Cargando…

Molecular docking and simulation of IcaC protein as O-succinyltransferase function in staphylococcus epidermidis biofilm formation

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Prabu, Ramachandira, Mohanty, Amaresh, Balakrishnan, Susmida Seni, Jayalakshmi, G., Sundar, Kothandapani
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8987812/
https://www.ncbi.nlm.nih.gov/pubmed/35399651
http://dx.doi.org/10.1016/j.crstbi.2022.03.002
_version_ 1784682825280126976
author Prabu, Ramachandira
Mohanty, Amaresh
Balakrishnan, Susmida Seni
Jayalakshmi, G.
Sundar, Kothandapani
author_facet Prabu, Ramachandira
Mohanty, Amaresh
Balakrishnan, Susmida Seni
Jayalakshmi, G.
Sundar, Kothandapani
author_sort Prabu, Ramachandira
collection PubMed
description 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.
format Online
Article
Text
id pubmed-8987812
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Elsevier
record_format MEDLINE/PubMed
spelling pubmed-89878122022-04-08 Molecular docking and simulation of IcaC protein as O-succinyltransferase function in staphylococcus epidermidis biofilm formation Prabu, Ramachandira Mohanty, Amaresh Balakrishnan, Susmida Seni Jayalakshmi, G. Sundar, Kothandapani Curr Res Struct Biol Research Article 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. Elsevier 2022-03-26 /pmc/articles/PMC8987812/ /pubmed/35399651 http://dx.doi.org/10.1016/j.crstbi.2022.03.002 Text en © 2022 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Research Article
Prabu, Ramachandira
Mohanty, Amaresh
Balakrishnan, Susmida Seni
Jayalakshmi, G.
Sundar, Kothandapani
Molecular docking and simulation of IcaC protein as O-succinyltransferase function in staphylococcus epidermidis biofilm formation
title Molecular docking and simulation of IcaC protein as O-succinyltransferase function in staphylococcus epidermidis biofilm formation
title_full Molecular docking and simulation of IcaC protein as O-succinyltransferase function in staphylococcus epidermidis biofilm formation
title_fullStr Molecular docking and simulation of IcaC protein as O-succinyltransferase function in staphylococcus epidermidis biofilm formation
title_full_unstemmed Molecular docking and simulation of IcaC protein as O-succinyltransferase function in staphylococcus epidermidis biofilm formation
title_short Molecular docking and simulation of IcaC protein as O-succinyltransferase function in staphylococcus epidermidis biofilm formation
title_sort molecular docking and simulation of icac protein as o-succinyltransferase function in staphylococcus epidermidis biofilm formation
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8987812/
https://www.ncbi.nlm.nih.gov/pubmed/35399651
http://dx.doi.org/10.1016/j.crstbi.2022.03.002
work_keys_str_mv AT praburamachandira moleculardockingandsimulationoficacproteinasosuccinyltransferasefunctioninstaphylococcusepidermidisbiofilmformation
AT mohantyamaresh moleculardockingandsimulationoficacproteinasosuccinyltransferasefunctioninstaphylococcusepidermidisbiofilmformation
AT balakrishnansusmidaseni moleculardockingandsimulationoficacproteinasosuccinyltransferasefunctioninstaphylococcusepidermidisbiofilmformation
AT jayalakshmig moleculardockingandsimulationoficacproteinasosuccinyltransferasefunctioninstaphylococcusepidermidisbiofilmformation
AT sundarkothandapani moleculardockingandsimulationoficacproteinasosuccinyltransferasefunctioninstaphylococcusepidermidisbiofilmformation