The chaperonin system GroEL / GroES is the most intensely studied member of a growing family of cellular nano-machines. These ring shaped oligomers are functionally diverse but share an ability to disrupt molecular and super-molecular complexes, driven by cycles of ATP binding and hydrolysis. They appear to act as mechano-chemical transducers. A better understanding of the structure and mechanism of these nano-machines is imperative since a growing number of diseases have been attributed to their malfunction. The chaperonins, ubiquitous and indispensable proteins, play an important role in vivo, assisting their substrate proteins (SP) to achieve and to maintain their native states. E. coil GroEL, the archetypic chaperonin, comprises two heptameric rings, stacked back to back. Each sub-unit comprises three distinct domains; the equatorial domain (the site for ATP hydrolysis), an intermediate domain, and an apical domain (the site for SP binding). The catalytic cycle involves large, concerted domain movements in GroEL, triggered allosterically by the binding of key ligands (K+ ion and ATP to the equatorial domain, SP and GroES to the apical domain). Allosteric communication occurs between the domains, within and between the rings. But the coupling between these allosteric T state to R state transitions is poorly understood. In this proposal, experiments designed to determine the role of each of the allosteric effectors on the TT to TR to RR transitions are outlined. With this experimental data, a more robust, all-inclusive model for nested cooperativity will be developed. The location, stoichiometry and affinity constants for the binding of the allosterically and catalytically essential K+ ion will be determined. The identity of the base in the ATP binding site in both the T state and the R state will be clarified. The importance of connectivity between the peptide binding sites in stabilizing the T state will be explored with model peptides of defined length. Methods utilized in the proposed work include site-directed mutagenesis, inter-domain cross-linking, steadystate and stopped-flow kinetics, isothermal titration calorimetry, fluorescence spectroscopy, x-ray crystallography, peptide synthesis, kinetic and computational modeling. These combined studies will provide information of specific significance to the mechanism of the chaperonins, but also of general significance to the mechanism of other ring-shaped nano-machines.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
1R01GM067851-01
Application #
6600841
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Program Officer
Wehrle, Janna P
Project Start
2003-06-01
Project End
2008-05-31
Budget Start
2003-06-01
Budget End
2004-05-31
Support Year
1
Fiscal Year
2003
Total Cost
$300,628
Indirect Cost
Name
University of Maryland College Park
Department
Chemistry
Type
Schools of Earth Sciences/Natur
DUNS #
790934285
City
College Park
State
MD
Country
United States
Zip Code
20742
Tehver, Riina; Chen, Jie; Thirumalai, D (2009) Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle. J Mol Biol 387:390-406
Zheng, Wenjun; Brooks, Bernard R; Thirumalai, D (2009) Allosteric transitions in biological nanomachines are described by robust normal modes of elastic networks. Curr Protein Pept Sci 10:128-32
Tehver, Riina; Thirumalai, D (2008) Kinetic model for the coupling between allosteric transitions in GroEL and substrate protein folding and aggregation. J Mol Biol 377:1279-95
Zheng, Wenjun; Brooks, Bernard R; Thirumalai, D (2007) Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. Biophys J 93:2289-99
Cheung, Margaret S; Thirumalai, D (2007) Effects of crowding and confinement on the structures of the transition state ensemble in proteins. J Phys Chem B 111:8250-7
Stan, George; Lorimer, George H; Thirumalai, D et al. (2007) Coupling between allosteric transitions in GroEL and assisted folding of a substrate protein. Proc Natl Acad Sci U S A 104:8803-8
Stan, George; Brooks, Bernard R; Lorimer, George H et al. (2006) Residues in substrate proteins that interact with GroEL in the capture process are buried in the native state. Proc Natl Acad Sci U S A 103:4433-8
Cheung, Margaret S; Thirumalai, D (2006) Nanopore-protein interactions dramatically alter stability and yield of the native state in restricted spaces. J Mol Biol 357:632-43
Hyeon, Changbong; Lorimer, George H; Thirumalai, D (2006) Dynamics of allosteric transitions in GroEL. Proc Natl Acad Sci U S A 103:18939-44
Zheng, Wenjun; Brooks, Bernard R; Thirumalai, D (2006) Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. Proc Natl Acad Sci U S A 103:7664-9

Showing the most recent 10 out of 13 publications