An insight into the general relationship between the three dimensional structures of enzymes and their electronic wave functions: Implication for the prediction of functional sites of enzymes

Proteins: Structure, Function and Genetics

Volumn 71, Issue 4, 2008, Pages 1940-1954

  Fukushima, K ^a   Wada, M ^b   Sakurai, M ^a  

^a Tokyo Institute of Technology ^*  (Japan)

^b FUJITSU LABORATORIES LTD   (Japan)

Author keywords

Catalytic residues; Enzyme; Hydration; Molecular orbital; Structural genomics; Wave functions of enzymes

Indexed keywords

ASPARAGINE; GLUTAMINE;

ARTICLE; CALCULATION; COVALENT BOND; ELECTRON; ELECTRONICS; ENZYME STRUCTURE; LINEAR SYSTEM; MOLECULAR DYNAMICS; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; WAVEFORM;

ALGORITHMS; AMINO ACID SEQUENCE; AMINO ACIDS; BINDING SITES; CATALYSIS; COMPUTER SIMULATION; DATABASES, FACTUAL; ELECTRONICS; ENZYMES; HYDROGEN BONDING; HYDROGEN-ION CONCENTRATION; HYDROPHOBICITY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PREDICTIVE VALUE OF TESTS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN SUBUNITS; STRUCTURE-ACTIVITY RELATIONSHIP; TEMPERATURE; TIME FACTORS; WATER;

EID: 44349123986     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21865     Document Type: Article

References (51)

