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 (AT-MD) simulations were performed using the GROMOS96 53a6 force field that has been widely used in simulation studies of membrane proteins.

Coarse-grained molecular dynamics simulations

Coarse-grained molecular dynamics (CG-MD) simulations were performed using the MARTINI force field [22].

Molecular dynamics (MD) simulations of membrane proteins in increasingly complex lipid bilayers [3] can now be applied with confidence to build dynamic models of membrane proteins in a native milieu [4,5].

Molecular dynamics simulations provide a powerful tool to analyze the structure and dynamics of membrane proteins in lipid bilayers of defined composition [4].

A molecular dynamics simulation of LacY, in various lipids identified specific interactions between the lipid head-groups and sites on the protein [70].

Molecular Dynamics Simulations (MD).

Constant pH molecular dynamics (CpHMD).

For constant pH molecular dynamics , unless explicitly stated, simulation parameters were the same as detailed above.

Determination of the reaction free energy profile using QM(DFTB)/MM and Multiple steered molecular dynamics (MSMD) strategy.

The brackets in equation (1) represent an average taken over an ensemble of molecular dynamics trajectories provided the initial ensemble is equilibrated.

In order to perform each trajectory, equilibrated snapshots were taken from classical Molecular Dynamics simulations of the reactant state and used as starting point for the QM/MM steering simulations.

psi Density function for a Cys-SOH containing peptide from molecular dynamics

In an attempt to guide experimental assessment of the identity of the minimal signaling unit for CBS, we conducted extensive coarse-grained (CG) molecular dynamics (MD) simulations of different combinations of the three major OR subtypes, i.e., u-OR, 6-OR, and K-OR, in an explicit lipid bilayer.

The inferences provided by the extensive molecular dynamics simulations reported herein constitute a first step in this direction.

Here, we carried out extensive, unbiased coarse-grained (CG) molecular dynamics (MD) simulations of freely diffusing ORs in an explicit lipid-water environment to evaluate differences and similarities in the supramolecular organization and preferred dimeric interfaces of all three major receptor subtypes.

Molecular Dynamics Simulations

Summary of all the molecular dynamics simulations of coarse-grained representations of opioid receptors reported in this manuscript.

Here, we examine the structural environment of the PC190723 binding pocket using Pock-etFEATURE, a statistical method that scores the similarity between pairs of small-molecule binding sites based on 3D structure information about the local microenvironment, and molecular dynamics (MD) simulations.

Here, we evaluate the PC190723 binding site with currently available crystallographic structures of FtsZ using the structural comparison algorithm PocketFEATURE and all-atom molecular dynamics simulations.

All-atom molecular dynamics (MD) simulations predicted that force generation may result from a dramatic bending in GDP-bound filaments induced by nucleotide hydrolysis [10]; this conformational change was later confirmed by X-ray crystallography [6].