literature relative to the Li systems, we predicted their ground state structures and found evidence for the existence of new structural motifs. PMID:26497381

  16. Structural Basis for WDR5 Interaction (Win) Motif Recognition in Human SET1 Family Histone Methyltransferases*

    PubMed Central

    Dharmarajan, Venkatasubramanian; Lee, Jeong-Heon; Patel, Anamika; Skalnik, David G.; Cosgrove, Michael S.

    2012-01-01

    Translocations and amplifications of the mixed lineage leukemia-1 (MLL1) gene are associated with aggressive myeloid and lymphocytic leukemias in humans. MLL1 is a member of the SET1 family of histone H3 lysine 4 (H3K4) methyltransferases, which are required for transcription of genes involved in hematopoiesis and development. MLL1 associates with a subcomplex containing WDR5, RbBP5, Ash2L, and DPY-30 (WRAD), which together form the MLL1 core complex that is required for sequential mono- and dimethylation of H3K4. We previously demonstrated that WDR5 binds the conserved WDR5 interaction (Win) motif of MLL1 in vitro, an interaction that is required for the H3K4 dimethylation activity of the MLL1 core complex. In this investigation, we demonstrate that arginine 3765 of the MLL1 Win motif is required to co-immunoprecipitate WRAD from mammalian cells, suggesting that the WDR5-Win motif interaction is important for the assembly of the MLL1 core complex in vivo. We also demonstrate that peptides that mimic SET1 family Win motif sequences inhibit H3K4 dimethylation by the MLL1 core complex with varying degrees of efficiency. To understand the structural basis for these differences, we determined structures of WDR5 bound to six different naturally occurring Win motif sequences at resolutions ranging from 1.9 to 1.2 Å. Our results reveal that binding energy differences result from interactions between non-conserved residues C-terminal to the Win motif and to a lesser extent from subtle variation of residues within the Win motif. These results highlight a new class of methylation inhibitors that may be useful for the treatment of MLL1-related malignancies. PMID:22665483

  17. Structural basis for the binding of tryptophan-based motifs by δ-COP

    PubMed Central

    Suckling, Richard J.; Poon, Pak Phi; Travis, Sophie M.; Majoul, Irina V.; Hughson, Frederick M.; Evans, Philip R.; Duden, Rainer; Owen, David J.

    2015-01-01

    Coatomer consists of two subcomplexes: the membrane-targeting, ADP ribosylation factor 1 (Arf1):GTP-binding βγδζ-COP F-subcomplex, which is related to the adaptor protein (AP) clathrin adaptors, and the cargo-binding αβ’ε-COP B-subcomplex. We present the structure of the C-terminal μ-homology domain of the yeast δ-COP subunit in complex with the WxW motif from its binding partner, the endoplasmic reticulum-localized Dsl1 tether. The motif binds at a site distinct from that used by the homologous AP μ subunits to bind YxxΦ cargo motifs with its two tryptophan residues sitting in compatible pockets. We also show that the Saccharomyces cerevisiae Arf GTPase-activating protein (GAP) homolog Gcs1p uses a related WxxF motif at its extreme C terminus to bind to δ-COP at the same site in the same way. Mutations designed on the basis of the structure in conjunction with isothermal titration calorimetry confirm the mode of binding and show that mammalian δ-COP binds related tryptophan-based motifs such as that from ArfGAP1 in a similar manner. We conclude that δ-COP subunits bind Wxn(1–6)[WF] motifs within unstructured regions of proteins that influence the lifecycle of COPI-coated vesicles; this conclusion is supported by the observation that, in the context of a sensitizing domain deletion in Dsl1p, mutating the tryptophan-based motif-binding site in yeast causes defects in both growth and carboxypeptidase Y trafficking/processing. PMID:26578768

  18. Computational study enlightens the structural role of the alcohol acyltransferase DFGWG motif.

    PubMed

    Morales-Quintana, Luis; Moya-León, María Alejandra; Herrera, Raúl

    2015-08-01

    Alcohol acyltransferases (AAT) catalyze the esterification reaction of alcohols and acyl-CoA into esters in fruits and flowers. Despite the high divergence between AAT enzymes, two important and conserved motifs are shared: the catalytic HxxxD motif, and the DFGWG motif. The latter is proposed to play a structural role; however, its function remains unclear. The DFGWG motif is located in loop 21 and stabilized by a hydrogen bond between residues Y52 and D381. Also, this motif is distant from the HxxxD motif, and most probably without a direct role in the substrate interaction. To evaluate the role of the DFGWG motif, in silico analysis was performed in the VpAAT1 protein. Three mutants (Y52F, D381A and D381E) were evaluated. Major changes (size and shape) in the solvent channels were found, although no differences were revealed in the entire 3D structure. Molecular dynamics simulations and docking studies described unfavorable energies for interaction of the mutant proteins with different substrates, as well as unfavored ligand orientations in the solvent channel. Additionally, we examined the contribution of different energetic parameters to the total free energy of protein-ligand complexes by the MM-GBSA method. The complexes differed mainly in their van der Waals contributions and have unfavorable electrostatic interactions. VpAAT1, Y52F and D381A mutants showed a dramatic reduction in the binding capacity to several substrates, which is related to differences in electrostatic potential on the protein surfaces, suggesting that D381 from the DFGWG motif and residue Y52 play a crucial role in maintenance of the adequate solvent channel structure required for catalysis. Graphical abstract Molecular docking, molecular dynamics (MD) simulations and MM-GBSA free energy calculations were employed to obtain quantitative estimates for the binding free energies of wild type Vasconcellea pubescens alcohol acyltransferase (VpAAT1-WT) and the protein mutants. Left VpAAT1

  19. Key Structural Motifs To Predict the Cage Topology in Endohedral Metallofullerenes.

    PubMed

    Wang, Yang; Díaz-Tendero, Sergio; Martín, Fernando; Alcamí, Manuel

    2016-02-10

    We show that the relative isomer stability of fullerene anions is essentially governed by a few simple structural motifs, requiring only the connectivity information between atoms. Relative energies of a large number of isomers of fullerene anions, C(2n)(q) (2n = 68-104; q = -2, -4, -6), can be satisfactorily reproduced by merely counting the numbers of seven kinds of hexagon-based motifs. The dependence of stability on these motifs varies with the charge state, which reflects the fact that the isomeric form of the carbon cage in endohedral metallofullerenes (EMFs) often differs from that in neutral empty fullerenes. The chemical origin of the stabilization differences between motifs is discussed on the basis of electronic and strain effects as well as aromaticity. On the basis of this simple model, the extraordinary abundance of the icosahedral C80 cage in EMFs can be easily understood. We also provide an explanation for why the well-known isolated pentagon rule is often violated in smaller EMFs. Finally, simple topological indices are proposed for quantitatively predicting the relative stability of fullerene anions, allowing a rapid determination of suitable hosting cages in EMFs by just counting three simple structural motifs. PMID:26762322

  20. [Conserved motifs in the primary and secondary ITS1 structures in bryophytes].

    PubMed

    Milyutina, I A; Ignatov, M S

    2015-01-01

    A study of the ITS1 nucleotide sequences of 1000 moss species of 62 families, 11 liverwort species from five orders, and one hornwort Anthoceros agrestis identified five highly conserved motifs (CM1-CM5), which are presumably involved in pre-rRNA processing. Although the ITS1 sequences substantially differ in length and the extent of divergence, the conserved motifs are found in all of them. ITS1 secondary structures were constructed for 76 mosses, and main regularities at conserved motif positioning were observed. The positions of processing sites in the ITS1 secondary structure of the yeast Saccharomyces cerevisiae were found to be similar to the positions of the conserved motifs in the ITS1 secondary structures of mosses and liverworts. In addition, a potential hairpin formation in the putative secondary structure of a pre-rRNA fragment was considered for the region between ITS1 CM4-CM5 and a highly conserved region between hairpins 49 and 50 (H49 and H50) of the 18S rRNA. PMID:26107892

  1. Structural basis for the indispensable role of a unique zinc finger motif in LNX2 ubiquitination

    PubMed Central

    Nayak, Digant; Sivaraman, J.

    2015-01-01

    LNX (Ligand of Numb Protein-X) proteins, LNX1 and LNX2, are RING- and PDZ-based E3-ubiquitin ligases known to interact with Numb. Silencing of LNX2 has been reported to down-regulate WNT and NOTCH, two key signaling pathways in tumorigenesis. Here we report the identification of the domain boundary of LNX2 to confer its ubiquitination activity, its crystal structure along with functional studies. We show that the RING domain in LNX2 is flanked by two Zinc-binding motifs (Zn-RING-Zn), in which the N-terminal Zinc-binding motif adopts novel conformation. Although this motif follows the typical Cys2His2-type zinc finger configuration, it is devoid of any secondary structure and forms an open circle conformation, which has not been reported yet. This unique N-terminal Zn-finger motif is indispensable for the activity and stability of LNX2, as verified using mutational studies. The Zn-RING-Zn domain of LNX2 is a dimer and assumes a rigid elongated structure that undergoes autoubiquitination and undergoes N-terminal polyubiquitination. The ubiquitin chains consist of all seven possible isopeptide linkages. These results were validated using full-length LNX2. Moreover we have demonstrated the ubiquitination of cell fate determinant protein, Numb by LNX2. Our study provides a structural basis for the functional machinery of LNX2 and thus provides the opportunity to investigate suitable drug targets against LNX2. PMID:26451611

  2. Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space

    PubMed Central

    Ahnert, S. E.; Fink, T. M. A.

    2016-01-01

    Network motifs have been studied extensively over the past decade, and certain motifs, such as the feed-forward loop, play an important role in regulatory networks. Recent studies have used Boolean network motifs to explore the link between form and function in gene regulatory networks and have found that the structure of a motif does not strongly determine its function, if this is defined in terms of the gene expression patterns the motif can produce. Here, we offer a different, higher-level definition of the ‘function’ of a motif, in terms of two fundamental properties of its dynamical state space as a Boolean network. One is the basin entropy, which is a complexity measure of the dynamics of Boolean networks. The other is the diversity of cyclic attractor lengths that a given motif can produce. Using these two measures, we examine all 104 topologically distinct three-node motifs and show that the structural properties of a motif, such as the presence of feedback loops and feed-forward loops, predict fundamental characteristics of its dynamical state space, which in turn determine aspects of its functional versatility. We also show that these higher-level properties have a direct bearing on real regulatory networks, as both basin entropy and cycle length diversity show a close correspondence with the prevalence, in neural and genetic regulatory networks, of the 13 connected motifs without self-interactions that have been studied extensively in the literature. PMID:27440255

  3. DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes

    PubMed Central

    Sebestyén, Endre; Nagy, Tibor; Suhai, Sándor; Barta, Endre

    2009-01-01

    Background The comparative genomic analysis of a large number of orthologous promoter regions of the chordate and plant genes from the DoOP databases shows thousands of conserved motifs. Most of these motifs differ from any known transcription factor binding site (TFBS). To identify common conserved motifs, we need a specific tool to be able to search amongst them. Since conserved motifs from the DoOP databases are linked to genes, the result of such a search can give a list of genes that are potentially regulated by the same transcription factor(s). Results We have developed a new tool called DoOPSearch for the analysis of the conserved motifs in the promoter regions of chordate or plant genes. We used the orthologous promoters of the DoOP database to extract thousands of conserved motifs from different taxonomic groups. The advantage of this approach is that different sets of conserved motifs might be found depending on how broad the taxonomic coverage of the underlying orthologous promoter sequence collection is (consider e.g. primates vs. mammals or Brassicaceae vs. Viridiplantae). The DoOPSearch tool allows the users to search these motif collections or the promoter regions of DoOP with user supplied query sequences or any of the conserved motifs from the DoOP database. To find overrepresented gene ontologies, the gene lists obtained can be analysed further using a modified version of the GeneMerge program. Conclusion We present here a comparative genomics based promoter analysis tool. Our system is based on a unique collection of conserved promoter motifs characteristic of different taxonomic groups. We offer both a command line and a web-based tool for searching in these motif collections using user specified queries. These can be either short promoter sequences or consensus sequences of known transcription factor binding sites. The GeneMerge analysis of the search results allows the user to identify statistically overrepresented Gene Ontology terms that

  4. Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif.

    PubMed

    Kim, Kuglae; Kwon, Soon-Kyeong; Jun, Sung-Hoon; Cha, Jeong Seok; Kim, Hoyoung; Lee, Weontae; Kim, Jihyun F; Cho, Hyun-Soo

    2016-01-01

    A novel light-driven chloride-pumping rhodopsin (ClR) containing an 'NTQ motif' in its putative ion conduction pathway has been discovered and functionally characterized in a genomic analysis study of a marine bacterium. Here we report the crystal structure of ClR from the flavobacterium Nonlabens marinus S1-08(T) determined under two conditions at 2.0 and 1.56 Å resolutions. The structures reveal two chloride-binding sites, one around the protonated Schiff base and the other on a cytoplasmic loop. We identify a '3 omega motif' formed by three non-consecutive aromatic amino acids that is correlated with the B-C loop orientation. Detailed ClR structural analyses with functional studies in E. coli reveal the chloride ion transduction pathway. Our results help understand the molecular mechanism and physiological role of ClR and provide a structural basis for optogenetic applications. PMID:27554809

  5. Beta-turn propensities as paradigms for the analysis of structural motifs to engineer protein stability.

    PubMed Central

    Ohage, E. C.; Graml, W.; Walter, M. M.; Steinbacher, S.; Steipe, B.

    1997-01-01

    The thermodynamic stability of a protein provides an experimental metric for the relationship of protein sequence and native structure. We have investigated an approach based on an analysis of the structural database for stability engineering of an immunoglobulin variable domain. The most frequently occurring residues in specific positions of beta-turn motifs were predicted to increase the folding stability of mutants that were constructed by site-directed mutagenesis. Even in positions in which different residues are conserved in immunoglobulin sequences, the predictions were confirmed. Frequently, mutants with increased beta-turn propensities display increased folding cooperativities, suggesting pronounced effects on the unfolded state independent of the expected effect on conformational entropy. We conclude that structural motifs with predominantly local interactions can serve as templates with which patterns of sequence preferences can be extracted from the database of protein structures. Such preferences can predict the stability effects of mutations for protein engineering and design. PMID:9007995

  6. Crystal structure of SEL1L: Insight into the roles of SLR motifs in ERAD pathway

    PubMed Central

    Jeong, Hanbin; Sim, Hyo Jung; Song, Eun Kyung; Lee, Hakbong; Ha, Sung Chul; Jun, Youngsoo; Park, Tae Joo; Lee, Changwook

    2016-01-01

    Terminally misfolded proteins are selectively recognized and cleared by the endoplasmic reticulum-associated degradation (ERAD) pathway. SEL1L, a component of the ERAD machinery, plays an important role in selecting and transporting ERAD substrates for degradation. We have determined the crystal structure of the mouse SEL1L central domain comprising five Sel1-Like Repeats (SLR motifs 5 to 9; hereafter called SEL1Lcent). Strikingly, SEL1Lcent forms a homodimer with two-fold symmetry in a head-to-tail manner. Particularly, the SLR motif 9 plays an important role in dimer formation by adopting a domain-swapped structure and providing an extensive dimeric interface. We identified that the full-length SEL1L forms a self-oligomer through the SEL1Lcent domain in mammalian cells. Furthermore, we discovered that the SLR-C, comprising SLR motifs 10 and 11, of SEL1L directly interacts with the N-terminus luminal loops of HRD1. Therefore, we propose that certain SLR motifs of SEL1L play a unique role in membrane bound ERAD machinery. PMID:27064360

  7. Identification of sequence–structure RNA binding motifs for SELEX-derived aptamers

    PubMed Central

    Hoinka, Jan; Zotenko, Elena; Friedman, Adam; Sauna, Zuben E.; Przytycka, Teresa M.

    2012-01-01

    Motivation: Systematic Evolution of Ligands by EXponential Enrichment (SELEX) represents a state-of-the-art technology to isolate single-stranded (ribo)nucleic acid fragments, named aptamers, which bind to a molecule (or molecules) of interest via specific structural regions induced by their sequence-dependent fold. This powerful method has applications in designing protein inhibitors, molecular detection systems, therapeutic drugs and antibody replacement among others. However, full understanding and consequently optimal utilization of the process has lagged behind its wide application due to the lack of dedicated computational approaches. At the same time, the combination of SELEX with novel sequencing technologies is beginning to provide the data that will allow the examination of a variety of properties of the selection process. Results: To close this gap we developed, Aptamotif, a computational method for the identification of sequence–structure motifs in SELEX-derived aptamers. To increase the chances of identifying functional motifs, Aptamotif uses an ensemble-based approach. We validated the method using two published aptamer datasets containing experimentally determined motifs of increasing complexity. We were able to recreate the author's findings to a high degree, thus proving the capability of our approach to identify binding motifs in SELEX data. Additionally, using our new experimental dataset, we illustrate the application of Aptamotif to elucidate several properties of the selection process. Contact: przytyck@ncbi.nlm.nih.gov, Zuben.Sauna@fda.hhs.gov PMID:22689764

  8. SiteBinder: an improved approach for comparing multiple protein structural motifs.

    PubMed

    Sehnal, David; Vařeková, Radka Svobodová; Huber, Heinrich J; Geidl, Stanislav; Ionescu, Crina-Maria; Wimmerová, Michaela; Koča, Jaroslav

    2012-02-27

    There is a paramount need to develop new techniques and tools that will extract as much information as possible from the ever growing repository of protein 3D structures. We report here on the development of a software tool for the multiple superimposition of large sets of protein structural motifs. Our superimposition methodology performs a systematic search for the atom pairing that provides the best fit. During this search, the RMSD values for all chemically relevant pairings are calculated by quaternion algebra. The number of evaluated pairings is markedly decreased by using PDB annotations for atoms. This approach guarantees that the best fit will be found and can be applied even when sequence similarity is low or does not exist at all. We have implemented this methodology in the Web application SiteBinder, which is able to process up to thousands of protein structural motifs in a very short time, and which provides an intuitive and user-friendly interface. Our benchmarking analysis has shown the robustness, efficiency, and versatility of our methodology and its implementation by the successful superimposition of 1000 experimentally determined structures for each of 32 eukaryotic linear motifs. We also demonstrate the applicability of SiteBinder using three case studies. We first compared the structures of 61 PA-IIL sugar binding sites containing nine different sugars, and we found that the sugar binding sites of PA-IIL and its mutants have a conserved structure despite their binding different sugars. We then superimposed over 300 zinc finger central motifs and revealed that the molecular structure in the vicinity of the Zn atom is highly conserved. Finally, we superimposed 12 BH3 domains from pro-apoptotic proteins. Our findings come to support the hypothesis that there is a structural basis for the functional segregation of BH3-only proteins into activators and enablers. PMID:22296449

  9. Analysis of BAC-end sequences in common bean (Phaseolus vulgaris L.) towards the development and characterization of long motifs SSRs.

    PubMed

    Müller, Bárbara Salomão de Faria; Sakamoto, Tetsu; de Menezes, Ivandilson Pessoa Pinto; Prado, Guilherme Souza; Martins, Wellington Santos; Brondani, Claudio; de Barros, Everaldo Gonçalves; Vianello, Rosana Pereira

    2014-11-01

    The increasing volume of genomic data on the Phaseolus vulgaris species have contributed to its importance as a model genetic species and positively affected the investigation of other legumes of scientific and economic value. To expand and gain a more in-depth knowledge of the common bean genome, the ends of a number of bacterial artificial chromosome (BAC) were sequenced, annotated and the presence of repetitive sequences was determined. In total, 52,270 BESs (BAC-end sequences), equivalent to 32 Mbp (~6 %) of the genome, were processed. In total, 3,789 BES-SSRs were identified, with a distribution of one SSR (simple sequence repeat) per 8.36 kbp and 2,000 were suitable for the development of SSRs, of which 194 were evaluated in low-resolution screening. From 40 BES-SSRs based on long motifs SSRs (≥ trinucleotides) analyzed in high-resolution genotyping, 34 showed an equally good amplification for the Andean and for the Mesoamerican genepools, exhibiting an average gene diversity (H E) of 0.490 and 5.59 alleles/locus, of which six classified as Class I showed a H E ≥ 0.7. The PCoA and structure analysis allowed to discriminate the gene pools (K = 2, FST = 0.733). From the 52,270 BESs, 2 % corresponded to transcription factors and 3 % to transposable elements. Putative functions for 24,321 BESs were identified and for 19,363 were assigned functional categories (gene ontology). This study identified highly polymorphic BES-SSRs containing tri- to hexanucleotides motifs and bringing together relevant genetic characteristics useful for breeding programs. Additionally, the BESs were incorporated into the international genome-sequencing project for the common bean. PMID:25164100

  10. Magnesium and manganese binding sites on proteins have the same predominant motif of secondary structure.

    PubMed

    Khrustalev, Vladislav Victorovich; Barkovsky, Eugene Victorovich; Khrustaleva, Tatyana Aleksandrovna

    2016-04-21

    Manganese ion (Mn(2+)) can substitute magnesium ion (Mg(2+)) in active sites of numerous enzymes. Binding sites for these two ions have been studied in two sets of protein 3D structures from the Protein Data Bank with the homology level lower than 25%. The structural motif "beta strand - binder - random coil" is predominant in both Mn(2+) and Mg(2+) coordination spheres, especially in functionally relevant ones. That predominant motif works as an active binder of those divalent cations which can then attract additional ligands, such as different phosphate-containing compounds. In contrast, such Mg(2+) and Mn(2+) binding motif as "GK(T/S)T" being the N-terminal part of alpha helices works as an active binder of phosphates which can then attract divalent cations. There are few differences between Mg(2+) and Mn(2+) coordination spheres responsible of the cation specificity. His residues are underrepresented in certain positions around Asp and Glu residues involved in Mg(2+) coordination, while they are overrepresented in certain positions around Asp and Glu residues coordinating Mn(2+). The random coil region in the "beta strand - random coil - alpha helix" motif for Mg(2+) binding is usually shorter than that in the same motif for Mn(2+) coordination. This feature is associated with the lower number of binding amino acids (and lower levels of usage of such "major" binders as Asp and Glu) for Mg(2+) (which is a hard Lewis acid) in comparison with those for Mn(2+) (an intermediate Lewis acid). PMID:26876751

  11. Structural motifs, mixing, and segregation effects in 38-atom binary clusters

    NASA Astrophysics Data System (ADS)

    Paz-Borbón, Lauro Oliver; Johnston, Roy L.; Barcaro, Giovanni; Fortunelli, Alessandro

    2008-04-01

    Thirty eight-atom binary clusters composed of elements from groups 10 and 11 of the Periodic Table mixing a second-row with a third-row transition metal (TM) (i.e., clusters composed of the four pairs: Pd-Pt, Ag-Au, Pd-Au, and Ag-Pt) are studied through a combined empirical-potential (EP)/density functional (DF) method. A "system comparison" approach is adopted in order to analyze a wide diversity of structural motifs, and the energy competition among different structural motifs is studied at the DF level for these systems, mainly focusing on the composition 24-14 (the first number refers to the second-row TM atom) but also considering selected motifs with compositions 19-19 (of interest for investigating surface segregation effects) and 32-6 (also 14-24 and 6-32 for the Pd-Au pair). The results confirm the EP predictions about the stability of crystalline structures at this size for the Au-Pd pair but with decahedral or mixed fivefold-symmetric/closed-packed structures in close competition with fcc motifs for the Ag-Au or Ag-Pt and Pd-Pt pairs, respectively. Overall, the EP description is found to be reasonably accurate for the Pd-Pt and Au-Pd pairs, whereas it is less reliable for the Ag-Au and Ag-Pt pairs due to electronic structure (charge transfer or directionality) effects. The driving force to core-shell chemical ordering is put on a quantitative basis, and surface segregation of the most cohesive element into the core is confirmed, with the exception of the Ag-Au pair for which charge transfer effects favor the segregation of Au to the surface of the clusters.

  12. Thermodynamic Features of Structural Motifs Formed by β-L-RNA

    PubMed Central

    Szabat, Marta; Gudanis, Dorota; Kotkowiak, Weronika; Gdaniec, Zofia; Kierzek, Ryszard; Pasternak, Anna

    2016-01-01

    This is the first report to provide comprehensive thermodynamic and structural data concerning duplex, hairpin, quadruplex and i-motif structures in β-L-RNA series. Herein we confirm that, within the limits of experimental error, the thermodynamic stability of enantiomeric structural motifs is the same as that of naturally occurring D-RNA counterparts. In addition, formation of D-RNA/L-RNA heterochiral duplexes is also observed; however, their thermodynamic stability is significantly reduced in reference to homochiral D-RNA duplexes. The presence of three locked nucleic acid (LNA) residues within the D-RNA strand diminishes the negative effect of the enantiomeric, complementary L-RNA strand in the formation of heterochiral RNA duplexes. Similar behavior is also observed for heterochiral LNA-2′-O-methyl-D-RNA/L-RNA duplexes. The formation of heterochiral duplexes was confirmed by 1H NMR spectroscopy. The CD curves of homochiral L-RNA structural motifs are always reversed, whereas CD curves of heterochiral duplexes present individual features dependent on the composition of chiral strands. PMID:26908023

  13. Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection

    PubMed Central

    Zheng, Heping; Shabalin, Ivan G.; Handing, Katarzyna B.; Bujnicki, Janusz M.; Minor, Wladek

    2015-01-01

    The ubiquitous presence of magnesium ions in RNA has long been recognized as a key factor governing RNA folding, and is crucial for many diverse functions of RNA molecules. In this work, Mg2+-binding architectures in RNA were systematically studied using a database of RNA crystal structures from the Protein Data Bank (PDB). Due to the abundance of poorly modeled or incorrectly identified Mg2+ ions, the set of all sites was comprehensively validated and filtered to identify a benchmark dataset of 15 334 ‘reliable’ RNA-bound Mg2+ sites. The normalized frequencies by which specific RNA atoms coordinate Mg2+ were derived for both the inner and outer coordination spheres. A hierarchical classification system of Mg2+ sites in RNA structures was designed and applied to the benchmark dataset, yielding a set of 41 types of inner-sphere and 95 types of outer-sphere coordinating patterns. This classification system has also been applied to describe six previously reported Mg2+-binding motifs and detect them in new RNA structures. Investigation of the most populous site types resulted in the identification of seven novel Mg2+-binding motifs, and all RNA structures in the PDB were screened for the presence of these motifs. PMID:25800744

  14. Structure and Mechanical Characterization of DNA i-Motif Nanowires by Molecular Dynamics Simulation

    PubMed Central

    Singh, Raghvendra Pratap; Blossey, Ralf; Cleri, Fabrizio

    2013-01-01

    We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm-long nanowires, based on a repeated TC5 sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual C⋅C+ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression, and bending deformations with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young’s and bending moduli of the nanowire, as well as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to that of a metal. Besides their yet to be clarified biological significance, i-motif nanowires may qualify as interesting candidates for nanotechnology templates, due to such outstanding mechanical properties. PMID:24359754

  15. X-ray analysis of butirosin biosynthetic enzyme BtrN redefines structural motifs for AdoMet radical chemistry

    PubMed Central

    Goldman, Peter J.; Grove, Tyler L.; Booker, Squire J.; Drennan, Catherine L.

    2013-01-01

    The 2-deoxy-scyllo-inosamine (DOIA) dehydrogenases are key enzymes in the biosynthesis of 2-deoxystreptamine–containing aminoglycoside antibiotics. In contrast to most DOIA dehydrogenases, which are NAD-dependent, the DOIA dehydrogenase from Bacillus circulans (BtrN) is an S-adenosyl-l-methionine (AdoMet) radical enzyme. To examine how BtrN employs AdoMet radical chemistry, we have determined its structure with AdoMet and substrate to 1.56 Å resolution. We find a previously undescribed modification to the core AdoMet radical fold: instead of the canonical (β/α)6 architecture, BtrN displays a (β5/α4) motif. We further find that an auxiliary [4Fe-4S] cluster in BtrN, thought to bind substrate, is instead implicated in substrate–radical oxidation. High structural homology in the auxiliary cluster binding region between BtrN, fellow AdoMet radical dehydrogenase anSME, and molybdenum cofactor biosynthetic enzyme MoaA provides support for the establishment of an AdoMet radical structural motif that is likely common to ∼6,400 uncharacterized AdoMet radical enzymes. PMID:24048029

  16. Structure/function relationships within the RNA recognition motif family applied to the hermes gene product.

    PubMed

    Thion, Laurent; Erard, Monique

    2002-04-01

    The RNA Recognition Motif (RRM) family of RNA-binding domains comprises distinct structural subclasses which can be equated to various types of cognate RNA(s) in relation to biological functions. By identifying structural templates within the appropriate RRM subclass, we have homology-modelled the three-dimensional structure of the hermes gene-encoded RRM. Our findings lead us to propose potential RNA targets for the corresponding protein and to predict possible functions in RNA metabolism during heart development. PMID:12141909

  17. Sequence, structure, and cooperativity in folding of elementary protein structural motifs

    PubMed Central

    Lai, Jason K.; Kubelka, Ginka S.; Kubelka, Jan

    2015-01-01

    Residue-level unfolding of two helix-turn-helix proteins—one naturally occurring and one de novo designed—is reconstructed from multiple sets of site-specific 13C isotopically edited infrared (IR) and circular dichroism (CD) data using Ising-like statistical-mechanical models. Several model variants are parameterized to test the importance of sequence-specific interactions (approximated by Miyazawa–Jernigan statistical potentials), local structural flexibility (derived from the ensemble of NMR structures), interhelical hydrogen bonds, and native contacts separated by intervening disordered regions (through the Wako–Saitô–Muñoz–Eaton scheme, which disallows such configurations). The models are optimized by directly simulating experimental observables: CD ellipticity at 222 nm for model proteins and their fragments and 13C-amide I′ bands for multiple isotopologues of each protein. We find that data can be quantitatively reproduced by the model that allows two interacting segments flanking a disordered loop (double sequence approximation) and incorporates flexibility in the native contact maps, but neither sequence-specific interactions nor hydrogen bonds are required. The near-identical free energy profiles as a function of the global order parameter are consistent with expected similar folding kinetics for nearly identical structures. However, the predicted folding mechanism for the two motifs is different, reflecting the order of local stability. We introduce free energy profiles for “experimental” reaction coordinates—namely, the degree of local folding as sensed by site-specific 13C-edited IR, which highlight folding heterogeneity and contrast its overall, average description with the detailed, local picture. PMID:26216963

  18. Sequence, structure, and cooperativity in folding of elementary protein structural motifs.

    PubMed

    Lai, Jason K; Kubelka, Ginka S; Kubelka, Jan

    2015-08-11

    Residue-level unfolding of two helix-turn-helix proteins--one naturally occurring and one de novo designed--is reconstructed from multiple sets of site-specific (13)C isotopically edited infrared (IR) and circular dichroism (CD) data using Ising-like statistical-mechanical models. Several model variants are parameterized to test the importance of sequence-specific interactions (approximated by Miyazawa-Jernigan statistical potentials), local structural flexibility (derived from the ensemble of NMR structures), interhelical hydrogen bonds, and native contacts separated by intervening disordered regions (through the Wako-Saitô-Muñoz-Eaton scheme, which disallows such configurations). The models are optimized by directly simulating experimental observables: CD ellipticity at 222 nm for model proteins and their fragments and (13)C-amide I' bands for multiple isotopologues of each protein. We find that data can be quantitatively reproduced by the model that allows two interacting segments flanking a disordered loop (double sequence approximation) and incorporates flexibility in the native contact maps, but neither sequence-specific interactions nor hydrogen bonds are required. The near-identical free energy profiles as a function of the global order parameter are consistent with expected similar folding kinetics for nearly identical structures. However, the predicted folding mechanism for the two motifs is different, reflecting the order of local stability. We introduce free energy profiles for "experimental" reaction coordinates--namely, the degree of local folding as sensed by site-specific (13)C-edited IR, which highlight folding heterogeneity and contrast its overall, average description with the detailed, local picture. PMID:26216963

  19. The structure of common-envelope remnants

    NASA Astrophysics Data System (ADS)

    Hall, Philip D.

