Mechanistic Studies of Protein Allostery at the Atomistic Scale
EMSL Project ID
25651
Abstract
Allostery refers to the change of protein conformation in response to ligand binding, biochemical modifications, or interactions with other proteins. In this proposal, we plan to study protein allostery at the atomistic scale by using various computational methodologies. The aims are to compute the free energy difference between the different conformational states of a protein molecule, to characterize the effects of ligand binding on the conformational flexibility of the protein molecule, and to elucidate the mechanism of conformational coupling and energy transduction in the protein molecule. The proposed research thus lies in the core of the "biological interactions and dynamics" theme of EMSL.The open-to-closed transition of adenylate kinase (AKE) upon binding to ATP and substrate will be the focus of this research. AKE allostery is one of the few examples that have been studied extensively via NMR techniques, thus allowing a direct comparison between computer simulation and experimental measurements. In addition to NMR methods, we will also compare our results with single molecule florescence resonance energy transfer (sFRET) experiments. In particular, the effects of dye modification will be simulated at the atomistic scale and compared with the results obtained without dye modification.
Preliminary molecular dynamics (MD) simulation performed on our local cluster have already generated very interesting results. In a ligand-free environment, direct transition from the closed state structure of AKE to the open state has been observed during a 60 ns trajectory, indicating that certain domain motions can now be observed via all-atom MD simulation. In this simulation, an explicit solvent representation was used and no external force was applied. Such dynamic trajectory also provides a series of structures for free energy calculations and reaction path sampling and optimization. The requested allocation from EMSL would allow us to significantly broaden the scope of our studies to include free energy calculations and reaction path optimization and sampling such that the question of how ligand-binding and dye modification affect AKE allostery can be analyzed in unprecedented detail. The justification of requested CPU hours (150,000) is stated in the research statement.
In summary, the proposed research constitutes a systematic computational study of AKE allostery at the atomistic level. Not only will this research advance the knowledge in protein allostery, new methodologies will also be developed to compare computer simulation results with experimental measurements. Due to the fundamental importance and technological implication of this project, we expect to have 3-4 publications in high-impact journals.
Project Details
Project type
Large-Scale EMSL Research
Start Date
2007-06-01
End Date
2010-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Brokaw JB, and J Chu. 2010. "On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase." Biophysical Journal 99(10):3420-3429. doi:10.1016/j.bpj.2010.09.040
Brokaw JB, KR Haas, and J Chu. 2009. "Reaction Path Optimization with Holonomic Constraints and Kinetic Energy Potentials." Journal of Chemical Theory and Computation 5(8):2050-2061. doi:10.1021/ct9001398
Hanson JA, K Dunderstadt, LP Watkins, S Bhattacharyya, JB Brokaw, J Chu, and H Yang. 2007. "Illuminating the Mechanistic Roles of Enzyme Conformational Dynamics." Proceedings of the National Academy of Sciences of the United States of America 104(46):18055-18060. doi:10.1073/pnas.0708600104
Lin Y, GT Beckham, ME Himmel, MF Crowley, and J Chu. 2013. "Endoglucanase Peripheral Loops Facilitate Complexation of Glucan Chains on Cellulose via Adaptive Coupling to the Emergent Substrate Structures." Journal of Physical Chemistry B 117(37):10750–10758. doi:10.1021/jp405897q