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Literature DB >> 14677926

Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange.

Michele Vendruscolo¹, Emanuele Paci, Christopher M Dobson, Martin Karplus.

Abstract

We present a method for determining the ensembles of native protein structures that result from the large fluctuations of low probability revealed by hydrogen-exchange experiments. The measured protection factors are used to bias Monte Carlo simulations to sample the structures of the exchange competent species. The approach is illustrated by its application to the case of alpha-lactalbumin.

Entities: Chemical Gene

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Year: 2003 PMID： 14677926 DOI： 10.1021/ja036523z

Source DB: PubMed Journal: J Am Chem Soc ISSN： 0002-7863 Impact factor: 15.419

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Cited

50 in total

1. Stability and fluctuations of amide hydrogen bonds in a bacterial cytochrome c: a molecular dynamics study.

Authors: Gernot Kieseritzky; Giulia Morra; Ernst-Walter Knapp
Journal: J Biol Inorg Chem Date: 2005-11-16 Impact factor: 3.358

2. Ensemble-based convergence analysis of biomolecular trajectories.

Authors: Edward Lyman; Daniel M Zuckerman
Journal: Biophys J Date: 2006-04-14 Impact factor: 4.033

3. Molecular statistics of cytochrome c: structural plasticity and molecular environment.

Authors: Giovanni La Penna; Sara Furlan; Lucia Banci
Journal: J Biol Inorg Chem Date: 2006-10-12 Impact factor: 3.358

4. Molecular crowding inhibits intramolecular breathing motions in proteins.

Authors: Lee Makowski; Diane J Rodi; Suneeta Mandava; David D L Minh; David B Gore; Robert F Fischetti
Journal: J Mol Biol Date: 2007-08-17 Impact factor: 5.469

5. The folding energy landscape of apoflavodoxin is rugged: hydrogen exchange reveals nonproductive misfolded intermediates.

Authors: Yves J M Bollen; Monique B Kamphuis; Carlo P M van Mierlo
Journal: Proc Natl Acad Sci U S A Date: 2006-03-06 Impact factor: 11.205

Review 6. CHARMM: the biomolecular simulation program.

Authors: B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal: J Comput Chem Date: 2009-07-30 Impact factor: 3.376

Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange.

1. Stability and fluctuations of amide hydrogen bonds in a bacterial cytochrome c: a molecular dynamics study.

2. Ensemble-based convergence analysis of biomolecular trajectories.

3. Molecular statistics of cytochrome c: structural plasticity and molecular environment.

4. Molecular crowding inhibits intramolecular breathing motions in proteins.

5. The folding energy landscape of apoflavodoxin is rugged: hydrogen exchange reveals nonproductive misfolded intermediates.

Review 6. CHARMM: the biomolecular simulation program.

7. An experimentally guided umbrella sampling protocol for biomolecules.

Review 8. Protein folding and misfolding: mechanism and principles.

Review 9. Hydrogen-exchange mass spectrometry for the study of intrinsic disorder in proteins.

10. Native State of Complement Protein C3d Analysed via Hydrogen Exchange and Conformational Sampling.