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Literature DB >> 7724609

Toward an outline of the topography of a realistic protein-folding funnel.

J N Onuchic¹, P G Wolynes, Z Luthey-Schulten, N D Socci.

Abstract

Experimental information on the structure and dynamics of molten globules gives estimates for the energy landscape's characteristics for folding highly helical proteins, when supplemented by a theory of the helix-coil transition in collapsed heteropolymers. A law of corresponding states relating simulations on small lattice models to real proteins possessing many more degrees of freedom results. This correspondence reveals parallels between "minimalist" lattice results and recent experimental results for the degree of native character of the folding transition state and molten globule and also pinpoints the needs of further experiments.

Mesh：

Year: 1995 PMID： 7724609 PMCID： PMC42220 DOI： 10.1073/pnas.92.8.3626

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

25 in total

1. Computer simulation of protein folding.

Authors: M Levitt; A Warshel
Journal: Nature Date: 1975-02-27 Impact factor: 49.962

2. New Monte Carlo technique for studying phase transitions.

Authors:
Journal: Phys Rev Lett Date: 1988-12-05 Impact factor: 9.161

Review 3. Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics.

Authors: J Skolnick; A Kolinski
Journal: J Mol Biol Date: 1991-09-20 Impact factor: 5.469

4. Phase transitions in a "many-letter" random heteropolymer.

Authors:
Journal: Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics Date: 1994-10

Review 5. Intermediates in the folding reactions of small proteins.

Authors: P S Kim; R L Baldwin
Journal: Annu Rev Biochem Date: 1990 Impact factor: 23.643

6. How does a protein fold?

Authors: A Sali; E Shakhnovich; M Karplus
Journal: Nature Date: 1994-05-19 Impact factor: 49.962

7. Solution structure of apocytochrome b562.

Authors: Y Feng; S G Sligar; A J Wand
Journal: Nat Struct Biol Date: 1994-01

8. Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding.

Authors: D E Otzen; L S Itzhaki; N F elMasry; S E Jackson; A R Fersht
Journal: Proc Natl Acad Sci U S A Date: 1994-10-25 Impact factor: 11.205

9. Specific nucleus as the transition state for protein folding: evidence from the lattice model.

Authors: V I Abkevich; A M Gutin; E I Shakhnovich
Journal: Biochemistry Date: 1994-08-23 Impact factor: 3.162

10. Spin glasses and the statistical mechanics of protein folding.

Authors: J D Bryngelson; P G Wolynes
Journal: Proc Natl Acad Sci U S A Date: 1987-11 Impact factor: 11.205

130 in total

1. Protein design is a key factor for subunit-subunit association.

Authors: C Clementi; P Carloni; A Maritan
Journal: Proc Natl Acad Sci U S A Date: 1999-08-17 Impact factor: 11.205

Review 2. Folding funnels, binding funnels, and protein function.

Authors: C J Tsai; S Kumar; B Ma; R Nussinov
Journal: Protein Sci Date: 1999-06 Impact factor: 6.725

3. Molecular dynamics simulation of Escherichia coli dihydrofolate reductase and its protein fragments: relative stabilities in experiment and simulations.

Authors: Y Y Sham; B Ma; C J Tsai; R Nussinov
Journal: Protein Sci Date: 2001-01 Impact factor: 6.725

Toward an outline of the topography of a realistic protein-folding funnel.

1. Computer simulation of protein folding.

2. New Monte Carlo technique for studying phase transitions.

Review 3. Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics.

4. Phase transitions in a "many-letter" random heteropolymer.

Review 5. Intermediates in the folding reactions of small proteins.

6. How does a protein fold?

7. Solution structure of apocytochrome b562.

8. Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding.

9. Specific nucleus as the transition state for protein folding: evidence from the lattice model.

10. Spin glasses and the statistical mechanics of protein folding.

1. Protein design is a key factor for subunit-subunit association.

Review 2. Folding funnels, binding funnels, and protein function.

3. Molecular dynamics simulation of Escherichia coli dihydrofolate reductase and its protein fragments: relative stabilities in experiment and simulations.

4. Hierarchies and logarithmic oscillations in the temporal relaxation patterns of proteins and other complex systems.

5. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures.

6. Entropic barriers, transition states, funnels, and exponential protein folding kinetics: a simple model.

Review 7. Folding and binding cascades: dynamic landscapes and population shifts.

8. A polar, solvent-exposed residue can be essential for native protein structure.

9. Investigation of routes and funnels in protein folding by free energy functional methods.

10. Protein folding and unfolding on a complex energy landscape.