Exploring the energy landscape of proteins: A characterization of the activation-relaxation technique

2002 ◽  
Vol 117 (24) ◽  
pp. 11379-11387 ◽  
Author(s):  
Guanghong Wei ◽  
Normand Mousseau ◽  
Philippe Derreumaux
Keyword(s):  
Energy Landscape ◽  
Relaxation Technique

scholarly journals Mechanical Characterization of Spray-Dried Granules by Compression and Stress-Relaxation Technique. Analysis of Relaxation Behavior.

1999 ◽  
Vol 107 (1252) ◽  
pp. 1183-1187 ◽  
Author(s):  
JunIchiro TSUBAKI ◽  
Takamasa MORI ◽  
Toshiyuki KONISHI ◽  
Akihisa TSURUTA ◽  
Hidetoshi MORI ◽  
...  
Keyword(s):  
Stress Relaxation ◽  
Mechanical Characterization ◽  
Relaxation Behavior ◽  
Relaxation Technique ◽  
Spray Dried ◽  
Technique Analysis

scholarly journals Multi-scale characterization of the energy landscape of proteins with application to the C3D/Efb-C complex

2009 ◽  
Vol 78 (4) ◽  
pp. 1004-1014 ◽  
Author(s):  
Nurit Haspel ◽  
Brian V. Geisbrecht ◽  
John Lambris ◽  
Lydia Kavraki
Keyword(s):  
Energy Landscape ◽  
Multi Scale ◽  
Scale Characterization ◽  
C Complex

Characterization of CeO2Ultrafine Particles Prepared Using a Thermal Relaxation Technique

1996 ◽  
Vol 25 (1) ◽  
pp. 75-76 ◽  
Author(s):  
Toshiyuki Masui ◽  
Ken-ichi Machida ◽  
Takao Sakata ◽  
Hirotaro Mori ◽  
Gin-ya Adachi
Keyword(s):  
Thermal Relaxation ◽  
Relaxation Technique

Optimized energy landscape exploration using the ab initio based activation-relaxation technique

2011 ◽  
Vol 135 (3) ◽  
pp. 034102 ◽  
Author(s):  
Eduardo Machado-Charry ◽  
Laurent Karim Béland ◽  
Damien Caliste ◽  
Luigi Genovese ◽  
Thierry Deutsch ◽  
...  
Keyword(s):  
Ab Initio ◽  
Energy Landscape ◽  
Relaxation Technique

Simulated silica

2004 ◽  
Vol 363 (1827) ◽  
pp. 525-535 ◽  
Author(s):  
Ivan Saika-Voivod ◽  
Francesco Sciortino ◽  
Tor Grande ◽  
Peter H. Poole
Keyword(s):  
Liquid Phase ◽  
Equation Of State ◽  
Energy Landscape ◽  
Average Energy ◽  
Configurational Entropy ◽  
Supercooled Liquid ◽  
Potential Energy Landscape ◽  
Comprehensive Picture ◽  
The Relationship

We review how molecular dynamics computer simulations are providing a comprehensive picture of the behaviour of silica, as modelled by the van Beest–Kramer–van Santen (BKS) potential. We have recently evaluated a number of key properties of this model system: the phase diagram, including melting lines of three crystal phases; the equation of state and free energy of the liquid phase; the dynamical equation of state; the average energy of inherent structures, and configurational entropy, associated with the potential energy landscape of the liquid; and a characterization of the local coordination environments in the supercooled liquid. The results reveal the interplay among a number of phenomena, in particular, the relationship between the energy landscape and the fragile–to–strong crossover of the liquid dynamics; and the relation of both of these to the possibility of a liquid–liquid phase transition in the supercooled liquid.

scholarly journals Folding Free Energy Landscape of Ordered and Intrinsically Disordered Proteins

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Song-Ho Chong ◽  
Sihyun Ham
Keyword(s):  
Free Energy ◽  
Intrinsically Disordered Proteins ◽  
Energy Landscape ◽  
Disordered Proteins ◽  
Free Energy Landscape ◽  
Ww Domain ◽  
Intrinsically Disordered ◽  
Ca 50 ◽  
Folding Free Energy

Abstract Folding funnel is the essential concept of the free energy landscape for ordered proteins. How does this concept apply to intrinsically disordered proteins (IDPs)? Here, we address this fundamental question through the explicit characterization of the free energy landscapes of the representative α-helical (HP-35) and β-sheet (WW domain) proteins and of an IDP (pKID) that folds upon binding to its partner (KIX). We demonstrate that HP-35 and WW domain indeed exhibit the steep folding funnel: the landscape slope for these proteins is ca. −50 kcal/mol, meaning that the free energy decreases by ~5 kcal/mol upon the formation of 10% native contacts. On the other hand, the landscape of pKID is funneled but considerably shallower (slope of −24 kcal/mol), which explains why pKID is disordered in free environments. Upon binding to KIX, the landscape of pKID now becomes significantly steep (slope of −54 kcal/mol), which enables otherwise disordered pKID to fold. We also show that it is the pKID–KIX intermolecular interactions originating from hydrophobic residues that mainly confer the steep folding funnel. The present work not only provides the quantitative characterization of the protein folding free energy landscape, but also establishes the usefulness of the folding funnel concept to IDPs.

Sign in / Sign up

Export Citation Format

Share Document