'New view' of protein folding reconciled with the old through multiple unfolding simulations

Science

Volumn 278, Issue 5345, 1997, Pages 1928-1931

  Lazaridis, Themis ^a   Karplus, Martin ^a,b  

^a HARVARD UNIVERSITY   (United States)

^b UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CHYMOTRYPSIN INHIBITOR;

ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

COMPUTER SIMULATION; MODELS, MOLECULAR; PEPTIDES; PLANT PROTEINS; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; THERMODYNAMICS;

EID: 0031465967     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.278.5345.1928     Document Type: Article

References (36)

1. R. L. Baldwin, Nature 369, 183 (1994).
2. C. Levinthal, J. Chim. Phys. 65, 44 (1968).
3. J. C. Bryngelson and P. G. Wolynes, J. Phys. Chem. 93, 6902 (1989).
4. E. I. Shakhnovich and A. M. Gutin, Biophys. Chem. 34, 187 (1989).
5. M. Karplus and E. Shakhnovich, in Protein Folding, T. Creighton, Ed. (Freeman, New York, 1992), pp. 127-195.
6. K. A. Dill et al., Protein Sci. 4, 561 (1995).
7. M. Karplus and A. Šali, Curr. Opin. Struct. Biol. 5, 58 (1995).
8. D. Thirumalai and S. A. Woodson, Accounts Chem. Res. 29, 433 (1996).
9. S. E. Jackson and A. R. Fersht, Biochemistry 30, 10428 (1991).
10. L. S. Itzhaki, D. E. Otzen, A. R. Fersht, J. Mol. Biol. 254, 260 (1995).
11. B. R. Brooks et al., J. Comp. Chem. 4, 187 (1983).
12. E. Neria, S. Fischer, M. Karplus, J. Chem. Phys. 105, 1902 (1996).
13. i is obtained from the solvation data making sure that the solvation free energy of deeply buried groups is zero. Ionic side chains are neutralized and a distance-dependent dielectric constant is used for the electrostatic interactions Simulations of proteins with the implicit solvent model yield satisfactory structural and thermodynamic properties for proteins (such as stable native structures under physiological conditions and appropriate energetics for the unfolding transition). Further, use of the implicit solvent model for simulations of dynamics, as well as thermodynamics, is justified by barnase unfolding simulations with explicit solvent (17), which have demonstrated that solvation is essentially simultaneous with the exposure of groups in the interior of the protein. Details and tests of the model will be presented separately.
14. The starting point for the simulations was the crystal structure of CI2 (PDB code 2ci2). Only residues 20 to 83 were modeled; the first 19 residues are disordered in the crystal and were not included in the simulations. Crystal water molecules were deleted. Hydrogen atoms were built with the HBUILD algorithm in CHARMM and 300 steps of energy minimization were performed by using the full potential followed by 50 ps of dynamics at 300 K. The 24 trajectories were started from the last structure obtained at 300 K. The only difference among the trajectories was the seed of the random number generator used to assign velocities corresponding to 500 K to the atoms at the beginning of each unfolding trajectory. The time step was 2 fs and the nonbonded interactions were updated every 20 steps. Coordinate frames were saved every 0.4 ps.
15. 2O (not shown).
16. A. Li and V. Daggett, J. Mol. Biol. 257, 412 (1996).
17. A. Caflisch and M. Karplus, J. Mol. Biol. 252, 672 (1995). In this simulation, there were about 9000 solvent atoms and 1100 protein atoms.
18. A. Šali, E. Shakhnovich, M. Karplus, Nature 369, 248 (1994).
19. J. N. Onuchic, P. G. Wolynes, Z. Luthey-Schulten, N. D. Socci, Proc. Natl. Acad. Sci. U.S.A. 92, 3626 (1995).
20. E. M. Boczko and C. L. Brooks III, Science 269, 393 (1995); Z. Guo, C. L. Brooks III, E. M. Boczko, Proc. Natl. Acad. Sci. USA 94, 10161 (1997).
21. E. M. Boczko and C. L. Brooks III, Science 269, 393 (1995); Z. Guo, C. L. Brooks III, E. M. Boczko, Proc. Natl. Acad. Sci. USA 94, 10161 (1997).
22. D. O. Alonso and V. Daggett, J. Mol. Biol. 247, 501 (1995).
23. We have made a number of simulated annealing runs starting with the unfolded state and found that all of them become trapped far from the native state; the best result had a decrease in energy from -1909 to -1955 kcal/mol and a decrease in rms from 8.9 to 7.1 Å.
24. The unfolding results of Li and Daggett (16) are very similar to those obtained here, except the β3-β4 sheet appears to unfold somewhat earlier in the present simulations.
25. J. L. Neira et al., Folding Design 1, 189 (1996).
26. A. R. Fersht, Curr. Opin. Struct. Biol. 7, 3 (1997).
27. J. K. Myers, C. N. Pace, J. M. Scholtz, Protein Sci. 4, 2138 (1995).
28. All values given in this paragraph are for the truncated protein used in the simulations and the protein engineering experiments. The first 19 residues, which are disordered, are assumed to be fully exposed in both the native state and the denatured state of the complete protein used in the expenments described in (9), so that they make no contribution to the change in surface area. The protein engineering experiments (10) used the truncated protein.
29. B. A. Schoemaker, J. Wang, P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 94, 777 (1997).
30. J. N. Onuchic, N. D. Socci, Z. Luthey-Schulten, P. G. Wolynes, Folding Design 1, 441 (1996).
31. MD(t) during the entire trajectory for some of the present simulations as well as those of Li and Daggett.
32. A. Chakrabartty, T. Kortemme, R. L. Baldwin, Protein Sci. 3, 843 (1994).
33. A. R. Fersht, Proc. Natl. Acad. Sci. U.S.A. 92, 10869 (1995).
34. B. Nölting et al., ibid. 94, 826 (1997).
35. There is a difference between the contact analysis from the simulations and the protein engineering experimants; for example, the protein engineering experiments deal only with the effect of side-chain mutations, whereas the contact analysis of the simulations is based on main-chain interactions for secondary structure and on side-chain interactions for tertiary structure (Fig. 1).
36. P. J. Kraulis, J. Appl. Crystallog. 24, 946 (1991).