Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity

Proteins: Structure, Function and Genetics

Volumn 37, Issue 3, 1999, Pages 379-387

  Blomberg, Niklas ^a   Gabdoulline, Razif R ^a   Nilges, Michael ^a   Wade, Rebecca C ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

Electrostatics; Homology modeling; PH domains; Phospholipid binding; Signal transduction; Similarity index

Indexed keywords

PLECKSTRIN; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CLASSIFICATION; CONTROLLED STUDY; ELECTRIC POTENTIAL; LIGAND BINDING; MATHEMATICAL COMPUTING; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

DATA INTERPRETATION, STATISTICAL; ELECTROSTATICS; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0032726693     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19991115)37:3<379::AID-PROT6>3.0.CO;2-K     Document Type: Article

References (27)

1. Honig B, Nicholls A. Classical electrostatics in biology and chemistry. Science 1995;268:1144-1149.
2. Botti S, Felder C, Sussman J, Silman I. Electrotactins: a class of adhesion proteins with conserved electrostatic and structural motifs. Protein Eng 1998;11:415-420.
3. 6 may be isofunctional with tyrosine 83 in plastocyanin. Biochemistry 1997;36:16187-16196.
4. Wade RC, Gabdoulline RR, Luty BA. Species dependence of enzyme-substrate encounter rates for triose phosphate isomerases. Proteins 1998;31:406-416.
5. Wade RC, Gabdoulline RR, Lüdemann SK, Lounnas V. Electrostatic steering and ionic tethering in enzyme-ligand binding: insights from simulations. Proc Natl Acad Sci USA 1998;95:5942-5949.
6. Demchuk E, Müller T, Oschkinat H, Sebald W, Wade RC. Receptor binding properties of four-helix-bundle growth factors deduced from electrostatic analysis. Protein Sci 1994;20:203-215.
7. Blomberg N, Nilges M. Functional diversity of PH domains: an exhaustive modelling study. Folding Design 1997;2(6):343-355.
8. Hodgkin EE, Richards WG. Molecular similarity based on electrostatic potential and electric field. Int J Quant Chem Quant Biol Symp 1987;14:105-110.
9. Good AC. 3D Molecular similarity indices and their application in QSAR studies. Molecular Similarity in drug design. Dean PM, editor. London: Blackie Academics, 1995. p 24-53.
10. Carbo R, Domingo L. LCAO-MO similarity measures and taxonomy. Int J Quant Chem 1987;17:517-545.
11. Burt C, Richards WG. The application of molecular similarity calculations. J Comput Chem 1990;11:1139-11.
12. Richard AM. Quantitative comparison of molecular electrostatic potentials for structure-activity studies. J Comp Chem 1991;12: 959-969.
13. Tomic S, Gabdoulline RR, Kojic-Prodic B, Wade RC. Classification of auxin plant hormones by interaction property similarity indices. J Comp Aid Mol Design 1998;12:1-17.
14. Abseher R, Horstink L, Hilbers CW, Nilges M. Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap. Proteins 1998;31:370-382.
15. Madura JD, Briggs JM, Wade RC, Davis ME, Luty BA, Ilin A, Antosiewicz J, Gilson MK, Bagheri B, Scott LR, McCammon JA. Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Browinian Dynamics program. Comp Phys Comm 1995;91:57-95.
16. Brünger AT. X-PLOR. A system for X-ray crystallography and NMR. New Haven: Yale University Press; 1992. 382 p.
17. Jorgensen WL, Tirado-Rives J. The OPLS potential function for proteins. Energy minimization for crystals of cyclic peptides and crambin. J Am Chem Soc 1988;110:1657-1666.
18. Macias MJ, Musacchio A, Ponstingl H, Nilges M, Saraste M, Oschkinat H. Structure of the pleckstrin homology domain from beta-spectrin. Nature 1994;369:675-677.
19. Yoon HS, Hajduk PJ, Petros AM, Olejniczak ET, Meadows RP, Fesik SW. Solution structure of a pleckstrin-homology domain. Nature 1994;369:672-675.
20. Zhang P, Talluri S, Deng H, Branton D, Wagner G. Solution structure of the pleckstrin homology domain of drosophila β-spectrin. Structure 1995;3(2):1185-1195.
21. Fushman D, Najmabadi-Haske T, Cahill S, Zheng J, LeVine III H, Cowburn D. The solution structure and dynamics of the pleckstrin homology domain of G-protein coupled receptor kinase 2 (β-ARK1): a binding partner of Gβγ subunit. J Biol Chem 1998;273: 2835-2843.
22. Koshiba S, Kigawa T, Kim J-H, Shirouzu M, Bowtell D, Yokoyama S. The solution structure of the pleckstrin homology domain of mouse son-of-sevenless 1 (mSos1). J Mol Biol 1997;269:579-591.
23. Zheng J, Chen R-H, Corblan-Garcia S, Cahill SM, Bar-Sagi D, Cowburn D. The solution structure of the pleckstrin homology domain of human Sos1: a possible structural role for the sequential association of dbl homology and pleckstrin homology domains. J Biol Chem 1997;272(48):30340-44.
24. Gower JC. Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 1966;53(3 and 4):325-38.
25. Mardia KV, Kent JT, Bibby JM. Multivariate analysis, 6th ed. Academic Press: London; 1997. 521 p.
26. Rost B. Marrying structure and genomics. Structure 1998;6:259-263.
27. Guex N, Peitsch MC. Swiss-model and the swiss-pdbviewer: an environment for comparative protein modeling. Electrophoresis 1997;18(15):2714-2723.