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Literature DB >> 9600893

Folding funnels and frustration in off-lattice minimalist protein landscapes.

Abstract

A full quantitative understanding of the protein folding problem is now becoming possible with the help of the energy landscape theory and the protein folding funnel concept. Good folding sequences have a landscape that resembles a rough funnel where the energy bias towards the native state is larger than its ruggedness. Such a landscape leads not only to fast folding and stable native conformations but, more importantly, to sequences that are robust to variations in the protein environment and to sequence mutations. In this paper, an off-lattice model of sequences that fold into a beta-barrel native structure is used to describe a framework that can quantitatively distinguish good and bad folders. The two sequences analyzed have the same native structure, but one of them is minimally frustrated whereas the other one exhibits a high degree of frustration.

Entities: Gene

Mesh：

Substances：
Proteins

Year: 1998 PMID： 9600893 PMCID： PMC34496 DOI： 10.1073/pnas.95.11.5921

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

60 in total

1. The kinetic folding intermediate of ribonuclease H resembles the acid molten globule and partially unfolded molecules detected under native conditions.

Authors: T M Raschke; S Marqusee
Journal: Nat Struct Biol Date: 1997-04

Review 2. 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

3. Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability.

Authors: M L Scalley; D Baker
Journal: Proc Natl Acad Sci U S A Date: 1997-09-30 Impact factor: 11.205

Folding funnels and frustration in off-lattice minimalist protein landscapes.

1. The kinetic folding intermediate of ribonuclease H resembles the acid molten globule and partially unfolded molecules detected under native conditions.

Review 2. Intermediates in the folding reactions of small proteins.

3. Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability.

Review 4. Time-resolved biophysical methods in the study of protein folding.

5. Building self-avoiding lattice models of proteins using a self-consistent field optimization.

6. Observation of distinct nanosecond and microsecond protein folding events.

7. Why are some proteins structures so common?

Review 8. Submillisecond kinetics of protein folding.

9. Simple model of protein folding kinetics.

10. Kinetic mechanism of cytochrome c folding: involvement of the heme and its ligands.

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

2. Folding of a pressure-denatured model protein.

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

4. How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta.

5. Pressure-induced protein-folding/unfolding kinetics.

6. Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A.

7. Thermodynamics and kinetics of a folded-folded' transition at valine-9 of a GCN4-like leucine zipper.

8. Three-helix-bundle protein in a Ramachandran model.

9. Nonglassy kinetics in the folding of a simple single-domain protein.

10. On hydrophobicity correlations in protein chains.