    2015-05-01

    We investigate the structure and evolution of the remnants of common-envelope evolution in binary star systems. In a common-envelope phase, two stars become engulfed in a gaseous envelope and, under the influence of drag forces, spiral to smaller separations. They may merge to form a single star or the envelope may be ejected to leave the stars in a shorter period orbit. This process explains the short orbital periods of many observed binary systems, such as cataclysmic variables and low-mass X-ray binary systems. Despite the importance of these systems, and of common-envelope evolution to their formation, it remains poorly understood. Specifically, we are unable to confidently predict the outcome of a common-envelope phase from the properties at its onset. After presenting a review of work on stellar evolution, binary systems, common-envelope evolution and the computer programs used, we describe the results of three computational projects on common-envelope evolution. Our work specifically relates to the methods and prescriptions which are used for predicting the outcome. We use the Cambridge stellar-evolution code STARS to produce detailed models of the structure and evolution of remnants of common-envelope evolution. We compare different assumptions about the uncertain end-of-common envelope structure and envelope mass of remnants which successfully eject their common envelopes. In the first project, we use detailed remnant models to investigate whether planetary nebulae are predicted after common-envelope phases initiated by low-mass red giants. We focus on the requirement that a remnant evolves rapidly enough to photoionize the nebula and compare the predictions for different ideas about the structure at the end of a common-envelope phase. We find that planetary nebulae are possible for some prescriptions for the end-of-common envelope structure. In our second contribution, we compute a large set of single-star models and fit new formulae to the core radii of

  20. Structures for common-cause failure analysis

    SciTech Connect

    Vaurio, J.K.

    1981-01-01

    Common-cause failure methodology and terminology have been reviewed and structured to provide a systematical basis for addressing and developing models and methods for quantification. The structure is based on (1) a specific set of definitions, (2) categories based on the way faults are attributable to a common cause, and (3) classes based on the time of entry and the time of elimination of the faults. The failure events are then characterized by their likelihood or frequency and the average residence time. The structure provides a basis for selecting computational models, collecting and evaluating data and assessing the importance of various failure types, and for developing effective defences against common-cause failure. The relationships of this and several other structures are described.

  1. Novel hinge-binding motifs for Janus kinase 3 inhibitors: a comprehensive structure-activity relationship study on tofacitinib bioisosteres.

    PubMed

    Gehringer, Matthias; Forster, Michael; Pfaffenrot, Ellen; Bauer, Silke M; Laufer, Stefan A

    2014-11-01

    The Janus kinases (JAKs) are a family of cytosolic tyrosine kinases crucially involved in cytokine signaling. JAKs have been demonstrated to be valid targets in the treatment of inflammatory and myeloproliferative disorders, and two inhibitors, tofacitinib and ruxolitinib, recently received their marketing authorization. Despite this success, selectivity within the JAK family remains a major issue. Both approved compounds share a common 7H-pyrrolo[2,3-d]pyrimidine hinge binding motif, and little is known about modifications tolerated at this heterocyclic core. In the current study, a library of tofacitinib bioisosteres was prepared and tested against JAK3. The compounds possessed the tofacitinib piperidinyl side chain, whereas the hinge binding motif was replaced by a variety of heterocycles mimicking its pharmacophore. In view of the promising expectations obtained from molecular modeling, most of the compounds proved to be poorly active. However, strategies for restoring activity within this series of novel chemotypes were discovered and crucial structure-activity relationships were deduced. The compounds presented may serve as starting point for developing novel JAK inhibitors and as a valuable training set for in silico models. PMID:25139757

  2. Tumor-associated mutations in a conserved structural motif alter physical and biochemical properties of human RAD51 recombinase

    PubMed Central

    Chen, Jianhong; Morrical, Milagros D.; Donigan, Katherine A.; Weidhaas, Joanne B.; Sweasy, Joann B.; Averill, April M.; Tomczak, Jennifer A.; Morrical, Scott W.

    2015-01-01

    Human RAD51 protein catalyzes DNA pairing and strand exchange reactions that are central to homologous recombination and homology-directed DNA repair. Successful recombination/repair requires the formation of a presynaptic filament of RAD51 on ssDNA. Mutations in BRCA2 and other proteins that control RAD51 activity are associated with human cancer. Here we describe a set of mutations associated with human breast tumors that occur in a common structural motif of RAD51. Tumor-associated D149N, R150Q and G151D mutations map to a Schellman loop motif located on the surface of the RecA homology domain of RAD51. All three variants are proficient in DNA strand exchange, but G151D is slightly more sensitive to salt than wild-type (WT). Both G151D and R150Q exhibit markedly lower catalytic efficiency for adenosine triphosphate hydrolysis compared to WT. All three mutations alter the physical properties of RAD51 nucleoprotein filaments, with G151D showing the most dramatic changes. G151D forms mixed nucleoprotein filaments with WT RAD51 that have intermediate properties compared to unmixed filaments. These findings raise the possibility that mutations in RAD51 itself may contribute to genome instability in tumor cells, either directly through changes in recombinase properties, or indirectly through changes in interactions with regulatory proteins. PMID:25539919

  3. Unique Structural Features and Sequence Motifs of Proline Utilization A (PutA)

    PubMed Central

    Singh, Ranjan K.; Tanner, John J.

    2013-01-01

    Proline utilization A proteins (PutAs) are bifunctional enzymes that catalyze the oxidation of proline to glutamate using spatially separated proline dehydrogenase and pyrroline-5-carboxylate dehydrogenase active sites. Here we use the crystal structure of the minimalist PutA from Bradyrhizobium japonicum (BjPutA) along with sequence analysis to identify unique structural features of PutAs. This analysis shows that PutAs have secondary structural elements and domains not found in the related monofunctional enzymes. Some of these extra features are predicted to be important for substrate channeling in BjPutA. Multiple sequence alignment analysis shows that some PutAs have a 17-residue conserved motif in the C-terminal 20–30 residues of the polypeptide chain. The BjPutA structure shows that this motif helps seal the internal substrate-channeling cavity from the bulk medium. Finally, it is shown that some PutAs have a 100–200 residue domain of unknown function in the C-terminus that is not found in minimalist PutAs. Remote homology detection suggests that this domain is homologous to the oligomerization beta-hairpin and Rossmann fold domain of BjPutA. PMID:22201760

  4. Unique structural features and sequence motifs of proline utilization A (PutA).

    PubMed

    Singh, Ranjan K; Tanner, John J

    2012-01-01

    Proline utilization A proteins (PutAs) are bifunctional enzymes that catalyze the oxidation of proline to glutamate using spatially separated proline dehydrogenase and pyrroline-5-carboxylate dehydrogenase active sites. Here we use the crystal structure of the minimalist PutA from Bradyrhizobium japonicum (BjPutA) along with sequence analysis to identify unique structural features of PutAs. This analysis shows that PutAs have secondary structural elements and domains not found in the related monofunctional enzymes. Some of these extra features are predicted to be important for substrate channeling in BjPutA. Multiple sequence alignment analysis shows that some PutAs have a 17-residue conserved motif in the C-terminal 20-30 residues of the polypeptide chain. The BjPutA structure shows that this motif helps seal the internal substrate-channeling cavity from the bulk medium. Finally, it is shown that some PutAs have a 100-200 residue domain of unknown function in the C-terminus that is not found in minimalist PutAs. Remote homology detection suggests that this domain is homologous to the oligomerization beta-hairpin and Rossmann fold domain of BjPutA. PMID:22201760

  5. Structure of a (Cys3His) zinc ribbon, a ubiquitous motif in archaeal and eucaryal transcription.

    PubMed

    Chen, H T; Legault, P; Glushka, J; Omichinski, J G; Scott, R A

    2000-09-01

    Transcription factor IIB (TFIIB) is an essential component in the formation of the transcription initiation complex in eucaryal and archaeal transcription. TFIIB interacts with a promoter complex containing the TATA-binding protein (TBP) to facilitate interaction with RNA polymerase II (RNA pol II) and the associated transcription factor IIF (TFIIF). TFIIB contains a zinc-binding motif near the N-terminus that is directly involved in the interaction with RNA pol II/TFIIF and plays a crucial role in selecting the transcription initiation site. The solution structure of the N-terminal residues 2-59 of human TFIIB was determined by multidimensional NMR spectroscopy. The structure consists of a nearly tetrahedral Zn(Cys)3(His)1 site confined by type I and "rubredoxin" turns, three antiparallel beta-strands, and disordered loops. The structure is similar to the reported zinc-ribbon motifs in several transcription-related proteins from archaea and eucarya, including Pyrococcus furiosus transcription factor B (PfTFB), human and yeast transcription factor IIS (TFIIS), and Thermococcus celer RNA polymerase II subunit M (TcRPOM). The zinc-ribbon structure of TFIIB, in conjunction with the biochemical analyses, suggests that residues on the beta-sheet are involved in the interaction with RNA pol II/TFIIF, while the zinc-binding site may increase the stability of the beta-sheet. PMID:11045620

  6. Structure of a (Cys3His) zinc ribbon, a ubiquitous motif in archaeal and eucaryal transcription.

    PubMed Central

    Chen, H. T.; Legault, P.; Glushka, J.; Omichinski, J. G.; Scott, R. A.

    2000-01-01

    Transcription factor IIB (TFIIB) is an essential component in the formation of the transcription initiation complex in eucaryal and archaeal transcription. TFIIB interacts with a promoter complex containing the TATA-binding protein (TBP) to facilitate interaction with RNA polymerase II (RNA pol II) and the associated transcription factor IIF (TFIIF). TFIIB contains a zinc-binding motif near the N-terminus that is directly involved in the interaction with RNA pol II/TFIIF and plays a crucial role in selecting the transcription initiation site. The solution structure of the N-terminal residues 2-59 of human TFIIB was determined by multidimensional NMR spectroscopy. The structure consists of a nearly tetrahedral Zn(Cys)3(His)1 site confined by type I and "rubredoxin" turns, three antiparallel beta-strands, and disordered loops. The structure is similar to the reported zinc-ribbon motifs in several transcription-related proteins from archaea and eucarya, including Pyrococcus furiosus transcription factor B (PfTFB), human and yeast transcription factor IIS (TFIIS), and Thermococcus celer RNA polymerase II subunit M (TcRPOM). The zinc-ribbon structure of TFIIB, in conjunction with the biochemical analyses, suggests that residues on the beta-sheet are involved in the interaction with RNA pol II/TFIIF, while the zinc-binding site may increase the stability of the beta-sheet. PMID:11045620

  7. Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif

    PubMed Central

    Kim, Kuglae; Kwon, Soon-Kyeong; Jun, Sung-Hoon; Cha, Jeong Seok; Kim, Hoyoung; Lee, Weontae; Kim, Jihyun F.; Cho, Hyun-Soo

    2016-01-01

    A novel light-driven chloride-pumping rhodopsin (ClR) containing an ‘NTQ motif' in its putative ion conduction pathway has been discovered and functionally characterized in a genomic analysis study of a marine bacterium. Here we report the crystal structure of ClR from the flavobacterium Nonlabens marinus S1-08T determined under two conditions at 2.0 and 1.56 Å resolutions. The structures reveal two chloride-binding sites, one around the protonated Schiff base and the other on a cytoplasmic loop. We identify a ‘3 omega motif' formed by three non-consecutive aromatic amino acids that is correlated with the B–C loop orientation. Detailed ClR structural analyses with functional studies in E. coli reveal the chloride ion transduction pathway. Our results help understand the molecular mechanism and physiological role of ClR and provide a structural basis for optogenetic applications. PMID:27554809

  8. Rationalizing the role of structural motif and underlying electronic structure in the finite temperature behavior of atomic clusters

    SciTech Connect

    Susan, Anju; Joshi, Kavita

    2014-04-21

    Melting in finite size systems is an interesting but complex phenomenon. Many factors affect melting and owing to their interdependencies it is a challenging task to rationalize their roles in the phase transition. In this work, we demonstrate how structural motif of the ground state influences melting transition in small clusters. Here, we report a case with clusters of aluminum and gallium having same number of atoms, valence electrons, and similar structural motif of the ground state but drastically different melting temperatures. We have employed Born-Oppenheimer molecular dynamics to simulate the solid-like to liquid-like transition in these clusters. Our simulations have reproduced the experimental trends fairly well. Further, the detailed analysis of isomers has brought out the role of the ground state structure and underlying electronic structure in the finite temperature behavior of these clusters. For both clusters, isomers accessible before cluster melts have striking similarities and does have strong influence of the structural motif of the ground state. Further, the shape of the heat capacity curve is similar in both the cases but the transition is more spread over for Al{sub 36} which is consistent with the observed isomerization pattern. Our simulations also suggest a way to characterize transition region on the basis of accessibility of the ground state at a specific temperature.

  9. The VirB4 Family of Proposed Traffic Nucleoside Triphosphatases: Common Motifs in Plasmid RP4 TrbE Are Essential for Conjugation and Phage Adsorption

    PubMed Central

    Rabel, Christian; Grahn, A. Marika; Lurz, Rudi; Lanka, Erich

    2003-01-01

    Proteins of the VirB4 family are encoded by conjugative plasmids and by type IV secretion systems, which specify macromolecule export machineries related to conjugation systems. The central feature of VirB4 proteins is a nucleotide binding site. In this study, we asked whether members of the VirB4 protein family have similarities in their primary structures and whether these proteins hydrolyze nucleotides. A multiple-sequence alignment of 19 members of the VirB4 protein family revealed striking overall similarities. We defined four common motifs and one conserved domain. One member of this protein family, TrbE of plasmid RP4, was genetically characterized by site-directed mutagenesis. Most mutations in trbE resulted in complete loss of its activities, which eliminated pilus production, propagation of plasmid-specific phages, and DNA transfer ability in Escherichia coli. Biochemical studies of a soluble derivative of RP4 TrbE and of the full-length homologous protein R388 TrwK revealed that the purified forms of these members of the VirB4 protein family do not hydrolyze ATP or GTP and behave as monomers in solution. PMID:12533481

  10. Immunity related genes in dipterans share common enrichment of AT-rich motifs in their 5' regulatory regions that are potentially involved in nucleosome formation

    PubMed Central

    Hernandez-Romano, Jesus; Carlos-Rivera, Francisco J; Salgado, Heladia; Lamadrid-Figueroa, Hector; Valverde-Garduño, Veronica; Rodriguez, Mario H; Martinez-Barnetche, Jesus

    2008-01-01

    Background Understanding the transcriptional regulation mechanisms in response to environmental challenges is of fundamental importance in biology. Transcription factors associated to response elements and the chromatin structure had proven to play important roles in gene expression regulation. We have analyzed promoter regions of dipteran genes induced in response to immune challenge, in search for particular sequence patterns involved in their transcriptional regulation. Results 5' upstream regions of D. melanogaster and A. gambiae immunity-induced genes and their corresponding orthologous genes in 11 non-melanogaster drosophilid species and Ae. aegypti share enrichment in AT-rich short motifs. AT-rich motifs are associated with nucleosome formation as predicted by two different algorithms. In A. gambiae and D. melanogaster, many immunity genes 5' upstream sequences also showed NFκB response elements, located within 500 bp from the transcription start site. In A. gambiae, the frequency of ATAA motif near the NFκB response elements was increased, suggesting a functional link between nucleosome formation/remodelling and NFκB regulation of transcription. Conclusion AT-rich motif enrichment in 5' upstream sequences in A. gambiae, Ae. aegypti and the Drosophila genus immunity genes suggests a particular pattern of nucleosome formation/chromatin organization. The co-occurrence of such motifs with the NFκB response elements suggests that these sequence signatures may be functionally involved in transcriptional activation during dipteran immune response. AT-rich motif enrichment in regulatory regions in this group of co-regulated genes could represent an evolutionary constrained signature in dipterans and perhaps other distantly species. PMID:18613977

  11. The mammalian heterochromatin protein 1 binds diverse nuclear proteins through a common motif that targets the chromoshadow domain

    SciTech Connect

    Lechner, Mark S. . E-mail: msl27@drexel.edu; Schultz, David C.; Negorev, Dmitri; Maul, Gerd G.; Rauscher, Frank J.

    2005-06-17

    The HP1 proteins regulate epigenetic gene silencing by promoting and maintaining chromatin condensation. The HP1 chromodomain binds to methylated histone H3. More enigmatic is the chromoshadow domain (CSD), which mediates dimerization, transcription repression, and interaction with multiple nuclear proteins. Here we show that KAP-1, CAF-1 p150, and NIPBL carry a canonical amino acid motif, PxVxL, which binds directly to the CSD with high affinity. We also define a new class of variant PxVxL CSD-binding motifs in Sp100A, LBR, and ATRX. Both canonical and variant motifs recognize a similar surface of the CSD dimer as demonstrated by a panel of CSD mutants. These in vitro binding results were confirmed by the analysis of polypeptides found associated with nuclear HP1 complexes and we provide the first evidence of the NIPBL/delangin protein in human cells, a protein recently implicated in the developmental disorder, Cornelia de Lange syndrome. NIPBL is related to Nipped-B, a factor participating in gene activation by remote enhancers in Drosophila melanogaster. Thus, this spectrum of direct binding partners suggests an expanded role for HP1 as factor participating in promoter-enhancer communication, chromatin remodeling/assembly, and sub-nuclear compartmentalization.

  12. The Solution Structural Ensembles of RNA Kink-turn Motifs and Their Protein Complexes

    PubMed Central

    Huang, Lin; Lilley, David M. J.

    2015-01-01

    With the growing number of crystal structures of RNA and RNA/protein complexes, a critical next step is understanding the dynamic behavior of these entities in solution in terms of conformational ensembles and energy landscapes. To this end, we have used X-ray scattering interferometry (XSI) to probe the widespread RNA kink-turn motif and its complexes with the canonical kink-turn binding protein L7Ae. XSI revealed that the folded kink-turn is best described as a restricted conformational ensemble. The ions present in solution alter the nature of this ensemble, and protein binding can perturb the kink-turn ensemble without collapsing it to a unique state. This study demonstrates how XSI can reveal structural and ensemble properties of RNAs and RNA/protein complexes in solution and uncovers the behavior of an important RNA/protein motif. This type of information will be necessary to understand, predict, and engineer the behavior and function of RNAs and their protein complexes. PMID:26727239

  13. The solution structural ensembles of RNA kink-turn motifs and their protein complexes.

    PubMed

    Shi, Xuesong; Huang, Lin; Lilley, David M J; Harbury, Pehr B; Herschlag, Daniel

    2016-03-01

    With the growing number of crystal structures of RNA and RNA-protein complexes, a critical next step is understanding the dynamic solution behavior of these entities in terms of conformational ensembles and energy landscapes. To this end, we have used X-ray scattering interferometry (XSI) to probe the ubiquitous RNA kink-turn motif and its complexes with the canonical kink-turn binding protein L7Ae. XSI revealed that the folded kink-turn is best described as a restricted conformational ensemble. The ions present in solution alter the nature of this ensemble, and protein binding can perturb the kink-turn ensemble without collapsing it to a unique state. This study demonstrates how XSI can reveal structural and ensemble properties of RNAs and RNA-protein complexes and uncovers the behavior of an important RNA-protein motif. This type of information will be necessary to understand, predict and engineer the behavior and function of RNAs and their protein complexes. PMID:26727239

  14. URS DataBase: universe of RNA structures and their motifs

    PubMed Central

    Baulin, Eugene; Yacovlev, Victor; Khachko, Denis; Spirin, Sergei; Roytberg, Mikhail

    2016-01-01

    The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 entries in October 2015). The content of the database is updated regularly. The database consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots. The user can also view and get information on an individual structure or its selected parts, e.g. RNA–protein hydrogen bonds. URSDB employs a new original definition of loops in RNA structures. That definition fits both pseudoknot-free and pseudoknotted secondary structures and coincides with the classical definition in case of pseudoknot-free structures. To our knowledge, URSDB is the first database supporting searches based on topological classification of pseudoknots and on extended loop classification. Database URL: http://server3.lpm.org.ru/urs/ PMID:27242032

  15. URS DataBase: universe of RNA structures and their motifs.

    PubMed

    Baulin, Eugene; Yacovlev, Victor; Khachko, Denis; Spirin, Sergei; Roytberg, Mikhail

    2016-01-01

    The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 entries in October 2015). The content of the database is updated regularly. The database consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots. The user can also view and get information on an individual structure or its selected parts, e.g. RNA-protein hydrogen bonds. URSDB employs a new original definition of loops in RNA structures. That definition fits both pseudoknot-free and pseudoknotted secondary structures and coincides with the classical definition in case of pseudoknot-free structures. To our knowledge, URSDB is the first database supporting searches based on topological classification of pseudoknots and on extended loop classification.Database URL: http://server3.lpm.org.ru/urs/. PMID:27242032

  16. Structural basis for the recognition of two consecutive mutually interacting DPF motifs by the SGIP1 μ homology domain

    PubMed Central

    Shimada, Atsushi; Yamaguchi, Atsuko; Kohda, Daisuke

    2016-01-01

    FCHo1, FCHo2, and SGIP1 are key regulators of clathrin-mediated endocytosis. Their μ homology domains (μHDs) interact with the C-terminal region of an endocytic scaffold protein, Eps15, containing fifteen Asp-Pro-Phe (DPF) motifs. Here, we show that the high-affinity μHD-binding site in Eps15 is a region encompassing six consecutive DPF motifs, while the minimal μHD-binding unit is two consecutive DPF motifs. We present the crystal structures of the SGIP1 μHD in complex with peptides containing two DPF motifs. The peptides bind to a novel ligand-binding site of the μHD, which is distinct from those of other distantly related μHD-containing proteins. The two DPF motifs, which adopt three-dimensional structures stabilized by sequence-specific intramotif and intermotif interactions, are extensively recognized by the μHD and are both required for binding. Thus, consecutive and singly scattered DPF motifs play distinct roles in μHD binding. PMID:26822536

  17. Structural basis for the recognition of two consecutive mutually interacting DPF motifs by the SGIP1 μ homology domain

    NASA Astrophysics Data System (ADS)

    Shimada, Atsushi; Yamaguchi, Atsuko; Kohda, Daisuke

    2016-01-01

    FCHo1, FCHo2, and SGIP1 are key regulators of clathrin-mediated endocytosis. Their μ homology domains (μHDs) interact with the C-terminal region of an endocytic scaffold protein, Eps15, containing fifteen Asp-Pro-Phe (DPF) motifs. Here, we show that the high-affinity μHD-binding site in Eps15 is a region encompassing six consecutive DPF motifs, while the minimal μHD-binding unit is two consecutive DPF motifs. We present the crystal structures of the SGIP1 μHD in complex with peptides containing two DPF motifs. The peptides bind to a novel ligand-binding site of the μHD, which is distinct from those of other distantly related μHD-containing proteins. The two DPF motifs, which adopt three-dimensional structures stabilized by sequence-specific intramotif and intermotif interactions, are extensively recognized by the μHD and are both required for binding. Thus, consecutive and singly scattered DPF motifs play distinct roles in μHD binding.

  18. Protein folding at atomic resolution: analysis of autonomously folding supersecondary structure motifs by nuclear magnetic resonance.

    PubMed

    Sborgi, Lorenzo; Verma, Abhinav; Sadqi, Mourad; de Alba, Eva; Muñoz, Victor

    2013-01-01

    The study of protein folding has been conventionally hampered by the assumption that all single-domain proteins fold by an all-or-none process (two-state folding) that makes it impossible to resolve folding mechanisms experimentally. Here we describe an experimental method for the thermodynamic analysis of protein folding at atomic resolution using nuclear magnetic resonance (NMR). The method is specifically developed for the study of small proteins that fold autonomously into basic supersecondary structure motifs, and that do so in the sub-millisecond timescale (folding archetypes). From the NMR experiments we obtain hundreds of atomic unfolding curves that are subsequently analyzed leading to the determination of the characteristic network of folding interactions. The application of this approach to a comprehensive catalog of elementary folding archetypes holds the promise of becoming the first experimental approach capable of unraveling the basic rules connecting protein structure and folding mechanism. PMID:22987355

  19. Zinc fingers as protein recognition motifs: Structural basis for the GATA-1/Friend of GATA interaction

    PubMed Central

    Liew, Chu Kong; Simpson, Raina J. Y.; Kwan, Ann H. Y.; Crofts, Linda A.; Loughlin, Fionna E.; Matthews, Jacqueline M.; Crossley, Merlin; Mackay, Joel P.

    2005-01-01

    GATA-1 and friend of GATA (FOG) are zinc-finger transcription factors that physically interact to play essential roles in erythroid and megakaryocytic development. Several naturally occurring mutations in the GATA-1 gene that alter the FOG-binding domain have been reported. The mutations are associated with familial anemias and thrombocytopenias of differing severity. To elucidate the molecular basis for the GATA-1/FOG interaction, we have determined the three-dimensional structure of a complex comprising the interaction domains of these proteins. The structure reveals how zinc fingers can act as protein recognition motifs. Details of the architecture of the contact domains and their physical properties provide a molecular explanation for how the GATA-1 mutations contribute to distinct but related genetic diseases. PMID:15644435

  20. Viroids: From Genotype to Phenotype Just Relying on RNA Sequence and Structural Motifs

    PubMed Central

    Flores, Ricardo; Serra, Pedro; Minoia, Sofía; Di Serio, Francesco; Navarro, Beatriz

    2012-01-01

    As a consequence of two unique physical properties, small size and circularity, viroid RNAs do not code for proteins and thus depend on RNA sequence/structural motifs for interacting with host proteins that mediate their invasion, replication, spread, and circumvention of defensive barriers. Viroid genomes fold up on themselves adopting collapsed secondary structures wherein stretches of nucleotides stabilized by Watson–Crick pairs are flanked by apparently unstructured loops. However, compelling data show that they are instead stabilized by alternative non-canonical pairs and that specific loops in the rod-like secondary structure, characteristic of Potato spindle tuber viroid and most other members of the family Pospiviroidae, are critical for replication and systemic trafficking. In contrast, rather than folding into a rod-like secondary structure, most members of the family Avsunviroidae adopt multibranched conformations occasionally stabilized by kissing-loop interactions critical for viroid viability in vivo. Besides these most stable secondary structures, viroid RNAs alternatively adopt during replication transient metastable conformations containing elements of local higher-order structure, prominent among which are the hammerhead ribozymes catalyzing a key replicative step in the family Avsunviroidae, and certain conserved hairpins that also mediate replication steps in the family Pospiviroidae. Therefore, different RNA structures – either global or local – determine different functions, thus highlighting the need for in-depth structural studies on viroid RNAs. PMID:22719735

  1. Ser/Thr Motifs in Transmembrane Proteins: Conservation Patterns and Effects on Local Protein Structure and Dynamics

    PubMed Central

    del Val, Coral; White, Stephen H.

    2014-01-01

    We combined systematic bioinformatics analyses and molecular dynamics simulations to assess the conservation patterns of Ser and Thr motifs in membrane proteins, and the effect of such motifs on the structure and dynamics of α-helical transmembrane (TM) segments. We find that Ser/Thr motifs are often present in β-barrel TM proteins. At least one Ser/Thr motif is present in almost half of the sequences of α-helical proteins analyzed here. The extensive bioinformatics analyses and inspection of protein structures led to the identification of molecular transporters with noticeable numbers of Ser/Thr motifs within the TM region. Given the energetic penalty for burying multiple Ser/Thr groups in the membrane hydrophobic core, the observation of transporters with multiple membrane-embedded Ser/Thr is intriguing and raises the question of how the presence of multiple Ser/Thr affects protein local structure and dynamics. Molecular dynamics simulations of four different Ser-containing model TM peptides indicate that backbone hydrogen bonding of membrane-buried Ser/Thr hydroxyl groups can significantly change the local structure and dynamics of the helix. Ser groups located close to the membrane interface can hydrogen bond to solvent water instead of protein backbone, leading to an enhanced local solvation of the peptide. PMID:22836667

  2. Ser/Thr motifs in transmembrane proteins: conservation patterns and effects on local protein structure and dynamics.

    PubMed

    Del Val, Coral; White, Stephen H; Bondar, Ana-Nicoleta

    2012-11-01

    We combined systematic bioinformatics analyses and molecular dynamics simulations to assess the conservation patterns of Ser and Thr motifs in membrane proteins, and the effect of such motifs on the structure and dynamics of α-helical transmembrane (TM) segments. We find that Ser/Thr motifs are often present in β-barrel TM proteins. At least one Ser/Thr motif is present in almost half of the sequences of α-helical proteins analyzed here. The extensive bioinformatics analyses and inspection of protein structures led to the identification of molecular transporters with noticeable numbers of Ser/Thr motifs within the TM region. Given the energetic penalty for burying multiple Ser/Thr groups in the membrane hydrophobic core, the observation of transporters with multiple membrane-embedded Ser/Thr is intriguing and raises the question of how the presence of multiple Ser/Thr affects protein local structure and dynamics. Molecular dynamics simulations of four different Ser-containing model TM peptides indicate that backbone hydrogen bonding of membrane-buried Ser/Thr hydroxyl groups can significantly change the local structure and dynamics of the helix. Ser groups located close to the membrane interface can hydrogen bond to solvent water instead of protein backbone, leading to an enhanced local solvation of the peptide. PMID:22836667

  3. Temporal motifs in time-dependent networks

    NASA Astrophysics Data System (ADS)

    Kovanen, Lauri; Karsai, Márton; Kaski, Kimmo; Kertész, János; Saramäki, Jari

    2011-11-01

    Temporal networks are commonly used to represent systems where connections between elements are active only for restricted periods of time, such as telecommunication, neural signal processing, biochemical reaction and human social interaction networks. We introduce the framework of temporal motifs to study the mesoscale topological-temporal structure of temporal networks in which the events of nodes do not overlap in time. Temporal motifs are classes of similar event sequences, where the similarity refers not only to topology but also to the temporal order of the events. We provide a mapping from event sequences to coloured directed graphs that enables an efficient algorithm for identifying temporal motifs. We discuss some aspects of temporal motifs, including causality and null models, and present basic statistics of temporal motifs in a large mobile call network.

