Using PocketFEATURE, we compared the PC190723-binding pocket from the SaFtsZ-PC190723 co-crystal with FtsZ crystal structures from multiple bacterial and archaeal species, including the Gram-positive S. aureus, B. subtilis, and Mycobacterium tuberculosis, the Gram-negative Pseudomonas aeruginosa, and the archaeon M ethanocaldococ-cus jannaschii (Table 1).

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.

PCt 97023 pocket scores from FtsZ crystal structures are highly species-dependent

Crystal structures of SaFtsZ bound to PC190723 (PDB ID: 4DXD and 3VOB) [17,18] suggest that PC190723 induces antimicrobial activity in this organism by specifically binding FtsZ, but no evidence of direct binding exists in other bacterial species.

Interestingly, crystal structures of SaFtsZ had similar pocket scores to each other whether or not PC190723 was bound (Fig.

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.

Despite the general change in pocket score to the SaFtsZ-PC190723 co-crystal in all simulations relative to the pocket score computed from static crystal structures , SaFtsZ and SeFtsZ monomers maintained better similarity to the SaFtsZ-PC190723 co-crystal compared to the BsFtsZ monomer.

Several interfaces observed in the simulations reported here are structurally similar to some of the putative dimer interfaces inferred from recent GPCR crystal structures (see 82 Table for a list of currently available GPCR crystal structures showing parallel receptor arrangements).

The calculated RMSD values of S3 and S4 Tables suggest that the dimer interface from simulations that is closest to one inferred from crystal structures is the TM1,2,H8/TM1,2,H8 interface.

The relatively small RMSD values listed in S3 Table, indicate that the simulations of the 5-OR system also reproduced both symmetric and asymmetric dimer interfaces inferred from CXCR4 crystal structures [24] (see S2 Table for details) with reasonable accuracy.

Preferred cholesterol interacting sites at the surface of GPCR molecules have been reported in some of the published crystal structures .

For instance, a cholesterol binding pocket was identified in a groove characterized by highly conserved residues (so-called “consensus-motif’ residues) between the intracellular ends of helices TM2 and TM4 in two B2AR crystal structures , i.e., the carazolol-bound 2RH1 [32] and the timolol-bound 3D4S [33].

While no cholesterol molecules were resolved in the K-OR or 5-OR crystal structures , electron density was attributed to a cholesterol molecule in the u-OR crystal structure (4DKL), at the same location between TM6 and TM7 as seen in the A2A crystal structure 4EIY.

Comparisons with available crystal structures of parallel interacting GPCRs (see 82 Table for a current list) were evaluated by calculating the overall COL RMSD.

In order to ignore the structural differences in the monomeric structures, and capture only the degree of similarity of the OR dimer interfaces from simulation with those inferred by crystal structures , we aligned the individual CG ORs to the receptors in each crystal dimer.

The recent X-ray crystal structures of the u-OR [12] and K-OR [13] have suggested specific receptor-receptor interactions involving transmembrane (TM) helices TM5 and TM6 or TM1, TM2, and helix 8 (H8).

For the evaluation cysteine conformation, all crystal structures depicted above were filtered considering only proteins that have a cysteine residue whose psi dihedral angle is between -50 and -90 degrees (i.e.

We also filtered crystals in which the constrained cysteine is involved in disulfide bonds and crystal structures with resolution of 2.5 A or higher.

Crystal structures of this protein family are generally homo-dimers, with a subunit presenting the Cys in the forbidden-psi conformation, while in the other one adopts a left handed heliX conformation.

Protein Crystal structures with sulfenyl amide deposited in Protein Data Bank.

Protein Crystal structures with cysteine sulfenic acid.

Protein Crystal structures with the cysteine between-150 and-90 psi angle (PDF)

Crystal structures of membrane proteins, particularly from bacterial sources, are being determined at an increasing rate (http://b1anco.biomol.uci.edu/mpstruc/).

Can we use MD simulations to detect specific lipid-protein interactions not often found in crystal structures and study their dynamics?

Tightly-bound lipids have been identified in a number of X-ray crystal structures of membrane proteins showing that there are specific binding sites for lipids on the surface of some membrane proteins, which may assist in their folding or functioning [7].