Abstract | Multiscale molecular dynamics simulations of the UraA symporter in phospholipid bilayers consisting of: 1) 1-palmitoyl 2—oIeoyl-phosphatidylcholine (POPC); 2) 1-palmitoyl 2—oleoyI-phosphatidylethanolamine (POPE); and 3) a mixture of 75% POPE, 20% 1-palmi-toyl 2—oleoyl-phosphatidylglycerol (POPG); and 5% 1-palmitoyl 2—oleoyI-diphosphatidylgly-cerol/cardiolipin (CL) to mimic the lipid composition of the bacterial inner membrane, were performed using the MARTINI coarse-grained force field to self-assemble lipids around the crystal structure of this membrane transport protein, followed by atomistic simulations. |
Atomistic molecular dynamics simulations | Atomistic molecular dynamics simulations |
Coarse-grained molecular dynamics simulations | Coarse-grained molecular dynamics simulations |
Membrane proteins in lipid bilayers | Molecular dynamics simulations provide a powerful tool to analyze the structure and dynamics of membrane proteins in lipid bilayers of defined composition [4]. |
Membrane proteins in lipid bilayers | A molecular dynamics simulation of LacY, in various lipids identified specific interactions between the lipid head-groups and sites on the protein [70]. |
Abstract | Molecular dynamics simulations on DNA hairpin stems containing A. . |
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. |
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. |
Author Summary | The inferences provided by the extensive molecular dynamics simulations reported herein constitute a first step in this direction. |
Molecular Dynamics Simulations | Molecular Dynamics Simulations |
Supporting Information | Summary of all the molecular dynamics simulations of coarse-grained representations of opioid receptors reported in this manuscript. |