Genomes and Genes
protein structural homology
Summary: The degree of 3-dimensional shape similarity between proteins. It can be an indication of distant AMINO ACID SEQUENCE HOMOLOGY and used for rational DRUG DESIGN.
- Durrant J, Amaro R, Xie L, Urbaniak M, Ferguson M, Haapalainen A, et al. A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. PLoS Comput Biol. 2010;6:e1000648 pubmed publisher..As it is capable of identifying potential secondary targets, the strategy described here may play a useful role in future efforts to reduce drug side effects and/or to increase polypharmacology. ..
- Brylinski M, Skolnick J. FINDSITE: a threading-based approach to ligand homology modeling. PLoS Comput Biol. 2009;5:e1000405 pubmed publisher..Thus, the rather accurate, computationally inexpensive FINDSITE(LHM) algorithm should be a useful approach to assist in the discovery of novel biopharmaceuticals. ..
- Hasegawa H, Holm L. Advances and pitfalls of protein structural alignment. Curr Opin Struct Biol. 2009;19:341-8 pubmed publisher..Advances have been made in algorithmic robustness, multiple alignment, and speeding up database searches. ..
- Angaran S, Bock M, Garutti C, Guerra C. MolLoc: a web tool for the local structural alignment of molecular surfaces. Nucleic Acids Res. 2009;37:W565-70 pubmed publisher..The MolLoc web server is available at http://bcb.dei.unipd.it/MolLoc. ..
- Margraf T, Schenk G, Torda A. The SALAMI protein structure search server. Nucleic Acids Res. 2009;37:W480-4 pubmed publisher..The alignment method is very tolerant of large gaps and insertions, and tends to produce slightly longer alignments than other similar programs. ..
- Launay G, Simonson T. Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations. BMC Bioinformatics. 2008;9:427 pubmed publisher..The results suggest that the simple modelling procedure applied here could help identify and characterize protein-protein complexes. The next step is to apply it on a genomic scale. ..
- Holden L, Prochnow C, Chang Y, Bransteitter R, Chelico L, Sen U, et al. Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications. Nature. 2008;456:121-4 pubmed publisher..These results provide a basis for understanding the underlying mechanisms of substrate specificity for the APOBEC family. ..
- Lo W, Lee C, Lee C, Lyu P. iSARST: an integrated SARST web server for rapid protein structural similarity searches. Nucleic Acids Res. 2009;37:W545-51 pubmed publisher..It can serve as a rapid annotation system for functionally unknown or hypothetical proteins, which are increasing rapidly in this post-genomics era. The server can be accessed at http://sarst.life.nthu.edu.tw/iSARST/. ..
- Huthoff H, Autore F, Gallois Montbrun S, Fraternali F, Malim M. RNA-dependent oligomerization of APOBEC3G is required for restriction of HIV-1. PLoS Pathog. 2009;5:e1000330 pubmed publisher..Accordingly, we propose that occupation of the positively charged pocket by RNA promotes A3G oligomerization, packaging into virions and antiviral function. ..
- Sivasubramanian A, Sircar A, Chaudhury S, Gray J. Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking. Proteins. 2009;74:497-514 pubmed publisher..This first large-scale antibody-antigen docking study using homology models reveals the level of "functional accuracy" of these structural models toward protein engineering applications. ..
- Lolkema J, Slotboom D. The major amino acid transporter superfamily has a similar core structure as Na+-galactose and Na+-leucine transporters. Mol Membr Biol. 2008;25:567-70 pubmed publisher..The APC superfamily contains the major amino acid transporter families that are found throughout life. Insight into their structure will significantly facilitate the studies of this important group of transporters. ..
- Cheng J. A multi-template combination algorithm for protein comparative modeling. BMC Struct Biol. 2008;8:18 pubmed publisher..We have developed a novel multi-template algorithm to improve protein comparative modeling. ..
- Guerler A, Knapp E. Novel protein folds and their nonsequential structural analogs. Protein Sci. 2008;17:1374-82 pubmed publisher..A web server is available at http://agknapp.chemie.fu-berlin.de/gplus for pairwise alignment, visualization, and database comparison. ..
