Understanding protein folding is crucial in both the prediction of protein structure from sequence and the design of novel functions. With the recent completion of multiple genome projects, much effort is now focused on the determination of protein structure and function. The long-term goal of this proposal is to understand how proteins fold. The last granting period witnessed the development of several new methods to investigate protein folding. These advances place us in a unique position to address a series of fundamental questions in the kinetics of protein folding.
Our first aim, utilizing kinetic isotope effects and specifically designed alpha-helical coiled coil variants, is to determine when hydrogen bonds from in the folding pathway and to test our hypothesis concerning the correlation between H-bond formation and surface burial for different protein types.
Our second aim, utilizing designed metal binding sites to stabilize particular regions of a protein, is to investigate whether there are single or multiple pathways (e.g. funnels) as well as the relative importance of short and long-range contacts on folding pathways.
Our third aim, utilizing hydrogen exchange/NMR techniques for the measurement of microsecond folding rates under native conditions, is to investigate how fast a protein can fold and to identify the ultimate limiting processes. Our multi-pronged approach applied to different structural classes will provide a comprehensive picture of how proteins adopt their biologically active structures.
Our fourth aim expands our focus to the kinetic determinants of protein folding when it is coupled to DNA binding. The goal is to learn how proteins expeditiously find a particular nucleotide sequence in a cellular context. Folding experiments using methodologies outlined above with the DNA binding domain of transcriptional activator GCN4 will extend our understanding of protein/DNA recognition beyond the static and into the kinetic realm. These results will have general implications for many dynamic cellular processes.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM055694-08
Application #
6637253
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Program Officer
Wehrle, Janna P
Project Start
1996-08-01
Project End
2005-07-31
Budget Start
2003-08-01
Budget End
2004-07-31
Support Year
8
Fiscal Year
2003
Total Cost
$252,826
Indirect Cost
Name
University of Chicago
Department
Biochemistry
Type
Schools of Medicine
DUNS #
005421136
City
Chicago
State
IL
Country
United States
Zip Code
60637
Lian, Huada; Qin, Jian; Freed, Karl F (2018) Dielectric virial expansion of polarizable dipolar spheres. J Chem Phys 149:163332
Wang, Zongan; Jumper, John M; Wang, Sheng et al. (2018) A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations. Biophys J 115:1872-1884
Riback, Joshua A; Bowman, Micayla A; Zmyslowski, Adam et al. (2018) Response to Comment on ""Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water"". Science 361:
Sachleben, Joseph R; Adhikari, Aashish N; Gawlak, Grzegorz et al. (2017) Aromatic claw: A new fold with high aromatic content that evades structural prediction. Protein Sci 26:208-217
Skinner, John J; Wang, Sheng; Lee, Jiyoung et al. (2017) Conserved salt-bridge competition triggered by phosphorylation regulates the protein interactome. Proc Natl Acad Sci U S A 114:13453-13458
French, Alexander R; Sosnick, Tobin R; Rock, Ronald S (2017) Investigations of human myosin VI targeting using optogenetically controlled cargo loading. Proc Natl Acad Sci U S A 114:E1607-E1616
Riback, Joshua A; Katanski, Christopher D; Kear-Scott, Jamie L et al. (2017) Stress-Triggered Phase Separation Is an Adaptive, Evolutionarily Tuned Response. Cell 168:1028-1040.e19
Gates, Zachary P; Baxa, Michael C; Yu, Wookyung et al. (2017) Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core. Proc Natl Acad Sci U S A 114:2241-2246
Riback, Joshua A; Bowman, Micayla A; Zmyslowski, Adam M et al. (2017) Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water. Science 358:238-241
Haddadian, Esmael J; Zhang, Hao; Freed, Karl F et al. (2017) Comparative Study of the Collective Dynamics of Proteins and Inorganic Nanoparticles. Sci Rep 7:41671

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