7 papers
Proteins associated with diseases show enhanced sequence correlation between charged residues
Ruxandra I. Dima, D. Thirumalai
Function of proteins or a network of interacting proteins often involves communication between residues that are well separated in sequence. The classic example is the participatio…
Asymmetry in the shapes of folded and denatured states of proteins
Ruxandra I. Dima, D. Thirumalai
The asymmetry in the shapes of folded and unfolded states are probed using two parameters, one being a measure of the sphericity and the other that describes the shape. For the fol…
Dependence of folding rates on protein length
Mai Suan Li, D. K. Klimov, D. Thirumalai
Using three-dimensional Go lattice models with side chains for proteins, we investigate the dependence of folding times on protein length. In agreement with previous theoretical pr…
Introducing Protein Folding Using Simple Models
D. Thirumalai, D. K. Klimov
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mech…
Kinetics of condensation of flexible polyelectrolytes in poor solvents: effects of solvent quality, valence and size of counterions
Namkyung Lee, D. Thirumalai
The collapse kinetics of strongly charged polyelectrolytes in poor solvents is investigated by Langevin simulations and scaling arguments. The rate of collapse increases sharply as…
Cooperativity in Protein Folding: From Lattice Models with Side Chains to Real Proteins
D. K. Klimov, D. Thirumalai
We consider equilibrium folding transitions in lattice protein models with and without side chains. A dimensionless measure, , is introduced to quantitatively assess the…