In silico Characterization of Biofilm-Associated Protein (Bap) Identified in a Multi-drug Resistant Acinetobacter baumannii Clinical Isolate
Introduction: Acinetobacter baumannii (AB) is a Gram-negative bacteria associated with various hospital infections. The present study deals with in silico analysis of the biofilm-associated protein (Bap) in this pathogen. Method: Sixty-eight multi-drug resistant (MDR) AB were isolated from two ho...
Saved in:
| Main Author: | |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Pasteur Institute of Iran
2021-12-01
|
| Series: | Journal of Medical Microbiology and Infectious Diseases |
| Subjects: | |
| Online Access: | https://jommid.pasteur.ac.ir/article-1-384-en.html |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850036364606701568 |
|---|---|
| author | Mohammad Reza Shakibaie1, 2 |
| author_facet | Mohammad Reza Shakibaie1, 2 |
| author_sort | Mohammad Reza Shakibaie1, 2 |
| collection | DOAJ |
| description | Introduction: Acinetobacter baumannii (AB) is a Gram-negative bacteria
associated with various hospital infections. The present study deals with in silico
analysis of the biofilm-associated protein (Bap) in this pathogen. Method:
Sixty-eight multi-drug resistant (MDR) AB were isolated from two hospitals in
Kerman, Iran. Biofilm-formation was investigated using the microtiter method
and PCR followed by sequencing to detect the bap gene in the strongest biofilmforming
isolate. The physicochemical parameters of Bap protein were
determined by the ProtParam tool using the ExPasy program. The 3D models
from the primary amino acid sequence were constructed using the I-TASSER
modeling platform based on multiple-threading alignments by LOMETS.
Nevertheless, to ensure the correct initial structure, the protein was minimized
in energy through the 3DRefine software of the deep learning system. For the
accuracy of predicted models, calculation of the orientation of dihedral angles,
including the phi (φ) and psi (ψ) and backbone conformation using the
PROCHECK module of the PDB Sum server was performed. The domains and
key amino acids involved in protein structure were studied by the Pfam and
Interpro softwares. Results: Analysis of the amino acid content of the Bap
protein revealed the absence of Arg and Cys in the protein structure. Our Bap
protein exhibited ~99.6% identity with other Bap sequences in the GenBank
database. Stereochemical simulation identified 19 antiparallel β-sheets with two
small α-helices. The N-terminal of Bap protein formed oligomers that mediate
cellular adhesion. Conclusion: This study adds considerable information about
Bap protein 3D structure, its conformation, domain analysis, and amino acids
involved in cellular attachment. |
| format | Article |
| id | doaj-art-3e1113444e474b4d950dbaba420e2ac8 |
| institution | DOAJ |
| issn | 2345-5349 2345-5330 |
| language | English |
| publishDate | 2021-12-01 |
| publisher | Pasteur Institute of Iran |
| record_format | Article |
| series | Journal of Medical Microbiology and Infectious Diseases |
| spelling | doaj-art-3e1113444e474b4d950dbaba420e2ac82025-08-20T02:57:12ZengPasteur Institute of IranJournal of Medical Microbiology and Infectious Diseases2345-53492345-53302021-12-019421022010.52547/JoMMID.9.4.210In silico Characterization of Biofilm-Associated Protein (Bap) Identified in a Multi-drug Resistant Acinetobacter baumannii Clinical IsolateMohammad Reza Shakibaie1, 20https://orcid.org/0000-0003-2524-125X1Department of Microbiology and Virology, Kerman University of Medical Sciences, Iran; 2 Environmental Health Engineering Research Center, Kerman University of Medical Sciences, Kerman, IranIntroduction: Acinetobacter baumannii (AB) is a Gram-negative bacteria associated with various hospital infections. The present study deals with in silico analysis of the biofilm-associated protein (Bap) in this pathogen. Method: Sixty-eight multi-drug resistant (MDR) AB were isolated from two hospitals in Kerman, Iran. Biofilm-formation was investigated using the microtiter method and PCR followed by sequencing to detect the bap gene in the strongest biofilmforming isolate. The physicochemical parameters of Bap protein were determined by the ProtParam tool using the ExPasy program. The 3D models from the primary amino acid sequence were constructed using the I-TASSER modeling platform based on multiple-threading alignments by LOMETS. Nevertheless, to ensure the correct initial structure, the protein was minimized in energy through the 3DRefine software of the deep learning system. For the accuracy of predicted models, calculation of the orientation of dihedral angles, including the phi (φ) and psi (ψ) and backbone conformation using the PROCHECK module of the PDB Sum server was performed. The domains and key amino acids involved in protein structure were studied by the Pfam and Interpro softwares. Results: Analysis of the amino acid content of the Bap protein revealed the absence of Arg and Cys in the protein structure. Our Bap protein exhibited ~99.6% identity with other Bap sequences in the GenBank database. Stereochemical simulation identified 19 antiparallel β-sheets with two small α-helices. The N-terminal of Bap protein formed oligomers that mediate cellular adhesion. Conclusion: This study adds considerable information about Bap protein 3D structure, its conformation, domain analysis, and amino acids involved in cellular attachment.https://jommid.pasteur.ac.ir/article-1-384-en.htmlacinetobacter baumanniigene ontologyprotein modelingmodel validityamino acids alignments |
| spellingShingle | Mohammad Reza Shakibaie1, 2 In silico Characterization of Biofilm-Associated Protein (Bap) Identified in a Multi-drug Resistant Acinetobacter baumannii Clinical Isolate Journal of Medical Microbiology and Infectious Diseases acinetobacter baumannii gene ontology protein modeling model validity amino acids alignments |
| title | In silico Characterization of Biofilm-Associated Protein (Bap) Identified in a Multi-drug Resistant Acinetobacter baumannii Clinical Isolate |
| title_full | In silico Characterization of Biofilm-Associated Protein (Bap) Identified in a Multi-drug Resistant Acinetobacter baumannii Clinical Isolate |
| title_fullStr | In silico Characterization of Biofilm-Associated Protein (Bap) Identified in a Multi-drug Resistant Acinetobacter baumannii Clinical Isolate |
| title_full_unstemmed | In silico Characterization of Biofilm-Associated Protein (Bap) Identified in a Multi-drug Resistant Acinetobacter baumannii Clinical Isolate |
| title_short | In silico Characterization of Biofilm-Associated Protein (Bap) Identified in a Multi-drug Resistant Acinetobacter baumannii Clinical Isolate |
| title_sort | in silico characterization of biofilm associated protein bap identified in a multi drug resistant acinetobacter baumannii clinical isolate |
| topic | acinetobacter baumannii gene ontology protein modeling model validity amino acids alignments |
| url | https://jommid.pasteur.ac.ir/article-1-384-en.html |
| work_keys_str_mv | AT mohammadrezashakibaie12 insilicocharacterizationofbiofilmassociatedproteinbapidentifiedinamultidrugresistantacinetobacterbaumanniiclinicalisolate |