bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors limiting the performance of prediction‐based fold recognition methods
Authors: Cruz Xavier De La , Thornton Janet M. 
Published: October 2010

AbstractIn the past few years, a new generation of fold recognition methods has been developed, in which the classical sequence information is combined with information obtained from secondary structure and, sometimes, accessibility predictions. The results are promising, indicating that this approach may compete with potential‐based methods (Rost B et al., 1997, J Mol Biol 270:471–480). Here we present a systematic study of the different factors contributing to the performance of these methods, in particular when applied to the problem of fold recognition of remote homologues.Our results indicate that secondary structure and accessibility prediction methods have reached an accuracy level where they are not the major factor limiting the accuracy of fold recognition. The pattern degeneracy problem is confirmed as the major source of error of these methods. On the basis of these results, we study three different options to overcome these limitations: normalization schemes, mapping of the coil state into the different zones of the Ramachandran plot, and post‐threading graphical analysis.
The use of dipolar couplings for determining the solution structure of rat apo‐S100B(ββ)
Authors: Drohat Alexander C. , Tjandra Nico , Baldisseri Donna M. , Weber David J. 
Published: October 2010

AbstractThe relative orientations of adjacent structural elements without many well‐defined NOE contacts between them are typically poorly defined in NMR structures. For apo‐S100B(ββ) and the structurally homologous protein calcyclin, the solution structures determined by conventional NMR exhibited considerable differences and made it impossible to draw unambiguous conclusions regarding the Ca2+‐induced conformational change required for target protein binding. The structure of rat apo‐S100B(ββ) was recalculated using a large number of constraints derived from dipolar couplings that were measured in a dilute liquid crystalline phase. The dipolar couplings orient bond vectors relative to a single‐axis system, and thereby remove much of the uncertainty in NOE‐based structures. The structure of apo‐S100B(ββ) indicates a minimal change in the first, pseudo‐EF‐hand Ca2+ binding site, but a large reorientation of helix 3 in the second, classical EF‐hand upon Ca2+ binding.
Structural and phylogenetic characterization of human SLURP‐1, the first secreted mammalian member of the Ly‐6/uPAR protein superfamily
Authors: Adermann Knut , Wattler Frank , Wattler Sigrid , Heine Gabriele , Meyer Markus , Forssmann Wolf‐Georg , Nehls Michael 
Published: October 2010

AbstractMembers of the Ly‐6/uPAR protein family share one or several repeat units of the Ly‐6/uPAR domain that is defined by a distinct disulfide bonding pattern between 8 or 10 cysteine residues. The Ly‐6/uPAR protein family can be divided into two subfamilies. One comprises GPI‐anchored glycoprotein receptors with 10 cysteine residues. The other subfamily includes the secreted single‐domain snake and frog cytotoxins, and differs significantly in that its members generally possess only eight cysteines and no GPI‐anchoring signal sequence. We report the purification and structural characterization of human SLURP‐1 (secreted mammalian Ly‐6/uPAR related protein 1) from blood and urine peptide libraries. SLURP‐1 is encoded by the ARS (component B)‐81/s locus, and appears to be the first mammalian member of the Ly‐6/uPAR family lacking a GPI‐anchoring signal sequence. A phylogenetic analysis based on the SLURP‐1 primary protein structure revealed a closer relationship to the subfamily of cytotoxins. Since the SLURP‐1 gene maps to the same chromosomal region as several members of the Ly‐6/uPAR subfamily of glycoprotein receptors, it is suggested that both biologically distinct subfamilies might have co‐evolved from local chromosomal duplication events.
The compact and expanded denatured conformations of apomyoglobin in the methanol‐water solvent
Authors: Kamatari Yuji O. , Ohji Shoko , Konno Takashi , Seki Yasutaka , Soda Kunitsugu , Kataoka Mikio , Akasaka Kazuyuki 
Published: October 2010

