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Insights from the analysis of alginate lyase protein model from Pseudomonas fluorescens towards the understanding of mucoid biofilm disruption



Gurjant Singh1, Mahesh Kulharia2,*



1Centre for Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda 151001, India;
2Centre for Computational Sciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda 151001, India;




Article Type




Received August 11, 2016; Accepted November 5, 2016; Published September 30, 2017



Bacterial biofilm is a protective, slippery and slimy coat secreted by bacterial cells. It helps in attaching to moisturized surfaces during colonization. Alginate is an important component as it is essential for retention of water and nutrients in biofilms. It is a polysaccharide consisting of β-D-mannuronic acid (M) and α-L-guluronic acid (G) monomers with 1-4 linkage. The alginate lyase (AlgL) secreted by certain bacteria is capable of degrading alginate into oligo-uronides by β-elimination of the glycosidic bond. Therefore, it is of interest to analyze the simulated (GROMACS force filed) structure protein model (homology based on template 4OZV) of AlgL from Pseudomonas fluorescens to gain functional insight mucoid biofilm disruption. We report root mean square deviation (RMSD) and radius of gyration (Rg) profiles of the simulated (molecular dynamics) AlgL protein homology model in this context towards biofilm discruption.



Bacterial Biofilms, Alginate Lyase, Alginate, Pseudomonas fluorescens, GROMACS, Homology modeling.



Singh & Kulkarni Bioinformation 13(9): 318-322 (2017)


Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.