Hydrogen bonds involving backbone C=O and NH groups constitute a large number of the native contacts in folded proteins. However, relatively little is known about the nature of their contribution to protein folding and stability. This is largely because backbone mutations in proteins are difficult to introduce by conventional site-directed mutagenesis protocols. Here we propose site-directed mutagenesis experiments utilizing total chemical synthesis strategies to study the role of backbone-backbone hydrogen bonds in the folding and stability of several model protein systems including: P22 Arc repressor, 4-oxalocrotonate tautomerase (40T), CopG, and protein L. Our experiments will involve the total chemical synthesis and the biophysical characterization of a series of different 40T, Arc repressor, CopG and protein L analogues that contain amide to ester bond mutations at specific locations in their polypeptide chains. The ester bond mutation is designed to modulate the hydrogen bonding characteristics of specific amide bonds in the polypeptide chains of these protein systems.The results of this work will be used to test five hypotheses about the fundamental role of backbone-backbone hydrogen bonds in protein folding reactions. We will determine: (1) if the stabilizing effects of all backbone-backbone hydrogen bonds in proteins are the same; (2) if the stabilizing effects of backbone-backbone hydrogen bonds located in similar regions (i.e. in the middle of an a-helix or at the end of a f3-sheet) of different protein structures are the same; (3) if the stabilizing effects of structurally equivalent backbone-backbone hydrogen bonds in protein's with the same backbone topology but different amino acid sequences (i.e. <25% sequence homology) are the same; (4) if the stabilizing effects of backbone-backbone hydrogen bonds protein folding intermediates are to those in the protein's native state; and (5) if backbone-backbone hydrogen bonds contribute to the stabilization of protein folding transition states.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
3R01GM061680-03S1
Application #
7006141
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Program Officer
Basavappa, Ravi
Project Start
2002-07-01
Project End
2007-06-30
Budget Start
2004-07-01
Budget End
2005-06-30
Support Year
3
Fiscal Year
2005
Total Cost
$25,513
Indirect Cost
Name
Duke University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
044387793
City
Durham
State
NC
Country
United States
Zip Code
27705
Hopper, Erin D; Roulhac, Petra L; Campa, Michael J et al. (2008) Throughput and efficiency of a mass spectrometry-based screening assay for protein-ligand binding detection. J Am Soc Mass Spectrom 19:1303-11
Roulhac, Petra L; Weaver, Katherine D; Adhikari, Pratima et al. (2008) Ex vivo analysis of synergistic anion binding to FbpA in Gram-negative bacteria. Biochemistry 47:4298-305
Yang, Xiaoye; Wang, Min; Fitzgerald, Michael C (2006) Direct analysis of backbone-backbone hydrogen bond formation in protein folding transition states. J Mol Biol 363:506-19
Yang, Xiaoye; Fitzgerald, Michael C (2006) Total chemical synthesis of the B1 domain of protein L from Peptostreptococcus magnus. Bioorg Chem 34:131-41
Wang, Min; Wales, Thomas E; Fitzgerald, Michael C (2006) Conserved thermodynamic contributions of backbone hydrogen bonds in a protein fold. Proc Natl Acad Sci U S A 103:2600-4
Cisneros, G Andres; Wang, Min; Silinski, Peter et al. (2004) The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: understanding from theory and experiment. Biochemistry 43:6885-92
Wales, Thomas E; Richardson, Jane S; Fitzgerald, Michael C (2004) Facile chemical synthesis and equilibrium unfolding properties of CopG. Protein Sci 13:1918-26
Yang, Xiaoye; Wang, Min; Fitzgerald, Michael C (2004) Analysis of protein folding and function using backbone modified proteins. Bioorg Chem 32:438-49
Silinski, Peter; Fitzgerald, Michael C (2003) Comparative analysis of two different amide-to-ester bond mutations in the beta-sheet of 4-oxalocrotonate tautomerase. Biochemistry 42:6620-30