Roles of native topology and chain-length scaling in protein folding: A simulation study with a ḡ-like model

Journal of Molecular Biology

Volumn 313, Issue 1, 2001, Pages 171-180

  Koga, Nobuyasu ^a   Takada, Shoji ^a,b  

^a KOBE UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

Contact order; Denatured state; Folding rate; Transition state; value

Indexed keywords

GUANINE NUCLEOTIDE BINDING PROTEIN; MYOGLOBIN; PROTEIN A;

AMINO ACID SEQUENCE; ARTICLE; CALCULATION; COMPUTER SIMULATION; DENATURATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE; TEMPERATURE DEPENDENCE;

EID: 0035850732     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.5037     Document Type: Article

References (34)

1. Theory of protein folding: The energy landscape perspective
2. Mechanisms of protein folding
3. A surprising simplicity to protein folding
4. Contact order, transition state placement and the refolding rates of single domain proteins
5. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: Evidence for a nucleation-condensation mechanism for protein folding
6. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved
7. Experiment and theory highlight role of native state topology in SH3 folding
8. Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding
9. Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain
10. A breakdown of symmetry in the folding transition state of protein L
11. Critical role of β-hairpin formation in protein G folding
12. From snapshot to movie: φ Analysis of protein folding transition states taken one step further
13. Chain length scaling of protein folding time
14. Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold
15. From minimal models to real proteins: Time scales for protein folding kinetics
16. Folding funnels and energy landscapes of larger proteins within the capillarity approximation
17. Structural correlations in protein folding funnels
18. Variational theory for site resolved protein folding free energy surfaces
19. A theoretical search for folding/unfolding nuclei in three-dimensional protein structures
20. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
21. A simple model for calculating the kinetics of protein folding from three-dimensional structures
22. The SH3-fold family: Experimental evidence and prediction of variations in the folding pathways
23. Theoretical studies of protein folding
24. Go-ing for the prediction of protein folding mechanisms
25. Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding?
26. How native-state topology affects the folding of dihydrofolate reductase and interleukin-1 β
27. Multidimensional free-energy calculations using the weighted histogram analysis method
28. Structural and dynamic characterization of partially folded states of apomyoglobin and implications for protein folding
29. Absence of a stable intermediate on the folding pathway of protein A
30. Scaling of folding properties in Gō models of proteins
31. Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach
32. Molecular dynamics with coupling to an external bath
33. A program to produce both detailed and schematic plots of protein structures