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

TY - JOUR

T1 - Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias

AU - Wang, Yong

AU - Tian, Pengfei

AU - Boomsma, Wouter

AU - Lindorff-Larsen, Kresten

PY - 2018/12/13

Y1 - 2018/12/13

N2 - Energy 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 that 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 the study of the folding of more complex proteins or to the study of conformational dynamics and integration with experimental data.

AB - Energy 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 that 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 the study of the folding of more complex proteins or to the study of conformational dynamics and integration with experimental data.

U2 - 10.1021/acs.jpcb.8b06335

DO - 10.1021/acs.jpcb.8b06335

M3 - Journal article

C2 - 30141937

AN - SCOPUS:85053338035

SN - 1520-6106

VL - 122

SP - 11174

EP - 11185

JO - Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical

JF - Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical

IS - 49

ER -