The influence of interdomain interactions on the intradomain motions in yeast phosphoglycerate kinase: A molecular dynamics study

Biophysical Journal

Volumn 92, Issue 5, 2007, Pages 1709-1716

  Balog, Erika ^a   Laberge, Monique ^a,b   Fidy, Judit ^a  

^a SEMMELWEIS UNIVERSITY   (Hungary)

^b HOSPITAL OF THE UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHOGLYCERATE KINASE;

ARTICLE; CONFORMATIONAL TRANSITION; CORRELATION ANALYSIS; ENZYME CONFORMATION; ENZYME SUBSTRATE; MOLECULAR DYNAMICS; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; SIMULATION; STRUCTURE ANALYSIS; YEAST;

EID: 33847773117     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.093195     Document Type: Article

References (42)

1. Banks, R. D., C. C. Blake, P. R. Evans, R. Haser, D. W. Rice, G. W. Hardy, M. Merrett, and A. W. Phillips. 1979. Sequence, structure and activity of phosphoglycerate kinase: a possible hinge-bending enzyme. Nature. 279:773-777.
2. Watson, H. C., N. P. C. Walker, P. J. Shaw, T. N. Bryant, P. L. Wemdell, L. A. Fothergill, R. E. Perkins, S. C. Conroy, M. J. Dobson, M. F. Tuite, A. J. Kingsman, and S. M. Kingsman. 1982. Sequence and structure of yeast phosphoglycerate kinase. The EMBO J. 1:1635-1640.
3. Harlos, K., M. Vas, and C. F. Blake. 1992. Crystal structure of the binary complex of pig muscle phosphoglycerate kinase and its substrate 3-phospho-D-glycerate. Proteins. 12:133-144.
4. Davies, G. J., S. J. Gamblin, J. A. Littlechid, Z. Dauter, K. S. Wilson, and H. C. Watson. 1994. The structure of a thermally stable 2 3-phosphoglycerate kinase and a comparison with its mesophilic equivalent. Acta Crystallogr. D. 50:202-209.
5. Blake, C. C., and P. R. Evans. 1974. Structure of horse muscle phosphoglycerate kinase. Some results on the chain conformation, substrate binding and evolution of the molecule from a 3 angstrom Fourier map. J. Mol. Biol. 84:585-601.
6. Bernstein, B. E., P. A. Michels, and W. G. Hol. 1997. Synergistic effects of substrate-induced conformational changes in phosphoglycerate kinase activation. Nature. 385:275-278.
7. Auerbach, G., R. Huber, M. Grattinger, K. Zaiss, H. Schurig, R. Jaenicke, and U. Jacob. 1997. Closed structure of phosphoglycerate kinase from Thermotoga maritima reveals the catalytic mechanism and determinants of thermal stability. Structure. 5:1475-1483.
8. Kovari, Z., and M. Vas. 2004. Protein conformer selection by sequence-dependent packing contacts in crystals of 3-phosphoglycerate kinase. Proteins. 55:198-209.
9. Vaidehi, N., and W. A. I. Goddard. 2000. Domain motions in phosphoglycerate kinase using hierarchical NEIMO molecular dynamics simulations. J. Phys. Chem. A. 104:2375-2383.
10. Guilbert, C., D. Perahia, and L. Mouawad. 1995. A method to explore transition paths in macromolecules. Applications to hemoglobin and phosphoglycerate kinase. Comput. Phys. Comm. 91:263-273.
11. Guilbert, C., F. Pecorari, D. Perahia, and L. Mouawad. 1996. Low frequency motions in phosphoglycerate kinase. A normal mode analysis. Chem. Phys. 204:324-336.
12. Haran, G., E. Haas, B. K. Szpikowska, and M. T. Mas. 1992. Domain motions in phosphoglycerate kinase: determination of interdomain distance distributions by site-specific labeling and time-resolved fluorescence energy transfer. Proc. Natl. Acad. Sci. USA. 89:11764-11768.
13. Adams, B., R. Fowler, M. Hudson, and R. H. Pain. 1996. The role of the C-terminal lysine in the hinge bending mechanism of yeast phosphoglycerate kinase. FEBS Lett. 385:101-104.
14. Mas, M. T., H. H. Chen, K. Aisaka, L. N. Lin, and J. F. Brandts. 1995. Effects of C-terminal deletions on the conformational state and denaturation of phosphoglycerate kinase. Biochemistry. 34:7931-7940.
15. Hosszu, L. L., C. J. Craven, J. Spencer, M. J. Parker, A. R. Clarke, M. Kelly, and J. P. Waltho. 1997. Is the structure of the N-domain of phosphoglycerate kinase affected by isolation from the intact molecule? Biochemistry. 36:333-340.
16. Minard, P., L. Hall, J. M. Betton, D. Missiakas, and J. M. Yon. 1989. Efficient expression and characterization of isolated structural domains of yeast phosphoglycerate kinase generated by site-directed mutagenesis. Protein Eng. 3:55-60.
