Prediction of functionally important residues in globular proteins from unusual central distances of amino acids

BMC Structural Biology

Volumn 11, Issue , 2011, Pages

  Kochańczyk, Marek ^a,b  

^a JAGIELLONIAN UNIVERSITY   (Poland)

^b INSTITUTE OF FUNDAMENTAL TECHNOLOGICAL RESEARCH   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; DOCKING PROTEIN; GLOBULAR PROTEIN; LIGAND;

AMINO ACID COMPOSITION; ARTICLE; BINDING SITE; COMPUTATIONAL FLUID DYNAMICS; NONHUMAN; PROTEIN INTERACTION; VALIDATION STUDY;

AMINO ACIDS; BINDING SITES; COMPUTER SIMULATION; LIGANDS; PROTEIN INTERACTION MAPPING; PROTEINS; SOFTWARE;

EID: 80052839469     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-11-34     Document Type: Article

References (93)

1. Computational modeling of structure-function of G protein-coupled receptors with applications for drug design. Li YY, Hou TJ, Goddard WA, Curr Med Chem 2010 17 12 1167 80 10.2174/092986710790827807 20158474
2. Binding site prediction and improved scoring during flexible protein-protein docking with ATTRACT. Fiorucci S, Zacharias M, Proteins 2010 78 15 3131 9 10.1002/prot.22808 20715290
3. Melamine deaminase and atrazine chlorohydrolase: 98 percent identical but functionally different. Seffernick JL, de Souza ML, Sadowsky MJ, Wackett LP, J Bacteriol 2001 183 8 2405 10 10.1128/JB.183.8.2405-2410.2001 11274097 (Pubitemid 32249746)
4. PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. Ivanisenko VA, Pintus SS, Grigorovich DA, Kolchanov NA, Nucleic Acids Res 2004 549 54 15215447
5. A new bioinformatic approach to detect common 3D sites in protein structures. Jambon M, Imberty A, Deléage G, Geourjon C, Proteins 2003 52 2 137 45 10.1002/prot.10339 12833538 (Pubitemid 36828938)
6. Fast and automated functional classification with MED-SuMo: an application on purinebinding proteins. Doppelt-Azeroual O, Delfaud F, Moriaud F, de Brevern AG, Protein Sci 2010 19 4 847 67 10.1002/pro.364 20162627
7. A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Brylinski M, Skolnick J, Proc Natl Acad Sci USA 2008 105 129 34 10.1073/pnas.0707684105 18165317
8. Knowledge-based annotation of small molecule binding sites in proteins. Thangudu RR, Tyagi M, Shoemaker BA, Bryant SH, Panchenko AR, Madej T, BMC Bioinformatics 2010 11 365 10.1186/1471-2105-11-365 20594344
9. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. Laskowski RA, J Mol Graph 1995 13 5 323 30, 307-8 10.1016/0263-7855(95)00073-9 8603061
10. Fast prediction and visualization of protein binding pockets with PASS. Brady GP Jr, Stouten PF, J Comput Aided Mol Des 2000 14 4 383 401 10.1023/A:1008124202956 10815774 (Pubitemid 30219399)
11. POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. Levitt DG, Banaszak LJ, J Mol Graph 1992 10 4 229 34 10.1016/0263-7855(92)80074-N 1476996 (Pubitemid 23018967)
12. LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. Hendlich M, Rippmann F, Barnickel G, J Mol Graph Model 1997 15 6 359 63, 389 10.1016/S1093-3263(98)00002-3 9704298 (Pubitemid 28409807)
13. PocketPicker: analysis of ligand binding-sites with shape descriptors. Weisel M, Proschak E, Schneider G, Chem Cent J 2007 1 7 10.1186/1752-153X-1-7 17880740
14. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Liang J, Edelsbrunner H, Woodward C, Protein Sci 1998 7 9 1884 97 10.1002/pro.5560070905 9761470 (Pubitemid 28432430)
15. Fpocket: an open source platform for ligand pocket detection. Le Guilloux V, Schmidtke P, Tuffery P, BMC Bioinformatics 2009 10 168 10.1186/1471-2105-10- 168 19486540