  4. Crystal Structure of a Luteoviral RNA Pseudoknot and Model for a Minimal Ribosomal Frameshifting Motif

    SciTech Connect

    Pallan, Pradeep S.; Marshall, William S.; Harp, Joel; Jewett III, Frederic C.; Wawrzak, Zdzislaw; Brown II, Bernard A.; Rich, Alexander; Egli, Martin

    2010-03-08

    To understand the role of structural elements of RNA pseudoknots in controlling the extent of -1-type ribosomal frameshifting, we determined the crystal structure of a high-efficiency frameshifting mutant of the pseudoknot from potato leaf roll virus (PLRV). Correlations of the structure with available in vitro frameshifting data for PLRV pseudoknot mutants implicate sequence and length of a stem-loop linker as modulators of frameshifting efficiency. Although the sequences and overall structures of the RNA pseudoknots from PLRV and beet western yellow virus (BWYV) are similar, nucleotide deletions in the linker and adjacent minor groove loop abolish frameshifting only with the latter. Conversely, mutant PLRV pseudoknots with up to four nucleotides deleted in this region exhibit nearly wild-type frameshifting efficiencies. The crystal structure helps rationalize the different tolerances for deletions in the PLRV and BWYV RNAs, and we have used it to build a three-dimensional model of the PRLV pseudoknot with a four-nucleotide deletion. The resulting structure defines a minimal RNA pseudoknot motif composed of 22 nucleotides capable of stimulating -1-type ribosomal frameshifts.

  5. Phylogenetic study of nine species of freshwater monogeneans using secondary structure and motif prediction from India

    PubMed Central

    Chaudhary, Anshu; Singh, Hridaya Shanker

    2012-01-01

    The present study was performed to identify and validate monogenean species from different piscine hosts using molecular tools. Nine species of freshwater monogeneans were collected from gills and skin of freshwater fishes at Hastinapur, Meerut, India. After microscopic examination, molecular analysis was performed utilizing 28S gene marker. Phylogenetic analysis indicated the validation and systematic position of these nine different monogeneans belongs to the Dactylogyridae and Gyrodactylidae families. The findings also confirm that the 28S rDNA sequence is highly conserved and may prove to be useful in taxonomic studies of parasitic platyhelminthes. Besides this, the study is also supplemented by molecular morphometrics that is based on 28S secondary structure homologies of nine monogenean species. The data indicate that 28S motifs i.e., ≤ 50bp in size can also be considered a promising tool for monogenean species identification and their validation. PMID:23144541

  6. Crystal structure of bacterial cell-surface alginate-binding protein with an M75 peptidase motif

    SciTech Connect

    Maruyama, Yukie; Ochiai, Akihito; Mikami, Bunzo; Hashimoto, Wataru; Murata, Kousaku

    2011-02-18

    Research highlights: {yields} Bacterial alginate-binding Algp7 is similar to component EfeO of Fe{sup 2+} transporter. {yields} We determined the crystal structure of Algp7 with a metal-binding motif. {yields} Algp7 consists of two helical bundles formed through duplication of a single bundle. {yields} A deep cleft involved in alginate binding locates around the metal-binding site. {yields} Algp7 may function as a Fe{sup 2+}-chelated alginate-binding protein. -- Abstract: A gram-negative Sphingomonas sp. A1 directly incorporates alginate polysaccharide into the cytoplasm via the cell-surface pit and ABC transporter. A cell-surface alginate-binding protein, Algp7, functions as a concentrator of the polysaccharide in the pit. Based on the primary structure and genetic organization in the bacterial genome, Algp7 was found to be homologous to an M75 peptidase motif-containing EfeO, a component of a ferrous ion transporter. Despite the presence of an M75 peptidase motif with high similarity, the Algp7 protein purified from recombinant Escherichia coli cells was inert on insulin B chain and N-benzoyl-Phe-Val-Arg-p-nitroanilide, both of which are substrates for a typical M75 peptidase, imelysin, from Pseudomonas aeruginosa. The X-ray crystallographic structure of Algp7 was determined at 2.10 A resolution by single-wavelength anomalous diffraction. Although a metal-binding motif, HxxE, conserved in zinc ion-dependent M75 peptidases is also found in Algp7, the crystal structure of Algp7 contains no metal even at the motif. The protein consists of two structurally similar up-and-down helical bundles as the basic scaffold. A deep cleft between the bundles is sufficiently large to accommodate macromolecules such as alginate polysaccharide. This is the first structural report on a bacterial cell-surface alginate-binding protein with an M75 peptidase motif.

  7. CAPS-DB: a structural classification of helix-capping motifs

    PubMed Central

    Segura, Joan; Oliva, Baldomero; Fernandez-Fuentes, Narcis

    2012-01-01

    The regions of the polypeptide chain immediately preceding or following an α-helix are known as Nt- and Ct cappings, respectively. Cappings play a central role stabilizing α-helices due to lack of intrahelical hydrogen bonds in the first and last turn. Sequence patterns of amino acid type preferences have been derived for cappings but the structural motifs associated to them are still unclassified. CAPS-DB is a database of clusters of structural patterns of different capping types. The clustering algorithm is based in the geometry and the (ϕ–ψ)-space conformation of these regions. CAPS-DB is a relational database that allows the user to search, browse, inspect and retrieve structural data associated to cappings. The contents of CAPS-DB might be of interest to a wide range of scientist covering different areas such as protein design and engineering, structural biology and bioinformatics. The database is accessible at: http://www.bioinsilico.org/CAPSDB. PMID:22021380

  8. Isoindigo-based polymer photovoltaics: modifying polymer molecular structures to control the nanostructural packing motif.

    PubMed

    Kim, Yu Jin; Lee, Yun-Ji; Kim, Yun-Hi; Park, Chan Eon

    2016-07-21

    Donor molecular structures, and their packing aspects in donor:acceptor active blends, play a crucial role in the photovoltaic performance of polymer solar cells. We systematically investigated a series of isoindigo-based donor polymers within the framework of a three-dimensional (3D) crystalline motif by modifying their chemical structures, thereby affecting device performances. Although our isoindigo-based polymer series contained polymers that differed only by their alkyl side chains and/or donating units, they showed quite different nanoscale morphological properties, which resulted in significantly different device efficiencies. Notably, blends of our isoindigo-based donor polymer systems with an acceptor compound, whereby the blends had more intermixed network morphologies and stronger face-on orientations of the polymer crystallites, provided better-performing photovoltaic devices. This behavior was analyzed using atomic force microscopy (AFM) and two-dimensional grazing incidence wide angle X-ray diffraction (2D-GIWAXD). To the best of our knowledge, no correlation has been reported previously between 3D nano-structural donor crystallites and device performances, particularly for isoindigo-based polymer systems. PMID:27326694

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

    PubMed Central

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

    2012-01-01

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

  10. From monomer to bulk: appearance of the structural motif of solid iodine in small clusters.

    PubMed

    Hulkko, Eero; Kiljunen, Toni; Kiviniemi, Tiina; Pettersson, Mika

    2009-01-28

    Formation of iodine clusters in a solid krypton matrix was studied using resonance Raman spectroscopy with a 1 cm(-1) resolution. The clusters were produced by annealing of the solid and recognized by appearance of additional spectral transitions. Two distinct regions, red-shifted from the fundamental vibrational wavenumber of the isolated I(2) at 211 cm(-1), were observed in the signal. The intermediate region spans the range 196-208 cm(-1), and the ultimate region consists of two peaks at 181 and 190 cm(-1) nearly identical to crystalline I(2). The experimental results were compared to DFT-D level electronic structure calculations of planar (I(2))(n) clusters (n = 1-7). The dimer, trimer, and tetramer structures, where the I(2) molecule is complexed from one end, were found to exhibit vibrational shifts corresponding to the intermediate size clusters. The larger, bulklike shift appears when the iodine molecule is coordinated from two opposite directions as in the case of a pentamer and higher clusters. Starting from the pentamer, the structural motif of crystalline iodine is clearly recognized in the clusters. PMID:19123809

  11. Defining RNA motif-aminoglycoside interactions via two-dimensional combinatorial screening and structure-activity relationships through sequencing.

    PubMed

    Velagapudi, Sai Pradeep; Disney, Matthew D

    2013-10-15

    RNA is an extremely important target for the development of chemical probes of function or small molecule therapeutics. Aminoglycosides are the most well studied class of small molecules to target RNA. However, the RNA motifs outside of the bacterial rRNA A-site that are likely to be bound by these compounds in biological systems is largely unknown. If such information were known, it could allow for aminoglycosides to be exploited to target other RNAs and, in addition, could provide invaluable insights into potential bystander targets of these clinically used drugs. We utilized two-dimensional combinatorial screening (2DCS), a library-versus-library screening approach, to select the motifs displayed in a 3×3 nucleotide internal loop library and in a 6-nucleotide hairpin library that bind with high affinity and selectivity to six aminoglycoside derivatives. The selected RNA motifs were then analyzed using structure-activity relationships through sequencing (StARTS), a statistical approach that defines the privileged RNA motif space that binds a small molecule. StARTS allowed for the facile annotation of the selected RNA motif-aminoglycoside interactions in terms of affinity and selectivity. The interactions selected by 2DCS generally have nanomolar affinities, which is higher affinity than the binding of aminoglycosides to a mimic of their therapeutic target, the bacterial rRNA A-site. PMID:23719281

  12. Tertiary structure and function of an RNA motif required for plant vascular entry to initiate systemic trafficking.

    PubMed

    Zhong, Xuehua; Tao, Xiaorong; Stombaugh, Jesse; Leontis, Neocles; Ding, Biao

    2007-08-22

    Vascular entry is a decisive step for the initiation of long-distance movement of infectious and endogenous RNAs, silencing signals and developmental/defense signals in plants. However, the mechanisms remain poorly understood. We used Potato spindle tuber viroid (PSTVd) as a model to investigate the direct role of the RNA itself in vascular entry. We report here the identification of an RNA motif that is required for PSTVd to traffic from nonvascular into the vascular tissue phloem to initiate systemic infection. This motif consists of nucleotides U/C that form a water-inserted cis Watson-Crick/Watson-Crick base pair flanked by short helices that comprise canonical Watson-Crick/Watson-Crick base pairs. This tertiary structural model was inferred by comparison with X-ray crystal structures of similar motifs in rRNAs and is supported by combined mutagenesis and covariation analyses. Hydration pattern analysis suggests that water insertion induces a widened minor groove conducive to protein and/or RNA interactions. Our model and approaches have broad implications to investigate the RNA structural motifs in other RNAs for vascular entry and to study the basic principles of RNA structure-function relationships. PMID:17660743

  13. Structural Determinants of Affinity Enhancement between GoLoco Motifs and G-Protein α Subunit Mutants*

    PubMed Central

    Bosch, Dustin E.; Kimple, Adam J.; Sammond, Deanne W.; Muller, Robin E.; Miley, Michael J.; Machius, Mischa; Kuhlman, Brian; Willard, Francis S.; Siderovski, David P.

    2011-01-01

    GoLoco motif proteins bind to the inhibitory Gi subclass of G-protein α subunits and slow the release of bound GDP; this interaction is considered critical to asymmetric cell division and neuro-epithelium and epithelial progenitor differentiation. To provide protein tools for interrogating the precise cellular role(s) of GoLoco motif/Gαi complexes, we have employed structure-based protein design strategies to predict gain-of-function mutations that increase GoLoco motif binding affinity. Here, we describe fluorescence polarization and isothermal titration calorimetry measurements showing three predicted Gαi1 point mutations, E116L, Q147L, and E245L; each increases affinity for multiple GoLoco motifs. A component of this affinity enhancement results from a decreased rate of dissociation between the Gα mutants and GoLoco motifs. For Gαi1Q147L, affinity enhancement was seen to be driven by favorable changes in binding enthalpy, despite reduced contributions from binding entropy. The crystal structure of Gαi1Q147L bound to the RGS14 GoLoco motif revealed disorder among three peptide residues surrounding a well defined Leu-147 side chain. Monte Carlo simulations of the peptide in this region showed a sampling of multiple backbone conformations in contrast to the wild-type complex. We conclude that mutation of Glu-147 to leucine creates a hydrophobic surface favorably buried upon GoLoco peptide binding, yet the hydrophobic Leu-147 also promotes flexibility among residues 511–513 of the RGS14 GoLoco peptide. PMID:21115486

  14. Structural determinants of affinity enhancement between GoLoco motifs and G-protein alpha subunit mutants.

    PubMed

    Bosch, Dustin E; Kimple, Adam J; Sammond, Deanne W; Muller, Robin E; Miley, Michael J; Machius, Mischa; Kuhlman, Brian; Willard, Francis S; Siderovski, David P

    2011-02-01

    GoLoco motif proteins bind to the inhibitory G(i) subclass of G-protein α subunits and slow the release of bound GDP; this interaction is considered critical to asymmetric cell division and neuro-epithelium and epithelial progenitor differentiation. To provide protein tools for interrogating the precise cellular role(s) of GoLoco motif/Gα(i) complexes, we have employed structure-based protein design strategies to predict gain-of-function mutations that increase GoLoco motif binding affinity. Here, we describe fluorescence polarization and isothermal titration calorimetry measurements showing three predicted Gα(i1) point mutations, E116L, Q147L, and E245L; each increases affinity for multiple GoLoco motifs. A component of this affinity enhancement results from a decreased rate of dissociation between the Gα mutants and GoLoco motifs. For Gα(i1)(Q147L), affinity enhancement was seen to be driven by favorable changes in binding enthalpy, despite reduced contributions from binding entropy. The crystal structure of Gα(i1)(Q147L) bound to the RGS14 GoLoco motif revealed disorder among three peptide residues surrounding a well defined Leu-147 side chain. Monte Carlo simulations of the peptide in this region showed a sampling of multiple backbone conformations in contrast to the wild-type complex. We conclude that mutation of Glu-147 to leucine creates a hydrophobic surface favorably buried upon GoLoco peptide binding, yet the hydrophobic Leu-147 also promotes flexibility among residues 511-513 of the RGS14 GoLoco peptide. PMID:21115486

  15. Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

    SciTech Connect

    Chojnowski, Grzegorz; Waleń, Tomasz; Piątkowski, Paweł; Potrzebowski, Wojciech; Bujnicki, Janusz M.

    2015-03-01

    A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.

  16. AptaTRACE Elucidates RNA Sequence-Structure Motifs from Selection Trends in HT-SELEX Experiments.

    PubMed

    Dao, Phuong; Hoinka, Jan; Takahashi, Mayumi; Zhou, Jiehua; Ho, Michelle; Wang, Yijie; Costa, Fabrizio; Rossi, John J; Backofen, Rolf; Burnett, John; Przytycka, Teresa M

    2016-07-01

    Aptamers, short RNA or DNA molecules that bind distinct targets with high affinity and specificity, can be identified using high-throughput systematic evolution of ligands by exponential enrichment (HT-SELEX), but scalable analytic tools for understanding sequence-function relationships from diverse HT-SELEX data are not available. Here we present AptaTRACE, a computational approach that leverages the experimental design of the HT-SELEX protocol, RNA secondary structure, and the potential presence of many secondary motifs to identify sequence-structure motifs that show a signature of selection. We apply AptaTRACE to identify nine motifs in C-C chemokine receptor type 7 targeted by aptamers in an in vitro cell-SELEX experiment. We experimentally validate two aptamers whose binding required both sequence and structural features. AptaTRACE can identify low-abundance motifs, and we show through simulations that, because of this, it could lower HT-SELEX cost and time by reducing the number of selection cycles required. PMID:27467247

  17. Novel Structural and Functional Motifs in cellulose synthase (CesA) Genes of Bread Wheat (Triticum aestivum, L.)

    PubMed Central

    Kaur, Simerjeet; Dhugga, Kanwarpal S.; Gill, Kulvinder; Singh, Jaswinder

    2016-01-01

    Cellulose is the primary determinant of mechanical strength in plant tissues. Late-season lodging is inversely related to the amount of cellulose in a unit length of the stem. Wheat is the most widely grown of all the crops globally, yet information on its CesA gene family is limited. We have identified 22 CesA genes from bread wheat, which include homoeologs from each of the three genomes, and named them as TaCesAXA, TaCesAXB or TaCesAXD, where X denotes the gene number and the last suffix stands for the respective genome. Sequence analyses of the CESA proteins from wheat and their orthologs from barley, maize, rice, and several dicot species (Arabidopsis, beet, cotton, poplar, potato, rose gum and soybean) revealed motifs unique to monocots (Poales) or dicots. Novel structural motifs CQIC and SVICEXWFA were identified, which distinguished the CESAs involved in the formation of primary and secondary cell wall (PCW and SCW) in all the species. We also identified several new motifs specific to monocots or dicots. The conserved motifs identified in this study possibly play functional roles specific to PCW or SCW formation. The new insights from this study advance our knowledge about the structure, function and evolution of the CesA family in plants in general and wheat in particular. This information will be useful in improving culm strength to reduce lodging or alter wall composition to improve biofuel production. PMID:26771740

  18. Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

    PubMed Central

    Chojnowski, Grzegorz; Waleń, Tomasz; Piątkowski, Paweł; Potrzebowski, Wojciech; Bujnicki, Janusz M.

    2015-01-01

    Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx. PMID:25760616

  19. Effect of trimerization motifs on quaternary structure, antigenicity, and immunogenicity of a noncleavable HIV-1 gp140 envelope glycoprotein

    SciTech Connect

    Du, Sean X.; Idiart, Rebecca J.; Mariano, Ellaine B.; Chen, Helen; Jiang Peifeng; Xu Li; Ostrow, Kristin M.; Wrin, Terri; Phung, Pham; Binley, James M.; Petropoulos, Christos J.; Ballantyne, John A.; Whalen, Robert G.

    2009-12-05

    The external domains of the HIV-1 envelope glycoprotein (gp120 and the gp41 ectodomain, collectively known as gp140) contain all known viral neutralization epitopes. Various strategies have been used to create soluble trimers of the envelope to mimic the structure of the native viral protein, including mutation of the gp120-gp41 cleavage site, introduction of disulfide bonds, and fusion to heterologous trimerization motifs. We compared the effects on quaternary structure, antigenicity, and immunogenicity of three such motifs: T4 fibritin, a GCN4 variant, and the Escherichia coli aspartate transcarbamoylase catalytic subunit. Fusion of each motif to the C-terminus of a noncleavable JRCSF gp140(-) envelope protein led to enhanced trimerization but had limited effects on the antigenic profile and CD4-binding ability of the trimers. Immunization of rabbits provided no evidence that the trimerized gp140(-) constructs induced significantly improved neutralizing antibodies to several HIV-1 pseudoviruses, compared to gp140 lacking a trimerization motif. However, modest differences in both binding specificity and neutralizing antibody responses were observed among the various immunogens.

  20. Novel Structural and Functional Motifs in cellulose synthase (CesA) Genes of Bread Wheat (Triticum aestivum, L.).

    PubMed

    Kaur, Simerjeet; Dhugga, Kanwarpal S; Gill, Kulvinder; Singh, Jaswinder

    2016-01-01

    Cellulose is the primary determinant of mechanical strength in plant tissues. Late-season lodging is inversely related to the amount of cellulose in a unit length of the stem. Wheat is the most widely grown of all the crops globally, yet information on its CesA gene family is limited. We have identified 22 CesA genes from bread wheat, which include homoeologs from each of the three genomes, and named them as TaCesAXA, TaCesAXB or TaCesAXD, where X denotes the gene number and the last suffix stands for the respective genome. Sequence analyses of the CESA proteins from wheat and their orthologs from barley, maize, rice, and several dicot species (Arabidopsis, beet, cotton, poplar, potato, rose gum and soybean) revealed motifs unique to monocots (Poales) or dicots. Novel structural motifs CQIC and SVICEXWFA were identified, which distinguished the CESAs involved in the formation of primary and secondary cell wall (PCW and SCW) in all the species. We also identified several new motifs specific to monocots or dicots. The conserved motifs identified in this study possibly play functional roles specific to PCW or SCW formation. The new insights from this study advance our knowledge about the structure, function and evolution of the CesA family in plants in general and wheat in particular. This information will be useful in improving culm strength to reduce lodging or alter wall composition to improve biofuel production. PMID:26771740

  1. Extending motifs in lithiocuprate chemistry: unexpected structural diversity in thiocyanate complexes.

    PubMed

    Peel, Andrew J; Hedidi, Madani; Bentabed-Ababsa, Ghenia; Roisnel, Thierry; Mongin, Florence; Wheatley, Andrew E H

    2016-04-14

    The new area of lithio(thiocyanato)cuprates has been developed. Using inexpensive, stable and safe CuSCN for their preparation, these complexes revealed Lipshutz-type dimeric motifs with solvent-dependent point group identities; planar, boat-shaped and chair shaped conformers are seen in the solid state. In solution, both Lipshutz-type and Gilman structures are clearly seen. Since the advent in 2007 of directed ortho cupration, effort has gone into understanding the structure-reactivity effects of amide ligand variation in and alkali metal salt abstraction from Lipshutz-type cuprates such as (TMP)2Cu(CN)Li2(THF) 1 (TMP = 2,2,6,6-tetramethylpiperidide). The replacement of CN(-) with SCN(-) is investigated presently as a means of improving the safety of lithium cuprates. The synthesis and solid state structural characterization of reference cuprate (TMP)2Cu(CN)Li2(THP) 8 (THP = tetrahydropyran) precedes that of the thiocyanate series (TMP)2Cu(SCN)Li2(L) (L = OEt29, THF 10, THP 11). For each of 9-11, preformed TMPLi was combined with CuSCN (2 : 1) in the presence of sub-stoichiometric Lewis base (0.5 eq. wrt Li). The avoidance of Lewis basic solvents incurs formation of the unsolvated Gilman cuprate (TMP)2CuLi 12, whilst multidimensional NMR spectroscopy has evidenced the abstraction of LiSCN from 9-11 in hydrocarbon solution and the in situ formation of Gilman reagents. The synthetic utility of 10 is established in the selective deprotometalation of chloropyridine substrates, including effecting transition metal-free homocoupling in 51-69% yield. PMID:26554572

  2. Structure and interactions of the first three RNA recognition motifs of splicing factor Prp24

    PubMed Central

    Bae, Euiyoung; Reiter, Nicholas J.; Bingman, Craig A.; Kwan, Sharon S.; Lee, Donghan; Phillips, George N.; Butcher, Samuel E.; Brow, David A.

    2007-01-01

    Summary The essential Saccharomyces cerevisiae pre-messenger RNA splicing protein 24 (Prp24) has four RNA recognition motifs (RRMs) and facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 is a component of the free U6 small nuclear ribonucleoprotein particle (snRNP) but not the U4/U6 bi-snRNP, and so is thought to be displaced from U6 by U4/U6 base-pairing. The interaction partners of each of the four RRMs of Prp24 and how these interactions direct U4/U6 pairing are not known. Here we report the crystal structure of the first three RRMs and the solution structure of the first two RRMs of Prp24. Strikingly, RRM 2 forms extensive inter-domain contacts with RRMs 1 and 3. These contacts occupy much of the canonical RNA-binding faces (β-sheets) of RRMs 1 and 2, but leave the β-sheet of RRM 3 exposed. Previously identified substitutions in Prp24 that suppress mutations in U4 and U6 spliceosomal RNAs cluster primarily in the β-sheet of RRM 3, but also in a conserved loop of RRM 2. RNA binding assays and chemical shift mapping indicate that a large basic patch evident on the surface of RRMs 1 and 2 is part of a high affinity U6 RNA binding site. Our results suggest that Prp24 binds free U6 RNA primarily with RRMs 1 and 2, which may remodel the U6 secondary structure. The β-sheet of RRM 3 then influences U4/U6 pairing through interaction with an unidentified ligand. PMID:17320109

  3. The Thiamin Pyrophosphate-Motif

    NASA Technical Reports Server (NTRS)

    Dominiak, Paulina M.; Ciszak, Ewa M.

    2003-01-01

    Using databases the authors have identified a common thiamin pyrophosphate (TPP)-motif in the family of functionally diverse TPP-dependent enzymes. This common motif consists of multimeric organization of subunits, two catalytic centers, common amino acid sequence, and specific contacts to provide a flip-flop, or alternate site, mechanism of action. Each catalytic center [PP:PYR] is formed at the interface of the PP-domain binding the magnesium ion, pyrophosphate and aminopyrimidine ring of TPP, and the PYR-domain binding the aminopyrimidine ring of that cofactor. A pair of these catalytic centers constitutes the catalytic core [PP:PYR]* within these enzymes. Analysis of the structural elements of this catalytic core reveals novel definition of the common amino acid sequences, which are GX@&(G)@XXGQ, and GDGX25-30 within the PP- domain, and the E&(G)@XXG@ within the PYR-domain, where Q, corresponds to a hydrophobic amino acid. This TPP-motif provides a novel tool for annotation of TPP-dependent enzymes useful in advancing functional proteomics.

  4. HMM-based prediction for protein structural motifs' two local properties: solvent accessibility and backbone torsion angles.

    PubMed

    Yu, Jianyong; Xiang, Leijun; Hong, Jiang; Zhang, Weidong

    2013-02-01

    Protein structure prediction is often assisted by predicting one-dimensional structural properties including relative solvent accessibility (RSA) surface and backbone torsion angles (BTA) of residues, and these two properties are continuously varying variables because proteins can move freely in a three-dimensional space. Instead of subdividing them into a few arbitrarily defined states that many popular approaches used, this paper proposes an integrated system for realvalue prediction of protein structural motifs' two local properties, based on the modified Hidden Markov Model that we previously presented. The model was used to capture the relevance of RSA and the dependency of BTA between adjacent residues along the local protein chain in motifs with definite probabilities. These two properties were predicted according to their own probability distribution. The method was applied to a protein fragment library. For nine different classes of motifs, real values of RSA were predicted with mean absolute error (MAE) of 0.122-0.175 and Pearson's correlation coefficient (PCC) of 0.623-0.714 between predicted and actual RSA. Meanwhile, real values of BTA were obtained with MAE of 8.5⁰-29.4⁰ for Φ angles, 11.2⁰-38.5⁰ for ψ angles and PCC of 0.601-0.716 for Φ, 0.597-0.713 for ψ. The results were compared with well-known Real-SPINE Server, and indicate the proposed method may at least serve as the foundation to obtain better local properties from structural motifs for protein structure prediction. PMID:22894152

  5. An unusual structural motif of antimicrobial peptides containing end-to-end macrocycle and cystine-knot disulfides.

    PubMed

    Tam, J P; Lu, Y A; Yang, J L; Chiu, K W

    1999-08-01

    Four macrocyclic cystine-knot peptides of 29-31 residues, kalata, circulin A and B (CirA and CirB), and cyclopsychotride, have been isolated from coffee plants but have undetermined physiological functions. These macrocycles and 10 of their analogs prepared by chemical synthesis were tested against nine strains of microbes. Kalata and CirA were specific for the Gram-positive Staphylococcus aureus with a minimum inhibition concentration of approximately 0.2 microM. They were relatively ineffective against Gram-negative bacteria such as Escherichia coli and Pseudomonas aeruginosa. However, CirB and cyclopsychotride were active against both Gram-positive and Gram-negative bacteria. In particular, CirB showed potent activity against E. coli with a minimum inhibitory concentration of 0.41 microM. All four cyclic peptides were moderately active against two strains of fungi, Candida kefyr and Candida tropicalis, but were inactive against Candida albicans. These macrocycles are cytotoxic and lysed human red blood cell with a lethal dose 50% of 400 microM. Modifying the Arg residue in kalata with a keto aldehyde significantly reduced its activity against S. aureus whereas blocking the arg in CirA produced no significant effect. The two-disulfide variants and their scrambled disulfide isomers exhibited antimicrobial profiles and potency similar to their native peptides. However, in high-salt assays (100 mM NaCl), few of these macrocyclic peptides, natives or analogs, retained antimicrobial activity. These results show that the macrocyclic peptides possess specific and potent antimicrobial activity that is salt-dependent and that their initial interactions with the microbial surfaces may be electrostatic, an effect commonly found in defensin antimicrobial peptides. Furthermore, their end-to-end cyclic structure with a cystine-knot motif represents a molecular structure of antimicrobials and may provide a useful template for the design of novel peptide antibiotics. PMID

  6. Structural basis for the regulatory role of the PPxY motifs in the thioredoxin-interacting protein TXNIP.

    PubMed

    Liu, Yanli; Lau, Johnathan; Li, Weiguo; Tempel, Wolfram; Li, Li; Dong, Aiping; Narula, Ashrut; Qin, Su; Min, Jinrong

    2016-01-15

    TXNIP (thioredoxin-interacting protein) negatively regulates the antioxidative activity of thioredoxin and participates in pleiotropic cellular processes. Its deregulation is linked to various human diseases, including diabetes, acute myeloid leukaemia and cardiovascular diseases. The E3 ubiquitin ligase Itch (Itchy homologue) polyubiquitinates TXNIP to promote its degradation via the ubiquitin-proteasome pathway, and this Itch-mediated polyubiquitination of TXNIP is dependent on the interaction of the four WW domains of Itch with the two PPxY motifs of TXNIP. However, the molecular mechanism of this interaction of TXNIP with Itch remains elusive. In the present study, we found that each of the four WW domains of Itch exhibited different binding affinities for TXNIP, whereas multivalent engagement between the four WW domains of Itch and the two PPxY motifs of TXNIP resulted in their strong binding avidity. Our structural analyses demonstrated that the third and fourth WW domains of Itch were able to recognize both PPxY motifs of TXNIP simultaneously, supporting a multivalent binding mode between Itch and TXNIP. Interestingly, the phosphorylation status on the tyrosine residue of the PPxY motifs of TXNIP serves as a molecular switch in its choice of binding partners and thereby downstream biological signalling outcomes. Phosphorylation of this tyrosine residue of TXNIP diminished the binding capability of PPxY motifs of TXNIP to Itch, whereas this phosphorylation is a prerequisite to the binding activity of TXNIP to SHP2 [SH2 (Src homology 2) domain-containing protein tyrosine phosphatase 2] and their roles in stabilizing the phosphorylation and activation of CSK (c-Src tyrosine kinase). PMID:26527736

  7. Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants.

    PubMed

    Cheng, Shifeng; Gutmann, Bernard; Zhong, Xiao; Ye, Yongtao; Fisher, Mark F; Bai, Fengqi; Castleden, Ian; Song, Yue; Song, Bo; Huang, Jiaying; Liu, Xin; Xu, Xun; Lim, Boon L; Bond, Charles S; Yiu, Siu-Ming; Small, Ian

    2016-02-01

    The pentatricopeptide repeat (PPR) proteins form one of the largest protein families in land plants. They are characterised by tandem 30-40 amino acid motifs that form an extended binding surface capable of sequence-specific recognition of RNA strands. Almost all of them are post-translationally targeted to plastids and mitochondria, where they play important roles in post-transcriptional processes including splicing, RNA editing and the initiation of translation. A code describing how PPR proteins recognise their RNA targets promises to accelerate research on these proteins, but making use of this code requires accurate definition and annotation of all of the various nucleotide-binding motifs in each protein. We have used a structural modelling approach to define 10 different variants of the PPR motif found in plant proteins, in addition to the putative deaminase motif that is found at the C-terminus of many RNA-editing factors. We show that the super-helical RNA-binding surface of RNA-editing factors is potentially longer than previously recognised. We used the redefined motifs to develop accurate and consistent annotations of PPR sequences from 109 genomes. We report a high error rate in PPR gene models in many public plant proteomes, due to gene fusions and insertions of spurious introns. These consistently annotated datasets across a wide range of species are valuable resources for future comparative genomics studies, and an essential pre-requisite for accurate large-scale computational predictions of PPR targets. We have created a web portal (http://www.plantppr.com) that provides open access to these resources for the community. PMID:26764122

  8. Structure of the central RNA recognition motif of human TIA-1 at 1.95 A resolution

    SciTech Connect

    Kumar, Amit O.; Swenson, Matthew C.; Benning, Matthew M.; Kielkopf, Clara L.

