A one-dimensional reaction coordinate for identification of transition states from explicit solvent Pfold-like calculations

Biophysical Journal

Volumn 93, Issue 10, 2007, Pages 3382-3391

  Beck, David A C ^a   Daggett, Valerie ^a  

^a University of Washington   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SOLVENT;

ARTICLE; CALCULATION; MOLECULAR DYNAMICS; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; PROTEOMICS; SIMULATION;

EID: 36549027538     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.100149     Document Type: Article

References (54)

1. Ladurner, A. G., L. S. Itzhaki, V. Daggett, and A. R. Fersht. 1998. Synergy between simulation and experiment in describing the energy landscape of protein folding. Proc. Natl. Acad. Sci. USA. 95:8473-8478.
2. Li, A., and V. Daggett. 1994. Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2. Proc. Natl. Acad. Sci. USA. 91:10430-10434.
3. Daggett, V., A. Li, L. S. Itzhaki, D. E. Otzen, and A. R. Fersht. 1996. Structure of the transition state for folding of a protein derived from experiment and simulation. J. Mol. Biol. 257:430-440.
4. Kearsley, S. K. 1989. On the orthogonal transformation used for structural comparisons. Acta Crystallogr. A. 45:208-210.
5. Kazmirski, S. L., A. J. Li, and V. Daggett. 1999. Analysis methods for comparison of multiple molecular dynamics trajectories: applications to protein unfolding pathways and denatured ensembles. J. Mol. Biol. 290:283-304.
6. DeMarco, M. D., D. O. V. Alonso, and V. Daggett. 2004. Diffusing and colliding: the atomic level folding/unfolding pathway of a small helical protein. J. Mol. Biol. 341:1109-1124.
7. Sander, J., M. Ester, H. P. Kriegel, and X. W. Xu. 1998. Density-based clustering in spatial databases: the algorithm GDBSCAN and its applications. Data Min. Knowl. Disc. 2:169-194.
8. Daggett, V., A. J. Li, and A. R. Fersht. 1998. Combined molecular dynamics and phi-value analysis of structure-reactivity relationships in the transition state and unfolding pathway of barnase: structural basis of Hammond and anti-Hammond effects. J. Am. Chem. Soc. 120:12740-12754.
9. De Jong, D., R. Riley, D. O. V. Alonso, and V. Daggett. 2002. Probing the energy landscape of protein folding/unfolding transition states. J. Mol. Biol. 319:229-242.
10. Mayor, U., C. M. Johnson, V. Daggett, and A. R. Fersht. 2000. Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc. Natl. Acad. Sci. USA. 97:13518-13522.
11. Gianni, S., N. R. Guydosh, F. Khan, T. D. Caldas, U. Mayor, G. W. White, M. L. DeMarco, V. Daggett, and A. R. Fersht. 2003. Unifying features in protein-folding mechanisms. Proc. Natl. Acad. Sci. USA. 100:13286-13291.
12. Mayor, U., N. R. Guydosh, C. M. Johnson, J. G. Grossmann, S. Sato, G. S. Jas, S. M. Freund, D. O. V. Alonso, V. Daggett, and A. R. Fersht. 2003. The complete folding pathway of a protein from nanoseconds to microseconds. Nature. 421:863-867.
13. Clarke, N. D., C. R. Kissinger, J. Desjarlais, G. L. Gilliland, and C. O. Pabo. 1994. Structural studies of the engrailed homeodomain. Protein Sci. 3:1779-1787.
14. Kissinger, C. R., B. S. Liu, E. Martinblanco, T. B. Kornberg, and C. O. Pabo. 1990. Crystal-structure of an engrailed homeodomain-DNA complex at 2.8-Å resolution - a framework for understanding homeodomain-DNA interactions. Cell. 63:579-590.