- Pei J, Kim B, Grishin N. PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res. 2008;36:2295-300 pubmed publisher..PROMALS3D outperforms a number of existing methods for constructing multiple sequence or structural alignments using both reference-dependent and reference-independent evaluation methods. ..
- Mosca R, Schneider T. RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes. Nucleic Acids Res. 2008;36:W42-6 pubmed publisher..The RAPIDO server, with related documentation, is available at http://webapps.embl-hamburg.de/rapido. ..
- Bauer R, Bourne P, Formella A, Frommel C, Gille C, Goede A, et al. Superimpose: a 3D structural superposition server. Nucleic Acids Res. 2008;36:W47-54 pubmed publisher..The search for structurally similar proteins allows the detection of similar folds with different backbone topology. The Superimposé server is available at: http://bioinformatics.charite.de/superimpose. ..
- Chiang R, Sali A, Babbitt P. Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PLoS Comput Biol. 2008;4:e1000142 pubmed publisher..Because the method is automated, it is suitable for large-scale characterization and comparison of fundamental functional capabilities of both characterized and uncharacterized enzyme superfamilies. ..
- Horsefield R, Nordén K, Fellert M, Backmark A, Törnroth Horsefield S, Terwisscha van Scheltinga A, et al. High-resolution x-ray structure of human aquaporin 5. Proc Natl Acad Sci U S A. 2008;105:13327-32 pubmed publisher..We postulate that a change in the conformation of the C terminus may arise from the phosphorylation of AQP5 and thereby signal trafficking. ..
- Ginzinger S, Coles M. SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database. J Biomol NMR. 2009;43:179-85 pubmed publisher..Thus SimShiftDB can be seen as a complement to currently available methods. ..
- Routsias J, Kyriakidis N, Latreille M, Tzioufas A. RNA recognition motif (RRM) of La/SSB: the bridge for interparticle spreading of autoimmune response to U1-RNP. Mol Med. 2010;16:19-26 pubmed publisher..Identification of key sequences that trigger and perpetuate the autoimmune process is particularly important for understanding pathogenetic mechanisms in autoimmunity. ..
- Faucher F, Wallace S, Doubli S. Structural basis for the lack of opposite base specificity of Clostridium acetobutylicum 8-oxoguanine DNA glycosylase. DNA Repair (Amst). 2009;8:1283-9 pubmed publisher..A structural comparison with human OGG1 provides a rationale for the lack of opposite base specificity displayed by the bacterial Ogg...
- Atanassova N, Grainge I. Biochemical characterization of the minichromosome maintenance (MCM) protein of the crenarchaeote Aeropyrum pernix and its interactions with the origin recognition complex (ORC) proteins. Biochemistry. 2008;47:13362-70 pubmed publisher..Further it was found that ORC2 could autophosphorylate in the presence of ATP and more remarkably could phosphorylate MCM in a species-specific manner...
- Pintilie G, Zhang J, Goddard T, Chiu W, Gossard D. Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. J Struct Biol. 2010;170:427-38 pubmed publisher..We describe both interactive and automated ways of using these two methods. Finally, we show segmentation and fitting results for several experimentally-obtained density maps. ..
- Sharma M, Khanna S, Bulusu G, Mitra A. Comparative modeling of thioredoxin glutathione reductase from Schistosoma mansoni: a multifunctional target for antischistosomal therapy. J Mol Graph Model. 2009;27:665-75 pubmed publisher..This also augments recent observations reported on the basis of X-ray structure data on SmTGR monomer lacking the C-terminal selenocysteine tail. ..
- Johansen N, Weber R, Ipsen H, Barber D, Broge L, Hejl C. Extensive IgE cross-reactivity towards the Pooideae grasses substantiated for a large number of grass-pollen-sensitized subjects. Int Arch Allergy Immunol. 2009;150:325-34 pubmed publisher..The data suggest equal effect upon use of any of the Pooideae species for diagnostic as well as therapeutic purposes. ..
