Sat, 18 Nov 2017

Molecular modeling approach and RMSD calibration for superimposed 3D structure of DHFR from Pneumocystis jiroveci (PCP)

 

Jayaprakash Chinnappan1. Palanisamy Thanga velan Lakshmi2*. Ondari Nyakundi Erick3

1.Phytomatics Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore-641 046, India.

2.Reader, Phytomatics Laboratory, Center for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry- 605 014, India.

3.Department of Bioinformatics, Bharathiar University, Coimbatore-641 046, India.


 

ABSTRACT

The research illuminates DHFR from Pneumocystis jiroveci as a newly potential drug target against pneumonia. P. jiroveci DHFR sequence Q9UUP5 was obtained from Swiss-Prot database and deployed for 3-dimensional structure prediction. Sequence similarity templates searching found between P.j DHFR against 1CD2, 1VJ3 and 1DR1 paved the modeling with high confidence. The superimposition of the predicted template structures revealed the sequence identity of more than 30% and  RMSD values of 4vs.1, 4vs.2, 4vs.3 and 4vs.5 and RMSD values 0.094, 0.093, 0.094 and 0.108 respectively; it comes under the expected range of <2Ȧ. The structure showed overall conservation domains involved in binding affinity, energy minimization value, as well as inter-subunit interactions. Our results provided a basis of structural modeling (threading), energy minimization, RMSD value, structural validation and evaluation, to compare the overall structure and functional amino acids dependent on P.j DHFR in Pneumocystis. Further analysis to show the differences found between the inter and intra species of P.j DHFR is a leeway to design inhibitors targeted specifically against Pneumocystis jiroveci pneumonia (PJP).

Keywords: Threading, RMSD value, Templates, Superimposition and Pneumonia.

 

Abbreviations: Pneumocystis carinii Pneumonia (PCP), Pneumocystis jiroveci Pneumonia (PJP), Dihydrofolate reductase (DHFR), Root Mean Square Deviation (RMSD).


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