Structure prediction and assessment of beta-lactamase tem-1 from s. Typhi using molecular dynamics and simulation studies

Research Article
Rakesh Kr Pandit.,Tapan K Mukherjee., Ashok Kumar., Varinder Kumar and Palki Sahib Kaur
DOI: 
xxx-xxxxx-xxxx
Subject: 
science
KeyWords: 
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Abstract: 

Beta lactamase is one of the main reasons behind the development of antibiotic resistance among pathogenic bacteria against beta lactam antibiotics. S. typhi, Gram negative bacteria is main causative agent among human population in developing countries has developed resistance against β-lactam antibiotics which are already in their fourth generation. The availability of a good quality three dimensional structure of target protein is necessary for the development of therapeutic drugs. A good quality three dimensional structure of Beta lactamase TEM-1 from S. typhi was not available. In this study, primary, secondary and tertiary structures of Beta lactamase TEM-1 from S. typhi were predicted using Expasy’s Protpram, PSIPRED and Homology modelling method respectively. The modelled structure was energy minimized and molecular dynamics and simulation studies were performed to investigate how the predicted model behaves structurally, dynamically and thermodynamically using Gromacs 5.1 molecular dynamics and simulation tool. The structure was predicted to be fast attaining the normal temperature (300 K), pressure (1 Bar) and density (1000 Kg/m3 ) values during NVT (constant volume and normal temperature) and NPT (constant normal pressure and normal temperature) simulation steps within the given timeframe using OPLS- AA force field and SPC/E water model. The predicted structure was also validated using PROCHECK. The predicted model was found to be stereo-chemically stable in Ramachandran plot produced by PROCHECK as more than 93% residues were falling under core regions of the plot. The structure will aid in discovery of more efficient alternative therapeutic drugs against typhoid causing