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 …
Recent successes in coarse‐grained modeling of DNA
The growing interest in the DNA‐based mesoscale systems of biological and nonbiological
nature has encouraged the computational molecular science community to develop coarse …
nature has encouraged the computational molecular science community to develop coarse …
Molecular crowding enhances native state stability and refolding rates of globular proteins
The presence of macromolecules in cells geometrically restricts the available space for
poplypeptide chains. To study the effects of macromolecular crowding on folding …
poplypeptide chains. To study the effects of macromolecular crowding on folding …
Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding
We combine experiment and computer simulation to show how macromolecular crowding
dramatically affects the structure, function, and folding landscape of phosphoglycerate …
dramatically affects the structure, function, and folding landscape of phosphoglycerate …
An all‐atom structure‐based potential for proteins: bridging minimal models with all‐atom empirical forcefields
Protein dynamics take place on many time and length scales. Coarse‐grained structure‐
based \bf(G\overlineo) models utilize the funneled energy landscape theory of protein …
based \bf(G\overlineo) models utilize the funneled energy landscape theory of protein …
Molecular crowding enhances native structure and stability of α/β protein flavodoxin
To investigate the consequences of macromolecular crowding on the behavior of a globular
protein, we performed a combined experimental and computational study on the 148 …
protein, we performed a combined experimental and computational study on the 148 …
Crowded, cell-like environment induces shape changes in aspherical protein
How the crowded environment inside cells affects the structures of proteins with aspherical
shapes is a vital question because many proteins and protein–protein complexes in vivo …
shapes is a vital question because many proteins and protein–protein complexes in vivo …
Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model
Interactions between denaturants and proteins are commonly used to probe the structures of
the denatured state ensemble and their stabilities. Osmolytes, a class of small intracellular …
the denatured state ensemble and their stabilities. Osmolytes, a class of small intracellular …
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 …
Nonnative electrostatic interactions can modulate protein folding: molecular dynamics with a grain of salt
A Azia, Y Levy - Journal of molecular biology, 2009 - Elsevier
In recent years, a growing number of protein folding studies have focused on the unfolded
state, which is now recognized as playing a major role in the folding process. Some of these …
state, which is now recognized as playing a major role in the folding process. Some of these …