17. Missiakas, D., J. M. Betton, P. Minard, and J. M. Yon. 1990. Unfolding-refolding of the domains in yeast phosphoglycerate kinase: comparison with the isolated engineered domains. Biochemistry. 29:8683-8689.
18. Pecorari, F., C. Guilbert, P. Minard, M. Desmadril, and J. M. Yon. 1996. Folding and functional complementation of engineered fragments from yeast phosphoglycerate kinase. Biochemistry. 35:3465-3476.
19. Hosszu, L. L., C. J. Craven, M. J. Parker, M. Lorch, J. Spencer, A. R. Clarke, and J. P. Waltho. 1997. Structure of a kinetic protein folding intermediate by equilibrium amide exchange. Nat. Struct. Biol. 4:801-804.
20. Szilagyi, A. N., and M. Vas. 1998. Sequential domain refolding of pig muscle 3-phosphoglycerate kinase: kinetic analysis of reactivation. Fold. Des. 3:565-575.
21. Parker, M. J., J. Spencer, G. S. Jackson, S. G. Burston, L. L. Hosszu, C. J. Craven, J. P. Waltho, and A. R. Clarke. 1996. Domain behavior during the folding of a thermostable phosphoglycerate kinase. Biochemistry. 35:15740-15752.
22. Ritco-Vonsovici, M., B. Mouratou, P. Minard, M. Desmadril, J. M. Yon, M. Andrieux, E. Leroy, and E. Guittet. 1995. Role of the C-terminal helix in the folding and stability of yeast phosphoglycerate kinase. Biochemistry. 34:833-841.
23. Osvath, S., G. Kohler, P. Zavodszky, and J. Fidy. 2005. Asymmetric effect of domain interactions on the kinetics of folding in yeast phosphoglycerate kinase. Protein Sci. 14:1609-1616.
24. Osvath, S., M. Jackel, G. Agocs, P. Zavodszky, G. Kohler, and J. Fidy. 2006. Domain interactions direct misfolding and amyloid formation of yeast phosphoglycerate kinase. Proteins. 62:909-917.
25. Varga, A., B. Flachner, E. Graczer, S. Osvath, A. N. Szilagyi, and M. Vas. 2005. Correlation between conformational stability of the ternary enzyme-substrate complex and domain closure of 3-phosphoglycerate kinase. FEBS J. 272:1867-1885.
26. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy, minimization and dynamics calculations. J. Comput. Chem. 4:187-217.
27. Phillips, J. C., R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, and K. Schulten. 2005. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26:1781-1802.
28. Luty, B. A., M. E. Davis, I. G. Tironi, and F. Van Gunsteren. 1994. A comparison of particle-particle, particle-mesh and Ewald methods for calculating electrostatic interactions. Mol. Simul. 14:11-20.
29. Yang, C., G. S. Jas, and K. Kuczera. 2001. Structure and dynamics of calcium-activated calmodulin in solution. J. Biomol. Struct. Dyn. 19:247-271.
30. Hoover, W. G. 1985. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A. 31:1695-1697.
31. Feller, S. E., Y. Zhang, R. W. Pastor, and B. R. Brooks. 1995. Constant pressure molecular dynamics simulation: the Langevin piston method. J. Chem. Phys. 103:4613-4621.
32. Ichiye, T., and M. Karplus. 1991. Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins. 11:205-217.
33. Henderson, S. J., E. H. Serpersu, B. S. Gerhardt, and G. J. Bunick. 1994. Conformational changes in yeast phosphoglycerate kinase upon substrate binding. Biophys. Chem. 53:95-104.
34. Rod, T. H., J. L. Radkiewicz, and C. L. Brooks 3rd. 2003. Correlated motion and the effect of distal mutations in dihydrofolate reductase. Proc. Natl. Acad. Sci. USA. 100:6980-6985.
35. Verma, C. S., L. S. Caves, R. E. Hubbard, and G. C. Roberts. 1997. Domain motions in dihydrofolate reductase: a molecular dynamics study. J. Mol. Biol. 266:776-796.
36. Blake, C. 1997. Phosphotransfer hinges in PGK. Nature. 385:204-205.
37. Gerstein, M., A. M. Lesk, and C. Chothia. 1994. Structural mechanisms for domain movements in proteins. Biochemistry. 33:6739-6749.
38. Radkiewicz, J. L., and C. L. Brooks III. 2000. Protein dynamics in enzymatic catalysis: exploration of dihydrofolate reductase. J. Am. Chem. Soc. 122:225-231.
39. Hunenberger, P. H., A. E. Mark, and W. F. van Gunsteren. 1995. Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations. J. Mol. Biol. 252:492-503.
40. Hayward, S., and H. J. Berendsen. 1998. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins. 30:144-154.
41. Hayward, S. 1999. Structural principles governing domain motions in proteins. Proteins. 36:425-435.
42. Sinha, N., S. Kumar, and R. Nussinov. 2001. Interdomain interactions in hinge-bending transitions. Structure. 9:1165-1181.