Dynamics of activated processes in globular proteins.

Thermally activated processes in polymer dynamics.

Jumps between neighboring minima in the energy landscape of both homopolymeric and heteropolymeric chains are numerically investigated by determining the average escape time from different valleys. The numerical results are compared to the theoretical expression derived by Langer [J.S. Langer, Ann. Phys. (N.Y.) 54, 258 (1969)] with reference to a 2N-dimensional space. Our simulations indicate t...

Quantification of structure/dynamics correlation of globular proteins

Volume Determination of Globular Proteins by Molecular Dynamics

Molecular dynamics simulations of myoglobin and aspartate aminotransferase, with explicit solvent, are shown to accurately reproduce the experimentally measured molar volumes. Single aminoacid substitution at VAL39 of aspartate aminotransferase is known to produce large volumetric changes in the enzyme, and this effect is demonstrated in simulation as well. This molecular dynamics approach, whi...

Folding energy landscape and network dynamics of small globular proteins.

The folding energy landscape of proteins has been suggested to be funnel-like with some degree of ruggedness on the slope. How complex the landscape, however, is still rather unclear. Many experiments for globular proteins suggested relative simplicity, whereas molecular simulations of shorter peptides implied more complexity. Here, by using complete conformational sampling of 2 globular protei...

Folding units in globular proteins.

We present a method to identify all compact, contiguous-chain, structural units in a globular protein from x-ray coordinates. These units are then used to describe a complete set of hierarchic folding pathways for the molecule. Our analysis shows that the larger units are combinations of smaller units, giving rise to a structural hierarchy ranging from the whole protein monomer through supersec...