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Literature DB >> 15295118

What can one learn from experiments about the elusive transition state?

Iksoo Chang¹, Marek Cieplak, Jayanth R Banavar, Amos Maritan.

Abstract

We present the results of an exact analysis of a model energy landscape of a protein to clarify the idea of the transition state and the physical meaning of the phi values determined in protein engineering experiments. We benchmark our findings to various theoretical approaches proposed in the literature for the identification and characterization of the transition state.

Mesh：

Substances：
Peptides

Year: 2004 PMID： 15295118 PMCID： PMC2280003 DOI： 10.1110/ps.04713804

Source DB: PubMed Journal: Protein Sci ISSN： 0961-8368 Impact factor: 6.725

40 in total

1. Understanding beta-hairpin formation.

Authors: A R Dinner; T Lazaridis; M Karplus
Journal: Proc Natl Acad Sci U S A Date: 1999-08-03 Impact factor: 11.205

2. Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G.

Authors: V S Pande; D S Rokhsar
Journal: Proc Natl Acad Sci U S A Date: 1999-08-03 Impact factor: 11.205

3. 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

4. Identifying the protein folding nucleus using molecular dynamics.

Authors: N V Dokholyan; S V Buldyrev; H E Stanley; E I Shakhnovich
Journal: J Mol Biol Date: 2000-03-10 Impact factor: 5.469

5. Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus.

Authors: L Li; L A Mirny; E I Shakhnovich
Journal: Nat Struct Biol Date: 2000-04

6. Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins.

Authors: C Clementi; H Nymeyer; J N Onuchic
Journal: J Mol Biol Date: 2000-05-19 Impact factor: 5.469

7. From snapshot to movie: phi analysis of protein folding transition states taken one step further.

Authors: T Ternström; U Mayor; M Akke; M Oliveberg
Journal: Proc Natl Acad Sci U S A Date: 1999-12-21 Impact factor: 11.205

Review 8. Characterisation of the transition states for protein folding: towards a new level of mechanistic detail in protein engineering analysis.

Authors: M Oliveberg
Journal: Curr Opin Struct Biol Date: 2001-02 Impact factor: 6.809

Review 9. Is protein folding hierarchic? II. Folding intermediates and transition states.

Authors: R L Baldwin; G D Rose
Journal: Trends Biochem Sci Date: 1999-02 Impact factor: 13.807

Review 10. Is protein folding hierarchic? I. Local structure and peptide folding.

Authors: R L Baldwin; G D Rose
Journal: Trends Biochem Sci Date: 1999-01 Impact factor: 13.807

7 in total

1. A simple and exact Laplacian clustering of complex networking phenomena: application to gene expression profiles.

Authors: Choongrak Kim; Mookyung Cheon; Minho Kang; Iksoo Chang
Journal: Proc Natl Acad Sci U S A Date: 2008-03-12 Impact factor: 11.205

2. Cooperative folding kinetics of BBL protein and peripheral subunit-binding domain homologues.

Authors: Wookyung Yu; Kwanghoon Chung; Mookyung Cheon; Muyoung Heo; Kyou-Hoon Han; Sihyun Ham; Iksoo Chang
Journal: Proc Natl Acad Sci U S A Date: 2008-02-12 Impact factor: 11.205

3. Analysis of oligomeric proteins during unfolding by pH and temperature.

Authors: Pradip Bhattacharya; Tamil Ganeshan; Soumiyadeep Nandi; Alok Srivastava; Prashant Singh; Mohommad Rehan; Reshmi Rashkush; Naidu Subbarao; Andrew Lynn
Journal: J Mol Model Date: 2009-02-11 Impact factor: 1.810

4. Minimal folding pathways for coarse-grained biopolymer fragments.

Authors: Ali R Mohazab; Steven S Plotkin
Journal: Biophys J Date: 2008-09-26 Impact factor: 4.033

5. Analyzing pathogenic mutations of C5 domain from cardiac myosin binding protein C through MD simulations.

Authors: Fabio Cecconi; Carlo Guardiani; Roberto Livi
Journal: Eur Biophys J Date: 2008-04-01 Impact factor: 1.733

Review 6. The Wako-Saitô-Muñoz-Eaton Model for Predicting Protein Folding and Dynamics.

Authors: Koji Ooka; Runjing Liu; Munehito Arai
Journal: Molecules Date: 2022-07-12 Impact factor: 4.927

7. Network measures for protein folding state discrimination.

Authors: Giulia Menichetti; Piero Fariselli; Daniel Remondini
Journal: Sci Rep Date: 2016-07-28 Impact factor: 4.379

7 in total