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Literature DB >> 10811910

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

Abstract

The overall structure of the transition-state and intermediate ensembles observed experimentally for dihydrofolate reductase and interleukin-1beta can be obtained by using simplified models that have almost no energetic frustration. The predictive power of these models suggests that, even for these very large proteins with completely different folding mechanisms and functions, real protein sequences are sufficiently well designed, and much of the structural heterogeneity observed in the intermediates and the transition-state ensembles is determined by topological effects.

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Year: 2000 PMID： 10811910 PMCID： PMC18526 DOI： 10.1073/pnas.100547897

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

26 in total

1. A simple model for calculating the kinetics of protein folding from three-dimensional structures.

Authors: V Muñoz; W A Eaton
Journal: Proc Natl Acad Sci U S A Date: 1999-09-28 Impact factor: 11.205

2. A theoretical search for folding/unfolding nuclei in three-dimensional protein structures.

Authors: O V Galzitskaya; A V Finkelstein
Journal: Proc Natl Acad Sci U S A Date: 1999-09-28 Impact factor: 11.205

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

Authors: E Alm; D Baker
Journal: Proc Natl Acad Sci U S A Date: 1999-09-28 Impact factor: 11.205

Review 4. The energy landscape theory of protein folding: insights into folding mechanisms and scenarios.

Authors: J N Onuchic; H Nymeyer; A E García; J Chahine; N D Socci
Journal: Adv Protein Chem Date: 2000

5. An essential intermediate in the folding of dihydrofolate reductase.

Authors: D K Heidary; J C O'Neill; M Roy; P A Jennings
Journal: Proc Natl Acad Sci U S A Date: 2000-05-23 Impact factor: 11.205

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

Authors: J E Shea; J N Onuchic; C L Brooks
Journal: Proc Natl Acad Sci U S A Date: 1999-10-26 Impact factor: 11.205

7. Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions.

Authors: H Taketomi; Y Ueda; N Gō
Journal: Int J Pept Protein Res Date: 1975

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

Authors: H Nymeyer; A E García; J N Onuchic
Journal: Proc Natl Acad Sci U S A Date: 1998-05-26 Impact factor: 11.205

9. Contact order, transition state placement and the refolding rates of single domain proteins.

Authors: K W Plaxco; K T Simons; D Baker
Journal: J Mol Biol Date: 1998-04-10 Impact factor: 5.469

10. Landscape approaches for determining the ensemble of folding transition states: success and failure hinge on the degree of frustration.

Authors: H Nymeyer; N D Socci; J N Onuchic
Journal: Proc Natl Acad Sci U S A Date: 2000-01-18 Impact factor: 11.205

67 in total

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

1. A simple model for calculating the kinetics of protein folding from three-dimensional structures.

2. A theoretical search for folding/unfolding nuclei in three-dimensional protein structures.

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

Review 4. The energy landscape theory of protein folding: insights into folding mechanisms and scenarios.

5. An essential intermediate in the folding of dihydrofolate reductase.

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

7. Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions.

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

9. Contact order, transition state placement and the refolding rates of single domain proteins.

10. Landscape approaches for determining the ensemble of folding transition states: success and failure hinge on the degree of frustration.

1. An essential intermediate in the folding of dihydrofolate reductase.

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

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

4. Buffed energy landscapes: another solution to the kinetic paradoxes of protein folding.

5. Protein topology determines binding mechanism.

6. Simulations of beta-hairpin folding confined to spherical pores using distributed computing.

7. Meeting halfway on the bridge between protein folding theory and experiment.

8. Simulation, experiment, and evolution: understanding nucleation in protein S6 folding.

9. The effects of nonnative interactions on protein folding rates: theory and simulation.

10. Variations in the fast folding rates of the lambda-repressor: a hybrid molecular dynamics study.