Steady-state parameter sensitivity in stochastic modeling via trajectory reweighting

Patrick B. Warren and Rosalind J. Allen

Parameter sensitivity analysis is effective in the building and analysis of biochemical network models, but requires multiple simulations for perturbed values of the parameters when used in stochastic simulations. This paper describes the use of trajectory reweighting to derive a method for computing sensitivity coefficients in stochastic simulations without explicitly perturbing the parameter values, which avoids the need for repeated simulations.

J. Chem. Phys. 136, 104106 (2012)

Dimethyl sulfoxide induced structural transformations and non-monotonic concentration dependence of conformational fluctuation around active site of lysozyme

Susmita Roy, Biman Jana, and Biman Bagchi

Dimethyl sulfoxide (DMSO) can have many effects on proteins such as stabilizing, denaturing, or inhibiting them depending on the concentration of DMSO. The authors use atomistic molecular dynamic simulations of Hen Egg White Lysozyme (HEWL) in solutions of water and DMSO to determine how the lysozyme changes with increasing DMSO concentration.

J. Chem. Phys. 136, 115103 (2012)

From protein denaturant to protectant: Comparative molecular dynamics study of alcohol∕protein interactions

Qiang Shao, Yubo Fan, Lijiang Yang, and Yi Qin Gao

The authors study how alcohols with varied hydrophobicity and different numbers of hydrophilic groups exert effects on the structure of the model polypeptide, BBA5 by using molecular dynamics simulations. Alcohols can denature or protect proteins and this study aids in the understanding of the molecular mechanisms.

J. Chem. Phys. 136, 115101 (2012)

Trapping of excess electrons at the microhydrated protonated amino groups in proteins

Wenchao Li, Zhenwei Zhang, Hongfang Yang, Xiuxiu Wu, Jinxiang Liu, and Yuxiang Bu

An excess electron in a condensed phase of a microhydrated protonated amino group in proteins is studied using a combined first-principles calculation and a molecular dynamics simulation. The study can be a basis for considering increasingly larger peptide fragments and charge migration mechanisms.

J. Chem. Phys. 136, 105101 (2012)

Kinetic pathways to peptide aggregation on surfaces: The effects of β-sheet propensity and surface attraction

Alex Morriss-Andrews and Joan-Emma Shea

The kinetics of peptide aggregation on a solid surface is studied using molecular dynamics simulations with a coarse-grained peptide representation. This work builds on previous work which examined the equilibrium structures of the system and provides details of aggregate growth mechanisms on scales inaccessible to either experiment or atomistic simulations.

J. Chem. Phys. 136, 065103 (2012)