- Rydberg E, Cellucci A, Bartholomew L, Mattu M, Barbato G, Ludmerer S, et al. Structural basis for resistance of the genotype 2b hepatitis C virus NS5B polymerase to site A non-nucleoside inhibitors. J Mol Biol. 2009;390:1048-59 pubmed publisher..Together, these data suggest that differences in the amino acid composition and shape of the indole-N-acetamide binding pocket are responsible for the resistance of the 2b polymerase to this class of inhibitors. ..
- Mukai Y, Shibata H, Nakamura T, Yoshioka Y, Abe Y, Nomura T, et al. Structure-function relationship of tumor necrosis factor (TNF) and its receptor interaction based on 3D structural analysis of a fully active TNFR1-selective TNF mutant. J Mol Biol. 2009;385:1221-9 pubmed publisher..This phage display technique can be used to efficiently construct functional mutants for analysis of the TNF structure-function relationship, which might facilitate in silico drug design based on receptor selectivity. ..
- Rossi K, Nayeem A, Weigelt C, Krystek S. Closing the side-chain gap in protein loop modeling. J Comput Aided Mol Des. 2009;23:411-8 pubmed publisher..In this study, we report on the ability to model loop side-chains accurately using a variety of commercially available algorithms that include rotamer libraries, systematic torsion scans and knowledge-based methods. ..
- Mares Sámano S, Badhan R, Penny J. Identification of putative steroid-binding sites in human ABCB1 and ABCG2. Eur J Med Chem. 2009;44:3601-11 pubmed publisher..No overlap between ATP- and RU-486-binding sites was predicted in either NBD, though overlaps between ATP- and steroid-binding sites were predicted in the vicinity of the P-Loop in both nucleotide-binding domains. ..
- Chen C, Nelson C, Khauv D, Bennett S, Radisky E, Hirai Y, et al. Homology with vesicle fusion mediator syntaxin-1a predicts determinants of epimorphin/syntaxin-2 function in mammary epithelial morphogenesis. J Biol Chem. 2009;284:6877-84 pubmed publisher..These results provide a dramatic demonstration of the use of structural information about one molecule to define a functional motif of a second molecule that is related at the sequence level but highly divergent functionally...
- Zhang M, Liu J, Kim Y, Dixon J, Pfaff S, Gill G, et al. Structural and functional analysis of the phosphoryl transfer reaction mediated by the human small C-terminal domain phosphatase, Scp1. Protein Sci. 2010;19:974-86 pubmed publisher..Our results strongly suggest that Asp206 and its equivalent residues in other HAD family members play important structural and possible mechanistic roles. ..
- Tuccinardi T, Botta M, Giordano A, Martinelli A. Protein kinases: docking and homology modeling reliability. J Chem Inf Model. 2010;50:1432-41 pubmed publisher..Our results suggest that in many cases this approach can give better results than the classical homology modeling procedure based exclusively on the sequence homology. ..
- Karpov P, Nadezhdina E, Yemets A, Matusov V, Nyporko A, Shashina N, et al. Bioinformatic search of plant microtubule-and cell cycle related serine-threonine protein kinases. BMC Genomics. 2010;11 Suppl 1:S14 pubmed publisher..Analysis of STALK's three-dimensional structure confirmed its relationship to the subgroup of AURKA-like protein kinases. ..
- Tsou H, MacEwan G, Birnberg G, Zhang N, Brooijmans N, Toral Barza L, et al. 4-Substituted-7-azaindoles bearing a ureidobenzofuranone moiety as potent and selective, ATP-competitive inhibitors of the mammalian target of rapamycin (mTOR). Bioorg Med Chem Lett. 2010;20:2259-63 pubmed publisher..Furthermore, modeling showed that the ureido group is best situated at C-5 of the benzofuranone. Syntheses of 4-ureido and 5-ureidobenzofuranones are presented. ..