    2008-03-21

    T-cell-restricted intracellular antigen-1 (TIA-1) regulates alternative pre-mRNA splicing in the nucleus, and mRNA translation in the cytoplasm, by recognizing uridine-rich sequences of RNAs. As a step towards understanding RNA recognition by this regulatory factor, the X-ray structure of the central RNA recognition motif (RRM2) of human TIA-1 is presented at 1.95 A resolution. Comparison with structurally homologous RRM-RNA complexes identifies residues at the RNA interfaces that are conserved in TIA-1-RRM2. The versatile capability of RNP motifs to interact with either proteins or RNA is reinforced by symmetry-related protein-protein interactions mediated by the RNP motifs of TIA-1-RRM2. Importantly, the TIA-1-RRM2 structure reveals the locations of mutations responsible for inhibiting nuclear import. In contrast with previous assumptions, the mutated residues are buried within the hydrophobic interior of the domain, where they would be likely to destabilize the RRM fold rather than directly inhibit RNA binding.

  9. 47 CFR 74.22 - Use of common antenna structure.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 4 2011-10-01 2011-10-01 false Use of common antenna structure. 74.22 Section... Applicable to All Services in Part 74 § 74.22 Use of common antenna structure. The simultaneous use of a common antenna structure by more than one station authorized under this part, or by one or more...

  10. 47 CFR 74.22 - Use of common antenna structure.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 4 2010-10-01 2010-10-01 false Use of common antenna structure. 74.22 Section... Applicable to All Services in Part 74 § 74.22 Use of common antenna structure. The simultaneous use of a common antenna structure by more than one station authorized under this part, or by one or more...

  11. 47 CFR 74.22 - Use of common antenna structure.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 4 2013-10-01 2013-10-01 false Use of common antenna structure. 74.22 Section... Applicable to All Services in Part 74 § 74.22 Use of common antenna structure. The simultaneous use of a common antenna structure by more than one station authorized under this part, or by one or more...

  12. 47 CFR 74.22 - Use of common antenna structure.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 4 2012-10-01 2012-10-01 false Use of common antenna structure. 74.22 Section... Applicable to All Services in Part 74 § 74.22 Use of common antenna structure. The simultaneous use of a common antenna structure by more than one station authorized under this part, or by one or more...

  13. 47 CFR 74.22 - Use of common antenna structure.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 4 2014-10-01 2014-10-01 false Use of common antenna structure. 74.22 Section... Applicable to All Services in Part 74 § 74.22 Use of common antenna structure. The simultaneous use of a common antenna structure by more than one station authorized under this part, or by one or more...

  14. The Thiamin Pyrophosphate-Motif

    NASA Technical Reports Server (NTRS)

    Dominiak, P.; Ciszak, E.

    2003-01-01

    Using databases the authors have identified a common thiamin pyrophosphate (TPP)-motif in the family of functionally diverse TPP-dependent enzymes. This common motif consists of multimeric organization of subunits and two catalytic centers. Each catalytic center (PP:PYR) is formed at the interface of the PP-domain binding the magnesium ion, pyrophosphate and amhopyrimidine ring of TPP, and the PYR-domain binding the aminopyrimidine ring of that cofactor. A pair of these catalytic centers constitutes the catalytic core (PP:PYR)(sub 2) within these enzymes. Analysis of the structural elements of this catalytic core reveals novel definition of the common amino acid sequences, which are GXPhiX(sub 4)(G)PhiXXGQ and GDGX(sub 25-30)NN in the PP-domain, and the EX(sub 4)(G)PhiXXGPhi in the PYR-domain, where Phi corresponds to a hydrophobic amino acid. This TPP-motif provides a novel tool for annotation of TPP-dependent enzymes useful in advancing functional proteomics.

  15. Crystal Structure of (+)-[delta]-Cadinene Synthase from Gossypium arboreum and Evolutionary Divergence of Metal Binding Motifs for Catalysis

    SciTech Connect

    Gennadios, Heather A.; Gonzalez, Veronica; Di Costanzo, Luigi; Li, Amang; Yu, Fanglei; Miller, David J.; Allemann, Rudolf K.; Christianson, David W.

    2009-09-11

    (+)-{delta}-Cadinene synthase (DCS) from Gossypium arboreum (tree cotton) is a sesquiterpene cyclase that catalyzes the cyclization of farnesyl diphosphate in the first committed step of the biosynthesis of gossypol, a phytoalexin that defends the plant from bacterial and fungal pathogens. Here, we report the X-ray crystal structure of unliganded DCS at 2.4 {angstrom} resolution and the structure of its complex with three putative Mg{sup 2+} ions and the substrate analogue inhibitor 2-fluorofarnesyl diphosphate (2F-FPP) at 2.75 {angstrom} resolution. These structures illuminate unusual features that accommodate the trinuclear metal cluster required for substrate binding and catalysis. Like other terpenoid cyclases, DCS contains a characteristic aspartate-rich D{sup 307}DTYD{sup 311} motif on helix D that interacts with Mg{sub A}{sup 2+} and Mg{sub C}{sup 2+}. However, DCS appears to be unique among terpenoid cyclases in that it does not contain the 'NSE/DTE' motif on helix H that specifically chelates Mg{sub B}{sup 2+}, which is usually found as the signature sequence (N,D)D(L,I,V)X(S,T)XXXE (boldface indicates Mg{sub B}{sup 2+} ligands). Instead, DCS contains a second aspartate-rich motif, D{sup 451}DVAE{sup 455}, that interacts with Mg{sub B}{sup 2+}. In this regard, DCS is more similar to the isoprenoid chain elongation enzyme farnesyl diphosphate synthase, which also contains two aspartate-rich motifs, rather than the greater family of terpenoid cyclases. Nevertheless, the structure of the DCS-2F-FPP complex shows that the structure of the trinuclear magnesium cluster is generally similar to that of other terpenoid cyclases despite the alternative Mg{sub B}{sup 2+} binding motif. Analyses of DCS mutants with alanine substitutions in the D{sup 307}DTYD{sup 311} and D{sup 451}DVAE{sup 455} segments reveal the contributions of these segments to catalysis.

  16. Dibromodiphenylstannane: isolated centrosymmetric dimers as a new structure motif for the intermolecular association of diorganotin(IV) dihalides.

    PubMed

    Ye, Fei; Reuter, Hans

    2012-04-01

    In the crystalline state, the low-melting title compound [common name: diphenyltin(IV) dibromide], [SnBr(2)(C(6)H(5))(2)], consists of distorted tetrahedral molecules with compressed halide and enlarged carbon opening angles of 102.741 (9) and 123.53 (8)°, respectively, and Sn-C and Sn-Br bond lengths of 2.109 (2)/2.113 (2) and 2.4710 (3)/2.4947 (3) Å, respectively. Intermolecular Sn...Br interactions, typical for diorganotin(IV) dihalides, R(2)SnHal(2) (with Hal = Cl, Br, I), and sterically less demanding organic groups lead to the formation of a hitherto unknown association pattern consisting of centrosymmetric dimers with an antiparallel orientation of the dipole moments and two weak intermolecular Sn...Br distances of 3.8482 (3) Å between one of the two Br atoms and its neighbouring Sn atom, and vice versa. The second Br atom is not involved in intermolecular interactions and lies somewhat outside the association plane that, therefore, is not coplanar [interplanar angle = 1.750 (2)°] with the tin-halide plane. The new structure motif of intermolecular tin-halide interaction can be classified as 2a(i), which indicates the number of molecules (i.e. '2') composing the oligomer, the antiparallel orientation (i.e. 'a') of their dipole moments and the centre of symmetry (i.e. 'i') giving rise to the association pattern. PMID:22476138

  17. Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs.

    PubMed

    Krepl, Miroslav; Cléry, Antoine; Blatter, Markus; Allain, Frederic H T; Sponer, Jiri

    2016-07-27

    RNA recognition motif (RRM) proteins represent an abundant class of proteins playing key roles in RNA biology. We present a joint atomistic molecular dynamics (MD) and experimental study of two RRM-containing proteins bound with their single-stranded target RNAs, namely the Fox-1 and SRSF1 complexes. The simulations are used in conjunction with NMR spectroscopy to interpret and expand the available structural data. We accumulate more than 50 μs of simulations and show that the MD method is robust enough to reliably describe the structural dynamics of the RRM-RNA complexes. The simulations predict unanticipated specific participation of Arg142 at the protein-RNA interface of the SRFS1 complex, which is subsequently confirmed by NMR and ITC measurements. Several segments of the protein-RNA interface may involve competition between dynamical local substates rather than firmly formed interactions, which is indirectly consistent with the primary NMR data. We demonstrate that the simulations can be used to interpret the NMR atomistic models and can provide qualified predictions. Finally, we propose a protocol for 'MD-adapted structure ensemble' as a way to integrate the simulation predictions and expand upon the deposited NMR structures. Unbiased μs-scale atomistic MD could become a technique routinely complementing the NMR measurements of protein-RNA complexes. PMID:27193998

  18. Common community structure in time-varying networks

    NASA Astrophysics Data System (ADS)

    Zhang, Shihua; Zhao, Junfei; Zhang, Xiang-Sun

    2012-05-01

    In this report we introduce the concept of common community structure in time-varying networks. We propose a novel optimization algorithm to rapidly detect common community structure in such networks. Both theoretical and numerical results show that the proposed method not only can resolve detailed common communities, but also can effectively identify the dynamical phenomena in time-varying networks.

  19. A common structure for the potexviruses

    SciTech Connect

    Kendall, Amy; Bian, Wen; Maris, Alexander; Azzo, Caitlin; Groom, Joseph; Williams, Dewight; Shi, Jian; Stewart, Phoebe L.; Wall, Joseph S.; Stubbs, Gerald

    2013-02-05

    We have used fiber diffraction, cryo-electron microscopy, and scanning transmission electron microscopy to confirm the symmetry of three potexviruses, potato virus X, papaya mosaic virus, and narcissus mosaic virus, and to determine their low-resolution structures. All three viruses have slightly less than nine subunits per turn of the viral helix. Our data strongly support the view that all potexviruses have approximately the same symmetry. The structures are dominated by a large domain at high radius in the virion, with a smaller domain, which includes the putative RNA-binding site, extending to low radius.

  20. Three-dimensional structure and mimetic-membrane association of consensus 11-amino-acid motif from soybean LEA3 protein.

    PubMed

    Xue, Rong; Liu, Yun; Zheng, Yizhi; Wu, Yijie; Li, Xiaojing; Pei, Fengkui; Ni, Jiazuan

    2012-01-01

    The occurrence of a highly conserved 11-mer repeating motif in the primary sequence is a major characteristic of group 3 late embryogenesis abundant (LEA3) proteins, which are strongly associated with abiotic stress tolerance of the plants. In this study, the three-dimensional structure, mimetic membrane association, and salt effect for consensus 11-mer motif from soybean PM2 protein (LEA3) were investigated in sodium dodecyl sulfate (SDS) micelles by NMR techniques. It was shown that the 11-mer motif was disordered in aqueous solution, but adopted an α-helix in SDS micelles. NMR diffusion measurements demonstrated that the 11-mer motif was associated with SDS micelles. Paramagnetic quenching NMR experiments further revealed the orientation of the 11-mer motif with respect to the mimetic membrane: the ordered N-terminal segment was inserted into the mimetic membrane, and the disordered C-terminal segment was exposed to water. In addition, salt addition could not change the secondary structure of the 11-mer motif, but might slightly alter the relative spatial position of some N-terminal residue atoms. These results implied that the 11-mer motif would take an important role in structural plasticity and membrane stabilization for LEA3 proteins. PMID:23325560

  1. Structure of common pili from Escherichia coli.

    PubMed Central

    McMichael, J C; Ou, J T

    1979-01-01

    Several important properties of the common pili from Escherichia coli are discussed. These pili were resistant to the gentle Folin-Ciocalteau reagent methods for protein detection and were not readily solubilized by sodium dodecyl sulfate. They were found to contain a reducing sugar but not peptidoglycan. The pilin had multiple conformations in sodium dodecyl sulfate solution, and the appearance of multiple bands on sodium dodecyl sulfate gels did not necessarily indicate heterogeneity of the preparation. The ilus subunit was found to be a different protein than outer membrane III, which has the same apparent molecular weight. In addition, we conformed the results of Brinton (Trans. N.Y. Acad. Sci 27:1003-1054, 1965): that there is a dramatic change in the properties of pili after they are heated at pH values below 2. Images PMID:37233

  2. Access to a CuII–O–CuII Motif: Spectroscopic Properties, Solution Structure, and Reactivity

    PubMed Central

    Haack, Peter; Kärgel, Anne; Greco, Claudio; Dokic, Jadranka; Braun, Beatrice; Pfaff, Florian F.; Mebs, Stefan; Ray, Kallol; Limberg, Christian

    2013-01-01

    We report a complex with a rare CuII–O–CuII structural motif that is stable at room temperature, which allows its in-depth characterization by a variety of spectroscopic methods. Interest in such compounds is fueled by the recent discovery that a CuII–O–CuII species on the surface of Cu-ZSM-5 is capable of oxidizing methane to methanol and this in turn ties into mechanistic discussions on the methane oxidation at the dicopper site within the particulate methane monooxygenase. For the synthesis of our Cu2O complex we have developed a novel, neutral ligand system, FurNeu, exhibiting two N-(N',N'-dimethylaminoethyl)(2-pyridylmethyl)amino binding pockets connected by a dibenzofuran spacer. The reaction of FurNeu with CuCl yielded [FurNeu](Cu2(μ-Cl))(CuCl2), 1, demonstrating the geometric potential of the ligand to stabilize Cu–X–Cu moieties. A CuI precursor with weakly coordinating anions was chosen in the next step, namely [Cu(NCCH3)4]OTf, which led to the formation of [FurNeu](Cu(NCCH3))2(OTf)2, 3. Treatment of 3 with O2 or PhIO led to identical green solutions, whose UV/Vis spectra were markedly different from the one displayed by [FurNeu](Cu)2(OTf)4, 4, prepared independently from FurNeu and Cu(OTf)2. Further investigations including PhIO consumption experiments, NMR and UV/Vis spectroscopy, HR-ESI mass spectrometry and protonation studies led to the identification of the green product as [FurNeu](Cu2(μ-O))(OTf)2, 5. DOSY NMR spectroscopy confirmed its monomeric character. Over longer periods of time 5 decomposes to give [Cu(picoloyl)2], formed through an oxidative N-dealkylation reaction followed by further oxidation of the ligand. Due to its slow decomposition reaction all attempts to crystallize 5 failed. However, its structure in solution could be determined by EXAFS analysis in combination with DFT calculations, which revealed a Cu–O–Cu angle that amounts to 105.17°. Moreover, TDDFT calculations helped to rationalize the UV/Vis absorptions

  3. Access to a Cu(II)-O-Cu(II) motif: spectroscopic properties, solution structure, and reactivity.

    PubMed

    Haack, Peter; Kärgel, Anne; Greco, Claudio; Dokic, Jadranka; Braun, Beatrice; Pfaff, Florian F; Mebs, Stefan; Ray, Kallol; Limberg, Christian

    2013-10-30

    We report a complex with a rare Cu(II)-O-Cu(II) structural motif that is stable at room temperature, which allows its in-depth characterization by a variety of spectroscopic methods. Interest in such compounds is fueled by the recent discovery that a Cu(II)-O-Cu(II) species on the surface of Cu-ZSM-5 is capable of oxidizing methane to methanol, and this in turn ties into mechanistic discussions on the methane oxidation at the dicopper site within the particulate methane monooxygenase. For the synthesis of our Cu2O complex we have developed a novel, neutral ligand system, FurNeu, exhibiting two N-(N',N'-dimethylaminoethyl)(2-pyridylmethyl)amino binding pockets connected by a dibenzofuran spacer. The reaction of FurNeu with CuCl yielded [FurNeu](Cu2(μ-Cl))(CuCl2), 1, demonstrating the geometric potential of the ligand to stabilize Cu-X-Cu moieties. A Cu(I) precursor with weakly coordinating anions was chosen in the next step, namely [Cu(NCCH3)4]OTf, which led to the formation of [FurNeu](Cu(NCCH3))2(OTf)2, 3. Treatment of 3 with O2 or PhIO led to identical green solutions, whose UV-vis spectra were markedly different from the one displayed by [FurNeu](Cu)2(OTf)4, 4, prepared independently from FurNeu and Cu(OTf)2. Further investigations including PhIO consumption experiments, NMR and UV-vis spectroscopy, HR-ESI mass spectrometry, and protonation studies led to the identification of the green product as [FurNeu](Cu2(μ-O))(OTf)2, 5. DOSY NMR spectroscopy confirmed its monomeric character. Over longer periods of time 5 decomposes to give [Cu(picoloyl)2], formed through an oxidative N-dealkylation reaction followed by further oxidation of the ligand. Due to its slow decomposition reaction, all attempts to crystallize 5 failed. However, its structure in solution could be determined by EXAFS analysis in combination with DFT calculations, which revealed a Cu-O-Cu angle that amounts to 105.17°. Moreover, TDDFT calculations helped to rationalize the UV-vis absorptions of 5

  4. Method of linear combination of structural motifs for surface and step energy calculations: Application to GaAs(001)

    SciTech Connect

    Zhang, S.B.; Zunger, A.

    1996-01-01

    First-principles calculations of atomic structure and formation energies of semiconductor surfaces and surface steps are often complicated by complex structural patterns. We suggest here a simpler, algebraic (not differential) approach that is based on two observations distilled from previous first-principles calculations. {ital First}, a relatively large collection of equilibrium structures of surfaces and bulk point defects can be built from a limited number of recurring local {open_quote}{open_quote}structural motifs,{close_quote}{close_quote} including for GaAs tetrahedrally bonded Ga and As and miscoordinated atoms such as threefold-coordinated pyramidal As. {ital Second}, the structure is such that band-gap levels are emptied, resulting in charged miscoordinated atoms. These charges compensate each other. We thus express the total energy of a given surface as a sum of the energies of the motifs, and an electrostatic term representing the Madelung energy of point charges. The motif energies are derived by fitting them to a set of pseudopotential total-energy calculations for {ital flat} GaAs(001) surfaces and for point defects in {ital bulk} GaAs. This set of parameters is shown to suffice to reproduce the energies of {ital other} (001) surfaces, calculated using the same pseudopotential approach. Application of the {open_quote}{open_quote}linear combination of structural motif{close_quote}{close_quote} (LCSM) method to flat GaAs(001) surfaces reveals the following: (i) The observed {ital h}(2{times}3) surface may be a disordered {ital c}(8{times}6) surface. (ii) The observed (2{times}6) surface is a metastable surface, only 0.03 eV/(1{times}1) higher than the {alpha}(2{times}4) surface having the same surface coverage. (iii) We confirm the recent suggestion by Hashizume {ital et} {ital al}. that the observed {gamma}(2{times}4) phase of the (2{times}4) surface is a mixture of the {beta}2(2{times}4) and {ital c}(4{times}4) surfaces. (Abstract Truncated)

  5. Crystal structure of a disulfide-linked "trefoil" motif found in a large family of putative growth factors.

    PubMed Central

    De, A; Brown, D G; Gorman, M A; Carr, M; Sanderson, M R; Freemont, P S

    1994-01-01

    Porcine pancreatic spasmolytic polypeptide (PSP) belongs to a large family of homologous growth factor-like polypeptides characterized by a disulfide-linked "trefoil motif," duplicated and conserved in various family members. PSP contains two trefoil motifs, has several pharmacological actions on the gut, and has growth factor properties on epithelial cells in vitro. The human PSP analogue, human spasmolytic polypeptide, appears to be involved in many regenerative situations and, especially, in healing gastrointestinal ulcers. One member of the trefoil family, pS2, is secreted in approximately 50% of estrogen-dependent human breast carcinomas, which has led to its use as a tumor prognostic marker. Both pS2 and human spasmolytic polypeptide are also widely expressed in chronic gastrointestinal ulcerative conditions such as Crohn disease. Here we report the three-dimensional structure at 2.6-A resolution of a trefoil-containing protein, namely PSP, purified from porcine pancreas. The structure shows two homologous domains that share a supersecondary structure and disulfide bond pattern. The two domains pack asymmetrically giving rise to a number of protruding loops, exposed clefts, and an unusual electrostatic surface potential. Knowledge of the structure of PSP should allow the design of mutants to investigate further the function of PSP and other trefoil-containing peptides. Images PMID:8302836

  6. The Thiamine-Pyrophosphate-Motif

    NASA Technical Reports Server (NTRS)

    Ciszak, Ewa; Dominiak, Paulina

    2004-01-01

    Thiamin pyrophosphate (TPP), a derivative of vitamin B1, is a cofactor for enzymes performing catalysis in pathways of energy production including the well known decarboxylation of a-keto acid dehydrogenases followed by transketolation. TPP-dependent enzymes constitute a structurally and functionally diverse group exhibiting multimeric subunit organization, multiple domains and two chemically equivalent catalytic centers. Annotation of functional TPP-dependcnt enzymes, therefore, has not been trivial due to low sequence similarity related to this complex organization. Our approach to analysis of structures of known TPP-dependent enzymes reveals for the first time features common to this group, which we have termed the TPP-motif. The TPP-motif consists of specific spatial arrangements of structural elements and their specific contacts to provide for a flip-flop, or alternate site, enzymatic mechanism of action. Analysis of structural elements entrained in the flip-flop action displayed by TPP-dependent enzymes reveals a novel definition of the common amino acid sequences. These sequences allow for annotation of TPP-dependent enzymes, thus advancing functional proteomics. Further details of three-dimensional structures of TPP-dependent enzymes will be discussed.

  7. New structural motifs and properties of squaric acid anions in the presence of the L-lysinium counterion

    NASA Astrophysics Data System (ADS)

    Kolev, Tsonko; Mayer-Figge, Heike; Seidel, Rüdiger W.; Sheldrick, William S.; Spiteller, Michael; Koleva, Bojidarka B.

    2009-02-01

    Two novel L-lysinium hydrogensquarate monohydrate ( 1) and the corresponding salt of the L-lysinium dication ( 2) are synthesized and their structure and properties elucidated in detail spectroscopically, thermally and structurally, using single crystal X-ray diffraction, linear-polarized solid-state IR-spectroscopy oriented colloid suspensions in nematic host, TGA, DSC, DTA methods, positive and negative HPLC tandem mass spectrometry (ESI-MS·MS). Quantum chemical methods are used to calculate the electronic structure, vibrational data and electronic spectra. Two novel structural motifs have been obtained, isolated [(HSq -)] and tetramolecular [(H 2Sq)(HSq) 2(Sq)] 4- anion, respectively. Preliminary second harmonic generation measurements are also performed.

  8. A non-canonical DNA structure is a binding motif for the transcription factor SP1 in vitro

    PubMed Central

    Raiber, Eun-Ang; Kranaster, Ramon; Lam, Enid; Nikan, Mehran; Balasubramanian, Shankar

    2012-01-01

    SP1 is a ubiquitous transcription factor that is involved in the regulation of various house-keeping genes. It is known that it acts by binding to a double-stranded consensus motif. Here, we have discovered that SP1 binds also to a non-canonical DNA structure, a G-quadruplex, with high affinity. In particular, we have studied the SP1 binding site within the promoter region of the c-KIT oncogene and found that this site can fold into an anti-parallel two-tetrad G-quadruplex. SP1 pull-down experiments from cellular extracts, together with biophysical binding assays revealed that SP1 has a comparable binding affinity for this G-quadruplex structure and the canonical SP1 duplex sequence. Using SP1 ChIP-on-chip data sets, we have also found that 87% of SP1 binding sites overlap with G-quadruplex forming sequences. Furthermore, while many of these immuoprecipitated sequences (36%) even lack the minimal SP1 consensus motif, 5′-GGGCGG-3′, we have shown that 77% of them are putative G-quadruplexes. Collectively, these data suggest that SP1 is able to bind both, canonical SP1 duplex DNA as well as G-quadruplex structures in vitro and we hypothesize that both types of interactions may occur in cells. PMID:22021377

  9. hCINAP is an atypical mammalian nuclear adenylate kinase with an ATPase motif: Structural and functional studies

    PubMed Central

    Drakou, Christina E.; Malekkou, Anna; Hayes, Joseph M.; Lederer, Carsten W.; Leonidas, Demetres D.; Lamond, Angus I.; Santama, Niovi; Zographos, Spyros E.

    2013-01-01

    Human coilin interacting nuclear ATPase protein (hCINAP) directly interacts with coilin, a marker protein of Cajal Bodies (CBs), nuclear organelles involved in the maturation of small nuclear ribonucleoproteins UsnRNPs and snoRNPs. hCINAP has previously been designated as an adenylate kinase (AK6), but is very atypical as it exhibits unusually broad substrate specificity, structural features characteristic of ATPase/GTPase proteins (Walker motifs A and B) and also intrinsic ATPase activity. Despite its intriguing structure, unique properties and cellular localization, the enzymatic mechanism and biological function of hCINAP have remained poorly characterized. Here, we offer the first high-resolution structure of hCINAP in complex with the substrate ADP (and dADP), the structure of hCINAP with a sulfate ion bound at the AMP binding site, and the structure of the ternary complex hCINAP-Mg2+ADP-Pi. Induced fit docking calculations are used to predict the structure of the hCINAP-Mg2+ATP-AMP ternary complex. Structural analysis suggested a functional role for His79 in the Walker B motif. Kinetic analysis of mutant hCINAP-H79G indicates that His79 affects both AK and ATPase catalytic efficiency and induces homodimer formation. Finally, we show that in vivo expression of hCINAP-H79G in human cells is toxic and drastically deregulates the number and appearance of CBs in the cell nucleus. Our findings suggest that hCINAP may not simply regulate nucleotide homeostasis, but may have broader functionality, including control of CB assembly and disassembly in the nucleus of human cells. PMID:22038794

  10. hCINAP is an atypical mammalian nuclear adenylate kinase with an ATPase motif: structural and functional studies.

    PubMed

    Drakou, Christina E; Malekkou, Anna; Hayes, Joseph M; Lederer, Carsten W; Leonidas, Demetres D; Oikonomakos, Nikos G; Lamond, Angus I; Santama, Niovi; Zographos, Spyros E

    2012-01-01

    Human coilin interacting nuclear ATPase protein (hCINAP) directly interacts with coilin, a marker protein of Cajal Bodies (CBs), nuclear organelles involved in the maturation of small nuclear ribonucleoproteins UsnRNPs and snoRNPs. hCINAP has previously been designated as an adenylate kinase (AK6), but is very atypical as it exhibits unusually broad substrate specificity, structural features characteristic of ATPase/GTPase proteins (Walker motifs A and B) and also intrinsic ATPase activity. Despite its intriguing structure, unique properties and cellular localization, the enzymatic mechanism and biological function of hCINAP have remained poorly characterized. Here, we offer the first high-resolution structure of hCINAP in complex with the substrate ADP (and dADP), the structure of hCINAP with a sulfate ion bound at the AMP binding site, and the structure of the ternary complex hCINAP-Mg(2+) ADP-Pi. Induced fit docking calculations are used to predict the structure of the hCINAP-Mg(2+) ATP-AMP ternary complex. Structural analysis suggested a functional role for His79 in the Walker B motif. Kinetic analysis of mutant hCINAP-H79G indicates that His79 affects both AK and ATPase catalytic efficiency and induces homodimer formation. Finally, we show that in vivo expression of hCINAP-H79G in human cells is toxic and drastically deregulates the number and appearance of CBs in the cell nucleus. Our findings suggest that hCINAP may not simply regulate nucleotide homeostasis, but may have broader functionality, including control of CB assembly and disassembly in the nucleus of human cells. PMID:22038794

  11. The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants.

    PubMed

    Mai, J C; Coleman, A W

    1997-03-01

    Sequences of the Internal Transcribed Spacer 2 (ITS-2) regions of the nuclear rDNA repeats from 111 organisms of the family Volvocaceae (Chlorophyta) and unicellular organisms of the Volvocales, including Chlamydomonas reinhardtii, were determined. The use of thermodynamic energy optimization to generate secondary structures and phylogenetic comparative analysis of the spacer regions revealed a common secondary structure that is conserved despite wide intra- and interfamilial primary sequence divergence. The existence of this conserved higher-order structure is supported by the presence of numerous compensating basepair changes as well as by an evolutionary history of insertions and deletions that nevertheless maintains major aspects of the overall structure. Furthermore, this general structure is preserved across broad phylogenetic lines, as it is observed in the ITS-2s of other chlorophytes, including flowering plants; previous reports of common ITS-2 secondary structures in other eukaryotes were restricted to the order level. The reported ITS-2 structure possesses important conserved structural motifs which may help to mediate cleavages in the ITS-2 that occur during rRNA transcript processing. Their recognition can guide further studies of eukaryotic rRNA processing, and their application to sequence alignments may contribute significantly to the value of ITS-2 sequences in phylogenetic analyses at several taxonomic levels, but particularly in characterizing populations and species. PMID:9060392

  12. Structural Basis for Phosphorylation and Lysine Acetylation Cross-talk in a Kinase Motif Associated with Myocardial Ischemia and Cardioprotection*

    PubMed Central

    Parker, Benjamin L.; Shepherd, Nicholas E.; Trefely, Sophie; Hoffman, Nolan J.; White, Melanie Y.; Engholm-Keller, Kasper; Hambly, Brett D.; Larsen, Martin R.; James, David E.; Cordwell, Stuart J.

