Atomic force microscopy (AFM) experiments and steered molecular dynamics (SMD) simulations have revealed much about the dynamics of protein-ligand binding and unbinding, as well as the stretching and unfolding of proteins. Both techniques induce ligand unbinding or protein unfolding by applying external mechanical forces to the ligand or stretched protein. However, comparing results from these ...

the internal structure of a molecule can be presented in terms of intra-molecular (i.e., inter atomic)and inter-molecular energies such as van der waals, bond and bending, torsion, and inversion energy.in this study, changes in molecular energies of individual asphalt components are evaluated as afunction of physical aging factors. the factors for physical aging such as temperature and pressure...

Computational studies of dynamics in complex systems require means for generating reactive trajectories with minimum knowledge about the processes of interest. Here, we introduce a method for generating transition paths when an existing one is not already available. Starting from biased paths obtained from steered molecular dynamics, we use a Monte Carlo procedure in the space of whole trajecto...

The inhibitors of class I histone deacetylases (HDACIs) have gained significant interest in cancer therapeutics. Virtual high throughput screening (vHTS) is one of the popular approaches used in the identification of novel scaffolds of HDACIs. However, an accurate description of ligand-protein flexibilities in the vHTS remains challenging. In this work, we implement an integrated approach, whic...

The design hypothesis, architectures, and computational modeling of a novel peptide-based nanoactuator are presented in this paper. We engineered the -helical coiled-coil portion of the yeast transcriptional activator peptide called GCN4 to obtain an environmentally responsive nanoactuator. The dimeric coiled-coil peptide consists of two identical approximately 4.5 nm long and approximately 3 n...

GPR17 is a hybrid G-protein-coupled receptor activated by two unrelated ligand families, extracellular nucleotides and cysteinyl-leukotrienes, and involved in brain damage and repair. Its exploitment as a target for novel neuroreparative strategies depends on the elucidation of the molecular determinants driving binding of its ligands. We applied docking and molecular dynamics simulations to an...

Escherichia coli lactose permease (LacY) transports sugar across the inner membrane of the bacterium using the proton motive force to accumulate sugar in the cytosol. We have probed lactose conduction across LacY using steered molecular dynamics, permitting us to follow molecular and energetic details of lactose interaction with the lumen of LacY during its permeation. Lactose induces a widenin...