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1.
Identifying calcium-binding sites in proteins is one of the first steps towards predicting and understanding the role of calcium in biological systems for protein structure and function studies. Due to the complexity and irregularity of calcium-binding sites, a fast and accurate method for predicting and identifying calcium-binding protein is needed. Here we report our development of a new fast algorithm (GG) to detect calcium-binding sites. The GG algorithm uses a graph theory algorithm to find oxygen clusters of the protein and a geometric algorithm to identify the center of these clusters. A cluster of four or more oxygen atoms has a high potential for calcium binding. High performance with about 90% site sensitivity and 80% site selectivity has been obtained for three datasets containing a total of 123 proteins. The results suggest that a sphere of a certain size with four or more oxygen atoms on the surface and without other atoms inside is necessary and sufficient for quickly identifying the majority of the calcium-binding sites with high accuracy. Our finding opens a new avenue to visualize and analyze calcium-binding sites in proteins facilitating the prediction of functions from structural genomic information. 相似文献
2.
Metals play a variety of roles in biological processes, and hence their presence in a protein structure can yield vital functional information. Because the residues that coordinate a metal often undergo conformational changes upon binding, detection of binding sites based on simple geometric criteria in proteins without bound metal is difficult. However, aspects of the physicochemical environment around a metal binding site are often conserved even when this structural rearrangement occurs. We have developed a Bayesian classifier using known zinc binding sites as positive training examples and nonmetal binding regions that nonetheless contain residues frequently observed in zinc sites as negative training examples. In order to allow variation in the exact positions of atoms, we average a variety of biochemical and biophysical properties in six concentric spherical shells around the site of interest. At a specificity of 99.8%, this method achieves 75.5% sensitivity in unbound proteins at a positive predictive value of 73.6%. We also test its accuracy on predicted protein structures obtained by homology modeling using templates with 30%-50% sequence identity to the target sequences. At a specificity of 99.8%, we correctly identify at least one zinc binding site in 65.5% of modeled proteins. Thus, in many cases, our model is accurate enough to identify metal binding sites in proteins of unknown structure for which no high sequence identity homologs of known structure exist. Both the source code and a Web interface are available to the public at http://feature.stanford.edu/metals. 相似文献
3.
David R. Cooper Katarzyna Grelewska Chang‐Yub Kim Andrzej Joachimiak Zygmunt S. Derewenda 《Acta Crystallographica. Section F, Structural Biology Communications》2010,66(3):219-224
The crystal structure of the dinB gene product from Geobacillus stearothermophilus (GsDinB) is reported at 2.5 Å resolution. The dinB gene is one of the DNA‐damage‐induced genes and the corresponding protein, DinB, is the founding member of a Pfam family with no known function. The protein contains a four‐helix up–down–down–up bundle that has previously been described in the literature in three disparate proteins: the enzyme MDMPI (mycothiol‐dependent maleylpyruvate isomerase), YfiT and TTHA0303, a member of a small DUF (domain of unknown function). However, a search of the DALI structural database revealed similarities to a further 11 new unpublished structures contributed by structural genomics centers. The sequences of these proteins are quite divergent and represent several Pfam families, yet their structures are quite similar and most (but not all) seem to have the ability to coordinate a metal ion using a conserved histidine‐triad motif. The structural similarities of these diverse proteins suggest that a new Pfam clan encompassing the families that share this fold should be created. The proteins that share this fold exhibit four different quaternary structures: monomeric and three different dimeric forms. 相似文献
4.
Hitomi Takahashi Eiji Inagaki Chizu Kuroishi Tahir H. Tahirov 《Acta Crystallographica. Section D, Structural Biology》2004,60(10):1846-1854
As part of a structural genomics project, the crystal structure of a 314‐amino‐acid protein encoded by Thermus thermophilus HB8 gene TT1099 was solved to 1.75 Å using the multiple‐wavelength anomalous dispersion (MAD) method and a selenomethionine‐incorporated protein. The native protein structure was solved to 1.5 Å using the molecular‐replacement method. Both structures revealed a bound ligand, l ‐glutamate or l ‐glutamine, and a fold related to the periplasmic substrate‐binding proteins (PSBP). Further comparative structural analysis with other PSBP‐fold proteins revealed the conservation of the predicted membrane permease binding surface area and indicated that the T. thermophilus HB8 molecule is most likely to be an l ‐glutamate and/or an l ‐glutamine‐binding protein related to the cluster 3 periplasmic receptors. However, the geometry of ligand binding is unique to the T. thermophilus HB8 molecule. 相似文献
5.