    2014-01-01

    Myocardial ischemia and cardioprotection by ischemic pre-conditioning induce signal networks aimed at survival or cell death if the ischemic period is prolonged. These pathways are mediated by protein post-translational modifications that are hypothesized to cross-talk with and regulate each other. Phosphopeptides and lysine-acetylated peptides were quantified in isolated rat hearts subjected to ischemia or ischemic pre-conditioning, with and without splitomicin inhibition of lysine deacetylation. We show lysine acetylation (acetyl-Lys)-dependent activation of AMP-activated protein kinase, AKT, and PKA kinases during ischemia. Phosphorylation and acetyl-Lys sites mapped onto tertiary structures were proximal in >50% of proteins investigated, yet they were mutually exclusive in 50 ischemic pre-conditioning- and/or ischemia-associated peptides containing the KXXS basophilic protein kinase consensus motif. Modifications in this motif were modeled in the C terminus of muscle-type creatine kinase. Acetyl-Lys increased proximal dephosphorylation by 10-fold. Structural analysis of modified muscle-type creatine kinase peptide variants by two-dimensional NMR revealed stabilization via a lysine-phosphate salt bridge, which was disrupted by acetyl-Lys resulting in backbone flexibility and increased phosphatase accessibility. PMID:25008320

  13. A coiled-coil motif in non-structural protein 3 (NS3) of bluetongue virus forms an oligomer.

    PubMed

    Chacko, Nirmal; Mohanty, Nihar Nalini; Biswas, Sanchay Kumar; Chand, Karam; Yogisharadhya, Revanaiah; Pandey, Awadh Bihari; Mondal, Bimalendu; Shivachandra, Sathish Bhadravati

    2015-10-01

    Bluetongue, an arthropod-borne non-contagious hemorrhagic disease of small ruminants, is caused by bluetongue virus (BTV). Several structural and non-structural proteins encoded by BTV have been associated with virulence mechanisms. In the present study, the NS3 protein sequences of bluetongue viral serotypes were analyzed for the presence of heptad regions and oligomer formation. Bioinformatic analysis of NS3 sequences of all 26 BTV serotypes revealed the presence of at least three coiled-coil motifs (CCMs). A conserved α-helical heptad sequence was identified at 14-26 aa (CCM-I), 185-198aa (CCM-II), and 94-116 aa (CCM-III). Among these, CCM-I occurs close to the N-terminus of NS3 and was presumed to be involved in oligomerization. Furthermore, the N-terminus of NS3 (1M-R117 aa) was over-expressed as a recombinant fusion protein in a prokaryotic expression system. Biochemical characterization of recombinant NS3Nt protein revealed that it forms SDS-resistant dimers and high-order oligomers (hexamer and/or octamer) under reducing or non-reducing conditions. Coiled-coil motifs are believed to be critical for NS protein oligomerization and have potential roles in the formation of viroporin ring/pore either with six/eight subunits and this is the first study toward characterization of CCMs in NS3 of bluetongue virus. PMID:26318174

  14. Triangle network motifs predict complexes by complementing high-error interactomes with structural information

    PubMed Central

    Andreopoulos, Bill; Winter, Christof; Labudde, Dirk; Schroeder, Michael

    2009-01-01

    Background A lot of high-throughput studies produce protein-protein interaction networks (PPINs) with many errors and missing information. Even for genome-wide approaches, there is often a low overlap between PPINs produced by different studies. Second-level neighbors separated by two protein-protein interactions (PPIs) were previously used for predicting protein function and finding complexes in high-error PPINs. We retrieve second level neighbors in PPINs, and complement these with structural domain-domain interactions (SDDIs) representing binding evidence on proteins, forming PPI-SDDI-PPI triangles. Results We find low overlap between PPINs, SDDIs and known complexes, all well below 10%. We evaluate the overlap of PPI-SDDI-PPI triangles with known complexes from Munich Information center for Protein Sequences (MIPS). PPI-SDDI-PPI triangles have ~20 times higher overlap with MIPS complexes than using second-level neighbors in PPINs without SDDIs. The biological interpretation for triangles is that a SDDI causes two proteins to be observed with common interaction partners in high-throughput experiments. The relatively few SDDIs overlapping with PPINs are part of highly connected SDDI components, and are more likely to be detected in experimental studies. We demonstrate the utility of PPI-SDDI-PPI triangles by reconstructing myosin-actin processes in the nucleus, cytoplasm, and cytoskeleton, which were not obvious in the original PPIN. Using other complementary datatypes in place of SDDIs to form triangles, such as PubMed co-occurrences or threading information, results in a similar ability to find protein complexes. Conclusion Given high-error PPINs with missing information, triangles of mixed datatypes are a promising direction for finding protein complexes. Integrating PPINs with SDDIs improves finding complexes. Structural SDDIs partially explain the high functional similarity of second-level neighbors in PPINs. We estimate that relatively little structural

  15. The 'WS motif' common to v-mpl and members of the cytokine receptor superfamily is dispensable for myeloproliferative leukemia virus pathogenicity.

    PubMed

    Bénit, L; Charon, M; Cocault, L; Wendling, F; Gisselbrecht, S

    1993-03-01

    Several motifs are conserved in the extracellular domain of the cloned chains of the recently described cytokine receptor superfamily. One of them, usually close to the transmembrane region, is the 'WS motif'. Its function remains unknown, but it has been recently shown that the integrity of this motif is essential for interleukin 2 receptor beta-chain and erythropoietin receptor activity [Miyazaki, T., Maruyama, M., Yamada, G., Hatakeyama, M. & Taniguchi, T. (1991). EMBO J., 10, 3191-3197; Watowich, S.S., Yoshimura, A., Longmore, G.D., Hilton, D.J., Hoshimura, Y. & Lodish, H.R. (1992). Proc. Natl. Acad. Sci. USA, 89, 2140-2144]. This WS motif is present in the v-mpl oncogene, which has been transduced in the myeloproliferative leukemia virus (MPLV). v-mpl encodes a truncated transmembrane protein that belongs to this growth factor receptor family. We demonstrate that determinants of MPLV pathogenesis are encoded by the env-mpl fusion gene and that the complete deletion of the WS motif does not abolish MPLV oncogenic properties. PMID:8382360

  16. Role of NH{sub 2}-terminal hydrophobic motif in the subcellular localization of ATP-binding cassette protein subfamily D: Common features in eukaryotic organisms

    SciTech Connect

    Lee, Asaka; Asahina, Kota; Okamoto, Takumi; Kawaguchi, Kosuke; Kostsin, Dzmitry G.; Kashiwayama, Yoshinori; Takanashi, Kojiro; Yazaki, Kazufumi; Imanaka, Tsuneo; Morita, Masashi

    2014-10-24

    Highlights: • ABCD proteins classifies based on with or without NH{sub 2}-terminal hydrophobic segment. • The ABCD proteins with the segment are targeted peroxisomes. • The ABCD proteins without the segment are targeted to the endoplasmic reticulum. • The role of the segment in organelle targeting is conserved in eukaryotic organisms. - Abstract: In mammals, four ATP-binding cassette (ABC) proteins belonging to subfamily D have been identified. ABCD1–3 possesses the NH{sub 2}-terminal hydrophobic region and are targeted to peroxisomes, while ABCD4 lacking the region is targeted to the endoplasmic reticulum (ER). Based on hydropathy plot analysis, we found that several eukaryotes have ABCD protein homologs lacking the NH{sub 2}-terminal hydrophobic segment (H0 motif). To investigate whether the role of the NH{sub 2}-terminal H0 motif in subcellular localization is conserved across species, we expressed ABCD proteins from several species (metazoan, plant and fungi) in fusion with GFP in CHO cells and examined their subcellular localization. ABCD proteins possessing the NH{sub 2}-terminal H0 motif were localized to peroxisomes, while ABCD proteins lacking this region lost this capacity. In addition, the deletion of the NH{sub 2}-terminal H0 motif of ABCD protein resulted in their localization to the ER. These results suggest that the role of the NH{sub 2}-terminal H0 motif in organelle targeting is widely conserved in living organisms.

  17. [Hemoglobin, from microorganisms to man: a single structural motif, multiple functions].

    PubMed

    Wajcman, Henri; Kiger, Laurent

    2002-12-01

    Haemoglobins from unicellular organisms, plants or animals, share a common structure, which results from the folding, around the heme group, of a polypeptide chain made from 6-8 helices. Nowadays, deciphering the genome of several species allows one to draw the evolutionary tree of this protein going back to 1800 millions of years, at a time when oxygen began to accumulate in the atmosphere. This permits to follow the evolution of the ancestral gene and of its product. It is likely that, only in complex multicellular species, transport and storage of oxygen became the main physiological function of this molecule. In addition, in unicellular organisms and small invertebrates, it is likely that the main function of this protein was to protect the organism from the toxic effect of O2, CO and NO*. The very high oxygen affinity of these molecules, leading them to act rather as a scavenger as an oxygen carrier, supports this hypothesis. Haemoglobins from microorganisms, which may probably be the closest vestiges to the ancestral molecules, are divided into three families. The first one is made from flavohaemoglobins, a group of chimerical proteins carrying a globin domain and an oxido-reduction FAD-dependant domain. The second corresponds to truncated haemoglobins, which are hexacoordinated with very high oxygen-affinity molecules, 20-40 residues shorter than classical haemoglobins. The third group is made from bacterial haemoglobins such as that of Vitreoscilla. Some specific structural arrangements in the region surrounding the heme are cause of their high oxygen affinity. In plants, two types of haemoglobins are present (non-symbiotic and symbiotic), that arose from duplication of an ancestral vegetal gene. Non-symbiotic haemoglobins, which are probably the oldest, are scarcely distributed within tissues having high energetic consumption. Conversely, symbiotic haemoglobins (also named leghaemoglobins) are present at a high concentration (mM) mostly in the rhizomes of

  18. Metal Ion Induced Pairing of Cytosine Bases: Formation of I-Motif Structures Identified by IR Ion Spectroscopy

    NASA Astrophysics Data System (ADS)

    Gao, Juehan; Berden, Giel; Oomens, J.

    2015-06-01

    While the Watson-Crick structure of DNA is among the most well-known molecular structures of our time, alternative base-pairing motifs are also known to occur, often depending on base sequence, pH, or presence of cations. Pairing of two cytosine (C) bases induced by the sharing of a single proton (C-H^+-C) gives rise to the so-called i-motif, occurring particularly in the telomeric region of DNA, and particularly at low pH. At physiological pH, silver cations were recently suggested to form cytosine dimers in a C-Ag^+-C structure analogous to the hemiprotonated cytosine dimer, which was later confirmed by IR spectroscopy.^1 Here we investigate whether Ag^+ is unique in this behavior. Using infrared action spectroscopy employing the free-electron laser FELIX and a tandem mass spectrometer in combination with quantum-chemical computations, we investigate a series of C-M^+-C complexes, where M is Cu, Li and Na. The complexes are formed by electrospray ionization (ESI) from a solution of cytosine and the metal chloride salt in acetonitrile/water. The complexes of interest are mass-isolated in the cell of a FT ion cyclotron resonance mass spectrometer, where they are irradiated with the tunable IR radiation from FELIX in the 600 - 1800 wn range. Spectra in the H-stretching range are obtained with a LaserVision OPO. Both experimental spectra as well as theoretical calculations indicate that while Cu behaves as Ag, the alkali metal ions induce a clearly different dimer structure, in which the two cytosine units are parallelly displaced. In addition to coordination to the ring nitrogen atom, the alkali metal ions coordinate to the carbonyl oxygen atoms of both cytosine bases, indicating that the alkali metal ion coordination favorably competes with hydrogen bonding between the two cytosine sub-units of the i-motif like structure. 1. Berdakin, Steinmetz, Maitre, Pino, J. Phys. Chem. A 2014, 118, 3804

  19. Role of GxxxG Motifs in Transmembrane Domain Interactions.

    PubMed

    Teese, Mark G; Langosch, Dieter

    2015-08-25

    Transmembrane (TM) helices of integral membrane proteins can facilitate strong and specific noncovalent protein-protein interactions. Mutagenesis and structural analyses have revealed numerous examples in which the interaction between TM helices of single-pass membrane proteins is dependent on a GxxxG or (small)xxx(small) motif. It is therefore tempting to use the presence of these simple motifs as an indicator of TM helix interactions. In this Current Topic review, we point out that these motifs are quite common, with more than 50% of single-pass TM domains containing a (small)xxx(small) motif. However, the actual interaction strength of motif-containing helices depends strongly on sequence context and membrane properties. In addition, recent studies have revealed several GxxxG-containing TM domains that interact via alternative interfaces involving hydrophobic, polar, aromatic, or even ionizable residues that do not form recognizable motifs. In multipass membrane proteins, GxxxG motifs can be important for protein folding, and not just oligomerization. Our current knowledge thus suggests that the presence of a GxxxG motif alone is a weak predictor of protein dimerization in the membrane. PMID:26244771

  20. Cryo-EM near-atomic structure of a dsRNA fungal virus shows ancient structural motifs preserved in the dsRNA viral lineage

    PubMed Central

    Luque, Daniel; Gómez-Blanco, Josué; Garriga, Damiá; Brilot, Axel F.; González, José M.; Havens, Wendy M.; Carrascosa, José L.; Trus, Benes L.; Verdaguer, Nuria; Ghabrial, Said A.; Castón, José R.

    2014-01-01

    Viruses evolve so rapidly that sequence-based comparison is not suitable for detecting relatedness among distant viruses. Structure-based comparisons suggest that evolution led to a small number of viral classes or lineages that can be grouped by capsid protein (CP) folds. Here, we report that the CP structure of the fungal dsRNA Penicillium chrysogenum virus (PcV) shows the progenitor fold of the dsRNA virus lineage and suggests a relationship between lineages. Cryo-EM structure at near-atomic resolution showed that the 982-aa PcV CP is formed by a repeated α-helical core, indicative of gene duplication despite lack of sequence similarity between the two halves. Superimposition of secondary structure elements identified a single “hotspot” at which variation is introduced by insertion of peptide segments. Structural comparison of PcV and other distantly related dsRNA viruses detected preferential insertion sites at which the complexity of the conserved α-helical core, made up of ancestral structural motifs that have acted as a skeleton, might have increased, leading to evolution of the highly varied current structures. Analyses of structural motifs only apparent after systematic structural comparisons indicated that the hallmark fold preserved in the dsRNA virus lineage shares a long (spinal) α-helix tangential to the capsid surface with the head-tailed phage and herpesvirus viral lineage. PMID:24821769

  1. Conserved structural motifs located in distal loops of aphthovirus internal ribosome entry site domain 3 are required for internal initiation of translation.

    PubMed Central

    López de Quinto, S; Martínez-Salas, E

    1997-01-01

    A comparison of picornavirus internal ribosome entry site (IRES) secondary structures revealed the existence of conserved motifs located on loops. We have carried out a mutational analysis to test their requirement for IRES-driven translation. The GUAA sequence, located in the aphthovirus 3A loop, did not tolerate substitutions that disrupt the GNRA motif. Interestingly, this motif was found at similar positions in all picornavirus IRESs, suggesting that it may form part of a tertiary-structure element. The RAAA tetranucleotide located in the 3B loop was conserved only in cardiovirus and aphthovirus. A mutational analysis of the RAAA motif revealed that activities of 3B loop mutants correlated with both the presence of a sequence close to CAAA at the new 3B loop and the absence of reorganization of the 3B and 3C stem-loops. In support of this conclusion, insertion of a large number of nucleotides close to the 3B loop, which was predicted to reorganize the 3B-3C stem-loop structure, led to defective IRES elements. We conclude that the aphthovirus IRES loops located at the most distal part of domain 3, which carries GNRA and RAAA motifs, are essential for IRES function. PMID:9094703

  2. BlockLogo: visualization of peptide and sequence motif conservation.

    PubMed

    Olsen, Lars Rønn; Kudahl, Ulrich Johan; Simon, Christian; Sun, Jing; Schönbach, Christian; Reinherz, Ellis L; Zhang, Guang Lan; Brusic, Vladimir

    2013-12-31

    BlockLogo is a web-server application for the visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from multiple sequence alignments. The user input consists of a multiple sequence alignment, selection of motif positions, type of sequence, and output format definition. The output has BlockLogo along with the sequence logo, and a table of motif frequencies. We deployed BlockLogo as an online application and have demonstrated its utility through examples that show visualization of T-cell epitopes and B-cell epitopes (both continuous and discontinuous). Our additional example shows a visualization and analysis of structural motifs that determine the specificity of peptide binding to HLA-DR molecules. The BlockLogo server also employs selected experimentally validated prediction algorithms to enable on-the-fly prediction of MHC binding affinity to 15 common HLA class I and class II alleles as well as visual analysis of discontinuous epitopes from multiple sequence alignments. It enables the visualization and analysis of structural and functional motifs that are usually described as regular expressions. It provides a compact view of discontinuous motifs composed of distant positions within biological sequences. BlockLogo is available at: http://research4.dfci.harvard.edu/cvc/blocklogo/ and http://met-hilab.bu.edu/blocklogo/. PMID:24001880

  3. The structure of the translational initiation factor IF1 from E.coli contains an oligomer-binding motif.

    PubMed Central

    Sette, M; van Tilborg, P; Spurio, R; Kaptein, R; Paci, M; Gualerzi, C O; Boelens, R

    1997-01-01

    The structure of the translational initiation factor IF1 from Escherichia coli has been determined with multidimensional NMR spectroscopy. Using 1041 distance and 78 dihedral constraints, 40 distance geometry structures were calculated, which were refined by restrained molecular dynamics. From this set, 19 structures were selected, having low constraint energy and few constraint violations. The ensemble of 19 structures displays a root-mean-square deviation versus the average of 0.49 A for the backbone atoms and 1.12 A for all atoms for residues 6-36 and 46-67. The structure of IF1 is characterized by a five-stranded beta-barrel. The loop connecting strands three and four contains a short 3(10) helix but this region shows considerably higher flexibility than the beta-barrel. The fold of IF1 is very similar to that found in the bacterial cold shock proteins CspA and CspB, the N-terminal domain of aspartyl-tRNA synthetase and the staphylococcal nuclease, and can be identified as the oligomer-binding motif. Several proteins of this family are nucleic acid-binding proteins. This suggests that IF1 plays its role in the initiation of protein synthesis by nucleic acid interactions. Specific changes of NMR signals of IF1 upon titration with 30S ribosomal subunit identifies several residues that are involved in the interaction with ribosomes. PMID:9135158

  4. Effect of packing motifs on the energy ranking and electronic properties of putative crystal structures of tricyano-1,4-dithiino[c]-isothiazole.

    PubMed

    Curtis, Farren; Wang, Xiaopeng; Marom, Noa

    2016-08-01

    We present an analysis of putative structures of tricyano-1,4-dithiino[c]-isothiazole (TCS3), generated within the sixth crystal structure prediction blind test. Typical packing motifs are identified and characterized in terms of distinct patterns of close contacts and regions of electrostatic and dispersion interactions. We find that different dispersion-inclusive density functional theory (DFT) methods systematically favor specific packing motifs, which may affect the outcome of crystal structure prediction efforts. The effect of crystal packing on the electronic and optical properties of TCS3 is investigated using many-body perturbation theory within the GW approximation and the Bethe-Salpeter equation (BSE). We find that a structure with Pna21 symmetry and a bilayer packing motif exhibits intermolecular bonding patterns reminiscent of π-π stacking and has markedly different electronic and optical properties than the experimentally observed P21/n structure with a cyclic dimer motif, including a narrower band gap, enhanced band dispersion and broader optical absorption. The Pna21 bilayer structure is close in energy to the observed structure and may be feasible to grow. PMID:27484377

  5. Institutional property rights structure, common pool resource (CPR), tragedy of the urban commons: A Review

    NASA Astrophysics Data System (ADS)

    Ling, G.; Ho, C. S.; Ali, H. M.

    2014-02-01

    There have been a plethora of researches on the significance of public open space (POS) in contributing to societies' sustainability. However, by virtue of identified maladaptive policy-based-property rights structure, such a shared good becomes vulnerable to tragedy of the urban commons (overexploitation) that subsequently leads to burgeoning number of mismanaged POS e.g., degraded and unkempt urban public spaces. By scrutinising the literatures within property rights domain and commons resources, an objective is highlighted in this paper which is to insightfully discourse institutional property rights structure pertaining to the mechanism, roles and interrelationship between property-rights regimes, bundle of property rights and resource domains; types of goods on how they act upon and tie in the POS with the social quandary. In summary, urban POS tragedy can potentially be triggered by the institutional structure especially if the ownership is left under open-access resource regime and ill-defined property rights which both successively constitute the natures of Common Pool Resource (CPR) within the commons, POS. Therefore, this paper sparks an idea to policy makers that property rights structure is a determinant in sustainably governing the POS in which adaptive assignment of property regimes and property rights are impelled.

  6. Structure for common access and support of fuel cell stacks

    DOEpatents

    Walsh, Michael M.

    2000-01-01

    A structure provides common support and access to multiple fuel cells externally mounted thereto. The structure has openings leading to passages defined therein for providing the access. Various other fuel cell power system components are connected at the openings, such as reactant and coolant sources.

  7. A motif of eleven amino acids is a structural adaptation that facilitates motor capability of eutherian prestin

    PubMed Central

    Tan, Xiaodong; Pecka, Jason L.; Tang, Jie; Lovas, Sándor; Beisel, Kirk W.; He, David Z. Z.

    2012-01-01

    Cochlear outer hair cells (OHCs) alter their length in response to transmembrane voltage changes. This so-called electromotility is the result of conformational changes of membrane-bound prestin. Prestin-based OHC motility is thought to be responsible for cochlear amplification, which contributes to the exquisite frequency selectivity and sensitivity of mammalian hearing. Prestin belongs to an anion transporter family, the solute carrier protein 26A (SLC26A). Prestin is unique in this family in that it functions as a voltage-dependent motor protein manifested by two hallmarks, nonlinear capacitance and motility. Evidence suggests that prestin orthologs from zebrafish and chicken are anion exchangers or transporters with no motor function. We identified a segment of 11 amino acid residues in eutherian prestin that is extremely conserved among eutherian species but highly variable among non-mammalian orthologs and SLC26A paralogs. To determine whether this sequence represents a motif that facilitates motor function in eutherian prestin, we utilized a chimeric approach by swapping corresponding residues from the zebrafish and chicken with those of gerbil. Motility and nonlinear capacitance were measured from chimeric prestin-transfected human embryonic kidney 293 cells using a voltage-clamp technique and photodiode-based displacement measurement system. We observed a gain of motor function with both of the hallmarks in the chimeric prestin without loss of transport function. Our results show, for the first time, that the substitution of a span of 11 amino acid residues confers the electrogenic anion transporters of zebrafish and chicken prestins with motor-like function. Thus, this motif represents the structural adaptation that assists gain of motor function in eutherian prestin. PMID:22399806

  8. A motif of eleven amino acids is a structural adaptation that facilitates motor capability of eutherian prestin.

    PubMed

    Tan, Xiaodong; Pecka, Jason L; Tang, Jie; Lovas, Sándor; Beisel, Kirk W; He, David Z Z

    2012-02-15

    Cochlear outer hair cells (OHCs) alter their length in response to transmembrane voltage changes. This so-called electromotility is the result of conformational changes of membrane-bound prestin. Prestin-based OHC motility is thought to be responsible for cochlear amplification, which contributes to the exquisite frequency selectivity and sensitivity of mammalian hearing. Prestin belongs to an anion transporter family, the solute carrier protein 26A (SLC26A). Prestin is unique in this family in that it functions as a voltage-dependent motor protein manifested by two hallmarks, nonlinear capacitance and motility. Evidence suggests that prestin orthologs from zebrafish and chicken are anion exchangers or transporters with no motor function. We identified a segment of 11 amino acid residues in eutherian prestin that is extremely conserved among eutherian species but highly variable among non-mammalian orthologs and SLC26A paralogs. To determine whether this sequence represents a motif that facilitates motor function in eutherian prestin, we utilized a chimeric approach by swapping corresponding residues from the zebrafish and chicken with those of gerbil. Motility and nonlinear capacitance were measured from chimeric prestin-transfected human embryonic kidney 293 cells using a voltage-clamp technique and photodiode-based displacement measurement system. We observed a gain of motor function with both of the hallmarks in the chimeric prestin without loss of transport function. Our results show, for the first time, that the substitution of a span of 11 amino acid residues confers the electrogenic anion transporters of zebrafish and chicken prestins with motor-like function. Thus, this motif represents the structural adaptation that assists gain of motor function in eutherian prestin. PMID:22399806

  9. Structural differences within the loop E motif imply alternative mechanisms of viroid processing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Viroids replicate via a rolling circle mechanism, and cleavage/ligation requires extensive rearrangement of the highly base-paired native structure. For Potato spindle tuber viroid (PSTVd), the switch from cleavage to ligation is driven by the change from a multi-branched tetraloop structure to a l...

  10. Novel structural motifs in low energy phases of LiAlH4.

    PubMed

    Amsler, Maximilian; Flores-Livas, José A; Huan, Tran Doan; Botti, Silvana; Marques, Miguel A L; Goedecker, Stefan

    2012-05-18

    We identify a class of novel low energy phases of the hydrogen storage material LiAlH4 by using the ab initio minima hopping crystal structure prediction method. These phases are, unlike previous predictions and known structures of similar materials, characterized by polymeric networks consisting of Al atoms interlinked with H atoms. The most stable structure is a layered ionic crystal with P21/c symmetry, and it has lower free energy than the previously reported structure over a wide range of temperatures. Furthermore, we carry out x-ray diffraction, phonon, and GW band-structure analysis in order to characterize this phase. Its experimental synthesis would have profound implications for the study of dehydrogenation and rehydrogenation processes and the stability problem of LiAlH4 for hydrogen storage applications. PMID:23003156

  11. Crystal Structure of the N-Terminal RNA Recognition Motif of mRNA Decay Regulator AUF1.

    PubMed

    Choi, Young Jun; Yoon, Je-Hyun; Chang, Jeong Ho

    2016-01-01

    AU-rich element binding/degradation factor 1 (AUF1) plays a role in destabilizing mRNAs by forming complexes with AU-rich elements (ARE) in the 3'-untranslated regions. Multiple AUF1-ARE complexes regulate the translation of encoded products related to the cell cycle, apoptosis, and inflammation. AUF1 contains two tandem RNA recognition motifs (RRM) and a Gln- (Q-) rich domain in their C-terminal region. To observe how the two RRMs are involved in recognizing ARE, we obtained the AUF1-p37 protein covering the two RRMs. However, only N-terminal RRM (RRM1) was crystallized and its structure was determined at 1.7 Å resolution. It appears that the RRM1 and RRM2 separated before crystallization. To demonstrate which factors affect the separate RRM1-2, we performed limited proteolysis using trypsin. The results indicated that the intact proteins were cleaved by unknown proteases that were associated with them prior to crystallization. In comparison with each of the monomers, the conformations of the β2-β3 loops were highly variable. Furthermore, a comparison with the RRM1-2 structures of HuR and hnRNP A1 revealed that a dimer of RRM1 could be one of the possible conformations of RRM1-2. Our data may provide a guidance for further structural investigations of AUF1 tandem RRM repeat and its mode of ARE binding. PMID:27437398

  12. Solution structure of gamma-bungarotoxin: the functional significance of amino acid residues flanking the RGD motif in integrin binding.

    PubMed

    Shiu, Jia-Hau; Chen, Chiu-Yueh; Chang, Long-Sen; Chen, Yi-Chun; Chen, Yen-Chin; Lo, Yu-Hui; Liu, Yu-Chen; Chuang, Woei-Jer

    2004-12-01

    Gamma-bungarotoxin, a snake venom protein isolated from Bungarus multicinctus, contains 68 amino acids, including 10 cysteine residues and a TAVRGDGP sequence at positions 30-37. The solution structure of gamma-bungarotoxin has been determined by nuclear magnetic resonance (NMR) spectroscopy. The structure is similar to that of the short-chain neurotoxins that contain three loops extending from a disulfide-bridged core. The tripeptide Arg-Gly-Asp (RGD) sequence is located at the apex of the flexible loop and is similar to that of other RGD-containing proteins. However, gamma-bungarotoxin only inhibits platelet aggregations with an IC50 of 34 microM. To understand its weak activity in inhibiting platelet aggregation, we mutated the RGD loop sequences of rhodostomin, a potent platelet aggregation inhibitor, from RIPRGDMP to TAVRGDGP, resulting in a 196-fold decrease in activity. In addition, the average Calpha-to-Calpha distance between R33 and G36 of gamma-bungarotoxin is 6.02 A, i.e., shorter than that of other RGD-containing proteins that range from 6.55 to 7.46 A. These results suggested that the amino acid residues flanking the RGD motif might control the width of the RGD loop. This structural difference may be responsible for its decrease in platelet aggregation inhibition compared with other RGD-containing proteins. PMID:15390258

  13. Crystal Structure of the N-Terminal RNA Recognition Motif of mRNA Decay Regulator AUF1

    PubMed Central

    Choi, Young Jun

    2016-01-01

    AU-rich element binding/degradation factor 1 (AUF1) plays a role in destabilizing mRNAs by forming complexes with AU-rich elements (ARE) in the 3′-untranslated regions. Multiple AUF1-ARE complexes regulate the translation of encoded products related to the cell cycle, apoptosis, and inflammation. AUF1 contains two tandem RNA recognition motifs (RRM) and a Gln- (Q-) rich domain in their C-terminal region. To observe how the two RRMs are involved in recognizing ARE, we obtained the AUF1-p37 protein covering the two RRMs. However, only N-terminal RRM (RRM1) was crystallized and its structure was determined at 1.7 Å resolution. It appears that the RRM1 and RRM2 separated before crystallization. To demonstrate which factors affect the separate RRM1-2, we performed limited proteolysis using trypsin. The results indicated that the intact proteins were cleaved by unknown proteases that were associated with them prior to crystallization. In comparison with each of the monomers, the conformations of the β2-β3 loops were highly variable. Furthermore, a comparison with the RRM1-2 structures of HuR and hnRNP A1 revealed that a dimer of RRM1 could be one of the possible conformations of RRM1-2. Our data may provide a guidance for further structural investigations of AUF1 tandem RRM repeat and its mode of ARE binding. PMID:27437398

  14. The nuclear magnetic resonance solution structure of the synthetic AhPDF1.1b plant defensin evidences the structural feature within the γ-motif.

    PubMed

    Meindre, Fanny; Lelièvre, Dominique; Loth, Karine; Mith, Oriane; Aucagne, Vincent; Berthomieu, Pierre; Marquès, Laurence; Delmas, Agnès F; Landon, Céline; Paquet, Françoise

    2014-12-16

    Plant defensins (PDF) are cysteine-rich peptides that are major actors in the innate immunity in plants. Besides their antifungal activity, some PDF such as Arabidopsis halleri PDF1.1b confer zinc tolerance in plants. Here we present (i) an efficient protocol for the production of AhPDF1.1b by solid-phase peptide synthesis followed by controlled oxidative folding to obtain the highly pure native form of the defensin and (ii) the three-dimensional (3D) nuclear magnetic resonance structure of AhPDF1.1b, the first 3D structure of plant defensin obtained with a synthetic peptide. Its fold is organized around the typical cysteine-stabilized α-helix β-sheet motif and contains the γ-core motif involved in the antifungal activity of all plant defensins. On the basis of our structural analysis of AhPDF1 defensins combined with previous biological data for antifungal and zinc tolerance activities, we established the essential role of cis-Pro41 within the γ-core. In fact, the four consecutive residues (Val39-Phe40-Pro41-Ala42) are strictly conserved for plant defensins able to tolerate zinc. We hypothesized that structural and/or dynamic features of this sequence are related to the ability of the defensin to chelate zinc. PMID:25419866

  15. The i-Motif in the bcl-2 P1 Promoter Forms an Unexpectedly Stable Structure with a Unique 8:5:7 Loop Folding Pattern

    PubMed Central

    Kendrick, Samantha; Akiyama, Yoshitsugu; Hecht, Sidney M.; Hurley, Laurence H.