15. Islam, S. A., M. Karplus, and D. L. Weaver. 2002. Application of the diffusion-collision model to the folding of three-helix bundle proteins. J. Mol. Biol. 318:199-215.
16. Religa, T. L., J. S. Markson, U. Mayor, S. M. V. Freund, and A. R. Fersht. 2005. Solution structure of a protein denatured state and folding intermediate. Nature. 437:1053-1056.
17. Li, L., and E. I. Shakhnovich. 2001. Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations. Proc. Natl. Acad. Sci. USA. 98:13014-13018.
18. Gsponer, J., and A. Caflisch. 2002. Molecular dynamics simulations of protein folding from the transition state. Proc. Natl. Acad. Sci. USA. 99:6719-6724.
19. Rao, F., and A. Caflisch. 2004. The protein folding network. J. Mol. Biol. 342:299-306.
20. Lenz, P., B. Zagrovic, J. Shapiro, and V. S. Pande. 2004. Folding probabilities: a novel approach to folding transitions and the two-dimensional Ising-model. J. Chem. Phys. 120:6769-6778.
21. Du, R., V. S. Pande, A. Y. Grosberg, T. Tanaka, and E. S. Shakhnovich. 1998. On the transition coordinate for protein folding. J. Chem. Phys. 108:334-350.
22. Shimada, J., and E. I. Shakhnovich. 2002. The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation. Proc. Natl. Acad. Sci. USA. 99:11175-11180.
23. Beck, D. A. C., and V. Daggett. 2004. Methods for molecular dynamics simulations of protein folding/unfolding in solution. Methods. 34:112-120.
24. Boczko, E. M., and C. L. Brooks. 1995. First-principles calculation of the folding free-energy of a 3-helix bundle protein. Science. 269:393-396.
25. Sheinerman, F. B., and C. L. Brooks. 1998. Molecular picture of folding of a small alpha/beta protein. Proc. Natl. Acad. Sci. USA. 95:1562-1567.
26. Sheinerman, F. B., and C. L. Brooks. 1998. Calculations on folding of segment B1 of streptococcal protein G. J. Mol. Biol. 278:439-456.
27. Dokholyan, N. V., L. Li, F. Ding, and E. I. Shakhnovich. 2002. Topological determinants of protein folding. Proc. Natl. Acad. Sci. USA. 99:8637-8641.
28. Alonso, D. O. V., and V. Daggett. 2000. Staphylococcal protein A: unfolding pathways, unfolded states, and differences between the B and E domains. Proc. Natl. Acad. Sci. USA. 97:133-138.
29. Yee, D. P., and K. A. Dill. 1993. Families and the structural relatedness among globular proteins. Protein Sci. 2:884-899.
30. Klimov, D. K., and D. Thirumalai. 2004. Progressing from folding trajectories to transition state ensemble in proteins. Chem. Phys. 307:251-258.
31. Tenenbaum, J. B., V. de Silva, and J. C. Langford. 2000. A global geometric framework for nonlinear dimensionality reduction. Science. 290:2319-2323.
32. Das, P., M. Moll, H. Stamati, L. E. Kavraki, and C. Clementi. 2006. Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction. Proc. Natl. Acad. Sci. USA. 103:9885-9890.
33. Kohonen, T. 1982. Self-organized formation of topologically correct feature maps. Biol. Cybern. 43:59-69.
34. Kell, G. S. 1967. Precise representation of volume properties of water at one atmosphere. J. Chem. Eng. Data. 12:66-69.
35. Haar, L., J. S. Gallagher, and G. S. Kell. 1984. NBS/NRC Steam Tables. Hemisphere, New York.
36. Levitt, M. 1990. ENCAD, Computer Program for Energy Calculation and Dynamics. Stanford University, Palo Alto, CA.
37. Pardi, A., M. Billeter, and K. Wuthrich. 1984. Calibration of the angular-dependence of the amide proton-C-α proton coupling-constants, 3jhn-α, in a globular protein - use of 3jhn-α for identification of helical secondary structure. J. Mol. Biol. 180:741-751.
