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

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.

Other studies have suggested that atomistic molecular dynamics simulations of AMPs require multi-microsecond timescales [36].

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.

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].

All simulations performed in this work used the GROMACS molecular dynamics software [53, 54], version 4.5.1 [55].

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].

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.

Molecular dynamics simulations on DNA hairpin stems containing A. .

In this context, we aim here to investigate the structure and dynamics of DNA duplex containing CAG repeat using molecular dynamics (MD) simulation technique.

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

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.

Estimates of protein stability using Molecular Dynamics are prohibitive for all but the smallest protein domains.

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].

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.

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.

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].

Live imaging of cell and molecular dynamics using fluorescently-tagged proteins is a key method to investigate these processes [4].

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].