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Exploring Energy Profiles of Protein-Protein Interactions (PPIs) Using DFT Method

[ Vol. 16 , Issue. 6 ]

Author(s):

Sanket Bapat, Renu Vyas* and Muthukumarasamy Karthikeyan   Pages 670 - 677 ( 8 )

Abstract:


Background: Large-scale energy landscape characterization of protein-protein interactions (PPIs) is important to understand the interaction mechanism and protein-protein docking methods. The experimental methods for detecting energy landscapes are tedious and the existing computational methods require longer simulation time.

Objective: The objective of the present work is to ascertain the energy profiles at the interface regions in a rapid manner to analyze the energy landscape of protein-protein interactions

Result: The atomic coordinates obtained from the X-ray and NMR spectroscopy data are considered as inputs to compute cumulative energy profiles for experimentally validated protein-protein complexes. The energies computed by the program were comparable to the standard molecular dynamics simulations. The PPI Profiler not only enables rapid generation of energy profiles but also facilitates the detection of hot spot residue atoms involved therein.

Conclusion: The hotspot residues and their computed energies matched with the experimentally determined hot spot residues and their energies which correlated well by employing the MM/GBSA method. The proposed method can be employed to scan entire proteomes across species at an atomic level to study the key PPI interactions.

Keywords:

Protein-protein interaction, energy profiles, DFT, energy landscape, hot spot residues, proteomes.

Affiliation:

CSIR-National Chemical Laboratory, Dr. HomiBhabha Road, Pune, Maharashtra, India- 411008, MIT school of Bioengineering Science and research, Loni, Kalbhor, Pune-412201, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Tathawade, Pune, Maharashtra



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