16. Protein pockets: inventory, shape, and comparison. Coleman RG, Sharp KA, J Chem Inf Model 2010 50 4 589 603 10.1021/ci900397t 20205445
17. Flexibility analysis of enzyme active sites by crystallographic temperature factors. Yuan Z, Zhao J, Wang ZX, Protein Eng 2003 16 2 109 14 10.1093/proeng/gzg014 12676979 (Pubitemid 36458649)
18. Prediction of functionally important residues based solely on the computed energetics of protein structure. Elcock AH, J Mol Biol 2001 312 4 885 96 10.1006/jmbi.2001.5009 11575940 (Pubitemid 33116748)
19. Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods. Bate P, Warwicker J, J Mol Biol 2004 340 2 263 76 10.1016/j.jmb.2004.04.070 15201051 (Pubitemid 38759909)
20. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Laurie ATR, Jackson RM, Bioinformatics 2005 21 9 1908 16 10.1093/bioinformatics/bti315 15701681 (Pubitemid 40668026)
21. Prediction of functional sites based on the fuzzy oil drop model. Brylinski M, Prymula K, Jurkowski W, Kochaczyk M, Stawowczyk E, Konieczny L, Roterman I, PLoS Comput Biol 2007 3 5 94 10.1371/journal.pcbi.0030094 17530916 (Pubitemid 46830599)
22. Evaluation of the searching abilities of HBOP and HBSITE for binding pocket detection. Oda A, Yamaotsu N, Hirono S, J Comput Chem 2009 30 16 2728 37 10.1002/jcc.21299 19399761
23. Characterizing the microenvironment surrounding protein sites. Bagley SC, Altman RB, Protein Sci 1995 4 4 622 35 7613462
24. Prediction of protein-protein interaction sites using patch analysis. Jones S, Thornton JM, J Mol Biol 1997 272 133 43 10.1006/jmbi.1997.1233 9299343 (Pubitemid 27395543)
25. THEMATICS: a simple computational predictor of enzyme function from structure. Ondrechen MJ, Clifton JG, Ringe D, Proc Natl Acad Sci USA 2001 98 22 12473 8 10.1073/pnas.211436698 11606719 (Pubitemid 33019970)
26. Predicting small ligand binding sites in proteins using backbone structure. Bordner AJ, Bioinformatics 2008 24 24 2865 71 10.1093/bioinformatics/ btn543 18940825
27. Automatic prediction of catalytic residues by modeling residue structural neighborhood. Cilia E, Passerini A, BMC Bioinformatics 2010 11 115 10.1186/1471-2105-11-115 20199672
28. Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery. Panjkovich A, Daura X, BMC Struct Biol 2010 10 9 10.1186/1472-6807-10-9 20356358
29. Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces. Burgoyne NJ, Jackson RM, Bioinformatics 2006 22 11 1335 42 10.1093/bioinformatics/btl079 16522669 (Pubitemid 43985269)
30. Partial order optimum likelihood (POOL): maximum likelihood prediction of protein active site residues using 3D structure and sequence properties. Tong W, Wei Y, Murga LF, Ondrechen MJ, Williams RJ, PLoS Comput Biol 2009 5 1000266 10.1371/journal.pcbi.1000266 19148270
31. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA, PLoS Comput Biol 2009 5 12 1000585 10.1371/journal.pcbi. 1000585 19997483
32. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. Huang B, Schroeder M, BMC Struct Biol 2006 6 19 10.1186/1472-6807-6-19 16995956 (Pubitemid 44570436)
33. SitesIdentify: a protein functional site prediction tool. Bray T, Chan P, Bougouffa S, Greaves R, Doig AJ, Warwicker J, BMC Bioinformatics 2009 10 379 10.1186/1471-2105-10-379 19922660
34. ProFunc: a server for predicting protein function from 3D structure. Laskowski RA, Watson JD, Thornton JM, Nucleic Acids Res 2005 89 93 15980588
35. MetaPocket: a meta approach to improve protein ligand binding site prediction. Huang B, OMICS 2009 13 4 325 30 10.1089/omi.2009.0045 19645590
