@article {46225, title = {Exploring energy profiles of protein-protein interactions (PPIs) Using DFT method}, journal = {Letters in Drug Design \& Discovery}, volume = {16}, year = {2019}, month = {JUN}, pages = {670-677}, type = {Article}, 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

Methods: 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.

Results: 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.

}, doi = {10.2174/1570180815666180815151141}, author = {Bapat, Sanket and Vyas, Renu and Karthikeyan, Muthukumarasamy} }