AbstractWe have performed a detailed study of methanol‐induced conformational transitions of horse heart apomyoglobin (apoMb) to investigate the existence of the compact and expanded denatured states. A combination of far‐ and nearultraviolet circular dichroism, NMR spectroscopy, and small‐angle X‐ray scattering (SAXS) was used, allowing a phase diagram to be constructed as a function of pH and the methanol concentration. The phase diagram contains four conformational states, the native (N), acid‐denatured (UA), compact denatured (IM), and expanded helical denatured (H) states, and indicates that the compact denatured state (IM) is stable under relatively mild denaturing conditions, whereas the expanded denatured states (UA and H) are realized under extreme conditions of pH (strong electric repulsion) or alcohol concentration (weak hydrophobic interaction). The results of this study, together with many previous studies in the literature, indicate the general existence of the compact denatured states not only in the salt‐pH plane but also in the alcohol‐pH plane. Furthermore, to determine the general feature of the H conformation we used several proteins including ubiquitin, ribonuclease A, α‐lactalbumin, β‐lactoglobulin, and Streptomyces subtilisin inhibitor (SSI) in addition to apoMb. SAXS studies of these proteins in 60% methanol showed that the H states of these all proteins have expanded and nonglobular conformations. The qualitative agreement of the experimental data with computer‐simulated Kratky profiles also supports this structural feature of the H state.
A minimal peptide substrate in biotin holoenzyme synthetase‐catalyzed biotinylation
Authors: Beckett Dorothy , Kovaleva Elena , Schatz Peter J. 
Published: October 2010

AbstractThe Escherichia coli biotin holoenzyme synthetase, BirA, catalyzes transfer of biotin to the epsilon amino group of a specific lysine residue of the biotin carboxyl carrier protein (BCCP) subunit of acetyl‐CoA carboxylase. Sequences of naturally biotinylated substrates are highly conserved across evolutionary boundaries, and cross‐species biotinylation has been demonstrated in several systems. To define the minimal substrate requirements in BirA‐catalyzed biotinylation, we have measured the kinetics of modification of a 23‐residue peptide previously identified by combinatorial methods. Although the sequence of the peptide bears little resemblance to the biotinylated sequence in BCCP, it is enzymatically biotinylated in vivo. Rates of biotin transfer to the 23‐residue peptide are similar to those determined for BCCP. To further elucidate the sequence requirements for biotinylation, transient kinetic measurements were performed on a series of amino‐ and carboxy‐terminal truncations of the 23‐mer. The results, determined by stopped‐flow fluorescence, allowed identification of a 14‐residue peptide as the minimum required sequence. Additional support was obtained using matrix‐assisted laser desorption ionization time‐of‐flight (MALDI‐TOF) mass spectrometric analysis of peptides that had been incubated with an excess of biotinyl‐5′‐adenylate intermediate and catalytic amounts of BirA. Results of these measurements indicate that while kinetically inactive truncations showed no significant shift in molecular mass to the values expected for biotinylated species, kinetically active truncations exhibited 100% biotinylation. The specificity constant (kcat/Km) governing BirA‐catalyzed biotinylation of the 14‐mer minimal substrate is similar to that determined for the natural substrate, BCCP. We conclude that the 14‐mer peptide efficiently mimics the biotin acceptor function of the much larger protein domain normally recognized by BirA.
Interaction with magnesium and ADP stabilizes both components of nitrogenase fromKlebsiella pneumoniaeagainst urea denaturation
Authors: Zou Lee , Baguinon Marilyn C. , Guo Xiaolu , Guo Sherry Yi , Yu Yong , Davis Lawrence C. 
Published: October 2010

AbstractThe nitrogenase enzyme ofKlebsiella pneumoniaeconsists of two separable proteins, each with multiple subunits and one or more oxygen sensitive metallocenters. The wild‐type nitrogenase proteins are stable to electrophoresis in high concentrations of urea under anaerobic conditions. Addition of Mg+2and ADP greatly increases the stability of the smaller Fe protein (from <4 to >6 M for full unfolding), an effect directly analogous to stabilization in p21ras induced by Mg+2and GDP. Stabilization by Mg+2is slight for the holo MoFe protein (from ∼1.5 to ∼2.4 M) but more dramatic for the apo protein form of the MoFe protein accumulated by certain Fe protein (nifHgene) mutants. The potent product inhibitor of nitrogenase function, MgADP, increases stability of the MoFe protein more than Mg+2alone, to ∼3.6 M, showing that nucleotides interact with the MoFe protein. Mutations of thenifMgene result in slower accumulation of less stable Fe protein, indicating that NifM is involved in correct folding of the Fe protein. Mutationally altered proteins are often difficult to purify for study because of their inherent instability, low expression level, or oxygen lability. Crude extracts of 11 different mutants of Fe protein (nifHgene) were examined by transverse urea gradient gels to rapidly screen for stabilizing interactions in the presence or absence of substrate or inhibitor analogs. Amino acid alterations D44N and R188C, at the interface of the dimer, in the vicinity of the nucleotide binding site(s), have significantly lower stability than the wild‐type enzyme in the absence of Mg+2but comparable stability in its presence, showing the importance of Mg+2in the subunit interactions. Mutations N163S and E266K, in which residues normally involved in hydrogen bonding far from the active site were altered, are more labile than the wild‐type even with Mg+2added. Seven other mutants, though nonfunctional, did not appear altered in stability compared to the wild‐type.
Anti‐HIV and anti‐tumor protein MAP30, a 30 kDa single‐strand type‐I RIP, shares similar secondary structure and β‐sheet topology with the A chain of ricin, a type‐II RIP
Authors: Wang Yun‐Xing , Jacob Jaison , Torchia Dennis A. , Wemgfteld Paul T. , Palmer Ira , Stahl Stephen J. , Kaufman Joshua D. , Huang Philip Lin , Huang Paul Lee , Lee‐Huang Sylvia 
Published: October 2010

