159 citations · 583 across the 11 of their papers we have counts for
11 papers
Coarse-grained molecular simulations of allosteric cooperativity
Prithviraj Nandigrami, John J. Portman
Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein'…
Comparing allosteric transitions in the domains of calmodulin through coarse-grained simulations
Prithviraj Nandigrami, John J. Portman
Calmodulin (CaM) is a ubiquitous calcium binding protein consisting of two structurally similar domains with distinct stabilities, binding affinities, and flexibilities. We present…
Inherent flexibility determines the transition mechanisms of the EF-hands of Calmodulin
Swarnendu Tripathi, John J. Portman
We explore how inherent flexibility of a protein molecule influences the mechanism controlling the kinetics of allosteric transitions using a variational model inspired from work i…
Capillarity-like growth of protein folding nuclei
Xianghon Qi, John J. Portman
We analyzed folding routes predicted by a variational model in terms of a generalized formalism of the capillarity scaling theory for 28 two-state proteins. The scaling exponent ra…
Inherent flexibility and protein function: the open/closed conformational transition of the N-terminal domain of calmodulin
Swarnendu Tripathi, John J. Portman
The key to understanding a protein's function often lies in its conformational dynamics. We develop a coarse-grained variational model to investigate the interplay between structur…
Excluded volume, local structural cooperativity,and the polymer physics of protein folding rates
Xianghong Qi, John J. Portman
A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding…