Supplementary Material for A Hybrid Potential Simulation of the Acylation of Enterococcus faecium L,D-transpeptidase by Carbapenems
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1 Supplementary Material for A Hybrid Potential Simulation of the Acylation of Enterococcus faecium L,D-transpeptidase by Carbapenems Nicholus Bhattacharjee 1, Martin J. Field 1 Jean-Pierre Simorre 2, Michel Arthur 3, Catherine Bougault 2 (1) Dynamo Team, DYNAMOP Group, (2) NMR Group, UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, Grenoble Cedex 9, France (3) Centre de Recherche des cordeliers, Equipe 12, UMR S 872 Université Pierre et Marie Curie-Paris 6, INSERM, Université Paris descartes, Sorbonne Paris Cité, 15 rue de l Ecole de Médecine,75006 Paris, France May 10, 2016 martin.field@ibs.fr catherine.bougault@ibs.fr S1
2 Figure S1: The waters present near the antibiotic binding site in the Model1 acyl-enzyme. Hydrogen bonds are shown as dotted lines. S2
3 Figure S2: The RMS coordinate deviations (top) and fluctuations (bottom) from 51 ns MD simulations of the apo- (left) and acyl-enzyme (right) forms of Ldt fm. The deviation data is plotted for the protein s Cα atoms, whereas the fluctuations were calculated residue-wise by averaging over 100 ps time blocks from the simulations. The colored lines in the fluctuation plots indicate the protein s secondary structure: helices in red and sheets in blue. S3
4 Figure S3: The distance between the phenol oxygen of Tyr403 and the nearest carboxylate oxygen atom of Ert442 during the MD simulation used to generate Model2. The initial distance is 4.6 Å, but increases rapidly. It then fluctuates substantially before assuming the value of 8.3 Å at 51 ns. S4
5 Figure S4: The RMS coordinate deviations for the catalytic center from the 51 ns MD simulations of the acyl- (left) and apo-enzyme (right) forms of Ldt fm : all atoms top; and backbone atoms bottom. For both the acyl- and apo-enzymes, the catalytic center was defined as the non-hydrogen protein and ertapenem atoms that were placed in the QC region during the QC/MM simulation (Figure 1 in the main manuscript). This resulted in 16 atoms for the calculation of the backbone-atom RMSDs for both forms of the enzyme. However, for the all-atom RMSDs, the choice gave 40 atoms for the acyl-enzyme, but only 24 atoms for the apo-enzyme due to the absence of ertapenem. S5
6 Table S1: Topology file in standard CHARMM format for the CHARMM force field used to describe the combined cysteine-ertapenem residue. RESI CER -1.00! Residue name and total charge. GROUP ATOM OAF OC -0.67! Atom type, name and partial charge. ATOM CAZ CC 0.34 ATOM OAJ OC ATOM CBF CA 0.00 ATOM CAP CA HAO ATOM HAP HP ATOM CAO CA CAO ATOM HAO HP (-)OAF // \ ATOM CAM CA \ // \ ATOM HAM HP CAZ--CBF CAM-HAM ATOM CAN CA // ATOM HAN HP OAJ ATOM CBE CPT 0.13 HAP-CAP CAN-HAN ATOM NAU NH \\ / ATOM HAU H 0.34 \\ / ATOM CBA C 0.51 CBE ATOM OAG O GROUP ATOM CBK CP NAU-HAU ATOM HBK HA ATOM CAS CP OAG=CBA ATOM HAS1 HA 0.09 ATOM HAS2 HA 0.09 ATOM NAT N HAT2 ATOM HAT1 H 0.41 \ ATOM HAT2 H 0.41 HAT1-NAT---CBK-HBK ATOM CAQ CP (+) ATOM HAQ1 HA 0.09 HAQ2 HAS2 ATOM HAQ2 HA 0.09 \ / ATOM CBJ CP CAQ CAS ATOM HBJ HA / \ / \ GROUP HAQ1 \ / HAS1 ATOM SAX S HBJ-CBJ ATOM CBD CP S6
7 ATOM CBI CP ATOM HBI HA 0.09 ATOM CAB CT ATOM HAB1 HA 0.09 SAX ATOM HAB2 HA 0.09 OAE ATOM HAB3 HA // ATOM CBC CP CBD---CBC--CAY ATOM CAY CC 0.62 HAB2 \ ATOM OAI OC OAI(-) ATOM OAE OC HAB1-CAB--CBI NAV-HAV ATOM NAV NH \ / ATOM HAV H 0.34 HAB3 HBI \ / ATOM CBL CP CBL-HBL ATOM HBL HA 0.09 GROUP ATOM CBM CT ATOM HBM HA 0.09 ATOM CBG CT HAA2 HBG ATOM HBG HA 0.09 ATOM CAA CT HAA1-CAA--CBG--CBM-HBM ATOM HAA1 HA 0.09 ATOM HAA2 HA 0.09 HAA3 OAK ATOM HAA3 HA 0.09 ATOM OAK OH HAK ATOM HAK H 0.34 Group ATOM CBB C 0.51 ATOM OAH O OAH=CBB ATOM SAW S ATOM CB CT SAW ATOM HB1 HA 0.09 ATOM HB2 HA 0.09 HB2-CB-HB1 ATOM CA CT ATOM HA HB 0.09 HN-N--CA--C=O ATOM C C 0.51 ATOM O O HA ATOM N NH ATOM HN H 0.41 BOND OAF CAZ CAZ OAJ CAZ CBF! Bonds. S7
8 BOND CBF CAP CBF CAO CAP HAP CAP CBE BOND CAO HAO CAO CAM CAM HAM CAM CAN BOND CAN CBE CAN HAN CBE NAU NAU HAU BOND NAU CBA CBA OAG CBA CBK CBK HBK BOND CBK NAT CBK CAS CAS HAS2 CAS HAS1 BOND CAS CBJ NAT HAT2 NAT HAT1 NAT CAQ BOND CAQ HAQ2 CAQ HAQ1 CAQ CBJ CBJ SAX BOND CBJ HBJ SAX CBD CBD CBC CBD CBI BOND CBI HBI CBI CAB CBI CBL CAB HAB3 BOND CAB HAB2 CAB HAB1 CBC NAV CBC CAY BOND CAY OAE CAY OAI NAV CBL NAV HAV BOND CBL HBL CBL CBM CBM HBM CBM CBB BOND CBM CBG CBG OAK CBG CAA CBG HBG BOND CAA HAA2 CAA HAA3 CAA HAA1 OAK HAK BOND CBB SAW CBB OAH SAW CB CB CA BOND CB HB2 CB HB1 CA HA CA C BOND CA N C O N HN IMPR CBA CBK NAU OAG NAU CBA CBE HAU! Improper dihedrals. IMPR CAZ CBF OAF OAJ CAY CBC OAE OAI END S8
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