The early folding kinetics of apomyoglobin

Protein Science

Volumn 7, Issue 2, 1998, Pages 480-490

  Pappu, Rohit V ^a,b   Weaver, David L ^b  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b TUFTS UNIVERSITY   (United States)

Author keywords

Apomyoglobin; Diffusion collision model; Folding kinetics; Microdomains; Nascent helices

Indexed keywords

APOMYOGLOBIN; MYOGLOBIN; UNCLASSIFIED DRUG;

ARTICLE; DIFFUSION; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY;

EID: 0031940406     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560070229     Document Type: Article

References (37)

1. Baldwin RL. 1996. Why is protein folding so fast? Proc Natl Acad Sci USA 93:2627-2628.
2. Ballew RM, Sabelko J, Gruebele M. 1996. Direct observation of fast protein folding: The initial collapse of apomyoglobin. Proc Natl Acad Sci USA 93:5759-5764.
3. Bashford D, Cohen FE, Karplus M, Kuntz ID, Weaver DL. 1988. Diffusion-collision model for the folding kinetics of myoglobin. Proteins 4:211-227.
4. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. 1977. The protein data bank: A computer based archival file for macromolecular structure. J Mol Biol 112:535-542.
5. Brooks CL, Karplus M, Pettitt BM. 1988. Proteins: A theoretical perspective of dynamics, structure and thermodynamics. New York: Wiley.
6. Dyson HJ, Merutka G, Waltho JP, Lerner RA, Wright PE. 1992. Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding I. Myohemerythrin. J Mol Bio 226:795-817.
7. Dyson HJ, Sayre JR, Merutka G, Shin H, Lerner RA, Wright PE. 1992. Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding II. Plastocyanin. J Mol Bio 226:819-835.
8. Eliezer D, Jennings PA, Wright PE, Doniach S, Hodgson KO, Tsuruta H. 1995. The radius of gyration of an apomyoglobin folding intermediate. Science 270:487-488.
9. Ermak DL, McCammon JA. 1978. Brownian dynamics with hydrodynamic interactions. J Chem Phy 69:1352-1360.
10. Hagen SJ, Hofrichter J, Szabo A, Eaton WA. 1996. Diffusion-limited contact formation in unfolded cytochrome c: Estimating the maximum rate of protein folding. Proc Natl Acad Sci USA 93:11615-11617.
11. Hirst JD, Brooks CL III. 1995. Molecular dynamics simulations of isolated helices of myoglobin. Biochemistry 34:7614-7621.
12. Hoffmann D, Knapp E-W. 1997. Folding pathways of a helix-turn-helix model protei. J Phys Chem. Forthcoming.
13. Hughson FM, Wright PE, Baldwin RL. 1990. Structural characterization of a partly folded apomyoglobin intermediate. Science 249:1544-1548.
14. Hughson FM, Barrick D, Baldwin RL. 1991. Probing the stability of a partly folded apomyoglobin intermediate by site-directed mutagenesis. Biochemistry 30:4113-4118.
15. Jacob M, Schindler T, Balbach J, Schmid. 1997. Diffusion control in an elementary protein folding reaction. Proc Natl Acad Sci USA 94:5622-5627.
16. Jennings PA, Wright PE. 1993. Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin. Science 262:892-896.
17. Jennings PA, Dyson HJ, Wright PE. 1994. In: S. Doniach, ed. The folding pathway of apomyoglobin, in statistical mechanics, protein structure and protein substrate interactions. New York: Plenum Press. pp 7-18.
18. Karplus M, Weaver DL. 1976. Protein-folding dynamics. Nature 260:404-406.
19. Karplus M, Weaver DL. 1994. Protein-folding dynamics: The diffusion-collision model and experimental data. Protein Sci 3:650-669.
20. Lee B, Richards FM. 1971. The interpretation of protein structure: Estimation of static accessibility. J Mol Bio 55:379-400.
21. Lee SY, Karplus M, Bashford D, Weaver DL. 1987. Brownian dynamics simulation of protein folding: A study of the diffusion-collision model. Biopolymers 26:481-506.
22. Levinthal C. 1968. Are there pathways for protein folding? J Chim Phys 65: 44-45.
23. Levinthal C. 1966. Molecular model building by computer. Scient Am 214: 42-45.
24. Loh SN, Kay MS, Baldwin RL. 1995. Structure and stability of a second molten globule intermediate in the apomyoglobin folding pathway. Proc Natl Acad Sci USA 92:5446-5450.
25. MATLAB. 1996. The language of technical computing. Natick, MA: The Math-Works, Inc.
26. McCammon JA, Northrup SH, Karplus M, Levy RM. 1980. Helix-coil transitions in a simple polypeptide model. Biopolymers 19:2033-2045.
27. McCammon JA. 1996. A speed limit for protein foldin. Proc Natl Acad Sci USA 93:11426-11427.
28. Pappu RV, Schneller W, Weaver DL. 1996. Electrostatic multipole representation of a polypeptide chain: An algorithm for simulation of polypeptide properties. J Comp Chem 17:1033-1055.
29. Reymond MT, Merutka G, Dyson HJ, Wright PE. 1997. Folding propensities of peptide fragments of myoglobin. Protein Sci 6:706-716.
30. Schneller W, Weaver D. 1993. Simulation of α-helix-coil transitions in simplified polyvaline: Equilibrium properties and Brownian dynamics. Biopolymers 33:1519-1535.
31. Shin H-C, Merutka G, Waltho JP, Wright PE, Dyson HJ. 1993. Peptide models of protein folding initiation sites. 2. The G-H turn region of myoglobin acts as a helix stop signal. J Am Chem Soc 32:6348-6355.
32. Shin H-C, Merutka G, Waltho JP, Tennant LL, Dyson HJ, Wright PE. 1993. Peptide models of protein folding initiation sites. 3. The G-H helical hairpin of myoglobin. J Am Chem Soc 32:6356-6364.
33. Waldburger CD, Jonsson T, Sauer RT. 1996. Barriers to protein folding: Formation of buried polar interactions is a slow step in acquisition of structure. Proc Natl Acad Sci USA 93:2629-2643.
34. Waltho JP, Feher VA, Merutka G, Dyson HJ, Wright PE. 1993. Peptide models of protein folding initiation sites. 1. Secondary structure formation by peptides corresponding to the G- and H-helices of myoglobin. J Am Chem Soc 32:6337-6347.
35. Weaver DL. 1992. Hydrophobic interaction between globin helices. Biopolymers 32:477-490.
36. Yapa K, Weaver DL, Karplus M. 1992. β-Sheet-coil transitions in a simple polypeptide model. Proteins 12:237-265.
37. Yapa KK, Weaver DL. 1996. Protein folding dynamics: Application of the diffusion-collision model to the folding of a four-helix bundle. J Phys Chem 100:2498-2509.