Abstract | To this end, we report the first molecular dynamics simulation study of the interaction of the antimicrobial peptide, polymyxin B1 with complex models of both the inner and outer membranes of E. coli. |
Discussion | Other studies have suggested that atomistic molecular dynamics simulations of AMPs require multi-microsecond timescales [36]. |
Discussion | The large molecular systems and extended timescales accessible to coarse-grain molecular dynamics (CG-MD) simulations provide an alternative and complementary route to studying antimicrobial peptides. |
Introduction | Because of experimental difficulties associated with characterizing dynamic, heterogeneous systems such as membrane-bound AMPs, molecular dynamics (MD) simulations provide a complementary approach to studying their modes of action, in unprecedented detail [14, 15]. |
Simulation Parameters and Protocol | All simulations performed in this work used the GROMACS molecular dynamics software [53, 54], version 4.5.1 [55]. |
Simulation Systems | the axis perpendicular to the plane of the membranes) and polymyxin molecules were manually added to the systems using the Visual Molecular Dynamics (VMD) software [52]. |
Abstract | Molecular dynamics simulations on DNA hairpin stems containing A. . |
Introduction | In this context, we aim here to investigate the structure and dynamics of DNA duplex containing CAG repeat using molecular dynamics (MD) simulation technique. |
Methods | Subsequently, the models are subjected to a total of 1.5us molecular dynamics simulations (MD) using Sander module of AMBER 12 package [40]. |
Molecular dynamics simulation protocol | Molecular dynamics simulation protocol |
Author Summary | However, commonly employed molecular dynamics simulations suffer from a limitation in accessible time scale, making it difficult to model large-scale unfolding events in a realistic amount of simulation time without employing unrealistically high temperatures. |
Discussion | Estimates of protein stability using Molecular Dynamics are prohibitive for all but the smallest protein domains. |
Introduction | Tm is obtainable by experiment and, in theory, from simulation, although current molecular dynamics simulations are limited in their ability to capture full folding or unfolding trajectories of most proteins (except very small fast folding domains [15]) in a tractable amount of simulation time [16]. |
Predicting the effects of mutations on protein stability from non-equilibrium unfolding simulations | Although the idea of obtaining equilibrium free energy differences from non-equilibrium measurements is not new [35], and protein stabilities have been calculated from molecular dynamics simulations using the Iarzynski equality, e.g., [36—38] , such simulations require application of an external steering force; in the present paper we report the use of multi-temperature Monte-Carlo unfolding simulations in obtaining protein stabilities. |
Discussion | The segmentation and tracking of AIs in 3D and the curation of vertices, edges, cells and trajectories would enable the extension of the pipeline to relate molecular dynamics with cell and tissue remodeling for multiscale analysis of epithelial tissue morphogenesis. |
Introduction | These behaviors, in turn, depend on intracellular molecular dynamics that allow cells to generate and transmit mechanical forces to one another, while maintaining epithelial cohesion [1, 2]. |
Introduction | Live imaging of cell and molecular dynamics using fluorescently-tagged proteins is a key method to investigate these processes [4]. |