1. Burley SK, Almo SC, Bonanno JB, Capel M, Chance MR, Gaasterland T. Lin D, Ŝali A, Studier WF, Swaminathan S. Structural genomics: beyond the human genome project. Nature Genet 1999;23:151-157.
2. Burley SK, Bonanno JB. Structural genomics of proteins from conserved biochemical pathways and processes. Curr Opin Struct Biol 2002;12:383-391.
3. Zhang C, Kim S-H. Overview of structural genomics: from structure to function. Curr Opin Chem Biol 2003;7:28-32.
4. Chandonia J-M, Brenner ES. The impact of structural genomics: expectations and outcomes. Science 2006;311:347-351.
5. Dietmann S, Holm L. Identification of homology in protein structure classification. Nat Struct Biol 2001;8:953-957.
6. Todd AE, Orengo CA, Thorton JM. Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol 2001;307:1113-1143.
7. Conte LL, Ailey B, Hubbard TJP, Brenner SE, Murzin AG, Chotia C. SCOP: a structural classification of protein database. Nucl Acids Res 2000;28:257-259.
8. Orengo CA, Miche AD, Jones S, Jones DT, Swindells MB, Thorton JM. CATH-a hierarchic classification of protein domain structures. Structure 1997;5:1093-1108.
9. Lankowski RA, Luscombe NM, Swindells MB, Thorton JM. Protein Clefts in molecular recognition and function. Protein Sci 1996;5:2438-2452.
10. Brady GP, Jr, Stouten PFW. Fast prediction and visualization of protein binding pockets with PASS. J Comput Aided Mol Des 2000;14:383-401.
11. Yao H, Kristensen DM, Mihalek I, Sowa ME, Shaw C, Kimmel M, Kavraki L, Lichtarge O. An accurate, sensitive, and scalable method to identify functional sites in protein structures. J Mol Biol 2003;326:255-261.
12. Chakrabarti R, Klibanov AM, Friesner RA. Computational prediction of native protein ligand-binding and enzyme active site sequences. Proc Natl Acad Sci USA 2005;102:10153-10158.
13. Wallace AC, Laskowski RA, Thornton JM. Derivation of 3D coordinate templates for searching structural databases: application to the Ser-His-Asp catalytic triads of the serine proteinases and lipases. Protein Sci 1996;5:1001-1013.
14. Wallace AC, Borkakoti N, Thornton JM. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases: application to enzyme active sites. Protein Sci 1997;6:2308-2323.
15. Pazos F, Sternberg MJ. Automated prediction of protein function and detection of functional sites from structure. Proc Natl Acad Sci USA 2004;101:14754-14759.
16. Ondrechen MJ, Clifton JG, Ringe D. THEMATICS: a simple computational predictor of enzyme function from structure. Proc Natl Acad Sci USA 1999;98:12473-12478.
17. Ko J, Murga LF, André P, Yang H, Ondrechen MJ, Williams RJ, Agunwamba A, Budil DE. Statistical criteria for the identification of protein active sites using theoretical microscopic titration curves. Proteins 2005;59:183-195.
18. Wei Y, Ko J, Murga LF, Ondrechen MJ. Selective prediction of interaction sites in protein structures with THEMATICS. BMC Bioinformatics 2007;8:119.
19. Laurie ATR, Jackson RM. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 2005;21:1908-1916.
20. Amitai G, Shemesh A, Sitbon E, Shklar M, Netanely D, Venger I, Pietrokovski S. Network analysis of protein structures identifies functional residues. J Mol Biol 2004;344:1135-1146.
21. Elcock AH. Prediction of functionally important residues based solely on the computed energetics of protein structure. J Mol Biol 2001;312:885-896.
22. Dessailly BH, Lensink MF, Wodak SJ. Relating destabilizing regions to known functional sites in proteins. BMC Bioinformatics 2007;8:141.
23. Ota M, Kinoshita K, Nishikawa K. Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation. J Mol Biol 2003;327:1053-1064.
24. Kinoshita K, Nakamura H. Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Sci 2003;12:1589-1595.
25. Bate P, Warwicker J. Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods. J Mol Biol 2004;340:263-276.
26. Greaves R, Warwicker J. Active site identification through geometry-based and sequence profile-based calculations: burial of catalytic clefts. J Mol Biol 2005;349:547-557.
27. Ben-Shimon A, Eisenstein M. 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. J Mol Biol 2005;351:309-326.
28. Yang L-W, Bahar I. Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes. Structure 2005;13:893-904.
29. Fukui K, Yonezawa T, Nagata C, Shing H. Molecular-orbital theory of orientation in aromatic, heteroaromatic, and other conjugated molecules. J Chem Phys 1954;20:722-725.
30. Ohno K, Kamioya N, Naoki A, Inoue Y, Sakurai M. Effects of hydration on the electronic structure of an enzyme: implications for the catalytic function. J Am Chem Soc 2001;123:8161-8162.
31. Ohno K, Wada M, Saito S, Inoue Y, Sakurai ,M. Quantum chemical study on the affinity maturation of 48G7 antibody. J Mol Struct THEOCHEM 2005;722:203-211.
32. Stewart JJP. Application of localized molecular orbitals to the solution of semiempirical self-consistent field equations. Int J Quantum Chem 1996;58:133-146.
33. Bartlett GJ, Porter CT, Borkakoti N, Thornton JM. Analysis of catalytic residues in enzyme active sites. J Mol Biol 2002;324:105-121.
34. Porter CT, Bartlett GJ, Thornton JM. The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucl Acids Res 2004;32:129-133.
35. Word JM, Lovell SC, Richardson JS, Richardson DC. Asparagine and glutamine: using hydrogen atom constants in the choice of side-chain amide orientation. J Mol Biol 1999;285:1735-1747.
36. Wada M, Sakurai M. A quantum chemical method for rapid optimization protein structures. J Comput Chem 2004;26:160-168.
37. Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP. AM1: a new general purpose quantum mechanical molecular model. J Am Chem Soc 1985;107:3902-3909.
38. Klamt A, Schüürmann G. COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J Chem Soc Perkin Trans 1993;2:799-805.
39. Klamt A, Jonas V, Burger T, Lohrentz JCW. Refinement and parametrization of COSMO-RS. J Phys Chem A 1998;102:5074-5085.
40. Stewart JJP. MOPAC2002. Tokyo, Japan: Fujitsu; 2002.
41. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA. Gaussian 03 Revision B 05. Wallingford, CT: Gaussian; 2004.
42. Pople JA, Beveridge DL. Approximate molecular orbital theory. New York: McGraw-Hill; 1970. Chapters 3 and 4.
43. Wilson KP, Malcolm BA, Matthews BW. Structural and thermodynamic analysis of compensating mutations within the core of chicken egg white lysozyme. J Biol Chem 1992;267:10842-10849.
44. Tsui V, Case DA. Theory and application of the generalized solvation model in macromolecular simulations. Nucl Acid Sci 2001;56:275-291.
45. Harvey SC, Tan RK, Cheatham TE. The flying ice cube: velocity scaling in molecular dynamics leads to violation of energy equipartition. J Comput Chem 1998;19:726-740.
46. Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ. The amber biomolecular simulation program. J Comput Chem 2005;26:1668-1688.
47. Warshel A, Levitt MJ. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol 1976;103:227-249.
48. Oliva G, Fontes MR, Garratt RC, Altamirano MM, Calcagno ML, Horjales E. Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 resolution. Structure 1995;3:1323-1332.
49. Horjales E, Altamirano MM, Calcagno ML, Garratt RC, Oliva G. The allosteric transition of glucosamine-6-phosphate deaminase: the structure of the state at 2.3 resolution. Structure Fold Des 1999;7:527-537.
50. Modis Y, Filppula SA, Novikov DK, Norledge B, Hiltunen JK, Wierenga RK. The crystal structure of dienoyl-CoA isomerase at 1.5 A resolution reveals the importance of aspartate and glutamate side-chains for catalysis. Structure 1998;6:957-970.
51. Singleton MR, Isupov MN, Littlechild JA. X-ray structure of pyrrolidone carboxyl peptidase from the hyperthermophilic archaeon Thermococcus litoralis. Structure 1999;7:237-244.