IJCRR - 9(3), February, 2017
Prediction of the Protein 3D Structure of Fimbrial Protein Fim a Type 1 of Porphyromonas Gingivalis - Strain ATCC 33277(A Keystone Periodontal Pathogen) using Homology Modeling and Structure Analysis
Author: Priyanka K. Cholan, Judith Grace Jenefa
Introduction: Porphyromonasgingivalis, is a bacterium that has high degree of association with periodontitis, specially due to the expression of a wide array of virulence factors, of which the fimbriae is of particular interest owing to its adherence and colonization potential in the subgingival niche. This study deals with the determination of the protein 3D structure of major fimbriaefim A type-1of the pathogen Porphyromonasgingivalis–strain ATCC 33277.
Materials Used: FASTA (Fast Adaptive Shrinkage Thresholding Algorithm) protein sequence from NCBI Database, Homology modeling server Swiss-model workspace, CASTp (Computed Atlas of Surface Topography of protein) server, Pro-Q (proetein quality predictor) and PROSESS ((Protein Structure Evaluation Suite and Server).
Methodology: The FASTA protein sequence of fimA type-1 of P. gingivalis– strain ATCC 33277 was retrieved from NCBI database (NCBI- National Centre for Biotechnology Information). The 3D structures of the protein were determined by homology modeling server Swiss-Model workspace. Three models were predicted, and the most relevant structure is estimated by passing various quality assessments steps like ProQand validating test –PROSESS
Results: The protein 3D modeling of major fimbriae fimA type-1 of the pathogen Porphyromonasgingivalis–strain ATCC 33277were subjected to a series of quality check steps and the three most relevant models were prognosticated. In association with this, model 3 was considered to be the most valid and likely structure of fim A type 1.
Conclusion: This study paves way for future studies to be performed in this field including the identification of the protein structure and functions, its pathogenic role in periodontitis and thereby targeting the active sites and hence disease prevention.
Keywords: Fim A type-1, 3D structure, FASTA, Swiss model, CASTp, Prosess
Priyanka K. Cholan, Judith Grace Jenefa. Prediction of the Protein 3D Structure of Fimbrial Protein Fim a Type 1 of Porphyromonas Gingivalis - Strain ATCC 33277(A Keystone Periodontal Pathogen) using Homology Modeling and Structure Analysis International Journal of Current Research and Review. 9(3), February, 18-23
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