36. Sequence-structure-function relation characterized in silico. Brylinski M, Kochaczyk M, Konieczny L, Roterman I, In Silico Biol 2006 6 6 589 600 17518766 (Pubitemid 47028647)
37. Analysis of protein-protein interaction sites using surface patches. Jones S, Thornton JM, J Mol Biol 1997 272 121 32 10.1006/jmbi.1997.1234 9299342 (Pubitemid 27395542)
38. Gauss-function-based model of hydrophobicity density in proteins. Konieczny L, Brylinski M, Roterman I, In Silico Biol 2006 6 1-2 15 22 16789910 (Pubitemid 43905152)
39. Description of atomic burials in compact globular proteins by Fermi-Dirac probability distributions. Gomes ALC, de Rezende JR, Pereira de Araújo AF, Shakhnovich EI, Proteins 2007 66 2 304 20 17109406 (Pubitemid 46053464)
40. Some factors in the interpretation of protein denaturation. Kauzmann W, Adv Protein Chem 1959 14 1 63 14404936
41. An analysis of packing in the protein folding problem. Richards FM, Lim WA, Q Rev Biophys 1993 26 4 423 98 10.1017/S0033583500002845 8058892 (Pubitemid 24141020)
42. Dominant forces in protein folding. Dill KA, Biochemistry 1990 29 31 7133 55 10.1021/bi00483a001 2207096 (Pubitemid 20230041)
43. Hydrophobicity, hydrophilicity, and the radial and orientational distributions of residues in native proteins. Rackovsky S, Scheraga HA, Proc Natl Acad Sci USA 1977 74 12 5248 51 10.1073/pnas.74.12.5248 271950
44. Amino acid interaction preferences in proteins. Jha AN, Vishveshwara S, Banavar JR, Protein Sci 2010 19 3 603 16 10.1002/pro.339 20073083
45. Correlation of the amino acid composition of a protein to its structural and biological characters. Nishikawa K, Ooi T, J Biochem 1982 91 5 1821 4 7096320
46. Application of amino acid occurrence for discriminating different folding types of globular proteins. Taguchi Yh, Gromiha MM, BMC Bioinformatics 2007 8 404 10.1186/1471-2105-8-404 17953741
47. What determines protein folding type? An investigation of intrinsic structural properties and its implications for understanding folding mechanisms. Ma BG, Chen LL, Zhang HY, J Mol Biol 2007 370 3 439 48 10.1016/j.jmb.2007.04. 051 17524416 (Pubitemid 46898431)
48. Global characteristics of protein sequences and their implications. Rackovsky S, Proc Natl Acad Sci USA 2010 107 19 8623 6 10.1073/pnas.1001299107 20421501
49. Exploiting amino acid composition for predicting protein-protein interactions. Roy S, Martinez D, Platero H, Lane T, Werner-Washburne M, PLoS One 2009 4 11 7813 10.1371/journal.pone.0007813 19936254
50. The Protein Data Bank. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE, Nucleic Acids Res 2000 28 235 42 10.1093/nar/28.1.235 10592235 (Pubitemid 30047768)
51. Shapes of flexible vesicles at constant volume. Baumgärtner A, J Chem Phys 1993 98 7496 7501 10.1063/1.464689
52. Compactness determines protein folding type. Galzitskaya OV, Bogatyreva NS, Ivankov DN, J Bioinform Comput Biol 2008 6 4 667 80 10.1142/ S0219720008003618 18763735
53. SCOP: a structural classification of proteins database for the investigation of sequences and structures. Murzin AG, Brenner SE, Hubbard T, Chothia C, J Mol Biol 1995 247 4 536 40 7723011
54. CATH-a hierarchic classification of protein domain structures. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM, Structure 1997 5 8 1093 108 10.1016/S0969-2126(97)00260-8 9309224 (Pubitemid 27393093)
55. Clustering of highly homologous sequences to reduce the size of large protein databases. Li W, Jaroszewski L, Godzik A, Bioinformatics 2001 17 3 282 3 10.1093/bioinformatics/17.3.282 11294794 (Pubitemid 32288218)