- Calderón Cortés N, Watanabe H, Cano Camacho H, Zavala Páramo G, Quesada M. cDNA cloning, homology modelling and evolutionary insights into novel endogenous cellulases of the borer beetle Oncideres albomarginata chamela (Cerambycidae). Insect Mol Biol. 2010;19:323-36 pubmed publisher..However, the presence of GHF45 cellulases in ancient molluscan taxa puts into question the hypothesis of horizontal gene transfer for the evolution of cellulases in animals. ..
- Potapov V, Cohen M, Inbar Y, Schreiber G. Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions. BMC Bioinformatics. 2010;11:374 pubmed publisher..The same methodology is applicable to other areas involving high-resolution modelling of biomolecules. ..
- Zhang Q, Petrey D, Norel R, Honig B. Protein interface conservation across structure space. Proc Natl Acad Sci U S A. 2010;107:10896-901 pubmed publisher..The performance of PredUs, as measured through comparisons with other methods, suggests that relationships across protein structure space can be successfully exploited in the prediction of protein-protein interactions. ..
- Jacoby E, Boettcher A, Mayr L, Brown N, Jenkins J, Kallen J, et al. Knowledge-based virtual screening: application to the MDM4/p53 protein-protein interaction. Methods Mol Biol. 2009;575:173-94 pubmed publisher..Novel, selective and dual hits are discovered for both systems. A hit rate analysis will be provided compared to the full HTS (High-throughput Screening). ..
- Li L, Cheng N, Hirschi K, Wang X. Structure of Arabidopsis chloroplastic monothiol glutaredoxin AtGRXcp. Acta Crystallogr D Biol Crystallogr. 2010;66:725-32 pubmed publisher..This study provides the first structural information on plant CGFS-type monothiol Grxs, allowing a better understanding of the redox-regulation mechanism mediated by these plant Grxs. ..
- Guerler A, Knapp E. GIS: a comprehensive source for protein structure similarities. Nucleic Acids Res. 2010;38:W46-52 pubmed publisher..75) or symmetry analysis. GIS is publicly available at http://agknapp.chemie.fu-berlin.de/gplus. ..
- Singh P, Patil K, Khanduja J, Kumar P, Williams A, Rossi F, et al. Mycobacterium tuberculosis UvrD1 and UvrA proteins suppress DNA strand exchange promoted by cognate and noncognate RecA proteins. Biochemistry. 2010;49:4872-83 pubmed publisher..These observations are consistent with a molecular mechanism, whereby M. tuberculosis UvrA and UvrD1, acting together, block DNA strand exchange promoted by cognate and noncognate RecA proteins...
- Seffernick J, Reynolds E, Fedorov A, Fedorov E, Almo S, Sadowsky M, et al. X-ray structure and mutational analysis of the atrazine Chlorohydrolase TrzN. J Biol Chem. 2010;285:30606-14 pubmed publisher..93 and 1.64 Å resolution, respectively. Both structure and kinetic determinations suggest that the Glu(241) side chain provides a proton to N-1 of the s-triazine substrate to facilitate nucleophilic displacement at the adjacent C-2. ..
- Mascarenhas N, Bhattacharyya D, Ghoshal N. Why pyridine containing pyrido[2,3-d]pyrimidin-7-ones selectively inhibit CDK4 than CDK2: insights from molecular dynamics simulation. J Mol Graph Model. 2010;28:695-706 pubmed publisher..Although these proteins have similar folds, the results from principal component analysis (PCA) indicate that CDK4 and CDK2 follow an anti-correlated behavior towards the accessibility of the active site. ..
- Chen Z, Jawhari A, Fischer L, Buchen C, Tahir S, Kamenski T, et al. Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry. EMBO J. 2010;29:717-26 pubmed publisher..This work establishes cross-linking/MS as an integrated structure analysis tool for large multi-protein complexes. ..
- Kanou K, Hirata T, Iwadate M, Terashi G, Umeyama H, Takeda Shitaka M. HUMAN FAMSD-BASE: high quality protein structure model database for the human genome using the FAMSD homology modeling method. Chem Pharm Bull (Tokyo). 2010;58:66-75 pubmed..The HUMAN FAMSD-BASE will have an important impact on the progress of biological science. ..