    2009-01-01

    Transcriptional regulation of the bcl-2 proto-oncogene is highly complex, with the majority of transcription driven by the P1 promoter site and the interaction of multiple regulatory proteins. A guanine- and cytosine-rich (GC-rich) region directly upstream of the P1 site has been shown to be integral to bcl-2 promoter activity, as deletion or mutation of this region significantly increases transcription. This GC-rich element consists of six contiguous runs of guanines and cytosines that have the potential to adopt DNA secondary structures, the G-quadruplex and i-motif, respectively. Our laboratory has previously demonstrated that the polypurine-rich strand of the bcl-2 promoter can form a mixture of three different G-quadruplex structures. In this current study, we demonstrate that the complementary polypyrimidine-rich strand is capable of forming one major intramolecular i-motif DNA secondary structure with a transition pH of 6.6. Characterization of the i-motif folding pattern using mutational studies coupled with circular dichroic spectra and thermal stability analyses revealed an 8:5:7 loop conformation as the predominant structure at pH 6.1. The folding pattern was further supported by chemical footprinting with bromine. In addition, a novel assay involving the sequential incorporation of a fluorescent thymine analog at each thymine position provided evidence of a capping structure within the top loop region of the i-motif. The potential of the GC-rich element within the bcl-2 promoter region to form DNA secondary structures suggests that the transition from the B-DNA to non-B-DNA conformation may play an important role in bcl-2 transcriptional regulation. Furthermore, the two adjacent large lateral loops in the i-motif structure provide an unexpected opportunity for protein and small molecule recognition. PMID:19908860

  16. A conserved secondary structural motif in 23S rRNA defines the site of interaction of amicetin, a universal inhibitor of peptide bond formation.

    PubMed Central

    Leviev, I G; Rodriguez-Fonseca, C; Phan, H; Garrett, R A; Heilek, G; Noller, H F; Mankin, A S

    1994-01-01

    The binding site and probable site of action have been determined for the universal antibiotic amicetin which inhibits peptide bond formation. Evidence from in vivo mutants, site-directed mutations and chemical footprinting all implicate a highly conserved motif in the secondary structure of the 23S-like rRNA close to the central circle of domain V. We infer that this motif lies at, or close to, the catalytic site in the peptidyl transfer centre. The binding site of amicetin is the first of a group of functionally related hexose-cytosine inhibitors to be localized on the ribosome. Images PMID:8157007

  17. Combined structural, biochemical and cellular evidence demonstrates that both FGDF motifs in alphavirus nsP3 are required for efficient replication

    PubMed Central

    Schulte, Tim; Liu, Lifeng; Panas, Marc D.; Thaa, Bastian; Dickson, Nicole; Götte, Benjamin; Achour, Adnane

    2016-01-01

    Recent findings have highlighted the role of the Old World alphavirus non-structural protein 3 (nsP3) as a host defence modulator that functions by disrupting stress granules, subcellular phase-dense RNA/protein structures formed upon environmental stress. This disruption mechanism was largely explained through nsP3-mediated recruitment of the host G3BP protein via two tandem FGDF motifs. Here, we present the 1.9 Å resolution crystal structure of the NTF2-like domain of G3BP-1 in complex with a 25-residue peptide derived from Semliki Forest virus nsP3 (nsP3-25). The structure reveals a poly-complex of G3BP-1 dimers interconnected through the FGDF motifs in nsP3-25. Although in vitro and in vivo binding studies revealed a hierarchical interaction of the two FGDF motifs with G3BP-1, viral growth curves clearly demonstrated that two intact FGDF motifs are required for efficient viral replication. Chikungunya virus nsP3 also binds G3BP dimers via a hierarchical interaction, which was found to be critical for viral replication. These results highlight a conserved molecular mechanism in host cell modulation. PMID:27383630

  18. The role of G-quadruplex/i-motif secondary structures as cis-acting regulatory elements

    PubMed Central

    Kendrick, Samantha; Hurley, Laurence H.

    2011-01-01

    The nature of DNA has captivated scientists for more than fifty years. The discovery of the double-helix model of DNA by Watson and Crick in 1953 not only established the primary structure of DNA, but also provided the mechanism behind DNA function. Since then, researchers have continued to further the understanding of DNA structure and its pivotal role in transcription. The demonstration of DNA secondary structure formation has allowed for the proposal that the dynamics of DNA itself can function to modulate transcription. This review presents evidence that DNA can exist in a dynamic equilibrium between duplex and secondary conformations. In addition, data demonstrating that intracellular proteins as well as small molecules can shift this equilibrium in either direction to alter gene transcription will be discussed, with a focus on the modulation of proto-oncogene expression. PMID:21796223

  19. On squaring triangles - Structural motifs in Cu-In-Sb compounds

    NASA Astrophysics Data System (ADS)

    Müller, C. J.; Lidin, S.

    2015-11-01

    Two new ternary Cu-In-Sb compounds Cu7In2.5Sb0.5 and Cu2In0.75Sb0.25 are presented. Both compounds are Ni2In type superstructures with vacancies in the pseudohexagonal network. Additionally, the pseudocubic nature of the compounds and Ni2In type (super)structures, in general, is discussed. Remarkably, a large number of pseudo-five-fold and pseudo-three-fold axes contribute to generate a pseudocubic symmetry in the crystal structure that is reflected in pseudocubic axial ratios in Ni2In type superstructures. We find that they belong to the family of tetrahedrally close packed structures which implies that pseudocubic axial relationships simply are to be expected.

  20. Evolutionary and taxonomic implications of conserved structural motifs between picornaviruses and insect picorna-like viruses.

    PubMed

    Liljas, L; Tate, J; Lin, T; Christian, P; Johnson, J E

    2002-01-01

    A comparison of the recently determined structure of an insect picorna-like virus, Cricket paralysis virus (CrPV), with that of the mammalian picornaviruses shows that several structural features are highly conserved between these viruses. These conserved features include the topology of the coat proteins, the conformation of most loops, and the general arrangement of the internally located N-terminal arms of the coat proteins. The conformational conservation of the N-termini of the three major coat proteins between CrPV and the picornaviruses suggests a putative ancestral T = 3 virus. Comparisons of the genome structure and amino-acid sequence of the coat proteins of CrPV with a number of other insect picorna-like viruses show that most of them belong to a novel group, recently given the interim name Cricket paralysis-like viruses. Two other insect picorna-like viruses, Infectious flacherie virus (IFV) and Sacbrood virus (SBV), for which the genome sequences have recently been determined, have very different coat protein sequences and a genome organization more like the picornaviruses. However, the position of the small VP4 protein in the structural protein polyprotein as well as the mechanism for its cleavage from VP3 upon assembly strongly suggests an evolutionary link to the "Cricket paralysis-like viruses". We propose that the picornaviruses, Cricket paralysis-like viruses and IFV/SBV group are a natural assemblage. The ancestor for this assemblage had a structure based upon the CrPV/picornavirus paradigm and a genome encoding a single major coat protein; gene duplication and rearrangements have subsequently produced the viruses that we observe today. We also discuss the possible relatives of the proposed assemblage and the likely implications of future structural studies that may be carried out on the putative relatives. PMID:11855636

  1. The alpha aneurism: a structural motif revealed in an insertion mutant of staphylococcal nuclease.

    PubMed Central

    Keefe, L J; Sondek, J; Shortle, D; Lattman, E E

    1993-01-01

    The x-ray crystal structure of a mutant of staphylococcal nuclease that contains a single glycine residue inserted in the C-terminal alpha-helix has been solved to 1.67 A resolution and refined to a crystallographic R value of 0.170. This inserted glycine residue is accommodated in the alpha-helix by formation of a previously uncharacterized bulge, which we term the alpha aneurism. A conformational search of known protein structures has identified the alpha aneurism in a number of protein families, including the histocompatibility antigens and hemoglobins. Images Fig. 1 Fig. 2 Fig. 3 Fig. 5 Fig. 6 PMID:8475069

  2. The solely motif-doped Au36-xAgx(SPh-tBu)24 (x = 1-8) nanoclusters: X-ray crystal structure and optical properties.

    PubMed

    Fan, Jiqiang; Song, Yongbo; Chai, Jinsong; Yang, Sha; Chen, Tao; Rao, Bo; Yu, Haizhu; Zhu, Manzhou

    2016-08-18

    We report the observation of new doping behavior in Au36-xAgx(SR)24 nanoclusters (NCs) with x = 1 to 8. The atomic arrangements of Au and Ag atoms are determined by X-ray crystallography. The new gold-silver bimetallic NCs share the same framework as that of the homogold counterpart, i.e. possessing an fcc-type Au28 kernel, four dimeric AuAg(SR)3 staple motifs and twelve simple bridging SR ligands. Interestingly, all the Ag dopants in the Au36-xAgx(SR)24 NCs are selectively incorporated into the surface motifs, which is in contrast to the previously reported Au-Ag alloy structures with the Ag dopants preferentially displacing the core gold atoms. This distinct doping behavior implies that the previous assignments of an fcc Au28 core with four dimers and 12 bridging thiolates for Au36(SR)24 are more justified than other assignments of core vs. surface motifs. The UV-Vis adsorption spectrum of Au36-xAgx(SR)24 is almost the same as that of Au36(SR)24, indicating that the Ag dopants in the motifs do not change the optical properties. The similar UV-Vis spectra are further confirmed by TD-DFT calculations. DFT also reveals that the energies of the HOMO and LUMO of the motif-doped AuAg alloy NC are comparable to those of the homogold Au36 NC, indicating that the electronic structure is not disturbed by the motif Ag dopants. Overall, this study reveals a new silver-doping mode in alloy NCs. PMID:27503279

  3. Structural motif of polyglutamine amyloid fibrils discerned with mixed-isotope infrared spectroscopy.

    PubMed

    Buchanan, Lauren E; Carr, Joshua K; Fluitt, Aaron M; Hoganson, Andrew J; Moran, Sean D; de Pablo, Juan J; Skinner, James L; Zanni, Martin T

    2014-04-22

    Polyglutamine (polyQ) sequences are found in a variety of proteins, and mutational expansion of the polyQ tract is associated with many neurodegenerative diseases. We study the amyloid fibril structure and aggregation kinetics of K2Q24K2W, a model polyQ sequence. Two structures have been proposed for amyloid fibrils formed by polyQ peptides. By forming fibrils composed of both (12)C and (13)C monomers, made possible by protein expression in Escherichia coli, we can restrict vibrational delocalization to measure 2D IR spectra of individual monomers within the fibrils. The spectra are consistent with a β-turn structure in which each monomer forms an antiparallel hairpin and donates two strands to a single β-sheet. Calculated spectra from atomistic molecular-dynamics simulations of the two proposed structures confirm the assignment. No spectroscopically distinct intermediates are observed in rapid-scan 2D IR kinetics measurements, suggesting that aggregation is highly cooperative. Although 2D IR spectroscopy has advantages over linear techniques, the isotope-mixing strategy will also be useful with standard Fourier transform IR spectroscopy. PMID:24550484

  4. Structural motifs of 2-(2-fluoro-phenyl)-ethylamine conformers.

    PubMed

    Mayorkas, Nitzan; Sachs, Hanan; Schütz, Markus; Ishiuchi, Shun-ichi; Fujii, Masaaki; Dopfer, Otto; Bar, Ilana

    2016-01-14

    Vibronic and vibrational spectra of 2-(2-fluoro-phenyl)-ethylamine (2-FPEA) conformers were measured in a molecular beam by resonant two-photon ionization (R2PI), ultraviolet-ultraviolet hole burning (UV-UV HB) spectroscopy, and ionization-loss stimulated Raman spectroscopy (ILSRS). The measured ILSR spectral signatures in the survey spectra of the amino group region and in the broad spectral range revealed the presence of five different conformers, which were confirmed by the HB spectra. The determination of the structures of the conformers of 2-FPEA was assisted by quantum chemical calculations of the torsional potential energy surface and of the scaled harmonic Raman spectra. Comparison of the measured ILSR spectra with the calculated Raman spectra allowed us to identify one gauche structure with the ethylamino side chain folded toward the fluorine atom, two gauche structures with the ethylamino side chain folded to the opposite side and two anti conformers with extended tails. The effect of fluorination on the spectra and on the stability and structures of these species is discussed. PMID:26660487

  5. Laser Spectroscopic and Theoretical Studies of the Structures and Encapsulation Motifs of Functional Molecules

    SciTech Connect

    Ebata, Takayuki; Kusaka, Ryoji; Xantheas, Sotiris S.

    2015-02-01

    Extensive laser spectroscopic and theoretical studies have been recently carried out with the aim to reveal the structure and dynamics of encapsulation complexes in the gas phase. The characteristics of the encapsulation complexes are governed by the fact that (i) most of the host molecules are flexible and (ii) the complexes form high dimensional structures by using weak non-covalent interactions. These characteristics result in the possibility of the coexistence of many conformers in close energetic proximity. The combination of supersonic jet/laser spectroscopy and high level quantum chemical calculations is essential in tackling these challenging problems. In this report we describe our recent studies on the structures and dynamics of the encapsulation complexes formed by calix[4]arene (C4A), dibenzo-18-crown-6-ether (DB18C6), and benzo-18-crown-6-ether (B18C6) "hosts" interacting with N2, acetylene, water, and ammonia "guest" molecules. The gaseous host-guest complexes are generated under jet-cooled conditions. We apply various laser spectroscopic methods to obtain the conformer- and isomer-specified electronic and IR spectra. The experimental results are complemented with quantum chemical calculations ranging from density functional theory to high level first principles calculations at the MP2 and CCSD(T) levels of theory. We discuss the possible conformations of the bare host molecules, the structural changes they undergo upon complexation, and the key interactions that are responsible in stabilizing the specific complexes

  6. Laser spectroscopic and theoretical studies of the structures and encapsulation motifs of functional molecules

    SciTech Connect

    Ebata, Takayuki; Kusaka, Ryoji; Xantheas, Sotiris S.

    2015-01-22

    Extensive laser spectroscopic and theoretical studies have been recently carried out with the aim to reveal the structure and dynamics of encapsulation complexes in the gas phase. The characteristics of the encapsulation complexes are governed by the fact that (i) most of the host molecules are flexible and (ii) the complexes form high dimensional structures by using weak non-covalent interactions. These characteristics result in the possibility of the coexistence of many conformers in close energetic proximity. The combination of supersonic jet/laser spectroscopy and high level quantum chemical calculations is essential in tackling these challenging problems. In this report we describe our recent studies on the structures and dynamics of the encapsulation complexes formed by calix[4]arene (C4A), dibenzo-18-crown-6-ether (DB18C6), and benzo-18-crown-6-ether (B18C6) 'hosts' interacting with N{sub 2}, acetylene, water, and ammonia 'guest' molecules. The gaseous host-guest complexes are generated under jet-cooled conditions. We apply various laser spectroscopic methods to obtain the conformer- and isomer-specified electronic and IR spectra. The experimental results are complemented with quantum chemical calculations ranging from density functional theory to high level first principles calculations at the MP2 and CCSD(T) levels of theory. We discuss the possible conformations of the bare host molecules, the structural changes they undergo upon complexation, and the key interactions that are responsible in stabilizing the specific complexes.

  7. Crystal structure and MD simulation of mouse EndoV reveal wedge motif plasticity in this inosine-specific endonuclease

    PubMed Central

    Nawaz, Meh Sameen; Vik, Erik Sebastian; Ronander, Mia Elise; Solvoll, Anne Marthe; Blicher, Pernille; Bjørås, Magnar; Alseth, Ingrun; Dalhus, Bjørn

    2016-01-01

    Endonuclease V (EndoV) is an enzyme with specificity for deaminated adenosine (inosine) in nucleic acids. EndoV from Escherichia coli (EcEndoV) acts both on inosines in DNA and RNA, whereas the human homolog cleaves only at inosines in RNA. Inosines in DNA are mutagenic and the role of EndoV in DNA repair is well established. In contrast, the biological function of EndoV in RNA processing is largely unexplored. Here we have characterized a second mammalian EndoV homolog, mouse EndoV (mEndoV), and show that mEndoV shares the same RNA selectivity as human EndoV (hEndoV). Mouse EndoV cleaves the same inosine-containing substrates as hEndoV, but with reduced efficiencies. The crystal structure of mEndoV reveals a conformation different from the hEndoV and prokaryotic EndoV structures, particularly for the conserved tyrosine in the wedge motif, suggesting that this strand separating element has some flexibility. Molecular dynamics simulations of mouse and human EndoV reveal alternative conformations for the invariant tyrosine. The configuration of the active site, on the other hand, is very similar between the prokaryotic and mammalian versions of EndoV. PMID:27108838

  8. Crystal structure and MD simulation of mouse EndoV reveal wedge motif plasticity in this inosine-specific endonuclease.

    PubMed

    Nawaz, Meh Sameen; Vik, Erik Sebastian; Ronander, Mia Elise; Solvoll, Anne Marthe; Blicher, Pernille; Bjørås, Magnar; Alseth, Ingrun; Dalhus, Bjørn

    2016-01-01

    Endonuclease V (EndoV) is an enzyme with specificity for deaminated adenosine (inosine) in nucleic acids. EndoV from Escherichia coli (EcEndoV) acts both on inosines in DNA and RNA, whereas the human homolog cleaves only at inosines in RNA. Inosines in DNA are mutagenic and the role of EndoV in DNA repair is well established. In contrast, the biological function of EndoV in RNA processing is largely unexplored. Here we have characterized a second mammalian EndoV homolog, mouse EndoV (mEndoV), and show that mEndoV shares the same RNA selectivity as human EndoV (hEndoV). Mouse EndoV cleaves the same inosine-containing substrates as hEndoV, but with reduced efficiencies. The crystal structure of mEndoV reveals a conformation different from the hEndoV and prokaryotic EndoV structures, particularly for the conserved tyrosine in the wedge motif, suggesting that this strand separating element has some flexibility. Molecular dynamics simulations of mouse and human EndoV reveal alternative conformations for the invariant tyrosine. The configuration of the active site, on the other hand, is very similar between the prokaryotic and mammalian versions of EndoV. PMID:27108838

  9. Crystal structure and MD simulation of mouse EndoV reveal wedge motif plasticity in this inosine-specific endonuclease

    NASA Astrophysics Data System (ADS)

    Nawaz, Meh Sameen; Vik, Erik Sebastian; Ronander, Mia Elise; Solvoll, Anne Marthe; Blicher, Pernille; Bjørås, Magnar; Alseth, Ingrun; Dalhus, Bjørn

    2016-04-01

    Endonuclease V (EndoV) is an enzyme with specificity for deaminated adenosine (inosine) in nucleic acids. EndoV from Escherichia coli (EcEndoV) acts both on inosines in DNA and RNA, whereas the human homolog cleaves only at inosines in RNA. Inosines in DNA are mutagenic and the role of EndoV in DNA repair is well established. In contrast, the biological function of EndoV in RNA processing is largely unexplored. Here we have characterized a second mammalian EndoV homolog, mouse EndoV (mEndoV), and show that mEndoV shares the same RNA selectivity as human EndoV (hEndoV). Mouse EndoV cleaves the same inosine-containing substrates as hEndoV, but with reduced efficiencies. The crystal structure of mEndoV reveals a conformation different from the hEndoV and prokaryotic EndoV structures, particularly for the conserved tyrosine in the wedge motif, suggesting that this strand separating element has some flexibility. Molecular dynamics simulations of mouse and human EndoV reveal alternative conformations for the invariant tyrosine. The configuration of the active site, on the other hand, is very similar between the prokaryotic and mammalian versions of EndoV.

  10. R22(8) motifs in Aminopyrimidine sulfonate/carboxylate interactions: Crystal structures of pyrimethaminium benzenesulfonate monohydrate (2:2:1) and 2-amino-4,6-dimethylpyrimidinium sulfosalicylate dihydrate (4:2:2)

    PubMed Central

    Balasubramani, Kasthuri; Muthiah, Packianathan Thomas; Lynch, Daniel E

    2007-01-01

    Background Pyrimethamine [2,4-diamino-5-(p-chlorophenyl)-6-ethylpyrimidine] is an antifolate drug used in anti-malarial chemotherapy. Pyrimidine and aminopyrimidine derivatives are biologically important compounds owing to their natural occurrence as components of nucleic acids. Results In the crystal structures of two organic salts, namely pyrimethaminium benzenesulfonate monohydrate 1 and 2-amino-4, 6-dimethylpyrimidinium 3-carboxy-4-hydroxy benzenesulfonate dihydrate 2, pyrimethamine (PMN) and 2-amino-4,6-dimethylpyrimidine (AMPY) are protonated at one of the nitrogens in the pyrimidine rings. In both the PMN and AMPY sulfonate complexes, the protonated pyrimidine rings are hydrogen bonded to the sulfonate groups, forming a hydrogen-bonded bimolecular ring motif with graph-set notation R22(8). The sulfonate group mimics the carboxylate anion's mode of association, which is more commonly seen when binding with 2-aminopyrimidines. In compound 1, the PMN moieties are centrosymmetrically paired through a complementary DADA array of hydrogen bonds. In compound 2, two types of bimolecular cyclic hydrogen bonded R22(8) motifs (one involving the carboxylate group and the other involving sulfonate group) coexist. Furthermore, this compound is stabilized by intra and intermolecular O-H...O hydrogen bonds. Conclusion The crystal structures of pyrimethaminium benzenesulfonate monohydrate and 2-amino-4,6-dimethylpyrimidinium sulfosalicylate dihydrate have been investigated in detail. In compound 1, the R22(8) motif involving the sulfonate group is present. The role the sulfonic acid group plays in mimicking the carboxylate anions is thus evident. In compound 2, two types of bimolecular cyclic hydrogen bonded R22(8) motifs (one involving the carboxylate group and the other involving sulfonate group) coexist. In both the compounds base pairing also occurs. Thus homo and hetero synthons are present. PMID:17999751

  11. Conserved Intramolecular Interactions Maintain Myosin Interacting-Heads Motifs Explaining Tarantula Muscle Super-Relaxed State Structural Basis.

    PubMed

    Alamo, Lorenzo; Qi, Dan; Wriggers, Willy; Pinto, Antonio; Zhu, Jingui; Bilbao, Aivett; Gillilan, Richard E; Hu, Songnian; Padrón, Raúl

    2016-03-27

    Tarantula striated muscle is an outstanding system for understanding the molecular organization of myosin filaments. Three-dimensional reconstruction based on cryo-electron microscopy images and single-particle image processing revealed that, in a relaxed state, myosin molecules undergo intramolecular head-head interactions, explaining why head activity switches off. The filament model obtained by rigidly docking a chicken smooth muscle myosin structure to the reconstruction was improved by flexibly fitting an atomic model built by mixing structures from different species to a tilt-corrected 2-nm three-dimensional map of frozen-hydrated tarantula thick filament. We used heavy and light chain sequences from tarantula myosin to build a single-species homology model of two heavy meromyosin interacting-heads motifs (IHMs). The flexibly fitted model includes previously missing loops and shows five intramolecular and five intermolecular interactions that keep the IHM in a compact off structure, forming four helical tracks of IHMs around the backbone. The residues involved in these interactions are oppositely charged, and their sequence conservation suggests that IHM is present across animal species. The new model, PDB 3JBH, explains the structural origin of the ATP turnover rates detected in relaxed tarantula muscle by ascribing the very slow rate to docked unphosphorylated heads, the slow rate to phosphorylated docked heads, and the fast rate to phosphorylated undocked heads. The conservation of intramolecular interactions across animal species and the presence of IHM in bilaterians suggest that a super-relaxed state should be maintained, as it plays a role in saving ATP in skeletal, cardiac, and smooth muscles. PMID:26851071

  12. Unusual conformation of the SxN motif in the crystal structure of penicillin-binding protein A from Mycobacterium tuberculosis.

    SciTech Connect

    Fedarovich, Alena; Nicholas, Robert A.; Davies, Christopher

    2010-07-19

    PBPA from Mycobacterium tuberculosis is a class B-like penicillin-binding protein (PBP) that is not essential for cell growth in M. tuberculosis, but is important for proper cell division in Mycobacterium smegmatis. We have determined the crystal structure of PBPA at 2.05 {angstrom} resolution, the first published structure of a PBP from this important pathogen. Compared to other PBPs, PBPA has a relatively small N-terminal domain, and conservation of a cluster of charged residues within this domain suggests that PBPA is more related to class B PBPs than previously inferred from sequence analysis. The C-terminal domain is a typical transpeptidase fold and contains the three conserved active-site motifs characterisitic of penicillin-interacting enzymes. While the arrangement of the SxxK and KTG motifs is similar to that observed in other PBPs, the SxN motif is markedly displaced away from the active site, such that its serine (Ser281) is not involved in hydrogen bonding with residues of the other two motifs. A disulfide bridge between Cys282 (the 'x' of the SxN motif) and Cys266, which resides on an adjacent loop, may be responsible for this unusual conformation. Another interesting feature of the structure is a relatively long connection between {beta}5 and {alpha}11, which restricts the space available in the active site of PBPA and suggests that conformational changes would be required to accommodate peptide substrate or {beta}-lactam antibiotics during acylation. Finally, the structure shows that one of the two threonines postulated to be targets for phosphorylation is inaccessible (Thr362), whereas the other (Thr437) is well placed on a surface loop near the active site.

  13. Structures and Encapsulation Motifs of Functional Molecules probed by Laser Spectroscopic and Theoretical methods

    SciTech Connect

    Kusaka, Ryoji; Inokuchi, Yoshiya; Xantheas, Sotiris S.; Ebata, Takayuki

    2010-04-01

    We report laser spectroscopic studies of host/guest hydration interactions between functional molecules (hosts) and water (guest) in supersonic jets. The examined hosts include dibenzo-18-crown-6-ether (DB18C6), benzo-18-crown-6-ether (B18C6) and calix[4]arene (C4A). The gaseous complexes between the functional molecular hosts and water are generated under jet-cooled conditions. Various laser spectroscopic methods are applied for these species: the electronic spectra are observed by laser-induced fluorescence (LIF) , massselected resonance enhanced multiphoton ionization (REMPI) and ultraviolet-ultraviolet holeburning (UV-UV HB) spectroscopy, whereas the vibrational spectra for each individual species are observed by infrared-ultraviolet double resonance (IR-UV DR) spectroscopy. The obained results are analyzed by first principles electronic structure calculations. We discuss the conformations of the host molecules, the various structures of the complexes and the key interactions that result in the complexation as well as the effect of the host conformation in the resulting complexation mechanism.

  14. Structure of GrlR and the Implication of its EDED Motif in Mediating the Regulation of Type III Secretion System in EHEC

    SciTech Connect

    Jobichen,C.; Li, M.; Yerushalmi, G.; Tan, Y.; Mok, Y.; Rosenshine, I.; Leung, K.; Sivaraman, J.

    2007-01-01

    Enterohemorrhagic Escherichia coli (EHEC) is a common cause of severe hemorrhagic colitis. EHEC's virulence is dependent upon a type III secretion system (TTSS) encoded by 41 genes. These genes are organized in several operons clustered in the locus of enterocyte effacement. Most of the locus of enterocyte effacement genes, including grlA and grlR, are positively regulated by Ler, and Ler expression is positively and negatively modulated by GrlA and GrlR, respectively. However, the molecular basis for the GrlA and GrlR activity is still elusive. We have determined the crystal structure of GrlR at 1.9 Angstroms resolution. It consists of a typical {beta}-barrel fold with eight {beta}-strands containing an internal hydrophobic cavity and a plug-like loop on one side of the barrel. Strong hydrophobic interactions between the two {beta}-barrels maintain the dimeric architecture of GrlR. Furthermore, a unique surface-exposed EDED (Glu-Asp-Glu-Asp) motif is identified to be critical for GrlA-GrlR interaction and for the repressive activity of GrlR. This study contributes a novel molecular insight into the mechanism of GrlR function.

  15. Interaction of Individual Structural Domains of hnRNP LL with the BCL2 Promoter i-Motif DNA.

    PubMed

    Roy, Basab; Talukder, Poulami; Kang, Hyun-Jin; Tsuen, Shujian S; Alam, Mohammad P; Hurley, Laurence H; Hecht, Sidney M

    2016-08-31

    The recently discovered role of the BCL2 (B-cell lymphoma 2 gene) promoter i-motif DNA in modulation of gene expression via interaction with the ribonucleoprotein hnRNP L-like (hnRNP LL) has prompted a more detailed study of the nature of this protein-DNA interaction. The RNA recognition motifs (RRMs) of hnRNP LL were expressed individually, and both RRM1 and RRM2 were found to bind efficiently to the BCL2 i-motif DNA, as well as being critical for transcriptional activation, whereas RRM3-4 bound only weakly to this DNA. Binding was followed by unfolding of the DNA as monitored by changes in the CD spectrum. Mutational analysis of the i-motif DNA revealed that binding involved primarily the lateral loops of the i-motif. The kinetics of binding of the DNA with RRM1 was explored by recording CD spectra at predetermined times following admixture of the protein and DNA. The change in molar ellipticity was readily apparent after 30 s and largely complete within 1 min. A more detailed view of protein-DNA interaction was obtained by introducing the fluorescence donor 6-CNTrp in RRM1 at position 137, and the acceptor 4-aminobenzo[g]quinazoline-2-one (Cf) in lieu of cytidine22 in the i-motif DNA. The course of binding of the two species was monitored by FRET, which reflected a steady increase in energy transfer over a period of several minutes. The FRET signal could be diminished by the further addition of (unlabeled) RRM2, no doubt reflecting competition for binding to the i-motif DNA. These experiments using the individual RRM domains from hnRNP LL confirm the role of this transcription factor in activation of BCL2 transcription via the i-motif in the promoter element. PMID:27483029

  16. The laminar structure of the common opossum masseter (Didelphis marsupialis).

    PubMed

    Deguchi, T; Takemura, A; Suwa, F

    2001-03-01

    Using three heads of the common opossum (Didelphis marsupialis), which may be considered to have a primitive mammalian form and therefore be appropriate for this study, the laminar structure of the masseter was investigated. We also attempted a comparative anatomical study of the relationships of food habits to the laminar structures of the masseter, zygomatic arch and mandibular ramus. In the common opossum masseter, a total of six layers, the primary and secondary sublayers of the superficial layer, the intermediate layer, and the primary, secondary and third sublayers of the deep layer as a proper masseter, were observed. These layers showed a typical reverse laminar structure, with the layers of tendons and muscles alternating. The maxillomandibularis and zygomaticomandibularis muscles were observed in one layer each, as an improper masseter. The laminar structure of the common opossum masseter was shown to be more similar to that of carnivorous placental animals than that of the herbivorous red kangaroo, a similar marsupial. In regard to the number of layers in the laminar structure of the masseter, the results of both this study and those of our predecessors' showed that differences in food habits affect the deep layer in the proper masseter of marsupials and placental mammals, and that of the maxillomandibularis muscle of placental mammals in the improper masseter. PMID:11392012

  17. Discovery of potent HIV-1 non-nucleoside reverse transcriptase inhibitors from arylthioacetanilide structural motif.

    PubMed

    Li, Wenxin; Li, Xiao; De Clercq, Erik; Zhan, Peng; Liu, Xinyong

    2015-09-18

    The poor pharmacokinetics, side effects and particularly the rapid emergence of drug resistance compromise the efficiency of the clinically used anti-HIV drugs. Therefore, the discovery of novel and effective NNRTIs is still an extremely primary mission. Arylthioacetanilide family is one of the highly active HIV-1 NNRTIs against wide-type (WT) HIV-1 and a wide range of drug-resistant mutant strains. Especially, VRX-480773 and RDEA806 have been chosen as candidates for further clinical studies. In this article, we review the discovery and development of the arylthioacetanilides, and, especially, pay much attention to the structural modifications, SARs conclusions and molecular modeling. Moreover, several medicinal chemistry strategies to overcome drug resistance involved in the optimization process of arylthioacetanilides are highlighted, providing valuable clues for further investigations. PMID:26276432

  18. Uncommon structural motifs dominate the antigen binding site in human autoantibodies reactive with basement membrane collagen.