Preethi Ragunathan Barbara Spellerberg Karthe Ponnuraj 《Acta Crystallographica. Section D, Structural Biology》2009,65(12):1262-1269
Adhesion/invasion of pathogenic bacteria is a critical step in infection and is mediated by surface‐exposed proteins termed adhesins. The crystal structure of recombinant Lmb, a laminin‐binding adhesin from Streptococcus agalactiae, has been determined at 2.5 Å resolution. Based on sequence and structural homology, Lmb was placed into the cluster 9 family of the ABC (ATP‐binding cassette) transport system. The structural organization of Lmb closely resembles that of ABC‐type solute‐binding proteins (SBPs), in which two structurally related globular domains interact with each other to form a metal‐binding cavity at the interface. The bound zinc in Lmb is tetrahedrally coordinated by three histidines and a glutamate from both domains. A comparison of Lmb with other metal transporters revealed an interesting feature of the dimerization of molecules in the crystallographic asymmetric unit in all zinc‐binding transporters. A closer comparison of Lmb with the zinc‐binding ZnuA from Escherichia coli and Synechocystis 6803 suggested that Lmb might undergo a unique structural rearrangement upon metal binding and release. The crystal structure of Lmb provides an impetus for further investigations into the molecular basis of laminin binding by human pathogens. Being ubiquitous in all serotypes of group B streptococcus (GBS), the structure of Lmb may direct the development of an efficient vaccine. 相似文献
6.
A structure alignment program aligns two structures by optimizing a scoring function that measures structural similarity. It is highly desirable that such scoring function is independent of the sizes of proteins in comparison so that the significance of alignment across different sizes of the protein regions aligned is comparable. Here, we developed a new score called SP‐score that fixes the cutoff distance at 4 Å and removed the size dependence using a normalization prefactor. We further built a program called SPalign that optimizes SP‐score for structure alignment. SPalign was applied to recognize proteins within the same structure fold and having the same function of DNA or RNA binding. For fold discrimination, SPalign improves sensitivity over TMalign for the chain‐level comparison by 12% and over DALI for the domain‐level comparison by 13% at the same specificity of 99.6%. The difference between TMalign and SPalign at the chain level is due to the inability of TMalign to detect single domain similarity between multidomain proteins. For recognizing nucleic acid binding proteins, SPalign consistently improves over TMalign by 12% and DALI by 31% in average value of Mathews correlation coefficients for four datasets. SPalign with default setting is 14% faster than TMalign. SPalign is expected to be useful for function prediction and comparing structures with or without domains defined. The source code for SPalign and the server are available at http://sparks.informatics.iupui.edu . Proteins 2012;. © 2012 Wiley Periodicals, Inc. 相似文献
7.
Shu‐Min Kuan Hsiao‐Chi Chen Chi‐Hung Huang Chi‐Huang Chang Sheng‐Chia Chen Chia Shin Yang Yeh Chen 《Acta Crystallographica. Section F, Structural Biology Communications》2013,69(1):80-82
MJ0927 is a member of the Nif3 family and is widely distributed across living organisms. Although several crystal structures of Nif3 proteins have been reported, structural information on archaeal Nif3 is still limited. To understand the structural differences between bacterial and archaeal Nif3 proteins, MJ0927 from Methanocaldococcus jannaschii was purified and crystallized using the sitting‐drop vapour‐diffusion method. The crystals diffracted to a resolution of 2.47 Å and belonged to the orthorhombic space group C222, with unit‐cell parameters a = 81.21, b = 172.94, c = 147.42 Å. Determination of this structure may provide insights into the function of MJ0927. 相似文献
8.
