φ-Value analysis by molecular dynamics simulations of reversible folding

Abstract

In Φ-value analysis, the effects of mutations on the folding kinetics are compared with the corresponding effects on thermodynamic stability to investigate the structure of the protein-folding transition state (TS). Here, molecular dynamics (MD) simulations (totaling 0.65 ms) have been performed for a large set of single-point mutants of a 20-residue three-stranded antiparallel β-sheet peptide. Between 57 and 120 folding events were sampled at near equilibrium for each mutant, allowing for accurate estimates of folding/unfolding rates and stability changes. The Φ values calculated from folding and unfolding rates extracted from the MD trajectories are reliable if the stability loss upon mutation is larger than ≈0.6 kcal/mol, which is observed for 8 of the 32 single-point mutants. The same heterogeneity of the TS of the wild type was found in the mutated peptides, showing two possible pathways for folding. Single-point mutations can induce significant TS shifts not always detected by Φ-value analysis. Specific nonnative interactions at the TS were observed in most of the peptides studied here. The interpretation of Φ values based on the ratio of atomic contacts at the TS over the native state, which has been used in the past in MD and Monte Carlo simulations, is in agreement with the TS structures of wild-type peptide. However, Φ values tend to overestimate the nativeness of the TS ensemble, when interpreted neglecting the nonnative interactions.

Autoren

Giovanni Settanni
Francesco Rao
Amedeo Caflisch

DOI

10.1073/pnas.0406754102

eISSN

1091-6490

ISSN

0027-8424

Ausgabe der Veröffentlichung

3

Zeitschrift

Proceedings of the National Academy of Sciences

Sprache

en

Online publication date

2005

Paginierung

628 - 633

Datum der Veröffentlichung

2005

Status

Published

Herausgeber

Proceedings of the National Academy of Sciences

Herausgeber URL

http://dx.doi.org/10.1073/pnas.0406754102

Datum der Datenerfassung

2022

Titel

Φ-Value analysis by molecular dynamics simulations of reversible folding

Ausgabe der Zeitschrift

102

Datenquelle: Crossref

Abstract

In Phi-value analysis, the effects of mutations on the folding kinetics are compared with the corresponding effects on thermodynamic stability to investigate the structure of the protein-folding transition state (TS). Here, molecular dynamics (MD) simulations (totaling 0.65 ms) have been performed for a large set of single-point mutants of a 20-residue three-stranded antiparallel beta-sheet peptide. Between 57 and 120 folding events were sampled at near equilibrium for each mutant, allowing for accurate estimates of folding/unfolding rates and stability changes. The Phi values calculated from folding and unfolding rates extracted from the MD trajectories are reliable if the stability loss upon mutation is larger than approximately 0.6 kcal/mol, which is observed for 8 of the 32 single-point mutants. The same heterogeneity of the TS of the wild type was found in the mutated peptides, showing two possible pathways for folding. Single-point mutations can induce significant TS shifts not always detected by Phi-value analysis. Specific nonnative interactions at the TS were observed in most of the peptides studied here. The interpretation of Phi values based on the ratio of atomic contacts at the TS over the native state, which has been used in the past in MD and Monte Carlo simulations, is in agreement with the TS structures of wild-type peptide. However, Phi values tend to overestimate the nativeness of the TS ensemble, when interpreted neglecting the nonnative interactions.

Addresses

Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.

Autoren

Giovanni Settanni
Francesco Rao
Amedeo Caflisch

DOI

10.1073/pnas.0406754102

eISSN

1091-6490

Externe Identifier

PubMed Identifier: 15644439
PubMed Central ID: PMC545520

Open access

false

ISSN

0027-8424

Ausgabe der Veröffentlichung

3

Zeitschrift

Proceedings of the National Academy of Sciences of the United States of America

Schlüsselwörter

Protein Folding
Kinetics
Point Mutation
Thermodynamics
Models, Molecular
Computer Simulation

Sprache

eng

Medium

Print-Electronic

Online publication date

2005

Paginierung

628 - 633

Datum der Veröffentlichung

2005

Status

Published

Datum der Datenerfassung

2005

Titel

Phi-value analysis by molecular dynamics simulations of reversible folding.

Sub types

Research Support, Non-U.S. Gov't
research-article
Journal Article

Ausgabe der Zeitschrift

102

Files

https://europepmc.org/articles/pmc545520?pdf=render

Datenquelle: Europe PubMed Central

Abstract

In Phi-value analysis, the effects of mutations on the folding kinetics are compared with the corresponding effects on thermodynamic stability to investigate the structure of the protein-folding transition state (TS). Here, molecular dynamics (MD) simulations (totaling 0.65 ms) have been performed for a large set of single-point mutants of a 20-residue three-stranded antiparallel beta-sheet peptide. Between 57 and 120 folding events were sampled at near equilibrium for each mutant, allowing for accurate estimates of folding/unfolding rates and stability changes. The Phi values calculated from folding and unfolding rates extracted from the MD trajectories are reliable if the stability loss upon mutation is larger than approximately 0.6 kcal/mol, which is observed for 8 of the 32 single-point mutants. The same heterogeneity of the TS of the wild type was found in the mutated peptides, showing two possible pathways for folding. Single-point mutations can induce significant TS shifts not always detected by Phi-value analysis. Specific nonnative interactions at the TS were observed in most of the peptides studied here. The interpretation of Phi values based on the ratio of atomic contacts at the TS over the native state, which has been used in the past in MD and Monte Carlo simulations, is in agreement with the TS structures of wild-type peptide. However, Phi values tend to overestimate the nativeness of the TS ensemble, when interpreted neglecting the nonnative interactions.

Autoren

Giovanni Settanni
Francesco Rao
Amedeo Caflisch

Autoren-URL

https://www.ncbi.nlm.nih.gov/pubmed/15644439

DOI

10.1073/pnas.0406754102

Externe Identifier

PubMed Central ID: PMC545520

ISSN

0027-8424

Ausgabe der Veröffentlichung

3

Zeitschrift

Proc Natl Acad Sci U S A

Schlüsselwörter

Computer Simulation
Kinetics
Models, Molecular
Point Mutation
Protein Folding
Thermodynamics

Sprache

eng

Country

United States

Paginierung

628 - 633

PII

0406754102

Datum der Veröffentlichung

2005

Status

Published

Datum, an dem der Datensatz öffentlich gemacht wurde

2005

Titel

Phi-value analysis by molecular dynamics simulations of reversible folding.

Sub types

Journal Article
Research Support, Non-U.S. Gov't

Ausgabe der Zeitschrift

102

Datenquelle: PubMed

φ-Value analysis by molecular dynamics simulations of reversible folding

Files

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