    PubMed

    Foster, Mary H; Buckley, Elizabeth S; Chen, Benny J; Hwang, Kwan-Ki; Clark, Amy G

    2016-08-01

    Autoantibodies mediate organ destruction in multiple autoimmune diseases, yet their origins in patients remain poorly understood. To probe the genetic origins and structure of disease-associated autoantibodies, we engrafted immunodeficient mice with human CD34+ hematopoietic stem cells and immunized with the non-collagenous-1 (NC1) domain of the alpha3 chain of type IV collagen. This antigen is expressed in lungs and kidneys and is targeted by autoantibodies in anti-glomerular basement membrane (GBM) nephritis and Goodpasture syndrome (GPS), prototypic human organ-specific autoimmune diseases. Using Epstein Barr virus transformation and cell fusion, six human anti-alpha3(IV)NC1 collagen monoclonal autoantibodies (mAb) were recovered, including subsets reactive with human kidney and with epitopes recognized by patients' IgG. Sequence analysis reveals a long to exceptionally long heavy chain complementarity determining region3 (HCDR3), the major site of antigen binding, in all six mAb. Mean HCDR3 length is 25.5 amino acids (range 20-36), generated from inherently long DH and JH genes and extended regions of non-templated N-nucleotides. Long HCDR3 are suited to forming noncontiguous antigen contacts and to binding recessed, immunologically silent epitopes hidden from conventional antibodies, as seen with self-antigen crossreactive broadly neutralizing anti-HIV Ig (bnAb). The anti-alpha3(IV)NC1 collagen mAb also show preferential use of unmutated variable region genes that are enriched among human chronic lymphocytic leukemia antibodies that share features with natural polyreactive Ig. Our findings suggest unexpected relationships between pathogenic anti-collagen Ig, bnAb, and autoreactive Ig associated with malignancy, all of which arise from B cells expressing unconventional structural elements that may require transient escape from tolerance for successful expansion. PMID:27450516

  19. Structure of a Bud6/Actin Complex Reveals a Novel WH2-like Actin Monomer Recruitment Motif.

    PubMed

    Park, Eunyoung; Graziano, Brian R; Zheng, Wei; Garabedian, Mikael; Goode, Bruce L; Eck, Michael J

    2015-08-01

    In budding yeast, the actin-binding protein Bud6 cooperates with formins Bni1 and Bnr1 to catalyze the assembly of actin filaments. The nucleation-enhancing activity of Bud6 requires both a "core" domain that binds to the formin and a "flank" domain that binds monomeric actin. Here, we describe the structure of the Bud6 flank domain in complex with actin. Two helices in Bud6(flank) interact with actin; one binds in a groove at the barbed end of the actin monomer in a manner closely resembling the helix of WH2 domains, a motif found in many actin nucleation factors. The second helix rises along the face of actin. Mutational analysis verifies the importance of these Bud6-actin contacts for nucleation-enhancing activity. The Bud6 binding site on actin overlaps with that of the formin FH2 domain and is also incompatible with inter-subunit contacts in F-actin, suggesting that Bud6 interacts only transiently with actin monomers during filament nucleation. PMID:26118535

  20. Modular motif, structural folds and affinity profiles of the PEVK segment of human fetal skeletal muscle titin.

    PubMed

    Gutierrez-Cruz, G; Van Heerden, A H; Wang, K

    2001-03-01

    The extension of the PEVK segment of the giant elastic protein titin is a key event in the elastic response of striated muscle to passive stretch. PEVK behaves mechanically as an entropic spring and is thought to be a random coil. cDNA sequencing of human fetal skeletal PEVK reveals a modular motif with tandem repeats of modules averaging 28 residues and with superrepeats of seven modules. Conformational studies of bacterially expressed 53-kDa fragment (TP1) by circular dichroism suggest that this soluble protein contains substantial polyproline II (PPII) type left-handed helices. Urea and thermal titrations cause gradual and reversible decrease in PPII content. The absence of sharp melting in urea and thermal titrations suggests that there is no long range cooperativity among the PPII helices. Studies with solid phase and surface plasmon resonance assays indicate that TP1 interacts with actin and some but not all cloned nebulin fragments with high affinity. Interestingly, Ca(2+)/calmodulin and Ca(2+)/S100 abolish nebulin/PEVK interaction. We suggest that in aqueous solution, PEVK is an open and flexible chain of relatively stable structural folds of the polyproline II type. PEVK region of titin may be involved in interfilament association with thin filaments in a calcium/calmodulin-sensitive manner. This adhesion may modulate titin extensibility and elasticity. PMID:11084039

  1. Cross-reactivity between the rheumatoid arthritis-associated motif EQKRAA and structurally related sequences found in Proteus mirabilis.

    PubMed

    Tiwana, H; Wilson, C; Alvarez, A; Abuknesha, R; Bansal, S; Ebringer, A

    1999-06-01

    Cross-reactivity or molecular mimicry may be one of the underlying mechanisms involved in the etiopathogenesis of rheumatoid arthritis (RA). Antiserum against the RA susceptibility sequence EQKRAA was shown to bind to a similar peptide ESRRAL present in the hemolysin of the gram-negative bacterium Proteus mirabilis, and an anti-ESRRAL serum reacted with EQKRAA. There was no reactivity with either anti-EQKRAA or anti-ESRRAL to a peptide containing the EDERAA sequence which is present in HLA-DRB1*0402, an allele not associated with RA. Furthermore, the EQKRAA and ESRRAL antisera bound to a mouse fibroblast transfectant cell line (Dap.3) expressing HLA-DRB1*0401 but not to DRB1*0402. However, peptide sequences structurally related to the RA susceptibility motif LEIEKDFTTYGEE (P. mirabilis urease), VEIRAEGNRFTY (collagen type II) and DELSPETSPYVKE (collagen type XI) did not bind significantly to cell lines expressing HLA-DRB1*0401 or HLA-DRB1*0402 compared to the control peptide YASGASGASGAS. It is suggested here that molecular mimicry between HLA alleles associated with RA and P. mirabilis may be relevant in the etiopathogenesis of the disease. PMID:10338479

  2. Motif for controllable toggle switch in gene regulatory networks

    NASA Astrophysics Data System (ADS)

    Zhao, Chen; Bin, Ao; Ye, Weiming; Fan, Ying; Di, Zengru

    2015-02-01

    Toggle switch as a common phenomenon in gene regulatory networks has been recognized important for biological functions. Despite much effort dedicated to understanding the toggle switch and designing synthetic biology circuit to achieve the biological function, we still lack a comprehensive understanding of the intrinsic dynamics behind such phenomenon and the minimum structure that is imperative for producing toggle switch. In this paper, we discover a minimum structure, a motif that enables a controllable toggle switch. In particular, the motif consists of a transformative double negative feedback loop (DNFL) that is regulated by an additional driver node. By enumerating all possible regulatory configurations from the driver node, we identify two types of motifs associated with the toggle switch that is captured by the existence of bistable states. The toggle switch is controllable in the sense that the gap between the bistable states is adjustable as determined by the regulatory strength from the driver nodes. We test the effect of the motifs in self-oscillating gene regulatory network (SON) with respect to the interplay between the motifs and the other genes, and find that the switching dynamics of the whole network can be successfully controlled insofar as the network contains a single motif. Our findings are important to uncover the underlying nonlinear dynamics of controllable toggle switch and can have implications in devising biology circuit in the field of synthetic biology.

  3. Transcription factor and microRNA-regulated network motifs for cancer and signal transduction networks

    PubMed Central

    2015-01-01

    Abstract Background Molecular networks are the basis of biological processes. Such networks can be decomposed into smaller modules, also known as network motifs. These motifs show interesting dynamical behaviors, in which co-operativity effects between the motif components play a critical role in human diseases. We have developed a motif-searching algorithm, which is able to identify common motif types from the cancer networks and signal transduction networks (STNs). Some of the network motifs are interconnected which can be merged together and form more complex structures, the so-called coupled motif structures (CMS). These structures exhibit mixed dynamical behavior, which may lead biological organisms to perform specific functions. Results In this study, we integrate transcription factors (TFs), microRNAs (miRNAs), miRNA targets and network motifs information to build the cancer-related TF-miRNA-motif networks (TMMN). This allows us to examine the role of network motifs in cancer formation at different levels of regulation, i.e. transcription initiation (TF → miRNA), gene-gene interaction (CMS), and post-transcriptional regulation (miRNA → target genes). Among the cancer networks and STNs we considered, it is found that there is a substantial amount of crosstalking through motif interconnections, in particular, the crosstalk between prostate cancer network and PI3K-Akt STN. Conclusions To validate the role of network motifs in cancer formation, several examples are presented which demonstrated the effectiveness of the present approach. A web-based platform has been set up which can be accessed at: http://ppi.bioinfo.asia.edu.tw/pathway/. It is very likely that our results can supply very specific CMS missing information for certain cancer types, it is an indispensable tool for cancer biology research. PMID:25707690

  4. Streptococcus salivarius Fimbriae Are Composed of a Glycoprotein Containing a Repeated Motif Assembled into a Filamentous Nondissociable Structure

    PubMed Central

    Lévesque, Céline; Vadeboncoeur, Christian; Chandad, Fatiha; Frenette, Michel

    2001-01-01

    Streptococcus salivarius, a gram-positive bacterium found in the human oral cavity, expresses flexible peritrichous fimbriae. In this paper, we report purification and partial characterization of S. salivarius fimbriae. Fimbriae were extracted by shearing the cell surface of hyperfimbriated mutant A37 (a spontaneous mutant of S. salivarius ATCC 25975) with glass beads. Preliminary experiments showed that S. salivarius fimbriae did not dissociate when they were incubated at 100°C in the presence of sodium dodecyl sulfate. This characteristic was used to separate them from other cell surface components by successive gel filtration chromatography procedures. Fimbriae with molecular masses ranging from 20 × 106 to 40 × 106 Da were purified. Examination of purified fimbriae by electron microscopy revealed the presence of filamentous structures up to 1 μm long and 3 to 4 nm in diameter. Biochemical studies of purified fimbriae and an amino acid sequence analysis of a fimbrial internal peptide revealed that S. salivarius fimbriae were composed of a glycoprotein assembled into a filamentous structure resistant to dissociation. The internal amino acid sequence was composed of a repeated motif of two amino acids alternating with two modified residues: A/X/T-E-Q-M/φ, where X represents a modified amino acid residue and φ represents a blank cycle. Immunolocalization experiments also revealed that the fimbriae were associated with a wheat germ agglutinin-reactive carbohydrate. Immunolabeling experiments with antifimbria polyclonal antibodies showed that antigenically related fimbria-like structures were expressed in two other human oral streptococcal species, Streptococcus mitis and Streptococcus constellatus. PMID:11292790

  5. Structural Analysis of a Repetitive Protein Sequence Motif in Strepsirrhine Primate Amelogenin

    PubMed Central

    Bromley, Keith M.; Hacia, Joseph G.; Bromage, Timothy G.; Snead, Malcolm L.; Moradian-Oldak, Janet; Paine, Michael L.

    2011-01-01

    Strepsirrhines are members of a primate suborder that has a distinctive set of features associated with the development of the dentition. Amelogenin (AMEL), the better known of the enamel matrix proteins, forms 90% of the secreted organic matrix during amelogenesis. Although AMEL has been sequenced in numerous mammalian lineages, the only reported strepsirrhine AMEL sequences are those of the ring-tailed lemur and galago, which contain a set of additional proline-rich tandem repeats absent in all other primates species analyzed to date, but present in some non-primate mammals. Here, we first determined that these repeats are present in AMEL from three additional lemur species and thus are likely to be widespread throughout this group. To evaluate the functional relevance of these repeats in strepsirrhines, we engineered a mutated murine amelogenin sequence containing a similar proline-rich sequence to that of Lemur catta. In the monomeric form, the MQP insertions had no influence on the secondary structure or refolding properties, whereas in the assembled form, the insertions increased the hydrodynamic radii. We speculate that increased AMEL nanosphere size may influence enamel formation in strepsirrhine primates. PMID:21437261

  6. First N-Heterocyclic Carbenes Relying on the Triazolone Structural Motif: Syntheses, Modifications and Reactivity.

    PubMed

    Jonek, Markus; Diekmann, Janina; Ganter, Christian

    2015-10-26

    4-Phenylsemicarbazide and 1,5-diphenylcarbazide are suitable starting materials for the syntheses of N-heterocyclic carbene (NHC) compounds with new backbone structures. In the first case, cyclisation and subsequent methylation leads to a cationic precursor whose deprotonation affords the triazolon-ylidene 2, which was converted to the corresponding sulfur and selenium adducts and a range of metal complexes. In contrast, cyclisation of diphenylcarbazide affords a neutral betain-type NHC-precursor 7, which is not in equilibrium with its carbene tautomer 7a. Precursor 7 can either be deprotonated to give the anionic NHC 8 or methylated at the N or O atom of the backbone resulting in two isomeric cationic species 16 and 20. Deprotonation of the latter two provides neutral NHC compounds with a carboxamide or carboximidate backbone, respectively. The ligand properties of the new NHC compounds were evaluated by IR and (77) Se NMR spectroscopy. Tolman electronic parameter (TEP) values range from 2050 to 2063 cm(-1) with the anionic NHC 8 being the best overall donor. PMID:26395132

  7. Structural analysis of a repetitive protein sequence motif in strepsirrhine primate amelogenin.

    PubMed

    Lacruz, Rodrigo S; Lakshminarayanan, Rajamani; Bromley, Keith M; Hacia, Joseph G; Bromage, Timothy G; Snead, Malcolm L; Moradian-Oldak, Janet; Paine, Michael L

    2011-01-01

    Strepsirrhines are members of a primate suborder that has a distinctive set of features associated with the development of the dentition. Amelogenin (AMEL), the better known of the enamel matrix proteins, forms 90% of the secreted organic matrix during amelogenesis. Although AMEL has been sequenced in numerous mammalian lineages, the only reported strepsirrhine AMEL sequences are those of the ring-tailed lemur and galago, which contain a set of additional proline-rich tandem repeats absent in all other primates species analyzed to date, but present in some non-primate mammals. Here, we first determined that these repeats are present in AMEL from three additional lemur species and thus are likely to be widespread throughout this group. To evaluate the functional relevance of these repeats in strepsirrhines, we engineered a mutated murine amelogenin sequence containing a similar proline-rich sequence to that of Lemur catta. In the monomeric form, the MQP insertions had no influence on the secondary structure or refolding properties, whereas in the assembled form, the insertions increased the hydrodynamic radii. We speculate that increased AMEL nanosphere size may influence enamel formation in strepsirrhine primates. PMID:21437261

  8. Structure of a CGI-58 motif provides the molecular basis of lipid droplet anchoring.

    PubMed

    Boeszoermenyi, Andras; Nagy, Harald Manuel; Arthanari, Haribabu; Pillip, Christoph Jens; Lindermuth, Hanna; Luna, Rafael Eulogio; Wagner, Gerhard; Zechner, Rudolf; Zangger, Klaus; Oberer, Monika

    2015-10-30

    Triacylglycerols (TGs) stored in lipid droplets (LDs) are hydrolyzed in a highly regulated metabolic process called lipolysis to free fatty acids that serve as energy substrates for β-oxidation, precursors for membrane lipids and signaling molecules. Comparative gene identification-58 (CGI-58) stimulates the enzymatic activity of adipose triglyceride lipase (ATGL), which catalyzes the hydrolysis of TGs to diacylglycerols and free fatty acids. In adipose tissue, protein-protein interactions between CGI-58 and the LD coating protein perilipin 1 restrain the ability of CGI-58 to activate ATGL under basal conditions. Phosphorylation of perilipin 1 disrupts these interactions and mobilizes CGI-58 for the activation of ATGL. We have previously demonstrated that the removal of a peptide at the N terminus (residues 10-31) of CGI-58 abrogates CGI-58 localization to LDs and CGI-58-mediated activation of ATGL. Here, we show that this tryptophan-rich N-terminal peptide serves as an independent LD anchor, with its three tryptophans serving as focal points of the left (harboring Trp(21) and Trp(25)) and right (harboring Trp(29)) anchor arms. The solution state NMR structure of a peptide comprising the LD anchor bound to dodecylphosphocholine micelles as LD mimic reveals that the left arm forms a concise hydrophobic core comprising tryptophans Trp(21) and Trp(25) and two adjacent leucines. Trp(29) serves as the core of a functionally independent anchor arm. Consequently, simultaneous tryptophan alanine permutations in both arms abolish localization and activity of CGI-58 as opposed to tryptophan substitutions that occur in only one arm. PMID:26350461

  9. Structure of a CGI-58 Motif Provides the Molecular Basis of Lipid Droplet Anchoring*

    PubMed Central

    Boeszoermenyi, Andras; Nagy, Harald Manuel; Arthanari, Haribabu; Pillip, Christoph Jens; Lindermuth, Hanna; Luna, Rafael Eulogio; Wagner, Gerhard; Zechner, Rudolf; Zangger, Klaus; Oberer, Monika

    2015-01-01

    Triacylglycerols (TGs) stored in lipid droplets (LDs) are hydrolyzed in a highly regulated metabolic process called lipolysis to free fatty acids that serve as energy substrates for β-oxidation, precursors for membrane lipids and signaling molecules. Comparative gene identification-58 (CGI-58) stimulates the enzymatic activity of adipose triglyceride lipase (ATGL), which catalyzes the hydrolysis of TGs to diacylglycerols and free fatty acids. In adipose tissue, protein-protein interactions between CGI-58 and the LD coating protein perilipin 1 restrain the ability of CGI-58 to activate ATGL under basal conditions. Phosphorylation of perilipin 1 disrupts these interactions and mobilizes CGI-58 for the activation of ATGL. We have previously demonstrated that the removal of a peptide at the N terminus (residues 10–31) of CGI-58 abrogates CGI-58 localization to LDs and CGI-58-mediated activation of ATGL. Here, we show that this tryptophan-rich N-terminal peptide serves as an independent LD anchor, with its three tryptophans serving as focal points of the left (harboring Trp21 and Trp25) and right (harboring Trp29) anchor arms. The solution state NMR structure of a peptide comprising the LD anchor bound to dodecylphosphocholine micelles as LD mimic reveals that the left arm forms a concise hydrophobic core comprising tryptophans Trp21 and Trp25 and two adjacent leucines. Trp29 serves as the core of a functionally independent anchor arm. Consequently, simultaneous tryptophan alanine permutations in both arms abolish localization and activity of CGI-58 as opposed to tryptophan substitutions that occur in only one arm. PMID:26350461

  10. The formation and characteristics of the i-motif structure within the promoter of the c-myb proto-oncogene.

    PubMed

    Li, Huihui; Hai, Jinhui; Zhou, Jiang; Yuan, Gu

    2016-09-01

    C-myb proto-oncogene is a potential therapeutic target for some human solid tumors and leukemias. A long cytosine-rich sequence, which locates the downstream of the transcription initiation site, is demonstrated to fold into an intramolecular i-motif DNA using electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy. Effects of factors, including the pH value, the number of C:C(+) dimers, the concentration of buffer, the molecular crowding condition, and the coexistence of the complementary DNA, on the formation and the structural stability of the i-motif DNA are systematically studied. We have demonstrated that the i-motif folding in the c-myb promoter could be accelerated upon synergistic physiological stimuli including intracellular molecular crowding and low pH values, as well as the large number of the i-motif C:C(+) dimers. Meanwhile, various inputs, such as acids/bases and metal ions, have exhibited their abilities in controlling the conformational switch of the c-myb GC-rich DNA. Acidic pH values and the presence of K(+) ions can induce the dissociation of the double helix. Our present strategy can greatly extend the potential usages of i-motif DNA molecules with specific sequences as conformational switch-controlled devices. Moreover, this work demonstrates the superiority of CD spectroscopy associated with ESI-MS as a rapid, more cost-effective and sensitive structural change responsive method in the research of DNA conformational switching. PMID:27487467

  11. The Annotation of RNA Motifs

    PubMed Central

    2002-01-01

    The recent deluge of new RNA structures, including complete atomic-resolution views of both subunits of the ribosome, has on the one hand literally overwhelmed our individual abilities to comprehend the diversity of RNA structure, and on the other hand presented us with new opportunities for comprehensive use of RNA sequences for comparative genetic, evolutionary and phylogenetic studies. Two concepts are key to understanding RNA structure: hierarchical organization of global structure and isostericity of local interactions. Global structure changes extremely slowly, as it relies on conserved long-range tertiary interactions. Tertiary RNA–RNA and quaternary RNA–protein interactions are mediated by RNA motifs, defined as recurrent and ordered arrays of non-Watson–Crick base-pairs. A single RNA motif comprises a family of sequences, all of which can fold into the same three-dimensional structure and can mediate the same interaction(s). The chemistry and geometry of base pairing constrain the evolution of motifs in such a way that random mutations that occur within motifs are accepted or rejected insofar as they can mediate a similar ordered array of interactions. The steps involved in the analysis and annotation of RNA motifs in 3D structures are: (a) decomposition of each motif into non-Watson–Crick base-pairs; (b) geometric classification of each basepair; (c) identification of isosteric substitutions for each basepair by comparison to isostericity matrices; (d) alignment of homologous sequences using the isostericity matrices to identify corresponding positions in the crystal structure; (e) acceptance or rejection of the null hypothesis that the motif is conserved. PMID:18629252

  12. Synthesis of the Tetrasaccharide Motif and Its Structural Analog Corresponding to the Lipopolysaccharide of Escherichia coli O75

    PubMed Central

    Sau, Abhijit; Misra, Anup Kumar

    2012-01-01

    Background Extraintestinal pathogenic E. coli are mostly responsible for a diverse spectrum of invasive human and animal infections leading to the urinary tract infections. Bacterial lipopolysaccharides are responsible for their pathogenicity and their interactions with host immune responses. In spite of several breakthroughs in the development of therapeutics to combat urinary tract infections and related diseases, the emergence of multidrug-resistant bacterial strains is a serious concern. Lipopolysaccharides are attractive targets for the development of long-term therapeutic agents to eradicate the infections. Since the natural sources cannot provide the required amount of oligosaccharides, development of chemical synthetic strategies for their synthesis is relevant to gain access to a reservoir of oligosaccharides and their close analogs. Methodology Two tetrasaccharide derivatives were synthesized from a single disaccharide intermediate. β-d-mannoside moiety was prepared from β-d-glucoside moiety following oxidation–reduction methodology. A [2+2] stereoselective block glycosylation strategy has been adopted for the preparation of tetrasaccharide derivative. α-d-Glucosamine moiety was prepared from α-d-mannosidic moiety following triflate formation at C-2 and SN2 substitution. A one-pot iterative glycosylation exploiting the orthogonal property of thioglycoside was carried out during the synthesis of tetrasaccharide analog. Results Synthesis of the tetrasaccharide motif (1) and its structural analog (2) corresponding to the lipopolysaccharide of Escherichia coli O75 was successfully achieved in excellent yield. Most of the reactions are clean and high yielding. Both compounds 1 and 2 were synthesized as their 4-methoxyphenyl glycoside, which can act as a temporary anomeric protecting group for further use of these tetrasaccharides in the preparation of glycoconjugates. PMID:22662142

  13. Comparing Class A GPCRs to bitter taste receptors: Structural motifs, ligand interactions and agonist-to-antagonist ratios.

    PubMed

    Di Pizio, Antonella; Levit, Anat; Slutzki, Michal; Behrens, Maik; Karaman, Rafik; Niv, Masha Y

    2016-01-01

    G protein-coupled receptors (GPCRs) are seven transmembrane (TM) proteins that play a key role in human physiology. The GPCR superfamily comprises about 800 members, classified into several classes, with rhodopsin-like Class A being the largest and most studied thus far. A huge component of the human repertoire consists of the chemosensory GPCRs, including ∼400 odorant receptors, 25 bitter taste receptors (TAS2Rs), which are thought to guard the organism from consuming poisons, and sweet and umami TAS1R heteromers, which indicate the nutritive value of food. The location of the binding site of TAS2Rs is similar to that of Class A GPCRs. However, most of the known bitter ligands are agonists, with only a few antagonists documented thus far. The agonist-to-antagonist ratios of Class A GPCRs vary, but in general are much lower than for TAS2Rs. For a set of well-studied GPCRs, a gradual change in agonists-to-antagonists ratios is observed when comparing low (10 μM)- and high (10 nM)-affinity ligand sets from ChEMBL and the DrugBank set of drugs. This shift reflects pharmaceutical bias toward the therapeutically desirable pharmacology for each of these GPCRs, while the 10 μM sets possibly represent the native tendency of the receptors toward either agonists or antagonists. Analyzing ligand-GPCR interactions in 56 X-ray structures representative of currently available structural data, we find that the N-terminus, TM1 and TM2 are more involved in binding of antagonists than of agonists. On the other hand, ECL2 tends to be more involved in binding of agonists. This is of interest, since TAS2Rs harbor variations on the typical Class A sequence motifs, including the absence of the ECL2-TM3 disulfide bridge. This suggests an alternative mode of regulation of conformational states for TAS2Rs, with potentially less stabilized inactive state. The comparison of TAS2Rs and Class A GPCRs structural features and the pharmacology of the their ligands highlights the intricacies of

  14. Syntax at Hand: Common Syntactic Structures for Actions and Language

    PubMed Central

    Roy, Alice C.; Curie, Aurore; Nazir, Tatjana; Paulignan, Yves; des Portes, Vincent; Fourneret, Pierre; Deprez, Viviane

    2013-01-01

    Evidence that the motor and the linguistic systems share common syntactic representations would open new perspectives on language evolution. Here, crossing disciplinary boundaries, we explore potential parallels between the structure of simple actions and that of sentences. First, examining Typically Developing (TD) children displacing a bottle with or without knowledge of its weight prior to movement onset, we provide kinematic evidence that the sub-phases of this displacing action (reaching + moving the bottle) manifest a structure akin to linguistic embedded dependencies. Then, using the same motor task, we reveal that children suffering from specific language impairment (SLI), whose core deficit affects syntactic embedding and dependencies, manifest specific structural motor anomalies parallel to their linguistic deficits. In contrast to TD children, SLI children performed the displacing-action as if its sub-phases were juxtaposed rather than embedded. The specificity of SLI’s structural motor deficit was confirmed by testing an additional control group: Fragile-X Syndrome patients, whose language capacity, though delayed, comparatively spares embedded dependencies, displayed slower but structurally normal motor performances. By identifying the presence of structural representations and dependency computations in the motor system and by showing their selective deficit in SLI patients, these findings point to a potential motor origin for language syntax. PMID:23991140

  15. Syntax at hand: common syntactic structures for actions and language.

    PubMed

    Roy, Alice C; Curie, Aurore; Nazir, Tatjana; Paulignan, Yves; des Portes, Vincent; Fourneret, Pierre; Deprez, Viviane

    2013-01-01

    Evidence that the motor and the linguistic systems share common syntactic representations would open new perspectives on language evolution. Here, crossing disciplinary boundaries, we explore potential parallels between the structure of simple actions and that of sentences. First, examining Typically Developing (TD) children displacing a bottle with or without knowledge of its weight prior to movement onset, we provide kinematic evidence that the sub-phases of this displacing action (reaching + moving the bottle) manifest a structure akin to linguistic embedded dependencies. Then, using the same motor task, we reveal that children suffering from specific language impairment (SLI), whose core deficit affects syntactic embedding and dependencies, manifest specific structural motor anomalies parallel to their linguistic deficits. In contrast to TD children, SLI children performed the displacing-action as if its sub-phases were juxtaposed rather than embedded. The specificity of SLI's structural motor deficit was confirmed by testing an additional control group: Fragile-X Syndrome patients, whose language capacity, though delayed, comparatively spares embedded dependencies, displayed slower but structurally normal motor performances. By identifying the presence of structural representations and dependency computations in the motor system and by showing their selective deficit in SLI patients, these findings point to a potential motor origin for language syntax. PMID:23991140

  16. Peptide binding motifs associated with MHC molecules common in Chinese rhesus macaques are analogous to those of human HLA supertypes, and include HLA-B27-like alleles

    PubMed Central

    Mothé, Bianca R.; Southwood, Scott; Sidney, John; English, A. Michelle; Wriston, Amanda; Hoof, Ilka; Shabanowitz, Jeffrey; Hunt, Donald F.; Sette, Alessandro

    2013-01-01

    Chinese rhesus macaques are of particular interest in SIV/HIV research as these animals have prolonged kinetics of disease progression to AIDS, compared to their Indian counterparts, suggesting that they may be a better model for HIV. Nevertheless, the specific mechanism(s) accounting for these kinetics remains unclear. The study of Major Histocompatibility Complex (MHC) molecules, including their MHC:peptide binding motifs, provides valuable information for measuring cellular immune responses and deciphering outcomes of infection and vaccine efficacy. In this study, we have provided detailed characterization of six prevalent Chinese rhesus macaque MHC class I alleles, yielding a combined phenotypic frequency of 29%. The peptide binding specificity of two of these alleles, Mamu-A2*01:02 and -B*010:01, as well as the previously characterized allele Mamu-B*003:01 (and Indian rhesus Mamu-B*003:01), was found to be analogous to that of alleles in the HLA-B27 supertype family. Specific alleles in the HLA-B27 supertype family, including HLA-B*27:05, have been associated with long-term non-progression to AIDS in humans. All six alleles characterized in the present study were found to have specificities analogous to HLA-supertype alleles. These data contribute to the concept that Chinese rhesus macaque MHC immunogenetics is more similar to HLA than their Indian rhesus macaque counterparts, and thereby warrant further studies to decipher the role of these alleles in the context of SIV infection. PMID:23417323

  17. Detecting correlations among functional-sequence motifs

    NASA Astrophysics Data System (ADS)

    Pirino, Davide; Rigosa, Jacopo; Ledda, Alice; Ferretti, Luca

    2012-06-01

    Sequence motifs are words of nucleotides in DNA with biological functions, e.g., gene regulation. Identification of such words proceeds through rejection of Markov models on the expected motif frequency along the genome. Additional biological information can be extracted from the correlation structure among patterns of motif occurrences. In this paper a log-linear multivariate intensity Poisson model is estimated via expectation maximization on a set of motifs along the genome of E. coli K12. The proposed approach allows for excitatory as well as inhibitory interactions among motifs and between motifs and other genomic features like gene occurrences. Our findings confirm previous stylized facts about such types of interactions and shed new light on genome-maintenance functions of some particular motifs. We expect these methods to be applicable to a wider set of genomic features.

