Molecular dynamics simulations of certain mutant peptide models from staphylococcal nuclease reveal that initial hydrophobic collapse associated with turn propensity drives β
-hairpin folding

Rashmi Tambe Shukla; Naveen Kumar; Yellamraju U. Sasidhar

doi:10.1002/psc.2530

Molecular dynamics simulations of certain mutant peptide models from staphylococcal nuclease reveal that initial hydrophobic collapse associated with turn propensity drives β -hairpin folding

Journal of Peptide Science ◽

10.1002/psc.2530 ◽

2013 ◽

Vol 19 (8) ◽

pp. 516-527

Author(s):

Rashmi Tambe Shukla ◽

Naveen Kumar ◽

Yellamraju U. Sasidhar

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Staphylococcal Nuclease ◽

Hydrophobic Collapse ◽

Mutant Peptide ◽

Peptide Models ◽

Dynamics Simulations

Download Full-text

Kinetic Folding andCis/TransProlyl Isomerization of Staphylococcal Nuclease. A Study by Stopped-Flow Absorption, Stopped-Flow Circular Dichroism, and Molecular Dynamics Simulations

Biochemistry ◽

10.1021/bi975017h ◽

1997 ◽

Vol 36 (36) ◽

pp. 11050-11050

Author(s):

Teikichi Ikura ◽

Galina P. Tsurupa ◽

Kunihiro Kuwajima

Keyword(s):

Molecular Dynamics ◽

Circular Dichroism ◽

Molecular Dynamics Simulations ◽

Staphylococcal Nuclease ◽

Stopped Flow ◽

Dynamics Simulations ◽

Circular Dichroïsm ◽

Kinetic Folding

Download Full-text

Molecular Dynamics Simulations of Simple Peptide Models: Solvent Effects and Comparison with Experiment

The Journal of Physical Chemistry ◽

10.1021/j100091a053 ◽

1994 ◽

Vol 98 (40) ◽

pp. 10294-10302 ◽

Cited By ~ 4

Author(s):

Gilad Haran ◽

Elisha Haas ◽

Dennis C. Rapaport

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Solvent Effects ◽

Comparison With Experiment ◽

Peptide Models ◽

Dynamics Simulations

Download Full-text

Correlation between changes in nuclear magnetic resonance order parameters and conformational entropy: Molecular dynamics simulations of native and denatured staphylococcal nuclease

Proteins Structure Function and Bioinformatics ◽

10.1002/(sici)1097-0134(20000201)38:2<123::aid-prot2>3.0.co;2-h ◽

2000 ◽

Vol 38 (2) ◽

pp. 123-133 ◽

Cited By ~ 25

Author(s):

James O. Wrabl ◽

David Shortle ◽

Thomas B. Woolf

Keyword(s):

Molecular Dynamics ◽

Nuclear Magnetic Resonance ◽

Magnetic Resonance ◽

Molecular Dynamics Simulations ◽

Staphylococcal Nuclease ◽

Order Parameters ◽

Conformational Entropy ◽

Dynamics Simulations ◽

Nuclear Magnetic

Download Full-text

Molecular dynamics simulations of hydrophobic collapse of ubiquitin

Protein Science ◽

10.1002/pro.5560070404 ◽

1998 ◽

Vol 7 (4) ◽

pp. 860-874 ◽

Cited By ~ 66

Author(s):

Darwin.V. Alonso ◽

Valerie Daggett

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Hydrophobic Collapse ◽

Dynamics Simulations

Download Full-text

Kinetic Folding andCis/TransProlyl Isomerization of Staphylococcal Nuclease. A Study by Stopped-Flow Absorption, Stopped-Flow Circular Dichroism, and Molecular Dynamics Simulations†

Biochemistry ◽

10.1021/bi963174v ◽

1997 ◽

Vol 36 (21) ◽

pp. 6529-6538 ◽

Cited By ~ 22

Author(s):

Teikichi Ikura ◽

Galina P. Tsurupa ◽

Kunihiro Kuwajima

Keyword(s):

Molecular Dynamics ◽

Circular Dichroism ◽

Molecular Dynamics Simulations ◽

Staphylococcal Nuclease ◽

Stopped Flow ◽

Dynamics Simulations ◽

Circular Dichroïsm ◽

Kinetic Folding

Download Full-text

Molecular Dynamics Simulations of Staphylococcal Nuclease: Properties of Water at the Protein Surface

The Journal of Physical Chemistry B ◽

10.1021/jp047579y ◽

2004 ◽

Vol 108 (40) ◽

pp. 15928-15937 ◽

Cited By ~ 56

Author(s):

Nikolai Smolin ◽

Roland Winter

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Staphylococcal Nuclease ◽

Protein Surface ◽

Dynamics Simulations

Download Full-text

Structure of phosphorus-selenium glasses: results from ab initio molecular dynamics simulations

Molecular Physics ◽

10.1080/002689700162045 ◽

2000 ◽

Vol 98 (11) ◽

pp. 701-707

Author(s):

Alessandro Sergi, Mauro Ferrario, Francesco Bu

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Ab Initio Molecular Dynamics ◽

Dynamics Simulations

Download Full-text

Tracer diffusion in perfectly aligned liquid crystalline phases Kinetic theory and molecular dynamics simulations

Molecular Physics ◽

10.1080/00268979709482789 ◽

1997 ◽

Vol 91 (6) ◽

pp. 993-1003 ◽

Cited By ~ 1

Author(s):

ANJALI KHARE ◽

DAVID KOFKE ◽

GLENN EVANS

Keyword(s):

Molecular Dynamics ◽

Kinetic Theory ◽

Molecular Dynamics Simulations ◽

Liquid Crystalline ◽

Tracer Diffusion ◽

Crystalline Phases ◽

Liquid Crystalline Phases ◽

Dynamics Simulations

Download Full-text

ERRATUM Molecular dynamics simulations of liquid crystal phases using atomistic potentials

Molecular Physics ◽

10.1080/002689798167430 ◽

1998 ◽

Vol 95 (1) ◽

pp. 121-121

Author(s):

CARL MCBRIDE MARK R. WILSON JUDITH A. K.

Keyword(s):

Molecular Dynamics ◽

Liquid Crystal ◽

Molecular Dynamics Simulations ◽

Crystal Phases ◽

Dynamics Simulations ◽

Liquid Crystal Phases

Download Full-text

Nonequilibrium Molecular Dynamics Simulations of 3-Methylhexane: The Effect of Inter- and Intramolecular Potential Models on Simulated Viscosity

The Journal of Physical Chemistry A ◽

10.1021/jp971476g ◽

1997 ◽

Vol 101 (27) ◽

pp. 5026-5026

Author(s):

Maija Lahtela ◽

Tapani A. Pakkanen ◽

Richard L. Rowley

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Nonequilibrium Molecular Dynamics ◽

Potential Models ◽

Dynamics Simulations

Download Full-text