56. Localization of ligand binding site in proteins identified in silico. Brylinski M, Kochanczyk M, Broniatowska E, Roterman I, J Mol Model 2007 13 6-7 665 75 10.1007/s00894-007-0191-x 17394030 (Pubitemid 47023390)
57. Scaling behavior of some molecular shape descriptors of polymer chains and protein backbones. Arteca GA, Phys Rev E 1994 49 3 2417 2428 10.1103/PhysRevE.49.2417
58. The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Porter CT, Bartlett GJ, Thornton JM, Nucleic Acids Res 2004 129 33 14681376
59. Reduced surface: an efficient way to compute molecular surfaces. Sanner MF, Olson AJ, Spehner JC, Biopolymers 1996 38 3 305 20 10.1002/(SICI)1097- 0282(199603)38:3<305::AID-BIP4>3.0.CO;2-Y 8906967
60. Protein-protein docking benchmark version 4.0. Hwang H, Vreven T, Janin J, Weng Z, Proteins 2010 78 15 3111 4 10.1002/prot.22830 20806234
61. Integrating statistical pair potentials into protein complex prediction. Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, Weng Z, Proteins 2007 69 3 511 20 10.1002/prot.21502 17623839 (Pubitemid 47628683)
62. ZRANK: reranking protein docking predictions with an optimized energy function. Pierce B, Weng Z, Proteins 2007 67 4 1078 86 10.1002/prot.21373 17373710 (Pubitemid 46753952)
63. ASPDock: protein-protein docking algorithm using atomic solvation parameters model. Li L, Guo D, Huang Y, Liu S, Xiao Y, BMC Bioinformatics 2011 12 36 10.1186/1471-2105-12-36 21269517
64. Modelling protein docking using shape complementarity, electrostatics and biochemical information. Gabb HA, Jackson RM, Sternberg MJ, J Mol Biol 1997 272 106 20 10.1006/jmbi.1997.1203 9299341 (Pubitemid 27395541)
65. Protein-protein docking benchmark version 3.0. Hwang H, Pierce B, Mintseris J, Janin J, Weng Z, Proteins 2008 73 3 705 9 10.1002/prot.22106 18491384 (Pubitemid 352788651)
66. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, Martz E, Ben-Tal N, Bioinformatics 2003 19:163 4 10.1093/bioinformatics/19.1.163 12499312 (Pubitemid 36150199)
67. The hydrophobic moment detects periodicity in protein hydrophobicity. Eisenberg D, Weiss RM, Terwilliger TC, Proc Natl Acad Sci USA 1984 81 140 4 10.1073/pnas.81.1.140 6582470 (Pubitemid 14180843)
68. Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues. Wu S, Liu T, Altman RB, BMC Struct Biol 2010 10 4 10.1186/1472-6807-10-4 20122268
69. Cysteine function governs its conservation and degeneration and restricts its utilization on protein surfaces. Marino SM, Gladyshev VN, J Mol Biol 2010 404 5 902 16 10.1016/j.jmb.2010.09.027 20950627
70. Comparison of molecular structures of proteins: helix content; distribution of apolar residues. Klotz IM, Arch Biochem Biophys 1970 138 2 704 6 10.1016/0003-9861(70)90401-7 4988452
71. Analysis of accessible surface of residues in proteins. Lins L, Thomas A, Brasseur R, Protein Sci 2003 12 7 1406 17 10.1110/ps.0304803 12824487 (Pubitemid 36759345)
72. Empirical studies of hydrophobicity. 1. Effect of protein size on the hydrophobic behavior of amino acids. Meirovitch H, Rackovsky S, Scheraga HA, Macromolecules 1980 13 6 1398 1405 10.1021/ma60078a013
73. Looking at enzymes from the inside out: the proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interfaces. Ben-Shimon A, Eisenstein M, J Mol Biol 2005 351 2 309 26 10.1016/j.jmb.2005.06.047 16019028 (Pubitemid 41007750)
74. Prediction of protein residue contacts with a PDB-derived likelihood matrix. Singer MS, Vriend G, Bywater RP, Protein Eng 2002 15 9 721 5 10.1093/protein/15.9.721 12456870 (Pubitemid 35470428)