AbstractMAP30 is a 30 kDa single‐stranded, type‐I ribosome inactivating protein (RIP) possessing anti‐tumor and anti‐HIV activities. It binds both ribosomal RNA and the HIV‐1 long‐terminal repeat DNA. To understand the structural basis for MAP30 activities, we undertook the study of MAP30 by solution NMR spectroscopy. We report nearly complete 1H, 13C, and 15N chemical shift assignments of its 263 amino acids. Based upon an analysis of secondary 13C chemical shifts, 1Jhnha coupling constants, hydrogen exchange data, and nuclear Overhauser effect patterns, we find that the secondary structure and β‐sheet topology of MAP30 are very similar to those of the ricin A chain, a subunit of the well‐known type‐II RIP, even though two proteins display distinct activities. We therefore suggest that MAP30 and ricin A chain share a similar three‐dimensional fold, and that the reported functional differences between two proteins arise primarily from differences in local three‐dimensional structure and other structural properties such as surface electrostatic potentials.
Common EF‐hand motifs in cholinesterases and neuroligins suggest a role for Ca2+ binding in cell surface associations
Authors: Tsigelny I. , Taylor P. , Bourne P.E. , Shindyalov I.N. , Südhof T.C. 
Published: October 2010

AbstractComparisons of protein sequence via cyclic training of Hidden Markov Models (HMMs) in conjunction with alignments of three‐dimensional structure, using the Combinatorial Extension (CE) algorithm, reveal two putative EF‐hand metal binding domains in acetylcholinesterase. Based on sequence similarity, putative EF‐hands are also predicted for the neuroligin family of cell surface proteins. These predictions are supported by experimental evidence. In the acetylcholinesterase crystal structure from Torpedo californica, the first putative EF‐hand region binds the Zn2+ found in the heavy metal replacement structure. Further, the interaction of neuroligin 1 with its cognate receptor neurexin depends on Ca2+. Thus, members of the α, β hydrolase fold family of proteins contain potential Ca2+ binding sites, which in some family members may be critical for heterologous cell associations.
The π‐helix translates structure into function
Authors: Weaver Todd M. 
Published: October 2010

AbstractA search for the occurrence of the rare π‐helix was performed with Iditis from the Oxford Molecular Group upon the Protein Data Bank. In 8 of the 10 confirmed crystal structures that harbor the π‐helix, its unique conformation has been linked directly to the formation or stabilization of a specific binding site within the protein. In the discussion to follow, the role for each of these eight π‐helices will be addressed in regard to protein function. It is clear upon closer examination that the conformation of the π‐helix has evolved to provide unique structural features within a variety of proteins.
Conformational substates in different crystal forms of the photoactive yellow protein—Correlation with theoretical and experimental flexibility
Authors: Van Aalten Daan M.F. , Joshua‐Tor Leemor , Crielaard Wim , Hellingwerf Klaas J. 
Published: October 2010

