Protein folding simulation with solvent-induced force field: Folding pathway ensemble of three-helix-bundle proteins

Proteins: Structure, Function and Genetics

Volumn 42, Issue 1, 2001, Pages 85-98

  Takada, Shoji ^a  

^a KOBE UNIVERSITY   (Japan)

Author keywords

Albumin binding domain; Coarse grained model; Folding nucleus; Helix capping; Phi value

Indexed keywords

ALBUMIN; HELICASE; PROTEIN A; SOLVENT;

ARTICLE; CARBOXY TERMINAL SEQUENCE; DIELECTRIC CONSTANT; ENTROPY; HYDROGEN BOND; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN LOCALIZATION; PROTEIN STABILITY; PROTEIN STRUCTURE; SIMULATION;

ALBUMINS; BACTERIAL PROTEINS; BINDING SITES; COMPUTER SIMULATION; ELECTROSTATICS; HYDROGEN BONDING; KINETICS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SOLVENTS; THERMODYNAMICS;

MUS;

EID: 0035189984     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/1097-0134(20010101)42:1<85::AID-PROT90>3.0.CO;2-3     Document Type: Article

References (44)

1. Theory of protein folding: The energy landscape perspective
2. Spin-glass and the statistical mechanics of protein folding
3. Contact order, transition state placement and the refolding rates of single domain proteins
4. Experiment and theory highlight role of native state topology in SH3 folding
5. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved
6. Structural correlations in protein folding funnels
7. Variational theory for site resolved protein folding free energy surfaces
8. A theoretical search for folding/unfolding nuclei in three-dimensional protein structures
9. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
10. A simple model for calculating the kinetics of protein folding from three-dimensional structures
11. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations
12. First principle calculation of the folding free energy of a three helix bundle protein
13. Exploring the folding free energy surface of a three helix bundle protein
14. Interpreting the folding kinetics of helical proteins
15. Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A
16. Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions
17. Principles of protein folding: A perspective from simple exact models
18. How does a protein fold?
19. Kinetics of protein folding: Nucleation mechanism, timescales, and pathways
20. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
21. A second generation force field for the simulation of proteins and nucleic acids
22. Monte Carlo simulations of protein folding. II. Application to protein A, ROP and crambin
23. Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignments
24. A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by Z-score optimization
25. Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer
26. Knowledge-based potentials for proteins
27. Free energy balance in protein folding
28. Roles of electrostatic interaction in proteins
29. LINCS A linear constraint solver for molecular simulations
30. Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
31. Intrinsic β-sheet propensities result from van der Waals interactions between side chain and the local backbone
32. Amino acid preferences for specific locations at the end of α helices
33. Free energy, entropy, and internal energy of hydrophobic interactions: Computer simulations
34. The GA module, a mobile albumin-binding bacterial domain, adopts a three-helix-bundle structure
35. Solution structure of the Albumin-binding GA module: A versatile bacterial protein domain
36. The weighted histogram analysis method for free-energy on biomolecules. I. The method
37. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometric features
38. A small engineered protein lacks structural uniqueness by increasing the side-chain conformational entropy
39. Pressure-induced protein folding/unfolding kinetics
40. Hydrophobicity at small and large length scales
41. MOLSCRIPT: A program to produce both detailed and schematic plots or protein structures