Prabu R, Mohanty A, Balakrishnan SS, Jayalakshmi G, Sundar K. Molecular docking and simulation of IcaC protein as O-succinyltransferase function in staphylococcus epidermidis biofilm formation.
Curr Res Struct Biol 2022;
4:78-86. [PMID:
35399651 PMCID:
PMC8987812 DOI:
10.1016/j.crstbi.2022.03.002]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/19/2022] [Accepted: 03/13/2022] [Indexed: 12/04/2022] Open
Abstract
Intercellular adhesion (IcaADBC) operon is necessary for PNAG (Polyβ-1,6-N-acetyl-D-glucosamine) biosynthesis of biofilm formation in Staphylococcus epidermidis. IcaC protein has a wide range of functions in terms of growth phase variation, migration, transposon insertion, PNAG modification, biofilm formation. Unusual TTTA signature motifs were identified from nucleotide sequence. Asparagine-linked glycosylation consensus motifs were identified at position 169 and 240. S. epidermidis was a close evolutionary association with S. haemolyticus and other Staphylococcus spp. Due to the non-availability of crystal structure, protein threading procedure was selected for constructing a full length IcaC three-dimensional structure. QMEANBrane structure quality assessment with model scores −100000 range within predicted integral membrane structure. IcaC motif constitutes 18 transmembrane helix, 37 helix-helix interaction, 8 beta turn, 2 gamma turn. Binding free energy was calculated with their succinate ligand docking form hydrogen bond with critical amino acids showed ΔG score −2.574 kJ/mol using Schrödinger. Serine (Ser96), Glutamic acid (Glu99), Tryptophan (Trp191) were active site amino acids form the catalytic core required for O-succinyltransferase function. Molecular dynamics simulation (MDS) was performed to evaluate the stability of IcaC protein and IcaC-Succinate binding complexes with the active site amino acids throughout trajectories captured with time scale 100 ns simulation period using GROMACS 4.5.
Structural characterization of Intercellular adhesion (IcaC) protein from Staphylococcus epidermidis.
Understanding of nucleotide, protein signature sequence, secondary structure motifs and phylogenetic association among Staphylococcus sp. homologs.
IcaC-Succinate docking and molecular dynamics simulation for determined structural stability of protein.
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