Importance of the lactate dehydrogenase quaternary structure in theoretical calculations

Journal of Physical Chemistry B

Volumn 114, Issue 9, 2010, Pages 3393-3397

  Świderek, Katarzyna ^a   Paneth, Piotr ^a  

^a LODZ UNIVERSITY OF TECHNOLOGY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CARRIER MOBILITY; HYDROGEN; ISOTOPES; ORGANIC ACIDS;

ACTIVE SITE; COVALENT CHARACTER; GEOMETRIC PARAMETER; ISOTOPE EFFECT; LACTATE DEHYDROGENASE; QUATERNARY STRUCTURE; STRUCTURAL INFORMATION; THEORETICAL CALCULATIONS;

HYDROGEN BONDS;

EID: 77749334410     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp100026z     Document Type: Article

References (35)

1. Warshel, A.; Levitt, M. J. Mol, Biol. 1976, 103, 227.
2. York, D. M., Lee, T.-S., Eds. Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications; Challenges and Advances in Computational Chemistry and Physics Series; Leszczynski, J., Series Ed.; Springer: New York, 2009; Vol.7.
3. (a) Lundberg, M; Siegbahn, P. E. M.; Morokuma, K. Biochemistry 2008, 47, 1031.
4. (b) Solt, L; Kulhanek, P.; Simon, L; Winfleld, S.; Payne, M. C.; Csanyi, G.; Fuxreiter, M. J. Phys. Chem. B 2009, 113, 5728.
5. Kwiecien, R.; Lewandowicz, A.; Paneth, P. Substrate-Enzyme Interactions from Modeling and Isotope Effects. In Molecular Materials with Specific Interactions: Modeling and Design; Sokalski, W. A., Ed.; Challenges and Advances in Computational Chemistry and Physics Series; Leszczynski, J., Series Ed.; Springer: New York, 2007; Vol.4, pp 341-363.
6. Schulz, R.; Lindner, B.; Petridis, L.; Smith, J. C. J. Chem. Theory Comput. 2009, 5, 2798.
7. (a) Mroginski M. A.; Mark, F.; Thiel, W.; Hildebrandt, P. Biophys. J. 2007, 93, 1885.
8. (b) Dyguda, E.; Grembecka, J.; Sokalski, W. A.; Leszczynski, J. J. Am. Chem. Soc. 2005, 127, 1658.
9. (c) Dýaz, N.; Suarez, D.; Merz, K. M. J. Am. Chem. Soc. 2000, 122, 4197.
10. (a) Hart, J. C.; David, W.; Sheppard, D. W.; Hillier, I. H.; Burton, N. A. Chem. Commun. 1999, 79.
11. (b) Ferrer, S.; Silla, E.; Tunon, I.; Oliva, M.; Moliner, V.; Williams, I. H. Chem. Commun. 2005, 5873.
12. (c) Faulder, P. F.; Tresadern, G.; Chohan, K. K.; Scrutton, N. S.; Sutcliffe, M. J.; Hillier, I. H.; Burton, N. A. J. Am. Chem. Soc. 2001, 123, 8604.
13. Schmidt, R. K.; Gready, J. E. J. Mol. Model. 1999, 5, 153.
14. Swiderek, K.; Panczakiewicz, A.; Bujacz, A.; .Bujacz, G.; Paneth, P. J. Phys. Chem. B 2009, 113, 12782.
15. (a) Becke, A. D. J. Chem. Phys. 1993, 98, 5648.
16. (b) Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785.
17. (c) Miehlich, B.; Savin, A.; Stoll, H.; Preuss, H. Chem. Phys. Lett. 1989, 157, 200.
18. (a) Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225.
19. (b) Jorgensen, W. L.; McDonald, N. A. J. Mol. Struct. (THEOCHEM) 1998, 424, 145.
20. (c) Jorgensen, W. L. BOSS, version 4.3; Yale University: New Haven, CT, 2001.
21. QSite, version 5.0; Schrodinger, LLC: New York, 2007.
22. Maestro, version 8.5; Schrodinger, LLC: New York, 2007.
23. Holm, L.; Park, J. Scince 1996, 273, 595.
24. Holm, L.; Park, J. Bioinformatics 2000, 16, 566.
25. Ramanchadran, G. N.; Ramanchadran, C.; Sasisekharan, V. J. Mol. Biol 1963, 7, 95.
26. Anisimov, V.; Paneth, P. J. Math. Chem. 1999, 26, 75.
27. HyperChem, release 8; Hypercube, Inc.: Gainesville, FL, 2007.
28. Gawlita, E.; Paneth, P.; Anderson, V. E. Biochemistry 1995, 34, 6050.
29. Bigeleisen, J. J. Chem. Phys. 1995, 23, 1164.
30. Grabowski, S. J.; Sokalski, W. A.; Dyguda, E.; Leszczynski, J. J. Phys. Chem. B 2006, 110, 6444.
31. Zhang, X.; DeChancie, J.; Gunaydin, H.; Chowdry, A. B.; Clemente, F. R.; Smith, A. J. T.; Handel, T. M.; Houk, K. N. J. Org. Chem. 2008, 73, 889.
32. Zhou, B.; Wong, C. F. J. Phys. Chem. A 2009, 113, 5144.
33. Idupulapati, N. B.; Mainardi, D. S.J. Phys. Chem A 2010, 114, 1887.
34. Dybala-Defratyka, A.; Paneth, P.; Banerjee, R.; Truhlar, D. G. Proc. Natl Acad. Sci. U.S.A. 2007, 104, 10779.
35. Shaik, S.; Cohen, S.; Wang, Y.; Chen, H.; Kumar, D.; Thiel, W. Chem. Rev. 2010, 100, 949.