Sodhi JS Bryson K McGuffin LJ Ward JJ Wernisch L Jones DT 《Journal of molecular biology》2004,342(1):307-320
The accurate prediction of the biochemical function of a protein is becoming increasingly important, given the unprecedented growth of both structural and sequence databanks. Consequently, computational methods are required to analyse such data in an automated manner to ensure genomes are annotated accurately. Protein structure prediction methods, for example, are capable of generating approximate structural models on a genome-wide scale. However, the detection of functionally important regions in such crude models, as well as structural genomics targets, remains an extremely important problem. The method described in the current study, MetSite, represents a fully automatic approach for the detection of metal-binding residue clusters applicable to protein models of moderate quality. The method involves using sequence profile information in combination with approximate structural data. Several neural network classifiers are shown to be able to distinguish metal sites from non-sites with a mean accuracy of 94.5%. The method was demonstrated to identify metal-binding sites correctly in LiveBench targets where no obvious metal-binding sequence motifs were detectable using InterPro. Accurate detection of metal sites was shown to be feasible for low-resolution predicted structures generated using mGenTHREADER where no side-chain information was available. High-scoring predictions were observed for a recently solved hypothetical protein from Haemophilus influenzae, indicating a putative metal-binding site. 相似文献
9.
Takashi Wada Mikako Shirouzu Takaho Terada Yoshiko Ishizuka Takayoshi Matsuda Takanori Kigawa Seiki Kuramitsu Sam‐Yong Park Jeremy R. H. Tame Shigeyuki Yokoyama 《Acta Crystallographica. Section D, Structural Biology》2003,59(7):1213-1218
TT1466 is a hypothetical protein from the extremely thermophilic bacterium Thermus thermophilus HB8 and is highly conserved in bacteria and archaea. The selenomethionyl protein was synthesized by a cell‐free system and the crystal structure was determined at 2.0 Å by MAD phasing. A native crystal was used for structure refinement to 1.7 Å. The structure is highly homologous to that of the CoA‐binding domain of the succinyl‐CoA synthetase from Escherichia coli, despite the protein having only 14% sequence identity to this domain. An isothermal titration calorimetry experiment was performed to investigate whether TT1466 binds CoA and revealed high‐affinity CoA binding of TT1466. 相似文献
10.
To identify functional structural motifs from protein structures of unknown function becomes increasingly important in recent years due to the progress of the structural genomics initiatives. Although certain structural patterns such as the Asp-His-Ser catalytic triad are easy to detect because of their conserved residues and stringently constrained geometry, it is usually more challenging to detect a general structural motifs like, for example, the betabetaalpha-metal binding motif, which has a much more variable conformation and sequence. At present, the identification of these motifs usually relies on manual procedures based on different structure and sequence analysis tools. In this study, we develop a structural alignment algorithm combining both structural and sequence information to identify the local structure motifs. We applied our method to the following examples: the betabetaalpha-metal binding motif and the treble clef motif. The betabetaalpha-metal binding motif plays an important role in nonspecific DNA interactions and cleavage in host defense and apoptosis. The treble clef motif is a zinc-binding motif adaptable to diverse functions such as the binding of nucleic acid and hydrolysis of phosphodiester bonds. Our results are encouraging, indicating that we can effectively identify these structural motifs in an automatic fashion. Our method may provide a useful means for automatic functional annotation through detecting structural motifs associated with particular functions. 相似文献
11.
Vladimir A. Meshcheryakov Inna Krieger Alla S. Kostyukova Fadel A. Samatey 《Acta Crystallographica. Section D, Structural Biology》2011,67(9):822-825
Tropomyosin (TM) is an elongated two‐chain protein that binds along actin filaments. Important binding sites are localized in the N‐terminus of tropomyosin. The structure of the N‐terminus of the long muscle α‐TM has been solved by both NMR and X‐ray crystallography. Only the NMR structure of the N‐terminus of the short nonmuscle α‐TM is available. Here, the crystal structure of the N‐terminus of the short nonmuscle α‐TM (αTm1bZip) at a resolution of 0.98 Å is reported, which was solved from crystals belonging to space group P31 with unit‐cell parameters a = b = 33.00, c = 52.03 Å, α = β = 90, γ = 120°. The first five N‐terminal residues are flexible and residues 6–35 form an α‐helical coiled coil. The overall fold and the secondary structure of the crystal structure of αTM1bZip are highly similar to the NMR structure and the atomic coordinates of the corresponding Cα atoms between the two structures superimpose with a root‐mean‐square deviation of 0.60 Å. The crystal structure validates the NMR structure, with the positions of the side chains being determined precisely in our structure. 相似文献
12.
