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Literature DB >> 18242977

Combining experiment and simulation in protein folding: closing the gap for small model systems.

R Dustin Schaeffer¹, Alan Fersht, Valerie Daggett.

Abstract

All-atom molecular dynamics (MD) simulations on increasingly powerful computers have been combined with experiments to characterize protein folding in detail over wider time ranges. The folding of small ultrafast folding proteins is being simulated on micros timescales, leading to improved structural predictions and folding rates. To what extent is 'closing the gap' between simulation and experiment for such systems providing insights into general mechanisms of protein folding?

Mesh：

Substances：
Proteins
Water
Urea

Year: 2008 PMID： 18242977 PMCID： PMC2291534 DOI： 10.1016/j.sbi.2007.11.007

Source DB: PubMed Journal: Curr Opin Struct Biol ISSN： 0959-440X Impact factor: 6.809

54 in total

Review 1. Generalized born models of macromolecular solvation effects.

Authors: D Bashford; D A Case
Journal: Annu Rev Phys Chem Date: 2000 Impact factor: 12.703

Review 2. Fast kinetics and mechanisms in protein folding.

Authors: W A Eaton; V Muñoz; S J Hagen; G S Jas; L J Lapidus; E R Henry; J Hofrichter
Journal: Annu Rev Biophys Biomol Struct Date: 2000

3. The role of aromatic residues in the hydrophobic core of the villin headpiece subdomain.

Authors: Benjamin S Frank; Didem Vardar; Deirdre A Buckley; C James McKnight
Journal: Protein Sci Date: 2002-03 Impact factor: 6.725

4. Experimental tests of villin subdomain folding simulations.

Authors: Jan Kubelka; William A Eaton; James Hofrichter
Journal: J Mol Biol Date: 2003-06-13 Impact factor: 5.469

5. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing.

Authors: Vijay S Pande; Ian Baker; Jarrod Chapman; Sidney P Elmer; Siraj Khaliq; Stefan M Larson; Young Min Rhee; Michael R Shirts; Christopher D Snow; Eric J Sorin; Bojan Zagrovic
Journal: Biopolymers Date: 2003-01 Impact factor: 2.505

Review 6. Is there a unifying mechanism for protein folding?

Authors: Valerie Daggett; Alan R Fersht
Journal: Trends Biochem Sci Date: 2003-01 Impact factor: 13.807

7. Parallel protein-unfolding pathways revealed and mapped.

Authors: Caroline F Wright; Kresten Lindorff-Larsen; Lucy G Randles; Jane Clarke
Journal: Nat Struct Biol Date: 2003-08

8. All-atom structure prediction and folding simulations of a stable protein.

Authors: Carlos Simmerling; Bentley Strockbine; Adrian E Roitberg
Journal: J Am Chem Soc Date: 2002-09-25 Impact factor: 15.419

9. Unifying features in protein-folding mechanisms.

Authors: Stefano Gianni; Nicholas R Guydosh; Faaizah Khan; Teresa D Caldas; Ugo Mayor; George W N White; Mari L DeMarco; Valerie Daggett; Alan R Fersht
Journal: Proc Natl Acad Sci U S A Date: 2003-10-31 Impact factor: 11.205

10. Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations.

Authors: G Settanni; J Gsponer; A Caflisch
Journal: Biophys J Date: 2004-03 Impact factor: 4.033

31 in total

1. Visualizing transient protein-folding intermediates by tryptophan-scanning mutagenesis.

Authors: Alexis Vallée-Bélisle; Stephen W Michnick
Journal: Nat Struct Mol Biol Date: 2012-06-10 Impact factor: 15.369

2. Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics simulations.

Authors: Whasil Lee; Xiancheng Zeng; Huan-Xiang Zhou; Vann Bennett; Weitao Yang; Piotr E Marszalek
Journal: J Biol Chem Date: 2010-09-24 Impact factor: 5.157

Combining experiment and simulation in protein folding: closing the gap for small model systems.

Review 1. Generalized born models of macromolecular solvation effects.

Review 2. Fast kinetics and mechanisms in protein folding.

3. The role of aromatic residues in the hydrophobic core of the villin headpiece subdomain.

4. Experimental tests of villin subdomain folding simulations.

5. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing.

Review 6. Is there a unifying mechanism for protein folding?

7. Parallel protein-unfolding pathways revealed and mapped.

8. All-atom structure prediction and folding simulations of a stable protein.

9. Unifying features in protein-folding mechanisms.

10. Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations.

1. Visualizing transient protein-folding intermediates by tryptophan-scanning mutagenesis.

2. Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics simulations.

Review 3. Structural determinants of protein folding.

4. The dual-basin landscape in GFP folding.

5. Molecular simulation of protein-surface interactions: benefits, problems, solutions, and future directions.

6. Implementation of Accelerated Molecular Dynamics in NAMD.

7. Protein folding in a reverse micelle environment: the role of confinement and dehydration.

8. Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

9. Stabilizing Effect of Inherent Knots on Proteins Revealed by Molecular Dynamics Simulations.

10. Emerging topics in structure-based virtual screening.