Squeezed exponential kinetics to describe a nonglassy downhill folding as observed in a lattice protein model

2004 ◽  
Vol 55 (1) ◽  
pp. 99-106 ◽  
Author(s):  
Hironori K. Nakamura ◽  
Masaki Sasai ◽  
Mitsunori Takano
Keyword(s):  
Downhill Folding ◽  
Protein Model

Improved Sampling Strategies for Protein Model Refinement based on Molecular Dynamics Simulation

2020 ◽  
Author(s):  
Lim Heo ◽  
Collin Arbour ◽  
Michael Feig
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Structure Prediction ◽  
Protein Structures ◽  
Conformational Space ◽  
Dynamics Simulation ◽  
Model Refinement ◽  
Protein Model ◽  
Lower Accuracy ◽  
Simulation Based

Protein structures provide valuable information for understanding biological processes. Protein structures can be determined by experimental methods such as X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, or cryogenic electron microscopy. As an alternative, in silico methods can be used to predict protein structures. Those methods utilize protein structure databases for structure prediction via template-based modeling or for training machine-learning models to generate predictions. Structure prediction for proteins distant from proteins with known structures often results in lower accuracy with respect to the true physiological structures. Physics-based protein model refinement methods can be applied to improve model accuracy in the predicted models. Refinement methods rely on conformational sampling around the predicted structures, and if structures closer to the native states are sampled, improvements in the model quality become possible. Molecular dynamics simulations have been especially successful for improving model qualities but although consistent refinement can be achieved, the improvements in model qualities are still moderate. To extend the refinement performance of a simulation-based protocol, we explored new schemes that focus on an optimized use of biasing functions and the application of increased simulation temperatures. In addition, we tested the use of alternative initial models so that the simulations can explore conformational space more broadly. Based on the insight of this analysis we are proposing a new refinement protocol that significantly outperformed previous state-of-the-art molecular dynamics simulation-based protocols in the benchmark tests described here. <br>

Minimalist Protein Model as a Diagnostic Tool for Misfolding and Aggregation

2006 ◽  
Vol 363 (1) ◽  
pp. 297-308 ◽  
Author(s):  
Silvina Matysiak ◽  
Cecilia Clementi
Keyword(s):  
Diagnostic Tool ◽  
Protein Model

scholarly journals A Survey of λ Repressor Fragments from Two-State to Downhill Folding

2010 ◽  
Vol 397 (3) ◽  
pp. 789-798 ◽  
Author(s):  
Feng Liu ◽  
Yi Gui Gao ◽  
Martin Gruebele
Keyword(s):  
Downhill Folding

scholarly journals Engineered Protein Model of the ATP synthase H+- Channel Shows No Salt Bridge at the Rotor-Stator Interface

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Hannah E. Pierson ◽  
Mandeep Kaler ◽  
Christopher O’Grady ◽  
Eva-Maria E. Uhlemann ◽  
Oleg Y. Dmitriev
Keyword(s):  
Atp Synthase ◽  
Salt Bridge ◽  
Protein Model
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