A data set of 89 protein-RNA complexes has been extracted from the Protein Data Bank, and the nucleic acid recognition sites characterized through direct contacts, accessible surface area, and secondary structure motifs. The differences between RNA recognition sites that bind to RNAs in functional classes has also been analyzed. Analysis of the complete data set revealed that van der Waals interactions are more numerous than hydrogen bonds and the contacts made to the nucleic acid backbone occur more frequently than specific contacts to nucleotide bases. Of the base-specific contacts that were observed, contacts to guanine and adenine occurred most frequently. The most favored amino acid-nucleotide pairings observed were lysine-phosphate, tyrosine-uracil, arginine-phosphate, phenylalanine-adenine and tryptophan-guanine. The amino acid propensities showed that positively charged and polar residues were favored as expected, but also so were tryptophan and glycine. The propensities calculated for the functional classes showed trends similar to those observed for the complete data set. However, the analysis of hydrogen bond and van der Waal contacts showed that in general proteins complexed with messenger RNA, transfer RNA and viral RNA have more base specific contacts and less backbone contacts than expected, while proteins complexed with ribosomal RNA have less base-specific contacts than the expected. Hence, whilst the types of amino acids involved in the interfaces are similar, the distribution of specific contacts is dependent upon the functional class of the RNA bound. 相似文献
13.
Spectroscopic methods were used to monitor the unfolding of the leucine specific (LS) and the leucine-isoleucine-valine (LIV) binding proteins. Our studies indicate that ligand-free protein undergoes a simple two-state unfolding, whereas the protein-ligand complex undergoes a three-state unfolding model. Ligand binding causes significant stabilization of both proteins. There is correlation between ligand hydrophobicity and protein stabilization: the most hydrophobic ligand, isoleucine, causes the most significant stabilization of LIV protein. A disulfide bond present in N-domain of both proteins makes a large contribution to the protein stability of these periplasmic binding receptors. 相似文献
14.
15.
Proteomic survey of copper-binding proteins in Arabidopsis roots by immobilized metal affinity chromatography and mass spectrometry 总被引：1，自引：0，他引：1
To plants, copper is vitally essential at low concentrations but extremely toxic at elevated concentrations. Plants have evolved a suite of mechanisms that modulate the uptake, distribution, and utilization of copper ions. These mechanisms require copper-interacting proteins for transporting, chelating, and sequestrating copper ions. In this study, we have systematically screened for copper-interacting proteins in Arabidopsis roots via copper-immobilized metal affinity chromatography (Cu-IMAC). We also compared Arabidopsis root metalloproteomes with affinity to Cu-IMAC and Zn-IMAC. From the identities of 38 protein spots with affinity to Cu-IMAC, 35 unique proteins were identified. Functional classification of these proteins includes redox/hydrolytic reactions, amino acid metabolism, glutathione metabolism, phosphorylation, translation machinery, membrane-associated proteins, and vegetative storage proteins. Potential copper-interacting motifs were predicted and scored. Six candidate motifs, H-(X)5 -H, H-(X)7 -H, H-(X)12 -H, H-(X)6 -M, M-(X)7 -H, and H-(X)3 -C, are present in Cu-IMAC-isolated proteins with higher frequency than in the whole Arabidopsis proteome. 相似文献
16.
17.