AbstractThe conformational changes during the photocycle of the photoactive yellow protein have been the subject of many recent studies. Spectroscopic measurements have shown that the photocycle also occurs in a crystalline environment, and this has been the basis for subsequent Laue diffraction and cryocrystallographic studies. These studies have shown that conformational changes during the photocycle are limited to the chromophore and its immediate environment. However, spectroscopic studies suggest the presence of large conformational changes in the protein. Here, we address this apparent discrepancy in two ways. First, we obtain a description of large concerted motions in the ground state of the yellow protein from NMR data and theoretical calculations. Second, we describe the high‐resolution structure of the yellow protein crystallized in a different space group. The structure of the yellow protein differs significantly between the two crystal forms. We show that these differences can be used to obtain a description of the flexibility of the protein that is consistent with the motions observed in solution.
Comparison of sequence profiles. Strategies for structural predictions using sequence information
Authors: Rychlewski Leszek , Li Weizhong , Jaroszewski Lukasz , Godzik Adam 
Published: October 2010

AbstractDistant homologies between proteins are often discovered only after three‐dimensional structures of both proteins are solved. The sequence divergence for such proteins can be so large that simple comparison of their sequences fails to identify any similarity. New generation of sensitive alignment tools use averaged sequences of entire homologous families (profiles) to detect such homologies. Several algorithms, including the newest generation of BLAST algorithms and BASIC, an algorithm used in our group to assign fold predictions for proteins from several genomes, are compared to each other on the large set of structurally similar proteins with little sequence similarity. Proteins in the benchmark are classified according to the level of their similarity, which allows us to demonstrate that most of the improvement of the new algorithms is achieved for proteins with strong functional similarities, with almost no progress in recognizing distant fold similarities. It is also shown that details of profile calculation strongly influence its sensitivity in recognizing distant homologies. The most important choice is how to include information from diverging members of the family, avoiding generating false predictions, while accounting for entire sequence divergence within a family. PSI‐BLAST takes a conservative approach, deriving a profile from core members of the family, providing a solid improvement without almost any false predictions. BASIC strives for better sensitivity by increasing the weight of divergent family members and paying the price in lower reliability. A new FFAS algorithm introduced here uses a new procedure for profile generation that takes into account all the relations within the family and matches BASIC sensitivity with PSI‐BLAST like reliability.
Structure of tick anticoagulant peptide at 1.6 Å resolution complexed with bovine pancreatic trypsin inhibitor
Authors: Charles Robert S. T. , Padmanabhan K. , Arni R. V. , Padmanabhan K. P. , Tulinsky A. 
Published: October 2010

AbstractThe structure of tick anticoagulant peptide (TAP) has been determined by X‐ray crystallography at 1.6 Å resolution complexed with bovine pancreatic trypsin inhibitor (BPTI). The TAP‐BPTI crystals are tetragonal, a = b = 46.87, c = 50.35 Å, space group P41, four complexes per unit cell. The TAP molecules are highly dipolar and form an intermolecular helical array along the c‐axis with a diameter of about 45 Å. Individual TAP units interact in a head‐to‐tail fashion, the positive end of one molecule associating with the distal negative end of another, and vice versa. The BPTI molecules have a uniformly distributed positively charged surface that interacts extensively through 14 hydrogen bonds and two hydrogen bonded salt bridges with the helical groove around the helical TAP chains. Comparing the structure of TAP in TAP‐BPTI with TAP bound to factor Xa(Xa) suggests a massive reorganization in the N‐terminal tetrapeptide and the first disulfide loop of TAP (Cys5T‐Cys15T) upon binding to Xa. The TyrlTOH atom of TAP moves 14.2 Å to interact with Asp 189 of the S1 specificity site, Arg3TCZ moves 5.0 Å with the guanidinium group forming a cation‐π‐electron complex in the S4 subsite of Xa, while Lys7TNZ differs in position by 10.6 Å in TAP‐BPTI and TAP‐Xa, all of which indicates a different pre‐Xa‐bound conformation for the N‐terminal of TAP in its native state. In contrast to TAP, the BPTI structure of TAP‐BPTI is practically the same as all those of previously determined structures of BPTI, only arginine and lysine side‐chain conformations showing significant differences.
Characterization of a comparative model of the extracellular domain of the epidermal growth factor receptor
Authors: Jorissen Robert N. , Treutlein Herbert R. , Burgess Antony W. , Epa V. Chandana , Garrett Thomas P. J. , Ward Colin W. 
Published: October 2010