75. A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites. Xie L, Bourne PE, BMC Bioinformatics 2007 8 Suppl 4 9 10.1186/1471-2105-8-S4-S9 18047732 (Pubitemid 351833828)
76. Pocket similarity: are alpha carbons enough? Feldman HJ, Labute P, J Chem Inf Model 2010 50 8 1466 75 10.1021/ci100210c 20690656
77. Ligand binding: functional site location, similarity and docking. Campbell SJ, Gold ND, Jackson RM, Westhead DR, Curr Opin Struct Biol 2003 13 3 389 95 10.1016/S0959-440X(03)00075-7 12831892 (Pubitemid 36782467)
78. Conservation of residue interactions in a family of Ca-binding proteins. Godzik A, Sander C, Protein Eng 1989 2 8 589 96 10.1093/protein/2.8.589 2813336 (Pubitemid 19212141)
79. Atom depth in protein structure and function. Pintar A, Carugo O, Pongor S, Trends Biochem Sci 2003 28 11 593 7 10.1016/j.tibs.2003.09.004 14607089 (Pubitemid 38352805)
80. Competition of electrostatic and hydrophobic interactions between small hydrophobes and model enclosures. Wang L, Friesner RA, Berne BJ, J Phys Chem B 2010 114 21 7294 301 10.1021/jp100772w 20443643
81. Ligand binding to protein-binding pockets with wet and dry regions. Wang L, Berne BJ, Friesner RA, Proc Natl Acad Sci USA 2011 108 4 1326 30 10.1073/pnas.1016793108 21205906
82. Principles of protein-protein interactions. Jones S, Thornton JM, Proc Natl Acad Sci USA 1996 93 13 20 10.1073/pnas.93.1.13 8552589 (Pubitemid 26038096)
83. Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy. Tuncbag N, Gursoy A, Keskin O, Bioinformatics 2009 25 12 1513 20 10.1093/bioinformatics/btp240 19357097
84. A sequence-compatible amount of native burial information is sufficient for determining the structure of small globular proteins. Pereira de Araujo AF, Onuchic JN, Proc Natl Acad Sci USA 2009 106 45 19001 4 10.1073/pnas.0910851106 19858496
85. Information-theoretic analysis of the reference state in contact potentials used for protein structure prediction. Solis AD, Rackovsky SR, Proteins 2010 78 6 1382 97 20034109
86. Principal eigenvector of contact matrices and hydrophobicity profiles in proteins. Bastolla U, Porto M, Roman HE, Vendruscolo M, Proteins 2005 58 22 30 15523667 (Pubitemid 39665613)
87. Internal motion in protein crystal structures. Schmidt A, Lamzin VS, Protein Sci 2010 19 5 944 53 20198682
88. Hydrophobicity of amino acid residues in globular proteins. Rose GD, Geselowitz AR, Lesser GJ, Lee RH, Zehfus MH, Science 1985 229 4716 834 8 10.1126/science.4023714 4023714 (Pubitemid 16246583)
89. Prediction of protein surface accessibility with information theory. Naderi-Manesh H, Sadeghi M, Arab S, Moosavi Movahedi AA, Proteins 2001 42 4 452 9 10.1002/1097-0134(20010301)42:4<452::AID-PROT40>3.0.CO;2-Q 11170200 (Pubitemid 32179855)
90. Secondary structure prediction: combination of three different methods. Biou V, Gibrat JF, Levin JM, Robson B, Garnier J, Protein Eng 1988 2 3 185 91 10.1093/protein/2.3.185 3237683
91. Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins. Cornette JL, Cease KB, Margalit H, Spouge JL, Berzofsky JA, DeLisi C, J Mol Biol 1987 195 3 659 85 10.1016/0022-2836(87) 90189-6 3656427
92. Amino acid side-chain partition energies and distribution of residues in soluble proteins. Guy HR, Biophys J 1985 47 61 70 10.1016/S0006-3495(85)83877-7 3978191
93. Physicochemical basis of amino acid hydrophobicity scales: evaluation of four new scales of amino acid hydrophobicity coefficients derived from RP-HPLC of peptides. Wilce MCJ, Aguilar MI, Hearn MTW, Analytical Chemistry 1995 67 7 1210 1219 10.1021/ac00103a012