Binding region of alanopine dehydrogenase predicted by unbiased molecular dynamics simulations of ligand diffusion

Journal of Chemical Information and Modeling

Volumn 53, Issue 10, 2013, Pages 2493-2498

  Gohlke, Holger ^a   Hergert, Ulrike ^a   Meyer, Tatu ^a   Mulnaes, Daniel ^a   Grieshaber, Manfred K ^a   Smits, Sander H J ^a   Schmitt, Lutz ^a  

^a HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS;

BIOCHEMICAL CHARACTERIZATION; HOMOLOGY MODELING; L-ALANINE; L-AMINO ACIDS; MOLECULAR DYNAMICS SIMULATIONS; PYRUVATES; SEQUENCE COMPARISONS;

MOLECULAR DYNAMICS;

ALANINE; ALANOPINE DEHYDROGENASE; HELMINTH PROTEIN; LIGAND; OXIDOREDUCTASE; PYRUVIC ACID; RECOMBINANT PROTEIN;

AMINO ACID SUBSTITUTION; ANIMAL; ARTICLE; BINDING SITE; CHEMISTRY; DIFFUSION; ENZYME SPECIFICITY; ENZYMOLOGY; GENETICS; KINETICS; METABOLISM; MOLECULAR DYNAMICS; POLYCHAETA; PROTEIN BINDING; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; STRUCTURAL HOMOLOGY;

ALANINE; AMINO ACID SUBSTITUTION; ANIMALS; BINDING SITES; DIFFUSION; HELMINTH PROTEINS; KINETICS; LIGANDS; MOLECULAR DYNAMICS SIMULATION; OXIDOREDUCTASES ACTING ON CH-NH GROUP DONORS; POLYCHAETA; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PYRUVIC ACID; RECOMBINANT PROTEINS; STRUCTURAL HOMOLOGY, PROTEIN; SUBSTRATE SPECIFICITY;

EID: 84887081813     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci400370y     Document Type: Article

References (25)

