Структура и функционирование белков. Применение методов биоинформатики - Джон Ригден 2014

Предсказание структуры мембранных белков
Литература

Altschul SF, Koonin EV (1998) Iterated profile searches with PSI-BLAST - a tool for discovery in protein databases. Trends Biochem Sсi 23:444—447

Altschul SF, Wootton JC, Gertz EM, et al. (2005) Protein database searches using compositionally adjusted substitution matrices. FEBS J 272:5099-5100

Amico M, Finelli M, Rossi I, et al. (2006) PONGO: a web server for multiple predictions of all alpha transmembrane proteins. Nucleic Acids Res 34:169—172

Bagos PG, Liakopoulos TD, Spyropoulos IC, et al. (2004) A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins. BMC Bioinformatics 5:29

Bahr A, Thompson JD, Thierry JC, et al. (2001) BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. Nucleic Acids Res 29:323-326

Barth P, Schonbrun J, Baker D (2007) Toward high-resolution prediction and design of transmembrane helical protein structures. Proc Natl Acad Sei USA 104:15682-15687

Bendtsen JD, Nielsen H, von Heijne G, et al. (2004). Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340:783-795

Bernstein FC, Koetzle TF, Williams GJB, et al. (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 112:535-542

Boeckmann B, Bairoch A, Apweiler R, et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31:365-370

Canutescu AA, Shelenkov AA, Dunbrack RL (2003) A graph-theory algorithm for rapid protein side-chain prediction. Protein Sei 12:2001-2014

Claras MG, von Heijne G (1994) TopPred П: an improved software for membrane protein structure predictions. Comput Appl Biosci 10:685-686

Dayhoff MO, Schwartz RM, Orcutt BC (1978) A model of evolutionary change in proteins. Atlas Protein Seq Struct 5:345-352

Donizelli M, Djite MA, Le Novere N (2006) LGICdb: a manually curated sequence database after the genomes. Nucleic Acids Res 34:267-269

Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797

Emanuelsson O, Brunak S, von Heijne G, et al. (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2:953-971

Engelman DM, Steitz ТА, Goldman А (1986) Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu Rev Biophys Biophys Chem 15:321-353

Forrest LR, Tang CL, Honig В (2006) On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins. Biophys J 91:508—517

Ghosh S, Liu XP, Zheng Y, et al. (2001) Rational design of potent and selective EGFR tyrosine kinase inhibitors as anticancer agents. Curr Cancer Drug Targets 1:129-140

Gromiha MM, Ponnuswamy PK (1993) Prediction of transmembrane beta-strands from hydrophobic characteristics of proteins. Int J Pept Protein Res 42:420-431

Gromiha MM, Ahmad S, Suwa M (2004) Neural network-based prediction of transmembrane betastrand segments in outer membrane proteins. J Comput Chem 25:762-767

Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sсi USA 89:10915-10919

Higgins D, Thompson J, Gibson T, et al. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680

Horn F, Bettler E, Oliveira L, et al. (2003) GPCRDB information system for G protein-coupled receptors. Nucleic Acids Res 31:294-297

Jacoboni I, Martelli PL, Fariselli P, et al. (2001) Prediction of the transmembrane regions of beta- barrel membrane proteins with a neural network-based predictor. Protein Sei 10:779-787 Jayasinghe S, Hristova K, White SH (2001) MPtopo: a database of membrane protein topology. Protein Sсi 10:455-458

Jones DT (2001) Predicting novel protein folds by using FRAGFOLD. Proteins 5:127-132

Jones DT (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics 23:538-544

Jones DT, Taylor WR, Thornton JM (1994a) A model recognition approach to the prediction of allhelical membrane protein structure and topology. Biochemsitiy 33:3038-3049

Jones DT, Taylor WR, Thornton JM (1994b) A mutation data matrix for transmembrane proteins. FEBS Lett 339:269-275

Klabunde T, Hessler G (2002) Drug design strategies for targeting G-protein-coupled receptors. ChemBioChem 3:928-944

Koehl P, Delame M (1996) Mean-field minimization methods for biological macromolecules. Curr Opin Struct Biol 6:222-226

Krogh A, Larsson B, von Heijne G, et al. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567-580

Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157:105-132

Kyttälä A, Dirke Q Vesa J, et al. (2004) Two motifs target Batten disease protein CLN3 to lysosomes in transfected nonneuronal and neuronal cells. Mol Biol Cell 15:1313-1323

Käll L, Krogh A, Sonnhammer E (2004) A combined transmembrane topology and signal peptide prediction method. J Mol Biol 338:1027-1036

Käll L, Krogh A, Sonnhammer E (2005) An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics 21:251-257

Li B, Gallin WJ (2004) VKCDB: voltage-gated potassium channel database. BMC Bioinformatics 5:3 Liu Q, Zhu YS, Wang BH, et al. (2003) A HMM-based method to predict the transmembrane regions of beta-barrel membrane proteins. Comput Biol Chem 27:69-76

Lo A, Chiu HS, Sung TY, et al. (2008) Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function. J Proteome Res 7:487-496

Lomize AL, Pogozheva ED, Lomize MA, et al. (2006a) Positioning of proteins in membranes: a computational approach. Protein Sci 15:1318—1333

Lomize MA, Ixjmize AL, Pogozheva ED, et al. (2006b) OPM: orientations of proteins in membranes database. Bioinformatics 22:623-625

Mahajan S, Ghosh S, Sudbeck EA, et al. (1999) Rational design and synthesis of a novel antileukemic agent targeting Bruton’s tyrosine kinase (ВТК), LFM-A13. J Biol Chem 274:9587-9599

