cAMP receptor protein (CRP) is the prototype of a super-family of transcription factors. One key feature of CRP's biological activity that has been the focus of this laboratory's research is the fundamental rules that govern the allosteric activation by cAMP of its sequence-specific DMA binding. Recently we established, for the first time in any allosteric system, that the energetics of allosteric parameters are linear functions of protein dynamics. Using protein dynamics as the focus, there is a convergence among the results derived from crystallographic, computational and functional energetic data. This preliminary success enables us to focus our research effort on protein dynamics as the fundamental physical property to establish quantitative linkages between CRP structure and mechanism(s) of allostery. For coming years we will address these issues: 1. Is protein dynamics one of the fundamental properties of protein that modulate allostery? Two strategies will be employed to test the validity of this relationship: a) loops which are solvent accessible are targeted as structural elements to alter protein dynamics and allostery;b) Osmolytes, which affect dynamic motions of proteins, will be employed as solvent additives to perturb protein dynamics and allostery. 2. Is there a network of structural elements that is particularly affected by allosteric regulation? The structural elements the perturbation of which can lead to changes in protein dynamics and allostery will be identified by: a) changes in the thermal B-factors in X-ray data due to mutation;b) H/D exchange measurements coupled with mass spectrometry;and c) computation evidence for structural connectivity. 3. Can one use the knowledge gained in Aims 1 and 2 to assist in defining the structural elements that exert long range effects in defining specificity of the activating effectors? CRP is activated most efficiently by cAMP, although it can bind other cNMP without being activated. Literature results imply that polypeptide outside of the cAMP binding site, specifically the DNA binding domain, dictates the ability of CRP to respond to the bound ligand. Based on the preliminary computation results which show connectivity between the cAMP binding site and the DNA binding domain, mutants will be used to test the connectivity pattern. X-ray structural data of the cAMP binding domain will be used to test if the presence of the DNA binding domain alters the structural connectivity pattern in the cAMP binding domain.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM077551-04
Application #
7578996
Study Section
Macromolecular Structure and Function C Study Section (MSFC)
Program Officer
Wehrle, Janna P
Project Start
2006-03-01
Project End
2012-02-29
Budget Start
2009-03-01
Budget End
2012-02-29
Support Year
4
Fiscal Year
2009
Total Cost
$285,911
Indirect Cost
Name
University of Texas Medical Br Galveston
Department
Biochemistry
Type
Schools of Medicine
DUNS #
800771149
City
Galveston
State
TX
Country
United States
Zip Code
77555
Evangelista, Wilfredo; Yeh, Lee-Chuan C; Gmyrek, Aleksandra et al. (2015) Long-Range Communication Network in the Type 1B Bone Morphogenetic Protein Receptor. Biochemistry 54:7079-88
Maillard, Rodrigo A; Liu, Tong; Beasley, David W C et al. (2014) Thermodynamic mechanism for the evasion of antibody neutralization in flaviviruses. J Am Chem Soc 136:10315-24
Yeh, Lee-Chuan C; Falcon, Wilfredo E; Garces, Andrea et al. (2012) A host-guest relationship in bone morphogenetic protein receptor-II defines specificity in ligand-receptor recognition. Biochemistry 51:6968-80
Yu, Shaoning; Maillard, Rodrigo A; Gribenko, Alexey V et al. (2012) The N-terminal capping propensities of the D-helix modulate the allosteric activation of the Escherichia coli cAMP receptor protein. J Biol Chem 287:39402-11
Lee, J Ching; Herman, Petr (2011) Structural and functional energetic linkages in allosteric regulation of muscle pyruvate kinase. Methods Enzymol 488:185-217
Li, Jianquan; Lee, J Ching (2011) Modulation of allosteric behavior through adjustment of the differential stability of the two interacting domains in E. coli cAMP receptor protein. Biophys Chem 159:210-6
Herman, Petr; Lee, J Ching (2009) Functional energetic landscape in the allosteric regulation of muscle pyruvate kinase. 1. Calorimetric study. Biochemistry 48:9448-55
Herman, Petr; Lee, J Ching (2009) Functional energetic landscape in the allosteric regulation of muscle pyruvate kinase. 2. Fluorescence study. Biochemistry 48:9456-65
Herman, Petr; Lee, J Ching (2009) Functional energetic landscape in the allosteric regulation of muscle pyruvate kinase. 3. Mechanism. Biochemistry 48:9466-70
Lee, J Ching (2008) Modulation of allostery of pyruvate kinase by shifting of an ensemble of microstates. Acta Biochim Biophys Sin (Shanghai) 40:663-9

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