Thermodynamics and Kinetics of Folding of Two Model Peptides Investigated by Molecular Dynamics Simulations

2000 ◽  
Vol 104 (20) ◽  
pp. 5000-5010 ◽  
Author(s):  
Philippe Ferrara ◽  
Joannis Apostolakis ◽  
Amedeo Caflisch
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Thermodynamics And Kinetics ◽  
Dynamics Simulations ◽  
Kinetics Of ◽  
Model Peptides

scholarly journals Folding Thermodynamics and Kinetics of Lambda-Repressor from All-Atom Molecular Dynamics Simulations

2012 ◽  
Vol 102 (3) ◽  
pp. 457a ◽  
Author(s):  
Yanxin Liu ◽  
Johan Strumpfer ◽  
Peter L. Freddolino ◽  
Martin Gruebele ◽  
Klaus Schulten
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lambda Repressor ◽  
Thermodynamics And Kinetics ◽  
Dynamics Simulations ◽  
Kinetics Of ◽  
Folding Thermodynamics

scholarly journals Morphology, energetics and growth kinetics of diphenylalanine fibres

2021 ◽  
Author(s):  
Phillip Mark Rodger ◽  
Caroline Montgomery ◽  
Giovanni Costantini ◽  
Alison Rodger
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Growth Kinetics ◽  
Dynamics Simulations ◽  
Kinetics Of

The formation and stability of diphenylalanine fibres are studied by combining molecular dynamics simulations with microscopy and spectroscopy experiments, quantitatively detailing their morphology, energetics and growth kinetics.

Solvent effects on the decarboxylation of trichloroacetic acid: insights from ab initio molecular dynamics simulations

2018 ◽  
Vol 20 (34) ◽  
pp. 21988-21998 ◽  
Author(s):  
Guilherme C. Q. da Silva ◽  
Thiago M. Cardozo ◽  
Giovanni W. Amarante ◽  
Charlles R. A. Abreu ◽  
Bruno A. C. Horta
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Solvent Effects ◽  
Trichloroacetic Acid ◽  
Ab Initio Molecular Dynamics ◽  
Aprotic Solvents ◽  
Protic Solvents ◽  
Dynamics Simulations ◽  
Kinetics Of

The kinetics of trichloroacetic acid (TCA) decarboxylation strongly depends on the solvent in which it occurs, proceeding faster in polar aprotic solvents compared to protic solvents.

scholarly journals THE RANGE OF THE CONTACT INTERACTIONS AND THE KINETICS OF THE GO MODELS OF PROTEINS

2002 ◽  
Vol 13 (09) ◽  
pp. 1231-1242 ◽  
Author(s):  
MAREK CIEPLAK ◽  
TRINH XUAN HOANG
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Van Der Waals ◽  
Contact Interactions ◽  
Residue Contact ◽  
Cutoff Distance ◽  
Dynamics Simulations ◽  
Kinetics Of ◽  
Van Der Waals Radii

We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue–residue contact interactions are selected based on a cutoff distance, Rc. The folding times strongly depend on the value of Rc and nonmonotonically. This indicates a need for a physically determined set of native contacts. One may accomplish it by considering the van der Waals radii of the residual atoms and checking if the atoms overlap. In the second model, non-native attractive contacts are added to the system. This leads to bad foldability. However, for a small number of such extra contacts there is a slight acceleration in the kinetics of folding.

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