Volume 11 Supplement 10
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.
- Li XF*, Moal I*, Bates PA: Detection and refinement of encounter complexes for protein-protein docking: taking account of macromolecular crowding. Proteins 2010, in press.Google Scholar
This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.