AbstractThe Epidermal Growth Factor (EGF) receptor is a tyrosine kinase that mediates the biological effects of ligands such as EGF and transforming growth factor alpha. An understanding of the molecular basis of its action has been hindered by a lack of structural and mutational data on the receptor. We have constructed comparative models of the four extracellular domains of the EGF receptor that are based on the structure of the first three domains of the insulin‐like growth factor‐1 (IGF‐1) receptor. The first and third domains of the EGF receptor, L1 and L2, are right‐handed beta helices. The second and fourth domains of the EGF receptor, S1 and S2, consist of the modules held together by disulfide bonds, which, except for the first module of the S1 domain, form rod‐like structures. The arrangement of the L1 and S1 domains of the model are similar to that of the first two domains of the IGF‐1 receptor, whereas that of the L2 and S2 domains appear to be significantly different. Using the EGF receptor model and limited information from the literature, we have proposed a number of regions that may be involved in the functioning of the receptor. In particular, the faces containing the large beta sheets in the L1 and L2 domains have been suggested to be involved with ligand binding of EGF to its receptor.
Copper binding to octarepeat peptides of the prion protein monitored by mass spectrometry
Authors: Whittal Randy M. , Ball Haydn L. , Cohen Fred E. , Burlingame Alma L. , Prusiner Stanley B. , Baldwin Michael A. 
Published: October 2010

AbstractElectrospray ionization mass spectrometry (ESI‐MS) was used to measure the binding of Cu2+ ions to synthetic peptides corresponding to sections of the sequence of the mature prion protein (PrP). ESI‐MS demonstrates that Cu2+ is unique among divalent metal ions in binding to PrP and defines the location of the major Cu2+ binding site as the octarepeat region in the N‐terminal domain, containing multiple copies of the repeat ProHisGlyGlyGlyTrpGlyGln. The stoichiometries of the complexes measured directly by ESI‐MS are pH dependent: a peptide containing four octarepeats chelates two Cu2+ ions at pH 6 but four at pH 7.4. At the higher pH, the binding of multiple Cu2+ ions occurs with a high degree of cooperativity for peptides C‐terminally extended to incorporate a fifth histidine. Dissociation constants for each Cu2+ ion binding to the octarepeat peptides, reported here for the first time, are mostly in the low micromolar range; for the addition of the third and fourth Cu2+ ions to the extended peptides at pH 7.4, KD's are <100 nm. n‐terminal acetylation of the peptides caused some reduction in the stoichiometry of binding at both ph's. cu2+ also binds to a peptide corresponding to the extreme N‐terminus of PrP that precedes the octarepeats, arguing that this region of the sequence may also make a contribution to the Cu2+ complexation. Although the structure of the four‐octarepeat peptide is not affected by pH changes in the absence of Cu2+, as judged by circular dichroism, Cu2+ binding induces a modest change at pH 6 and a major structural perturbation at pH 7.4. It is possible that PrP functions as a Cu2+ transporter by binding Cu2+ ions from the extracellular medium under physiologic conditions and then releasing some or all of this metal upon exposure to acidic pH in endosomes or secondary lysosomes.
Amyloid protofilament formation of hen egg lysozyme in highly concentrated ethanol solution
Authors: Goda Shuichiro , Takano Kazufumi , Yutani Katsuhide , Yamagata Yuriko , Nagata Ryou , Akutsu Hideo , Maki Saori , Namba Keiichi 
Published: October 2010

AbstractMutant human lysozymes (Ile56Thr & Asp67His) have been reported to form amyloid deposits in the viscera. From the standpoint of understanding the mechanism of amyloid formation, we searched for conditions of amyloid formation in vitro using hen egg lysozyme, which has been extensively studied from a physicochemical standpoint. It was found that the circular dichroism spectra in the far‐ultraviolet region of the hen egg lysozyme changed to those characteristic of a β‐structure from the native α‐helix rich spectrum in 90% ethanol solution. When the concentration of protein was increased to 10 mg/mL, the protein solution formed a gel in the presence of 90% ethanol, and precipitated on further addition of 10 mM NaCl. The precipitates were examined by electron microscopy, their ability to bind Congo red, and X‐ray diffraction to determine whether amyloid fibrils were formed in the precipitates. Electron micrographs displayed unbranched protofilament with a diameter of ∼70 Å. The peak point of the difference spectrum for the Congo red binding assay was 541 nm, which is characteristic of amyloid fibrils. The X‐ray diffraction pattern showed a sharp and intense diffraction ring at 4.7 Å, a reflection that arises from the interstrand spacing in β‐sheets. These results indicate that the precipitates of hen egg lysozyme are amyloid protofilament, and that the amyloid protofilament formation of hen egg lysozyme closely follows upon the destruction of the helical and tertiary structures.