Since there are no GTP-bound crystal structures of SaFtsZ, we conducted MD simulations of the APO state and GTP-bound SaFtsZ monomers (Fig.

Based on PocketFEATURE analysis of MD simulations of S. aureus FtsZ bound to GTP or with mutations that are known to confer PC190723 resistance, we predict that PC190723 strongly prefers to bind Staphylococcus FtsZ in the nucleotide-bound state.

Furthermore, MD simulations of an FtsZ dimer indicated that polymerization may enhance PC190723 binding.

Using all-atom MD simulations to quantify perturbations to the PC190723-binding pocket due to re-sistance-inducing mutations, we have provided an indirect assessment of PC190723 binding affinity that can be used as a point of comparison for at least two relevant applications.

We conducted MD simulations of GDP-bound dimers of wild-type SaFtsZ (Fig.

At later times in the MD simulation , the PC190723 pocket score of the wild-type dimer subunit with the better pocket score rapidly shifted to a value similar to that of the other subunit with poorer similarity (82A Fig).

Given that this biologically relevant release of GDP at the dimer interface has a corresponding drastic affect on the PC190723-binding pocket in our MD simulations (82A Fig), this further confirms the allosteric coupling between the bound nucleotide and PC190723 binding.

Similarity scores computed from the coordinates of all-atom MD simulations preserved the ranking order determined by their static crystal structures counterparts, with PC190723-resistant SaFtsZ mutants harboring pockets that were less similar to the SaFtsZ-PC190723 co-crystal than wild-type SaFtsZ pockets.

Since crystal structures of these mutants do not exist, we conducted all-atom MD simulations on SaFtsZ GDP-bound wildtype and drug-resistant (mutant) monomers in order to evaluate how the mutations affected the PC190723-binding pocket.

To compare pocket scores from MD trajectories across species, we also carried out MD simulations of SeFtsZ and BsFtsZ monomers initialized from their crystal structures (PDB IDs: 2RHL and 4M81, respectively); we observed similar initial decreases in pocket similarity (Fig.

2A), indicating that important features of the PC190723-binding pocket are conserved in MD simulations .

All atomistic systems were equilibrated for 2.5 ns with the protein backbone Coc atoms restrained, followed by unrestrained atomistic MD simulations from 100 to 500 ns with a time step of 2 fs.

In particular, UraA in a lipid bilayer containing POPE (75%), POPG (20%) and CL (5%) was subjected to MD simulations at coarse-grained and atomistic resolutions (see Methods and Table 1 for more information).

Thus, the MD simulation produced a closed state of the carrier, i.e.

MD simulations allow us to explore molecular motions and the dynamic interactions between lipids and proteins, providing a complementary approach to the temporal and spatially averaged static structures determined by X-ray crystallography.

Recent studies using MD simulations have identified cardiolipin (CL) binding sites in the cytochrome bc1 transporter [8] and in the cytochrome c oxidase [9], and PIPZ binding sites in Kir channels [10,11].

MD simulations were also used to identify interactions of lipids with the aquaporin family [12,13] and other proteins [14,15].

MD simulation showing the diffusion of two single CL molecules (green) and a POPG molecule (red) in a lipid bilayer and their binding to the CL site 1 on UraA (shown using the residues R4 and R299).

The starting structure for the MD simulations was retrieved from the Protein Data Bank [38], corresponding to PTPIB with Cys215 in the sulfenic acid state, (PDBid IOET) with a crystal resolution of 2.3 A.

This optimization was followed by 100 ps long constant volume MD, where the temperature of the system was slowly raised to 300 K. The heating was followed by a 100 ps long constant temperature and constant pressure MD simulation to equilibrate the system's density.

We used constant pH MD simulations to determine Cys pKa in both a constrained model peptide in the forbidden-psi conformation and a small peptide harboring the whole secondary structure motif taken from the crystal structure of PTPIB.

We then performed 100ns long MD simulations for the peptide containing Cys-OH in water.

In order to analyze the cyclic sulfenyl amide reaction mechanism in PTP1B (see below) and the role played by His214 (in all possible tautomeric states) we performed 10ns long MD simulations starting from the Cys215-SCH modified PTP1B setting histidine tautomeric states either as HIE, HID or HIP (see Methods for details).

(C) Density functions plot for Cys 215-S and Ser 216 HN distance taken from PTP1B MD simulations with His 214 in the HIE (Red), HID (Blue) and HIP (Green) tautomer.

Specifically, we ran multiple, independent MD simulations of each homomeric u-OR/u-OR, 6-OR/6-OR, and K-OR/K-OR complex, as well as two of the most studied heteromeric complexes, i.e., 6-OR/u-OR and 6-OR/K-OR, to derive the preferred supramolecular organization and dimer interfaces of ORs in a cell membrane model.

We estimated the free-energy associated with such a rotation using the results of steered MD simulations , and assuming no conformational changes occurring within the individual protomers based on the CG model we employed.

A summary of all the MD simulations we carried out on CG molecular models based on the crystallographic structures of inactive 5-OR [15] , u-OR [12] , and K-OR [13] is provided in 81 Table.