Resolving molecular determinants of mechanical stability of proteins is crucial in the rational design of advanced biomaterials for use in biomedical and nanotechnological applications. Here we present an interdisciplinary study combining bioinformatics screening, steered molecular dynamics simulations, protein engineering, and single-molecule force spectroscopy that explores the mechanical pro...

The mechanism of action of cellulose-degrading enzymes is illuminated through a multidisciplinary collaboration that uses molecular dynamics (MD) simulations and expands the capabilities of MD codes to allow simulations of enzymes and substrates on petascale computational facilities. There is a class of glycoside hydrolase enzymes called cellulases that are thought to decrystallize and processi...

This data article contains the results of molecular dynamics (MD) simulations performed to assess the stability of the previously computed complex between the hCES1 structure and the Amplex Red (AR) substrate (Miwa et al., 2015) [1] and to compare the dynamic behavior of this complex with that of the corresponding hCES1-deacetylAR product. The study involves both standard molecular dynamics (MD...

The knowledge of the dynamics and conformational particularities of bone morphogenetic protein-2 (BMP-2) are important for predicting its bioactivity in the process of osteoblasts differentiation and proliferation while using it in bone implants and scaffolds. Molecular dynamics simulations were performed to investigate the conformational stability of bone morphogenetic protein-2 in water envir...

In this paper, we present a novel approach that makes use of multiscale and multiphysics modeling coupled to virtual reality for nanorobotic prototyping systems. First, a CAD-assisted assembly system that integrates principles for a multiscale approach into a nanorobotics structure design is presented. Then, we focus on the different design levels, more specifically, the optimization of geometr...

Single-molecule force experiments in vitro enable the characterization of the mechanical response of biological matter at the nanometer scale. However, they do not reveal the molecular mechanisms underlying mechanical function. These can only be readily studied through molecular dynamics simulations of atomic structural models: "in silico" (by computer analysis) single-molecule experiments. Ste...

The determination of gyration radius is a strong research for configuration of a Macromolecule. Italso reflects molecular compactness shape. In this work, to characterize the behavior of theprotein, we observe quantities such as the radius of gyration and the average energy. We studiedthe changes of these factors as a function of temperature for Acetylcholine receptor protein in gasphase with n...