Insights from coarse-grained Gō models for protein folding and dynamics
Exploring the landscape of large scale conformational changes such as protein folding at
atomistic detail poses a considerable computational challenge. Coarse-grained …
atomistic detail poses a considerable computational challenge. Coarse-grained …
Reaching new levels of realism in modeling biological macromolecules in cellular environments
An increasing number of studies are aimed at modeling cellular environments in a
comprehensive and realistic fashion. A major challenge in these efforts is how to bridge …
comprehensive and realistic fashion. A major challenge in these efforts is how to bridge …
Factors Defining Effects of Macromolecular Crowding on Protein Stability: An in Vitro/in Silico Case Study Using Cytochrome c
Previous experiments with two single-domain proteins showed that macromolecular
crowding can stabilize dramatically toward heat perturbation and modulate native-state …
crowding can stabilize dramatically toward heat perturbation and modulate native-state …
Self-assembly of β-sheet forming peptides into chiral fibrillar aggregates
The authors introduce a novel mid-resolution off-lattice coarse-grained model to investigate
the self-assembly of β-sheet forming peptides. The model retains most of the peptide …
the self-assembly of β-sheet forming peptides. The model retains most of the peptide …
How efficient is replica exchange molecular dynamics? An analytic approach
H Nymeyer - Journal of chemical theory and computation, 2008 - ACS Publications
Replica exchange molecular dynamics (REMD) has become a standard technique for
accelerating relaxation in biosimulations. Despite its widespread use, questions remain …
accelerating relaxation in biosimulations. Despite its widespread use, questions remain …
Macromolecular crowding extended to a heptameric system: the co-chaperonin protein 10
Experiments on monomeric proteins have shown that macromolecular crowding can
stabilize toward heat perturbation and also modulate native-state structure. To assess the …
stabilize toward heat perturbation and also modulate native-state structure. To assess the …
Exploring the unfolding pathway of maltose binding proteins: an integrated computational approach
Recent single-molecule force spectroscopy experiments on the Maltose Binding Proteins
(MBPs) identified four stable structural units, termed unfoldons, that resist mechanical stress …
(MBPs) identified four stable structural units, termed unfoldons, that resist mechanical stress …
Protein–cofactor binding and ultrafast electron transfer in riboflavin binding protein under the spatial confinement of nanoscopic reverse micelles
In this contribution, we study the effect of confinement on the ultrafast electron transfer (ET)
dynamics of riboflavin binding protein (RBP) to the bound cofactor riboflavin (Rf, vitamin B2) …
dynamics of riboflavin binding protein (RBP) to the bound cofactor riboflavin (Rf, vitamin B2) …
Coarse grained modeling and approaches to protein folding
The theoretical prediction of protein structures has become a field of increasing importance
in both biology and physics. Reliable prediction methods in fact, would spare time …
in both biology and physics. Reliable prediction methods in fact, would spare time …
The physics of the interactions governing folding and association of proteins
W Guo, JE SHEA, RS Berry - Annals of the New York Academy …, 2006 - Wiley Online Library
The review discusses the molecular origins of the forces and free energies that determine
several things about proteins, and how experiment and theory reveal this information. The …
several things about proteins, and how experiment and theory reveal this information. The …