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.

The overall fold of the protein in lipid bilayers remained similar to the crystal structure in detergent on the timescale of our simulations.

Alignment of the crystal structure with the final snapshot of the extended simulations demonstrates that the integrity of all 14 transmembrane helices was maintained during the simulation, however the positions and angles of the helices that form the gate domain changed from the crystal structure (Fig.

To study the preferential interaction of UraA with the anionic lipids in a membrane, the crystal structure of UraA (3QE7) was assembled in a lipid bilayer that resembles its native environment in the bacterial inner membrane.

Note that in all simulations the uracil molecule was absent, as was the detergent molecule present in the crystal structure , producing an empty carrier.

The starting structure of the UraA transporter, without the bound uracil or single detergent molecule, was taken from the protein coordinates of 2.8 A crystal structure deposited in the PDB (3QE7).

It is therefore important to relate the crystal structure back to the state of the protein in a native lipid bilayer [1,2].

A key question to be explored is to what extent the crystal structure determined in the presence of detergents is the same as the structure of the membrane protein in a lipid bilayer.

We explored these questions using the E. coli UraA H+-uracil symporter, the crystal structure of which was determined with bound uracil in the detergent n-nonyl-B-D-glucopyrano-side (NG; Fig.

To allow a quantitative comparison, we calculated the minimum Cor root mean square deviation (RMSD) distance between members of the cluster of dimeric complexes that formed during the simulations and each crystal structure listed in 82 Table.

In particular, 5-OR and K-OR form TM1,2,H8/TM1,2,H8 interfaces in both homo and hetero-dimers that are very close (RMSDs below 4.3 A) to that seen in the crystal structure of K-OR (4DIH [13]).

The closest crystal structure to the TM1,2,H8/TM1,2,H8 interface that forms during u-OR simulations is not the one inferred by the u-OR crystal structure (4DKL [12] ), but rather the one suggested by a [31 -adrenergic receptor (B lAR) crystal structure

This observation provides a possible explanation why the TM5,6/TM5,6 interface seen in the u-OR crystal structure did not form during the 10 us simulations, notwithstanding its thermodynamical stability [14].

Cholesterol molecules were also observed in the ultrahigh resolution crystal structure of the A2A adenosine receptor corresponding to PDB code 4EIY [34].

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.

Notably, the root mean square deviation (RMSD) of this loop conformation from the resolved loop of the newest high-resolution crystal structure of 5-OR [40] is 0.46 A overall.

The sulfenyl amide intermediate was first observed in the crystal structure of human protein tyrosine phosphatase 1B (PTP1B) [7].

Standard protonation states were assigned to all other titrable residues, D and Q were negatively charged, K and R positively charged and Histidine protonation was assigned favoring formation of hydrogen bonds in the crystal structure , but in the case of the already mentioned Histidine 214.

The most important in terms of available experimental information is the protein tyrosine phosphatase family where the first cyclic sulfenyl amide was identified in the crystal structure of PTP1B[87].

In this case, 95% proteins with crystal structure have the constrained cysteine.

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.

The lack of crystal structure for several proteins in other datasets prompted us to build a new dataset of approved drugs.

This example also illustrates the nAnnoLyze capacity of predicting interactions when no crystal structure is available for the target.

In spite of it, we were able to cover 42% of the human proteome with either a crystal structure or a reliable model.

Those ligands are predicted to bind the same predicted binding site of the human COX-1 thanks to its similarity to the crystal structure of optimal cutoff (max value)

Interestingly, most of the links have been previously annotated either in DrugBank, PubChem or in the PDB as a crystal structure .

Our analysis indicates that the PC190723-binding pocket in BsFtsZ is less similar to the SaFtsZ-PC190723 co-crystal than the non-drug bound SaFtsZ structure, both as a static crystal structure (Fig.

All water molecules retained in the crystal structure were removed prior to simulation and the structures were then resolvated in a box of water molecules described by the TIP3P model [36] with 14 A padding and neutralized with NaCl using the solvate and auto-ionize VMD extensions [37].

Single point mutations were introduced into the S. aureus crystal structure with the mutate residue VMD modeling extension [37].

All SaFtsZ simulations were initialized from the crystal structure of the GDP-bound SaFtsZ without PC190723 (PDB ID: 3V08) (Fig.

The crystal structure of colchicine-bound tubulin was downloaded from the PDB database (PDB code: ISAO) and the beta tubulin monomer with bound colchicine (chain D) was extracted from the protein model [69].

To test this hypothesis, we performed a structural alignment of compound 6 with colchicine and docked the aligned conformations onto the ligand-bound tubulin crystal structure (PDB: 1SAO) (Fig.

Structural alignment of compounds 6—12 within the colchicine-binding pocket of the colchicine-tubulin crystal structure (PDB: lSAO) using the MOE FlexAlign protocol followed by an energy minimization procedure to simulate the “induced-fit” effect.