1. Shan, Y. B.; Kim, E. T.; Eastwood, M. P.; Dror, R. O.; Seeliger, M. A.; Shaw, D. E. How Does a Drug Molecule Find Its Target Binding Site? J. Am. Chem. Soc. 2011, 133 (24) 9181-9183
2. Dror, R. O.; Pan, A. C.; Arlow, D. H.; Borhani, D. W.; Maragakis, P.; Shan, Y.; Xu, H.; Shaw, D. E. Pathway and mechanism of drug binding to G-protein-coupled receptors Proc. Natl. Acad. Sci. U.S.A. 2011, 108 (32) 13118-23
3. Giorgino, T.; Buch, I.; De Fabritiis, G. Visualizing the Induced Binding of SH2-Phosphopeptide J. Chem. Theory. Comput. 2012, 8 (4) 1171-1175
4. Buch, I.; Giorgino, T.; De Fabritiis, G. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations Proc. Natl. Acad. Sci. U.S.A. 2011, 108 (25) 10184-10189
5. Kruse, A. C.; Hu, J.; Pan, A. C.; Arlow, D. H.; Rosenbaum, D. M.; Rosemond, E.; Green, H. F.; Liu, T.; Chae, P. S.; Dror, R. O.; Shaw, D. E.; Weis, W. I.; Wess, J.; Kobilka, B. K. Structure and dynamics of the M3 muscarinic acetylcholine receptor Nature 2012, 482 (7386) 552-6
6. Zebe, E.; Schiedeck, D. The lugworm Arenicola marina: a model of physiological adaptation to life in intertidal sediments Helgoländer Meeresunters 1996, 30, 37-68
7. Grieshaber, M. K.; Hardewig, I.; Kreutzer, U.; Portner, H. O. Physiological and metabolic responses to hypoxia in invertebrates Rev. Physiol. Biochem. Pharmacol. 1994, 125, 43-147
8. van Thoai, N.; Huc, C.; Pho, D. B.; Olomucki, A. Octopine dehydrogenase. Purification and catalytic properties Biochim. Biophys. Acta 1969, 191 (1) 46-57
9. Pho, D. B.; Olomucki, A.; Huc, C.; Thoai, N. V. Spectrophotometric studies of binary and ternary complexes of octopine dehydrogenase Biochim. Biophys. Acta 1970, 206 (1) 46-53
10. Muller, A.; Janssen, F.; Grieshaber, M. K. Putative reaction mechanism of heterologously expressed octopine dehydrogenase from the great scallop, Pecten maximus (L) Febs. J. 2007, 274 (24) 6329-6339
11. Smits, S. H.; Mueller, A.; Schmitt, L.; Grieshaber, M. K. A structural basis for substrate selectivity and stereoselectivity in octopine dehydrogenase from Pecten maximus J. Mol. Biol. 2008, 381 (1) 200-11
12. Smits, S. H.; Meyer, T.; Mueller, A.; van Os, N.; Stoldt, M.; Willbold, D.; Schmitt, L.; Grieshaber, M. K. Insights into the mechanism of ligand binding to octopine dehydrogenase from Pecten maximus by NMR and crystallography PLoS One 2010, 5 (8) e12312
13. van Os, N.; Smits, S. H. J.; Schmitt, L.; Grieshaber, M. K. Control of D-octopine formation in scallop adductor muscle as revealed through thermodynamic studies of octopine dehydrogenase J. Exp. Biol. 2012, 215 (9) 1515-1522
14. Siegmund, B.; Grieshaber, M.; Reitze, M.; Zebe, E. Alanopine and Strombine Are End Products of Anaerobic Glycolysis in the Lugworm, Arenicola-Marina-L (Annelida, Polychaeta) Comp. Biochem. Physiol. B: Biochem. Mol. Biol. 1985, 82 (2) 337-345
15. Siegmund, B.; Grieshaber, M. K. Determination of meso-alanopine and D-strombine by high pressure liquid chromatography in extracts from marine invertebrates Hoppe Seylers Z. Physiol. Chem. 1983, 364 (7) 807-12
16. Britton, K. L.; Asano, Y.; Rice, D. W. Crystal structure and active site location of N-(1- d -carboxylethyl)- l -norvaline dehydrogenase Nat. Struct. Biol. 1998, 5 (7) 593-601
17. Gade, G.; Grieshaber, M. K. Pyruvate Reductases Catalyze the Formation of Lactate and Opines in Anaerobic Invertebrates Comp. Biochem. Physiol. B: Biochem. Mol. Biol. 1986, 83 (2) 255-272
18. Endo, N.; Kan-No, N.; Nagahisa, E. Purification, characterization, and cDNA cloning of opine dehydrogenases from the polychaete rockworm Marphysa sanguinea Comp. Biochem. Physiol. B: Biochem. Mol. Biol. 2007, 147 (2) 293-307
19. Sali, A.; Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 1993, 234 (3) 779-815
20. Altschul, S. F.; Gish, W.; Miller, W.; Myers, E. W.; Lipman, D. J. Basic Local Alignment Search Tool J. Mol. Biol. 1990, 215 (3) 403-410
21. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28 (1) 235-242
22. Gohlke, H.; Kiel, C.; Case, D. A. Insights into protein-protein binding by free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes J. Mol. Biol. 2003, 330, 891-913
23. Bryngelson, J. D.; Onuchic, J. N.; Socci, N. D.; Wolynes, P. G. Funnels, pathways, and the energy landscape of protein folding: a synthesis Proteins 1995, 21 (3) 167-195
24. Wang, J.; Verkhivker, G. M. Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding Phys. Rev. Lett. 2003, 90 (18) 188101
25. Tsai, C.-J.; Kumar, S.; Ma, B.; Nussinov, R. Folding funnels, binding funnels, and protein function Protein Sci. 1999, 8, 1181-1190