38. Lee, B., and F. M. Richards. 1971. Interpretation of protein structures - estimation of static accessibility. J. Mol. Biol. 55:379-400.
39. Galassi, M., J. Davies, J. Theiler, B. Gough, G. Jungman, M. Booth, and F. Rossi. 2005. GNU Scientific Library Reference Manual. Network Theory, Bristol, UK.
40. Snow, C. D., Y. M. Rhee, and V. S. Pande. 2006. Kinetic definition of protein folding transition state ensembles and reaction coordinates. Biophys. J. 91:14-24.
41. Day, R., D. A. C. Beck, R. S. Armen, and V. Daggett. 2003. A consensus view of fold space: combining SCOP, CATH, and the Dali domain dictionary. Protein Sci. 12:2150-2160.
42. Beck, D. A. C., A. L. Jonsson, D. Schaeffer, K. A. Scott, R. Day, R. D. Toofanny, D. O. V. Alonso, and V. Daggett. 2007. Dyanameomics: Mass annotation of protein dynamics and unfolding in water by high-throughput all-atom molecular dynamics simulations. Genome Biol. In press.
43. Day, R., and V. Daggett. 2005. Sensitivity of the folding/unfolding transition state ensemble of chymotrypsin inhibitor 2 to changes in temperature and solvent. Protein Sci. 14:1242-1252.
44. Gutmanas, A., and M. Billeter. 2004. Specific DNA recognition by the Antp homeodomain: MD simulations of specific and nonspecific complexes. Proteins. 57:772-782.
45. Sato, K., M. D. Simon, A. M. Levin, K. M. Shokat, and G. A. Weiss. 2004. Dissecting the engrailed homeodomain-DNA interaction by phage-displayed shotgun scanning. Chem. Biol. 11:1017-1023.
46. Simon, M. D., K. Sato, G. A. Weiss, and K. M. Shokat. 2004. A phage display selection of engrailed homeodomain mutants and the importance of residue Q50. Nucleic Acids Res. 32:3623-3631.
47. Ades, S. E., and R. T. Sauer. 1995. Specificity of minor-groove and major-groove interactions in a homeodomain-DNA complex. Biochemistry. 34:14601-14608.
48. Duan, J. X., and L. Nilsson. 2002. The role of residue 50 and hydration water molecules in homeodomain DNA recognition. Eur. Biophys. J. 31:306-316.
49. Fraenkel, E., M. A. Rould, K. A. Chambers, and C. O. Pabo. 1998. Engrailed homeodomain-DNA complex at 2.2 Å resolution: a detailed view of the interface and comparison with other engrailed structures. J. Mol. Biol. 284:351-361.
50. Grant, R. A., M. A. Rould, J. D. Klemm, and C. O. Pabo. 2000. Exploring the role of glutamine 50 in the homeodomain-DNA interface: crystal structure of engrailed (Gln50 → Ala) complex at 2.0 Å. Biochemistry. 39:8187-8192.
51. Ledneva, R. K., A. V. Alexeevskii, S. A. Vasil'ev, S. A. Spirin, and A. S. Karyagina. 2001. Structural aspects of interaction of homeodomains with DNA. Mol. Biol. 35:647-659.
52. Tucker-Kellogg, L., M. A. Rould, K. A. Chambers, S. E. Ades, R. T. Sauer, C. O. Pabo. 1997. Engrailed (Gln50/Lys) homeodomain-DNA complex at 1.9 Å resolution: structural basis for enhanced affinity and altered specificity. Structure. 5:1047-1054.
53. White, G. W., S. Gianni, J. G. Grossmann, P. Jemth, A. R. Fersht, and V. Daggett. 2005. Simulation and experiment conspire to reveal cryptic intermediates and a slide from the nucleation-condensation to framework mechanism of folding. J. Mol. Biol. 350:757-775.
54. Day, R., and V. Daggett. 2007. Direct observation of microscopic reversibility in protein folding. J. Mol. Biol. 366:677-686.