Protein structure selection, search parameters and Cys environment characterization | For all residues, except the sulfenic acid, the AMBER99SB force field was used [44,45]. |
Protein structure selection, search parameters and Cys environment characterization | Sulfenic acid force field parameters were built using AMBER recommended procedure. |
Protein structure selection, search parameters and Cys environment characterization | All bonded and VdW parameters were taken from the General AMBER Force Field [47]. |
Introduction | From this information the traction force field can be reconstructed (Fig 1C) and correlated with the internal actin structure, including actin retrograde flow and SFs [19,20]. |
Regularlzation | If it is chosen too large, the details of the force field are smoothed out and the overall force magnitude is too small. |
Robustness of the method | The deviation between the theoretical prediction and experimental measurement is represented by the relative LZ-norm that ranges between 0 for perfect agreement and 1 for a vanishing force field . |
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 (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]. |
Dynamic Behavior of Lipid Molecules | ), corresponding to a lipid diffusion coefficient Dmdz/ (tX) = 10—6 cmZ/s, (or Dm2.5><10_7 cmZ/s, when accounting for the effective time scaling for the CG force field we used). |
Dynamic Behavior of Lipid Molecules | Notably, similar values of lipid diffusion constants have recently been reported in the literature [26,27] for comparable CG force fields , and a similar behavior was implied. |
System Preparation | The receptors were converted to a CG representation under the MARTINI force field (version 2.1) [16—18] and a modified elastic network was applied, as reported previously in the literature [42]. |