Gregory A Babbitt, Madhusudan Rajendran, Miranda L Lynch, Richmond Asare-Bediako, Leora T Mouli, Cameron J Ryan, Harsh Srivastava, Patrick Rynkiewicz, Kavya Phadke, Makayla L Reed, Nadia Moore, Maureen C Ferran, Ernest P Fokoue
Comparative methods in molecular evolution and structural biology rely heavily upon the site-wise analysis of DNA sequence and protein structure, both static forms of information. However, it is widely accepted that protein function results from nanoscale non-random machine-like motions induced by evolutionarily conserved molecular interactions. Comparisons of molecular dynamics (MD) simulations conducted between homologous sites representative of different functional or mutational states can potentially identify local effects on binding interaction and protein evolution...
March 21, 2024: Biophysical Journal