Mao Q, Foster BJ, Xia H, et al. (2003) Membrane topology of CLN3, the protein underlying Batten disease. FEBS Lett 541:40-46

Martelli PL, Fariselli P, Krogh A, et al. (2002) A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. Bioinformatics 18:46-53

Martelli PL, Fariselli P, Casadio R (2003) An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins. Bioinformatics 19:205-211

Marti-Renom MA, Stuart AC, Fiser A, et al. (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29:291-325

Melen K, Krogh A, von Heijne G (2003) Reliability measures for membrane protein topology prediction algorithms. J Mol Biol 327:735-744

Möller S, Kriventseva EV, Apweiler R (2000) A collection of well characterised integral membrane proteins. Bioinformatics 16:1159-1160

Müller T, Rahmann S, Rehmsmeier M (2001) Non-symmetric score matrices and the detection of homologous transmembrane proteins. Bioinformatics 17:182-189

Ng PC, HenikofF JQ HenikofFS (2000) PHAT: a transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane. Bioinformatics 16:760-676

Nilsson J, Persson B, von Heijne G (2002) Prediction of partial membrane protein topologies using a consensus approach. Protein Sсi 11:2974—2980

Notredame C, Higgins D, Heringa J (2000) Т-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302:205-217

Park KJ, Gromiha MM, Horton P, et al. (2005) Discrimination of outer membrane proteins using support vector machines. Bioinformatics 21:4223-4229

Peitsch MC (1996) ProMod and Swiss-Model: internet-based tools for automated comparative protein modelling. Biochem Soc Trans 24:274-279

Pellegrini-Calace M, Carotti A, Jones DT (2003) Folding in lipid membranes (FILM): a novel method for the prediction of small membrane protein 3D structures. Proteins 50:537-545

Pirovano W, Feenstra KA, Heringa J (2008). PRALINETM: a strategy for improved multiple alignment of transmembrane proteins. Bioinformatics 24:492-497

Pomillos O, Chen Y, Chen AP, et al. (2005) X-ray structure of the EmrE multidrug transporter in complex with a substrate. Science 310:1950-1953

Raman P, Cherezov V, Caffrey M (2006) The membrane protein data bank. Cell Mol Life Sсi 63:36-51

Rohl CA, Strauss CE, Misura KM, et al. (2004) Protein structure prediction using Rosetta. Method Enzymol 383:66-93

Rost B, Fariselli P, Casadio R (1996) Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci 4:521-533

Saier MH, Tran CV, Barabote RD (2006) TCDB: the Transporter Classification Database for membrane transport protein analyses and information. Nucleic Acids Res 34:181-186.

Samatey FA, Xu C, Popot JL (1995) On the distribution of amino acid residues in transmembrane alpha-helix bundles. Proc Natl Acad Sci USA 92:4577-4581

Sansom SP, Scott KA, Bond PJ (2008) Coarse-grained simulation: a high-throughput computational approach to membrane proteins. Biochem Soc Trans 36:27-32

Schirmer T, Cowan SW (1993) Prediction of membrane-spanning beta-strands and its application to maltoporin. Protein Sci 2:1361—1363

Senes A, Gerstein M, Engelman DM (2000) Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions. J Mol Biol 296:921-936

Shafrir Y, Guy HR (2004) STAM: simple transmembrane alignment method. Bioinformatics 20:758-769

Sanchez R, Sali A (1997) Advances in comparative protein-structure modelling. Curr Opin Struct Biol 7:206-214

Sudbeck EA, Liu XP, Narla RK, et al. (1999) Structure-based design of specific inhibitors of Janus kinase 3 as apoptosis-inducing antileukemic agents. Clin Cancer Res 5:1569-1582

Tang CL, Xie L, Koh IY, et al. (2003) On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles. J Mol Biol 334:1043-1062

Taylor PD, Attwood TK, Flower DR (2003) BPROMPT: a consensus server for membrane protein prediction. Nucleic Acids Res 31:3698-3700

Tusnśdy GE, Simon I (1998) Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J Mol Biol 283:489-506

Tusnśdy GE, Dosztśnyi Z, Simon I (2005a) TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates. Bioinformatics 21:1276-1277

Tusnśdy GE, Dosztśnyi Z, Simon I (2005b) PDB TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res. 33:275-278

Tusnśdy GE, Kalmśr L, Simon I (2008) TOPDB: topology data bank of transmembrane proteins. Nucleic Acids Res 36:234-239

Viklund H, Elofsson A (2008) OCTOPUS: improving topology prediction by two-track ANNbased preference scores and an extended topological grammar. Bioinformatics 24:1662-1668

Viklund H, Granseth E, Elofsson A (2006) Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes. J Mol Biol 361:591-603

Wallin E, Tsukihara T, Yoshikawa S, et al. (1997) Architecture of helix bundle membrane proteins: an analysis of cytochrome c oxidase from bovine mitochondria. Protein Sei 6:808-815

Wallner B, Elofsson A (2005) Pcons5: combining consensus, structural evaluation and fold recognition scores. Protein Sci 14:1315-1327

White S (2004) The progress of membrane protein structure determination. Protein Sci 13:1948-1949

Wimley WC (2003) The versatile beta-barrel membrane protein. Curr Opin Struct Biol 13:404-411

Wimley WC, White SH (1996) Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat Struct Biol 3:842-848

Yarov-Yarovoy V, Baker D, Catterall WA (2006) Voltage sensor conformations in the open and closed states in ROSETTA structural models of K(+) channels. Proc Natl Acad Sci USA 103:7292-7297

Yuan Z, Mattick JS, Teasdale RD (2004) SVMtm: support vector machines to predict trans-membrane segments. J Comput Chem 25:632-636

von Heijne G (1992) Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J Mol Biol 225:487-494