- Qiu L, Ma J, Wang J, Zhang F, Wang Y. Thermal stability properties of an antifreeze protein from the desert beetle Microdera punctipennis. Cryobiology. 2010;60:192-7 pubmed publisher..This study suggests that MpAFP698 has a high thermal stability and could be used to improve the thermal stability of the less stable proteins by producing fusion proteins, which could be used for biotechnological purposes. ..
- Arafat Y, Fenalti G, Whisstock J, Mackay I, Garcia de la Banda M, Rowley M, et al. Structural determinants of GAD antigenicity. Mol Immunol. 2009;47:493-505 pubmed publisher..This could well apply to the various other enzyme autoantigens and, if so, these features could be used as the basis of future predictive strategies. ..
- Koopmann R, Muhammad K, Perbandt M, Betzel C, Duszenko M. Trypanosoma brucei ATG8: structural insights into autophagic-like mechanisms in protozoa. Autophagy. 2009;5:1085-91 pubmed..1. Thus membrane formation during appearance of the autophagic bodies seems very similar in trypanosomes and their higher eukaryotic counterpart. ..
- Tamura H, Saito Y, Ashida H, Kai Y, Inoue T, Yokota A, et al. Structure of the apo decarbamylated form of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus subtilis. Acta Crystallogr D Biol Crystallogr. 2009;65:942-51 pubmed publisher..Based on these results, the characteristic structural features of DK-MTP-1P enolase are discussed. ..
- Yamamura A, Okada A, Kameda Y, Ohtsuka J, Nakagawa N, Ebihara A, et al. Structure of TTHA1623, a novel metallo-beta-lactamase superfamily protein from Thermus thermophilus HB8. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009;65:455-9 pubmed publisher..However, TTHA1623 exhibits a putative substrate-binding pocket with a unique shape...
- Vallat B, Pillardy J, Májek P, Meller J, Blom T, Cao B, et al. Building and assessing atomic models of proteins from structural templates: learning and benchmarks. Proteins. 2009;76:930-45 pubmed publisher..This algorithm is a component of the prediction server LOOPP (http://www.loopp.org). Large-scale training and tests sets were designed and are presented. Recent results of the LOOPP server in CASP8 are discussed. ..
- Torrent G, Benito A, Castro J, Ribo M, Vilanova M. Contribution of the C30/C75 disulfide bond to the biological properties of onconase. Biol Chem. 2008;389:1127-36 pubmed publisher..These results suggest that the C30/C75 disulfide bond could easily be reduced under physiological redox conditions. ..
- Han W, Wang Y, Zhou Y, Yao Y, Li Z, Feng Y. Understanding structural/functional properties of amidase from Rhodococcus erythropolis by computational approaches. J Mol Model. 2009;15:481-7 pubmed publisher..The new structural and mechanistic insights gained from this computational study should be useful in elucidating the detailed structures and mechanisms of amidase and other homologous members of the amidase signature family. ..
- Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T. The SWISS-MODEL Repository and associated resources. Nucleic Acids Res. 2009;37:D387-92 pubmed publisher..proteinmodelportal.org) of the PSI Structural Genomics Knowledge Base facilitates the navigation between protein sequence and structure resources. ..
- Schulman S, Wang B, Li W, Rapoport T. Vitamin K epoxide reductase prefers ER membrane-anchored thioredoxin-like redox partners. Proc Natl Acad Sci U S A. 2010;107:15027-32 pubmed publisher..Taken together, our results demonstrate that human VKOR employs the same electron transfer pathway as its bacterial homologs and that VKORs generally prefer membrane-bound Trx-like redox partners. ..
- Agarwal V, Remmert M, Biegert A, Söding J. PDBalert: automatic, recurrent remote homology tracking and protein structure prediction. BMC Struct Biol. 2008;8:51 pubmed publisher..PDBalert will accelerate the information flow from the PDB database to all those who can profit from the newly released protein structures for predicting the 3D structure or function of their proteins of interest. ..