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Small-world communication of residues and significance for protein dynamics.
Elucidating the structural mechanisms for biological activity of the chemokine family
A basis for the construction of hybrids of chemokines to bind and/or activate various chemokine receptors is presented and the 30s‐loop, although not directly involved in the binding interface like the N‐terminus and the N-loop, is identified as having a prominent role in both binding/activation and dimerization.
Relaxation kinetics and the glassiness of proteins: the case of bovine pancreatic trypsin inhibitor.
Coordination topology and stability for the native and binding conformers of chymotrypsin inhibitor 2
It is demonstrated that the stabilization of the binding region is accomplished at the expense of a loss in the stability of the rest of the protein, indicating the effective propagation of perturbation and the presence of remotely controlling residues.
Conformational features of poly(1,1-dihydroperfluorooctyl acrylate) and poly(vinyl acetate) diblock oligomers in supercritical carbon dioxide
We report detailed molecular dynamics calculations of single chain diblocks of poly(1,1- dihydroperfluorooctyl acrylate) (PFOA) and poly(vinyl acetate) (PVAc) in supercritical carbon dioxide, SCCO2.…
Free energy based populations of interconverting microstates of a cyclic peptide lead to the experimental NMR data.
The validity of these atomic solvation parameters (ASPs) within the framework of the entire methodology is verified and a very good agreement is obtained between experimental and calculated NOEs and 3J coupling constants.
Relaxation kinetics and the glassiness of native proteins: coupling of timescales.
It is shown that the onset of functional dynamics of folded proteins with elevated temperatures is associated with the effective sampling of its energy landscape under physiological conditions, and that at the temperature window where motions corresponding to all three timescales become operative that the protein becomes active.
DETERMINATION OF THE STABLE MICROSTATES OF A PEPTIDE FROM NOE DISTANCE CONSTRAINTS AND OPTIMIZATION OF ATOMIC SOLVATION PARAMETERS
A methodology for analyzing nuclear Overhauser effect (NOE) data of interconverting microstates of a peptide has been suggested recently, which is based on pure statistical mechanical considerations.…
Ab initio prediction of the solution structures and populations of a cyclic pentapeptide in DMSO based on an implicit solvation model
Using a recently developed statistical mechanics methodology, the solution structures and populations of the cyclic pentapeptide cyclo in DMSO are obtained ab initio, i.e., without using experimental restraints, and the theoretical values of proton–proton distances and 3J coupling constants agree very well with the NMR results.
Efficiency of the Local Torsional Deformations Method for Identifying the Stable Structures of Cyclic Molecules
A new method for generating the low-energy structures of a chain molecule was proposed recently by us. This is a stochastic process where at each step an energy-minimized structure is changed by…