Ying Zhang Florence Reddish Shen Tang You Zhuo Yuan‐Fang Wang Jenny J. Yang Irene T. Weber 《Acta Crystallographica. Section D, Structural Biology》2013,69(12):2309-2319
Calcium ions, which are important signaling molecules, can be detected in the endoplasmic reticulum by an engineered mutant of green fluorescent protein (GFP) designated CatchER with a fast off‐rate. High resolution (1.78–1.20 Å) crystal structures were analyzed for CatchER in the apo form and in complexes with calcium or gadolinium to probe the binding site for metal ions. While CatchER exhibits a 1:1 binding stoichiometry in solution, two positions were observed for each of the metal ions bound within the hand‐like site formed by the carboxylate side chains of the mutated residues S147E, S202D, Q204E, F223E and T225E that may be responsible for its fast kinetic properties. Comparison of the structures of CatchER, wild‐type GFP and enhanced GFP confirmed that different conformations of Thr203 and Glu222 are associated with the two forms of Tyr66 of the chromophore which are responsible for the absorbance wavelengths of the different proteins. Calcium binding to CatchER may shift the equilibrium for conformational population of the Glu222 side chain and lead to further changes in its optical properties. 相似文献
18.
Escherichia coli Hsp100 ClpB plays critical roles in multi‐chaperone systems in cell physiology. After being activated by protein or peptide binding, ClpB disaggregates denatured polypeptides by employing ATP hydrolysis and allows other molecular chaperones such as Hsp70 DnaK and Hsp40 DnaJ to refold the non‐native polypeptides. ClpB contains two nucleotide‐binding domains with Walker A and B motifs within their primary sequences. Therefore, ClpB can be classified as a member of the large ATPase family known as ATPases associated with various cellular activities (AAAs). The mechanisms by which the ClpB acts as a molecular chaperone to disaggregate denatured polypeptides are unknown. To investigate how the nucleotide‐binding domain participates in ClpB chaperone activity, we have cloned and crystallized ClpB nucleotide‐binding domain 1 (NBD1). The ClpB NBD1 crystals diffract to 1.80 Å using a synchrotron X‐ray source and belong to the space group P212121, with unit‐cell parameters a = 38.41, b = 65.48, c = 79.13 Å. Structure determination by the MAD method is under way. 相似文献
19.
Viviana Job Anne Marie Di Guilmi Lydie Martin Thierry Vernet Otto Dideberg Andra Dessen 《Acta Crystallographica. Section D, Structural Biology》2003,59(6):1067-1069
The synthesis of the bacterial cell wall requires enzymes which are localized both in the cytoplasm and in the periplasm. Penicillin‐binding proteins (PBPs) catalyze the last, crucial steps in peptidoglycan biosynthesis and several of them are essential for bacterial survival. High‐molecular‐mass PBPs can be bifunctional (class A) or monofunctional (class B) and to date no structural information on any class A PBP is available. To initiate the determination of the three‐dimensional structure of a class A PBP, crystals of the transpeptidase domain of PBP1a from Streptococcus pneumoniae were prepared by limited proteolysis of the full‐length molecule and purification by anion‐exchange chromatography and gel filtration. The samples crystallize in space group C2221, contain one molecule per asymmetric unit and diffract X‐rays to 2.7 Å. Selenomethionine‐labelled crystals have been prepared and structure solution is under way. 相似文献
20.
Ganggang Wang Rong Guo Mark Bartlam Hong Xue Haitao Yang Yiwei Liu Li Huang Zihe Rao 《Acta Crystallographica. Section D, Structural Biology》2002,58(7):1240-1242
A small DNA‐binding protein of 87 amino‐acid residues from the hyperthermophilic archaeon Methanococcus jannaschii (Mja10b) was cloned and overexpressed in Escherichia coli. The protein was crystallized and the crystals belong to the space group P6122/P6522, with unit‐cell parameters a = b = 50.85, c = 124.02 Å, α = β = 90, γ = 120°. The crystals diffracted to a maximum resolution of 2.2 Å at 100 K using Cu Kα radiation. The presence of one molecule per asymmetric unit gives a crystal volume per protein mass (VM) of 2.4 Å3 Da−1 and a solvent content of 49% by volume. A full set of X‐ray diffraction data was collected to 2.2 Å from the native crystal. 相似文献