  18. Detecting correlations among functional-sequence motifs.

    PubMed

    Pirino, Davide; Rigosa, Jacopo; Ledda, Alice; Ferretti, Luca

    2012-06-01

    Sequence motifs are words of nucleotides in DNA with biological functions, e.g., gene regulation. Identification of such words proceeds through rejection of Markov models on the expected motif frequency along the genome. Additional biological information can be extracted from the correlation structure among patterns of motif occurrences. In this paper a log-linear multivariate intensity Poisson model is estimated via expectation maximization on a set of motifs along the genome of E. coli K12. The proposed approach allows for excitatory as well as inhibitory interactions among motifs and between motifs and other genomic features like gene occurrences. Our findings confirm previous stylized facts about such types of interactions and shed new light on genome-maintenance functions of some particular motifs. We expect these methods to be applicable to a wider set of genomic features. PMID:23005179

  19. Structure of the Small Dictyostelium discoideum Myosin Light Chain MlcB Provides Insights into MyoB IQ Motif Recognition*

    PubMed Central

    Liburd, Janine; Chitayat, Seth; Crawley, Scott W.; Munro, Kim; Miller, Emily; Denis, Chris M.; Spencer, Holly L.; Côté, Graham P.; Smith, Steven P.

    2014-01-01

    Dictyostelium discoideum MyoB is a class I myosin involved in the formation and retraction of membrane projections, cortical tension generation, membrane recycling, and phagosome maturation. The MyoB-specific, single-lobe EF-hand light chain MlcB binds the sole IQ motif of MyoB with submicromolar affinity in the absence and presence of Ca2+. However, the structural features of this novel myosin light chain and its interaction with its cognate IQ motif remain uncharacterized. Here, we describe the NMR-derived solution structure of apoMlcB, which displays a globular four-helix bundle. Helix 1 adopts a unique orientation when compared with the apo states of the EF-hand calcium-binding proteins calmodulin, S100B, and calbindin D9k. NMR-based chemical shift perturbation mapping identified a hydrophobic MyoB IQ binding surface that involves amino acid residues in helices I and IV and the functional N-terminal Ca2+ binding loop, a site that appears to be maintained when MlcB adopts the holo state. Complementary mutagenesis and binding studies indicated that residues Ile-701, Phe-705, and Trp-708 of the MyoB IQ motif are critical for recognition of MlcB, which together allowed the generation of a structural model of the apoMlcB-MyoB IQ complex. We conclude that the mode of IQ motif recognition by the novel single-lobe MlcB differs considerably from that of stereotypical bilobal light chains such as calmodulin. PMID:24790102

  20. Nuclear Magnetic Resonance Solution Structures of Lacticin Q and Aureocin A53 Reveal a Structural Motif Conserved among Leaderless Bacteriocins with Broad-Spectrum Activity.

    PubMed

    Acedo, Jeella Z; van Belkum, Marco J; Lohans, Christopher T; Towle, Kaitlyn M; Miskolzie, Mark; Vederas, John C

    2016-02-01

    Lacticin Q (LnqQ) and aureocin A53 (AucA) are leaderless bacteriocins from Lactococcus lactis QU5 and Staphylococcus aureus A53, respectively. These bacteriocins are characterized by the absence of an N-terminal leader sequence and are active against a broad range of Gram-positive bacteria. LnqQ and AucA consist of 53 and 51 amino acids, respectively, and have 47% identical sequences. In this study, their three-dimensional structures were elucidated using solution nuclear magnetic resonance and were shown to consist of four α-helices that assume a very similar compact, globular overall fold (root-mean-square deviation of 1.7 Å) with a highly cationic surface and a hydrophobic core. The structures of LnqQ and AucA resemble the shorter two-component leaderless bacteriocins, enterocins 7A and 7B, despite having low levels of sequence identity. Homology modeling revealed that the observed structural motif may be shared among leaderless bacteriocins with broad-spectrum activity against Gram-positive organisms. The elucidated structures of LnqQ and AucA also exhibit some resemblance to circular bacteriocins. Despite their similar overall fold, inhibition studies showed that LnqQ and AucA have different antimicrobial potency against the Gram-positive strains tested, suggesting that sequence disparities play a crucial role in their mechanisms of action. PMID:26771761

  1. Mass Efficiencies for Common Large-Scale Precision Space Structures

    NASA Technical Reports Server (NTRS)

    Williams, R. Brett; Agnes, Gregory S.

    2005-01-01

    This paper presents a mass-based trade study for large-scale deployable triangular trusses, where the longerons can be monocoque tubes, isogrid tubes, or coilable longeron trusses. Such structures are typically used to support heavy reflectors, solar panels, or other instruments, and are subject to thermal gradients that can vary a great deal based on orbital altitude, location in orbit, and self-shadowing. While multi layer insulation (MLI) blankets are commonly used to minimize the magnitude of these thermal disturbances, they subject the truss to a nonstructural mass penalty. This paper investigates the impact of these add-on thermal protection layers on selecting the lightest precision structure for a given loading scenario.

  2. Structural and functional studies of a phosphatidic acid-binding antifungal plant defensin MtDef4: Identification of an RGFRRR motif governing fungal cell entry

    SciTech Connect

    Sagaram, Uma S.; El-Mounadi, Kaoutar; Buchko, Garry W.; Berg, Howard R.; Kaur, Jagdeep; Pandurangi, Raghoottama; Smith, Thomas J.; Shah, Dilip

    2013-12-04

    A highly conserved plant defensin MtDef4 potently inhibits the growth of a filamentous fungus Fusarium graminearum. MtDef4 is internalized by cells of F. graminearum. To determine its mechanism of fungal cell entry and antifungal action, NMR solution structure of MtDef4 has been determined. The analysis of its structure has revealed a positively charged patch on the surface of the protein consisting of arginine residues in its γ-core signature, a major determinant of the antifungal activity of MtDef4. Here, we report functional analysis of the RGFRRR motif of the γ-core signature of MtDef4. The replacement of RGFRRR to AAAARR or to RGFRAA not only abolishes fungal cell entry but also results in loss of the antifungal activity of MtDef4. MtDef4 binds strongly to phosphatidic acid (PA), a precursor for the biosynthesis of membrane phospholipids and a signaling lipid known to recruit cytosolic proteins to membranes. Mutations of RGFRRR which abolish fungal cell entry of MtDef4 also impair its binding to PA. Our results suggest that RGFRRR motif is a translocation signal for entry of MtDef4 into fungal cells and that this positively charged motif likely mediates interaction of this defensin with PA as part of its antifungal action.

  3. Crystal Structure of pb9, the Distal Tail Protein of Bacteriophage T5: a Conserved Structural Motif among All Siphophages

    PubMed Central

    Flayhan, Ali; Vellieux, Frédéric M. D.; Lurz, Rudi; Maury, Olivier; Contreras-Martel, Carlos; Girard, Eric; Boulanger, Pascale

    2014-01-01

    The tail of Caudovirales bacteriophages serves as an adsorption device, a host cell wall-perforating machine, and a genome delivery pathway. In Siphoviridae, the assembly of the long and flexible tail is a highly cooperative and regulated process that is initiated from the proteins forming the distal tail tip complex. In Gram-positive-bacterium-infecting siphophages, the distal tail (Dit) protein has been structurally characterized and is proposed to represent a baseplate hub docking structure. It is organized as a hexameric ring that connects the tail tube and the adsorption device. In this study, we report the characterization of pb9, a tail tip protein of Escherichia coli bacteriophage T5. By immunolocalization, we show that pb9 is located in the upper part of the cone of the T5 tail tip, at the end of the tail tube. The crystal structure of pb9 reveals a two-domain protein. Domain A exhibits remarkable structural similarity with the N-terminal domain of known Dit proteins, while domain B adopts an oligosaccharide/oligonucleotide-binding fold (OB-fold) that is not shared by these proteins. We thus propose that pb9 is the Dit protein of T5, making it the first Dit protein described for a Gram-negative-bacterium-infecting siphophage. Multiple sequence alignments suggest that pb9 is a paradigm for a large family of Dit proteins of siphophages infecting mostly Gram-negative hosts. The modular structure of the Dit protein maintains the basic building block that would be conserved among all siphophages, combining it with a more divergent domain that might serve specific host adhesion properties. PMID:24155371

  4. Common genetic variants influence human subcortical brain structures

    PubMed Central

    Hibar, Derrek P.; Stein, Jason L.; Renteria, Miguel E.; Arias-Vasquez, Alejandro; Desrivières, Sylvane; Jahanshad, Neda; Toro, Roberto; Wittfeld, Katharina; Abramovic, Lucija; Andersson, Micael; Aribisala, Benjamin S.; Armstrong, Nicola J.; Bernard, Manon; Bohlken, Marc M.; Boks, Marco P.; Bralten, Janita; Brown, Andrew A.; Chakravarty, M. Mallar; Chen, Qiang; Ching, Christopher R. K.; Cuellar-Partida, Gabriel; den Braber, Anouk; Giddaluru, Sudheer; Goldman, Aaron L.; Grimm, Oliver; Guadalupe, Tulio; Hass, Johanna; Woldehawariat, Girma; Holmes, Avram J.; Hoogman, Martine; Janowitz, Deborah; Jia, Tianye; Kim, Sungeun; Klein, Marieke; Kraemer, Bernd; Lee, Phil H.; Olde Loohuis, Loes M.; Luciano, Michelle; Macare, Christine; Mather, Karen A.; Mattheisen, Manuel; Milaneschi, Yuri; Nho, Kwangsik; Papmeyer, Martina; Ramasamy, Adaikalavan; Risacher, Shannon L.; Roiz-Santiañez, Roberto; Rose, Emma J.; Salami, Alireza; Sämann, Philipp G.; Schmaal, Lianne; Schork, Andrew J.; Shin, Jean; Strike, Lachlan T.; Teumer, Alexander; van Donkelaar, Marjolein M. J.; van Eijk, Kristel R.; Walters, Raymond K.; Westlye, Lars T.; Whelan, Christopher D.; Winkler, Anderson M.; Zwiers, Marcel P.; Alhusaini, Saud; Athanasiu, Lavinia; Ehrlich, Stefan; Hakobjan, Marina M. H.; Hartberg, Cecilie B.; Haukvik, Unn K.; Heister, Angelien J. G. A. M.; Hoehn, David; Kasperaviciute, Dalia; Liewald, David C. M.; Lopez, Lorna M.; Makkinje, Remco R. R.; Matarin, Mar; Naber, Marlies A. M.; McKay, D. Reese; Needham, Margaret; Nugent, Allison C.; Pütz, Benno; Royle, Natalie A.; Shen, Li; Sprooten, Emma; Trabzuni, Daniah; van der Marel, Saskia S. L.; van Hulzen, Kimm J. E.; Walton, Esther; Wolf, Christiane; Almasy, Laura; Ames, David; Arepalli, Sampath; Assareh, Amelia A.; Bastin, Mark E.; Brodaty, Henry; Bulayeva, Kazima B.; Carless, Melanie A.; Cichon, Sven; Corvin, Aiden; Curran, Joanne E.; Czisch, Michael; de Zubicaray, Greig I.; Dillman, Allissa; Duggirala, Ravi; Dyer, Thomas D.; Erk, Susanne; Fedko, Iryna O.; Ferrucci, Luigi; Foroud, Tatiana M.; Fox, Peter T.; Fukunaga, Masaki; Gibbs, J. Raphael; Göring, Harald H. H.; Green, Robert C.; Guelfi, Sebastian; Hansell, Narelle K.; Hartman, Catharina A.; Hegenscheid, Katrin; Heinz, Andreas; Hernandez, Dena G.; Heslenfeld, Dirk J.; Hoekstra, Pieter J.; Holsboer, Florian; Homuth, Georg; Hottenga, Jouke-Jan; Ikeda, Masashi; Jack, Clifford R.; Jenkinson, Mark; Johnson, Robert; Kanai, Ryota; Keil, Maria; Kent, Jack W.; Kochunov, Peter; Kwok, John B.; Lawrie, Stephen M.; Liu, Xinmin; Longo, Dan L.; McMahon, Katie L.; Meisenzahl, Eva; Melle, Ingrid; Mohnke, Sebastian; Montgomery, Grant W.; Mostert, Jeanette C.; Mühleisen, Thomas W.; Nalls, Michael A.; Nichols, Thomas E.; Nilsson, Lars G.; Nöthen, Markus M.; Ohi, Kazutaka; Olvera, Rene L.; Perez-Iglesias, Rocio; Pike, G. Bruce; Potkin, Steven G.; Reinvang, Ivar; Reppermund, Simone; Rietschel, Marcella; Romanczuk-Seiferth, Nina; Rosen, Glenn D.; Rujescu, Dan; Schnell, Knut; Schofield, Peter R.; Smith, Colin; Steen, Vidar M.; Sussmann, Jessika E.; Thalamuthu, Anbupalam; Toga, Arthur W.; Traynor, Bryan J.; Troncoso, Juan; Turner, Jessica A.; Valdés Hernández, Maria C.; van ’t Ent, Dennis; van der Brug, Marcel; van der Wee, Nic J. A.; van Tol, Marie-Jose; Veltman, Dick J.; Wassink, Thomas H.; Westman, Eric; Zielke, Ronald H.; Zonderman, Alan B.; Ashbrook, David G.; Hager, Reinmar; Lu, Lu; McMahon, Francis J.; Morris, Derek W.; Williams, Robert W.; Brunner, Han G.; Buckner, Randy L.; Buitelaar, Jan K.; Cahn, Wiepke; Calhoun, Vince D.; Cavalleri, Gianpiero L.; Crespo-Facorro, Benedicto; Dale, Anders M.; Davies, Gareth E.; Delanty, Norman; Depondt, Chantal; Djurovic, Srdjan; Drevets, Wayne C.; Espeseth, Thomas; Gollub, Randy L.; Ho, Beng-Choon; Hoffmann, Wolfgang; Hosten, Norbert; Kahn, René S.; Le Hellard, Stephanie; Meyer-Lindenberg, Andreas; Müller-Myhsok, Bertram; Nauck, Matthias; Nyberg, Lars; Pandolfo, Massimo; Penninx, Brenda W. J. H.; Roffman, Joshua L.; Sisodiya, Sanjay M.; Smoller, Jordan W.; van Bokhoven, Hans; van Haren, Neeltje E. M.; Völzke, Henry; Walter, Henrik; Weiner, Michael W.; Wen, Wei; White, Tonya; Agartz, Ingrid; Andreassen, Ole A.; Blangero, John; Boomsma, Dorret I.; Brouwer, Rachel M.; Cannon, Dara M.; Cookson, Mark R.; de Geus, Eco J. C.; Deary, Ian J.; Donohoe, Gary; Fernández, Guillén; Fisher, Simon E.; Francks, Clyde; Glahn, David C.; Grabe, Hans J.; Gruber, Oliver; Hardy, John; Hashimoto, Ryota; Hulshoff Pol, Hilleke E.; Jönsson, Erik G.

    2015-01-01

    The highly complex structure of the human brain is strongly shaped by genetic influences1. Subcortical brain regions form circuits with cortical areas to coordinate movement2, learning, memory3 and motivation4, and altered circuits can lead to abnormal behaviour and disease2. To investigate how common genetic variants affect the structure of these brain regions, here we conduct genome-wide association studies of the volumes of seven subcortical regions and the intracranial volume derived from magnetic resonance images of 30,717 individuals from 50 cohorts. We identify five novel genetic variants influencing the volumes of the putamen and caudate nucleus. We also find stronger evidence for three loci with previously established influences on hippocampal volume5 and intracranial volume6. These variants show specific volumetric effects on brain structures rather than global effects across structures. The strongest effects were found for the putamen, where a novel intergenic locus with replicable influence on volume (rs945270; P = 1.08 × 10−33; 0.52% variance explained) showed evidence of altering the expression of the KTN1 gene in both brain and blood tissue. Variants influencing putamen volume clustered near developmental genes that regulate apoptosis, axon guidance and vesicle transport. Identification of these genetic variants provides insight into the causes of variability inhuman brain development, and may help to determine mechanisms of neuropsychiatric dysfunction. PMID:25607358

  5. Common genetic variants influence human subcortical brain structures.

    PubMed

    Hibar, Derrek P; Stein, Jason L; Renteria, Miguel E; Arias-Vasquez, Alejandro; Desrivières, Sylvane; Jahanshad, Neda; Toro, Roberto; Wittfeld, Katharina; Abramovic, Lucija; Andersson, Micael; Aribisala, Benjamin S; Armstrong, Nicola J; Bernard, Manon; Bohlken, Marc M; Boks, Marco P; Bralten, Janita; Brown, Andrew A; Chakravarty, M Mallar; Chen, Qiang; Ching, Christopher R K; Cuellar-Partida, Gabriel; den Braber, Anouk; Giddaluru, Sudheer; Goldman, Aaron L; Grimm, Oliver; Guadalupe, Tulio; Hass, Johanna; Woldehawariat, Girma; Holmes, Avram J; Hoogman, Martine; Janowitz, Deborah; Jia, Tianye; Kim, Sungeun; Klein, Marieke; Kraemer, Bernd; Lee, Phil H; Olde Loohuis, Loes M; Luciano, Michelle; Macare, Christine; Mather, Karen A; Mattheisen, Manuel; Milaneschi, Yuri; Nho, Kwangsik; Papmeyer, Martina; Ramasamy, Adaikalavan; Risacher, Shannon L; Roiz-Santiañez, Roberto; Rose, Emma J; Salami, Alireza; Sämann, Philipp G; Schmaal, Lianne; Schork, Andrew J; Shin, Jean; Strike, Lachlan T; Teumer, Alexander; van Donkelaar, Marjolein M J; van Eijk, Kristel R; Walters, Raymond K; Westlye, Lars T; Whelan, Christopher D; Winkler, Anderson M; Zwiers, Marcel P; Alhusaini, Saud; Athanasiu, Lavinia; Ehrlich, Stefan; Hakobjan, Marina M H; Hartberg, Cecilie B; Haukvik, Unn K; Heister, Angelien J G A M; Hoehn, David; Kasperaviciute, Dalia; Liewald, David C M; Lopez, Lorna M; Makkinje, Remco R R; Matarin, Mar; Naber, Marlies A M; McKay, D Reese; Needham, Margaret; Nugent, Allison C; Pütz, Benno; Royle, Natalie A; Shen, Li; Sprooten, Emma; Trabzuni, Daniah; van der Marel, Saskia S L; van Hulzen, Kimm J E; Walton, Esther; Wolf, Christiane; Almasy, Laura; Ames, David; Arepalli, Sampath; Assareh, Amelia A; Bastin, Mark E; Brodaty, Henry; Bulayeva, Kazima B; Carless, Melanie A; Cichon, Sven; Corvin, Aiden; Curran, Joanne E; Czisch, Michael; de Zubicaray, Greig I; Dillman, Allissa; Duggirala, Ravi; Dyer, Thomas D; Erk, Susanne; Fedko, Iryna O; Ferrucci, Luigi; Foroud, Tatiana M; Fox, Peter T; Fukunaga, Masaki; Gibbs, J Raphael; Göring, Harald H H; Green, Robert C; Guelfi, Sebastian; Hansell, Narelle K; Hartman, Catharina A; Hegenscheid, Katrin; Heinz, Andreas; Hernandez, Dena G; Heslenfeld, Dirk J; Hoekstra, Pieter J; Holsboer, Florian; Homuth, Georg; Hottenga, Jouke-Jan; Ikeda, Masashi; Jack, Clifford R; Jenkinson, Mark; Johnson, Robert; Kanai, Ryota; Keil, Maria; Kent, Jack W; Kochunov, Peter; Kwok, John B; Lawrie, Stephen M; Liu, Xinmin; Longo, Dan L; McMahon, Katie L; Meisenzahl, Eva; Melle, Ingrid; Mohnke, Sebastian; Montgomery, Grant W; Mostert, Jeanette C; Mühleisen, Thomas W; Nalls, Michael A; Nichols, Thomas E; Nilsson, Lars G; Nöthen, Markus M; Ohi, Kazutaka; Olvera, Rene L; Perez-Iglesias, Rocio; Pike, G Bruce; Potkin, Steven G; Reinvang, Ivar; Reppermund, Simone; Rietschel, Marcella; Romanczuk-Seiferth, Nina; Rosen, Glenn D; Rujescu, Dan; Schnell, Knut; Schofield, Peter R; Smith, Colin; Steen, Vidar M; Sussmann, Jessika E; Thalamuthu, Anbupalam; Toga, Arthur W; Traynor, Bryan J; Troncoso, Juan; Turner, Jessica A; Valdés Hernández, Maria C; van 't Ent, Dennis; van der Brug, Marcel; van der Wee, Nic J A; van Tol, Marie-Jose; Veltman, Dick J; Wassink, Thomas H; Westman, Eric; Zielke, Ronald H; Zonderman, Alan B; Ashbrook, David G; Hager, Reinmar; Lu, Lu; McMahon, Francis J; Morris, Derek W; Williams, Robert W; Brunner, Han G; Buckner, Randy L; Buitelaar, Jan K; Cahn, Wiepke; Calhoun, Vince D; Cavalleri, Gianpiero L; Crespo-Facorro, Benedicto; Dale, Anders M; Davies, Gareth E; Delanty, Norman; Depondt, Chantal; Djurovic, Srdjan; Drevets, Wayne C; Espeseth, Thomas; Gollub, Randy L; Ho, Beng-Choon; Hoffmann, Wolfgang; Hosten, Norbert; Kahn, René S; Le Hellard, Stephanie; Meyer-Lindenberg, Andreas; Müller-Myhsok, Bertram; Nauck, Matthias; Nyberg, Lars; Pandolfo, Massimo; Penninx, Brenda W J H; Roffman, Joshua L; Sisodiya, Sanjay M; Smoller, Jordan W; van Bokhoven, Hans; van Haren, Neeltje E M; Völzke, Henry; Walter, Henrik; Weiner, Michael W; Wen, Wei; White, Tonya; Agartz, Ingrid; Andreassen, Ole A; Blangero, John; Boomsma, Dorret I; Brouwer, Rachel M; Cannon, Dara M; Cookson, Mark R; de Geus, Eco J C; Deary, Ian J; Donohoe, Gary; Fernández, Guillén; Fisher, Simon E; Francks, Clyde; Glahn, David C; Grabe, Hans J; Gruber, Oliver; Hardy, John; Hashimoto, Ryota; Hulshoff Pol, Hilleke E; Jönsson, Erik G; Kloszewska, Iwona; Lovestone, Simon; Mattay, Venkata S; Mecocci, Patrizia; McDonald, Colm; McIntosh, Andrew M; Ophoff, Roel A; Paus, Tomas; Pausova, Zdenka; Ryten, Mina; Sachdev, Perminder S; Saykin, Andrew J; Simmons, Andy

    2015-04-01

    The highly complex structure of the human brain is strongly shaped by genetic influences. Subcortical brain regions form circuits with cortical areas to coordinate movement, learning, memory and motivation, and altered circuits can lead to abnormal behaviour and disease. To investigate how common genetic variants affect the structure of these brain regions, here we conduct genome-wide association studies of the volumes of seven subcortical regions and the intracranial volume derived from magnetic resonance images of 30,717 individuals from 50 cohorts. We identify five novel genetic variants influencing the volumes of the putamen and caudate nucleus. We also find stronger evidence for three loci with previously established influences on hippocampal volume and intracranial volume. These variants show specific volumetric effects on brain structures rather than global effects across structures. The strongest effects were found for the putamen, where a novel intergenic locus with replicable influence on volume (rs945270; P = 1.08 × 10(-33); 0.52% variance explained) showed evidence of altering the expression of the KTN1 gene in both brain and blood tissue. Variants influencing putamen volume clustered near developmental genes that regulate apoptosis, axon guidance and vesicle transport. Identification of these genetic variants provides insight into the causes of variability in human brain development, and may help to determine mechanisms of neuropsychiatric dysfunction. PMID:25607358

  6. Revision of pyrrhotite structures within a common superspace model.

    PubMed

    Izaola, Zunbeltz; González, Santiago; Elcoro, Luis; Perez-Mato, J M; Madariaga, Gotzon; García, Alberto

    2007-10-01

    The structure of pyrrhotite (Fe(1 - x)S with 0.05 < or = x < or = 0.125) has been reinvestigated in the framework of the superspace formalism. A common model with a centrosymmetric superspace group is proposed for the whole family. The atomic domains in the internal space representing the Fe atoms are parametrized as crenel functions that fulfil the closeness condition. The proposed model explains the x-dependent space groups observed and the basic features of the structures reported up to now. Our model yields for any x value a well defined ordered distribution of Fe vacancies in contrast to some of the structural models proposed in the literature. A new (3 + 1)-dimensional refinement of Fe(0.91)S using the deposited dataset [Yamamoto & Nakazawa (1982). Acta Cryst. A38, 79-86] has been performed as a benchmark of the model. The consistency of the proposed superspace symmetry and its validity for other compositions has been further checked by means of ab initio calculations of both atomic forces and equilibrium atomic positions in non-relaxed and relaxed structures, respectively. PMID:17873438

  7. Crystal form III of beta-cyclodextrin-ethanol inclusion complex: layer-type structure with dimeric motif.

    PubMed

    Aree, Thammarat; Chaichit, Narongsak

    2008-09-01

    The crystal form III of the beta-cyclodextrin (beta-CD)-ethanol inclusion complex [2(C(6)H(10)O(5))(7).1.5C(2)H(5)OH.19H(2)O] belongs to the triclinic space group P1 with unit cell constants: a=15.430(1), b=15.455(1), c=17.996(1)A, alpha=99.30(1) degrees , beta=113.18(1) degrees , gamma=103.04(1) degrees . beta-CD forms dimers comprising two identical monomers that adopt a 'round' conformation stabilized by intramolecular, interglucose O-3(n)cdots, three dots, centeredO-2(n+1) hydrogen bonds. The two beta-CD monomers of form III are isostructural to that of form I in the monoclinic space group P2(1) [Steiner, T.; Mason, S. A.; Saenger, W. J. Am. Chem. Soc.1991, 113, 5676-5687], but exhibit a striking difference from that of form II in the monoclinic space group C2 [Aree, T.; Chaichit, N. Carbohydr. Res.2003, 338, 1581-1589]. The small guest EtOH molecule orients differently in the large beta-CD cavity. In form III, two disordered EtOH molecules are embedded in the beta-CD-dimer cavity. A half occupied EtOH molecule (#1) is located above the O-4 plane of beta-CD #1, whereas another doubly disordered EtOH molecule (#2, #3) is situated at about the middle of the beta-CD-dimer cavity. The three EtOH sites are maintained in positions by making van der Waals contacts to each other and to the surrounding water sites and beta-CD O-3-H group. The EtOH molecules disordered (occupancy 0.3) above the beta-CD O-4 plane in form I and fully occupied beneath the O-4 plane in form II are strongly held in positions by hydrogen bonding with the surrounding water site and beta-CD O-6-H, O-3-H groups. Occurrence of the beta-CD dimer as a structural motif of channel-type packing (form II) and layer-type packing (form III) is attributed to the higher tendency for self aggregation under the moderate acidic conditions. At weak acidic conditions, beta-CD prefers a herringbone mode (form I). PMID:18490008

  8. Mining Conditional Phosphorylation Motifs.

    PubMed

    Liu, Xiaoqing; Wu, Jun; Gong, Haipeng; Deng, Shengchun; He, Zengyou

    2014-01-01

    Phosphorylation motifs represent position-specific amino acid patterns around the phosphorylation sites in the set of phosphopeptides. Several algorithms have been proposed to uncover phosphorylation motifs, whereas the problem of efficiently discovering a set of significant motifs with sufficiently high coverage and non-redundancy still remains unsolved. Here we present a novel notion called conditional phosphorylation motifs. Through this new concept, the motifs whose over-expressiveness mainly benefits from its constituting parts can be filtered out effectively. To discover conditional phosphorylation motifs, we propose an algorithm called C-Motif for a non-redundant identification of significant phosphorylation motifs. C-Motif is implemented under the Apriori framework, and it tests the statistical significance together with the frequency of candidate motifs in a single stage. Experiments demonstrate that C-Motif outperforms some current algorithms such as MMFPh and Motif-All in terms of coverage and non-redundancy of the results and efficiency of the execution. The source code of C-Motif is available at: https://sourceforge. net/projects/cmotif/. PMID:26356863

  9. DILIMOT: discovery of linear motifs in proteins.

    PubMed

    Neduva, Victor; Russell, Robert B

    2006-07-01

    Discovery of protein functional motifs is critical in modern biology. Small segments of 3-10 residues play critical roles in protein interactions, post-translational modifications and trafficking. DILIMOT (DIscovery of LInear MOTifs) is a server for the prediction of these short linear motifs within a set of proteins. Given a set of sequences sharing a common functional feature (e.g. interaction partner or localization) the method finds statistically over-represented motifs likely to be responsible for it. The input sequences are first passed through a set of filters to remove regions unlikely to contain instances of linear motifs. Motifs are then found in the remaining sequence and ranked according to a statistic that measure over-representation and conservation across homologues in related species. The results are displayed via a visual interface for easy perusal. The server is available at http://dilimot.embl.de. PMID:16845024

  10. Alliance: a common factor of psychotherapy modeled by structural theory

    PubMed Central

    Tschacher, Wolfgang; Haken, Hermann; Kyselo, Miriam

    2015-01-01

    There is broad consensus that the therapeutic alliance constitutes a core common factor for all modalities of psychotherapy. Meta-analyses corroborated that alliance, as it emerges from therapeutic process, is a significant predictor of therapy outcome. Psychotherapy process is traditionally described and explored using two categorically different approaches, the experiential (first-person) perspective and the behavioral (third-person) perspective. We propose to add to this duality a third, structural approach. Dynamical systems theory and synergetics on the one hand and enactivist theory on the other together can provide this structural approach, which contributes in specific ways to a clarification of the alliance factor. Systems theory offers concepts and tools for the modeling of the individual self and, building on this, of alliance processes. In the enactive perspective, the self is conceived as a socially enacted autonomous system that strives to maintain identity by observing a two-fold goal: to exist as an individual self in its own right (distinction) while also being open to others (participation). Using this conceptualization, we formalized the therapeutic alliance as a phase space whose potential minima (attractors) can be shifted by the therapist to approximate therapy goals. This mathematical formalization is derived from probability theory and synergetics. We draw the conclusion that structural theory provides powerful tools for the modeling of how therapeutic change is staged by the formation, utilization, and dissolution of the therapeutic alliance. In addition, we point out novel testable hypotheses and future applications. PMID:25954215