Gibbs adsorption isotherm combined with Monte Carlo sampling to see action of cosolutes on protein folding

2004 ◽  
Vol 57 (2) ◽  
pp. 311-321 ◽  
Author(s):  
Daniel Harries ◽  
V. Adrian Parsegian
Keyword(s):  
Monte Carlo ◽  
Protein Folding ◽  
Adsorption Isotherm ◽  
Monte Carlo Sampling

scholarly journals Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias

2018 ◽  
Author(s):  
Yong Wang ◽  
Pengfei Tian ◽  
Wouter Boomsma ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Monte Carlo ◽  
Protein Folding ◽  
Conformational Changes ◽  
Conformational Dynamics ◽  
Coarse Graining ◽  
Monte Carlo Sampling ◽  
Implicit Solvent ◽  
Great Success ◽  
Native State ◽  
Dynamics Simulations

AbstractEnergy landscape theory suggests that native interactions are a major determinant of the folding mechanism of a protein. Thus, structure-based (Gō) models have, aided by coarse-graining techniques, shown great success in capturing the mechanisms of protein folding and conformational changes. In certain cases, however, non-native interactions and atomic details are also essential to describe the protein dynamics, prompting the development of a variety of structure-based models which include non-native interactions, and differentiate between different types of attractive potentials. Here, we describe an all-protein-atom hybrid model, termed ProfasiGo, that integrates an implicit solvent all-atom physics-based model (called Profasi) and a structure-based Gō potential, and its implementation in two software packages (PHAISTOS and ProFASi) that are developed for Monte Carlo sampling of protein molecules. We apply the ProfasiGo model to study the folding free energy landscapes of four topologically similar proteins, one of which can be folded by the simplified potential Profasi, and two that have been folded by explicit solvent, all-atom molecular dynamics simulations with the CHARMM22∗ force field. Our results reveal that the hybrid ProfasiGo model is able to capture many of the details present in the physics-based potentials, while retaining the advantages of Gō models for sampling and guiding to the native state. We expect that the model will be widely applicable to study the folding of more complex proteins, or to study conformational dynamics and integration with experimental data.

scholarly journals Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias

2018 ◽  
Vol 122 (49) ◽  
pp. 11174-11185 ◽  
Author(s):  
Yong Wang ◽  
Pengfei Tian ◽  
Wouter Boomsma ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Monte Carlo ◽  
Protein Folding ◽  
Monte Carlo Sampling ◽  
Native State

Monte Carlo Sampling with Hierarchical Move Sets: POSH Monte Carlo

2009 ◽  
Vol 5 (8) ◽  
pp. 1968-1984 ◽  
Author(s):  
Jerome Nilmeier ◽  
Matthew P. Jacobson
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Sampling
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