Bridging the gaps: atomic simulation of macromolecular environment brings together protein docking, interaction kinetics and the crowding effects
© Li et al; licensee BioMed Central Ltd. 2010
Published: 07 December 2010
Cellular structures and functions rely on a complex network of regulated protein interactions, which are further based on complex molecular binding mechanisms. Three key questions are usually asked: a) how does a protein find its partner, b) at what rate do they interact and c) how they achieve the previous 2 goals in vivo. While these questions are usually studied in isolation, we believe that unique observations will be made by carrying out holistic investigation of the three problems under one roof, bringing together molecular docking, interaction kinetics and macromolecular crowding.
Our simulation effectively bridges the gap between structural studies of individual macromolecular complexes and their kinetic behaviour in a physiologically crowded condition. Potentially, this offers further connection to systemic approaches of studying regulatory network kinetics, as well as the enhancement of our ability to probe, manipulate and engineer molecular interactions in a simulated, but more realistic cellular environment.
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