Protein docking and molecular dynamics simulation of predicted IcaA and IcaD protein structure from Staphylococcus epidermidis involved in PNAG biosynthesis and trafficking

IcaA is poly-beta-1,6-N-acetyl-D-glucosamine (PNAG) synthase, an enzyme producing activated homopolymer chain of N-acetylglucosamine from Staphylococcus epidermidis. IcaA is an integral membrane-associated N-Acetylglucosamine transferase that requires accessory IcaD protein for maximal expression and synthesis. We identified icaA gene sequence carries reputed G-quadruplexes region and characterized 164 bp upstream promoter sequence of IcaADBC operon. We characterized transcription factor binding sequence derived from promoter region as PurR, DegU transcription factor and E-Box invariant sequence. We identified IcaD gene sequence carries E-Box sequence overlap with IcaB gene of the operon which may act as transcription start site (TSS) for IcaB gene expression. Due to lack of crystal structure in PDB database, protein threading methodology was used for construct IcaA and IcaD three-dimensional structure. Our findings reveal that IcaA C-terminal helices region between Phe295-Arg394 connected by loops, may act as lid domain of the protein. Asp134, Ile224, Glu226, Asp227, Arg266, Trp267 are active site amino acids and binding free energy was calculated as ΔG score −5.13 KJ/mol using Autodock 4.2.6. Molecular dynamics simulation (MDS) was performed to evaluate stability of IcaA protein, IcaA-UDP-GluNAc binding complex and IcaD protein throughout trajectories captured within time scale 100 ns simulation period using GROMACS 4.5. Different binding energies were calculated for IcaA-UDP-GluNAc complex using GROMACS tools MM-PBSA.