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Research Summary
Our research focus is on understanding how proteins fold, incorporate metal ions and perform catalysis. We approach this challenge from a coordination chemistry perspective by using protein ligands to test biochemical hypotheses about metalloprotein structure-function relationships. We design and synthesize novel proteins from first principles using de novo protein design to reveal the structure-function relationships of natural metalloproteins.
Our interdisciplinary research program in de novo metalloprotein design represents a novel approach in the field of bioinorganic chemistry. Our research begins with the computational design of the protein ligand followed by construction via solid phase peptide synthesis or biochemical expression. After purification, inorganic self-assembly reactions are developed to incorporate the metal ions into the peptide ligands. Detailed chemical and biophysical characterizations of these metalloproteins under physiological conditions are then performed, allowing a direct comparison to natural proteins. We seek to design simplified metalloproteins with all the structural, spectroscopic, and functional hallmarks of their biological counterparts to provide the fullest understanding of natural protein design and function. The insight gained can then be utilized to design chemical catalysts without the limitations imposed by genomic biology.
Using modular protein scaffolds containing natural and nonnatural amino acids ligands, the Gibney lab is assembling a variety of metalloproteins including heme, iron-sulfur clusters, Co(II), Ni(II) and Zn(II). We are delineating the absolute thermodynamic stability of metalloproteins to improve potential energy functions for computation metalloprotein design. These thermodynamic data provide detailed insight into the chemical underpinnings of biology including the role of ligands in proton coupled electron transfer at [4Fe-4S] clusters and the sequence of the reactions in the biosynthetic pathway of hemes a, o and c from heme b. Using this insight, the Gibney lab has designed a five-coordinate heme protein that is spectroscopically identical to deoxymyoglobin as well as peptides which bind Zn(II) tighter than any natural Zn(II) protein.
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Reddi, A.R.; Guzman, T.R.; Breece, R.M.; Tierney, D.L.; Gibney, B.R. Deducing the Energetic Cost of Protein Folding in Zinc Finger Proteins Using Designed Metallopeptides, J. Am. Chem. Soc., 2007, 129, 12815-12827.
Reddi, A.R.; Gibney, B.R. The Role of Protons in the Thermodynamic Contribution of a Zn(II)-Cys4 Site Toward Metalloprotein Stability, Biochemistry, 2007, 46, 3745-3758.
Reddi, A.R.; Reedy, C.J.; Mui, S.; Gibney, B.R. Thermodynamic Investigation into the Mechanisms of Proton-Coupled Electron Transfer in Heme Protein Maquettes, Biochemistry, 2007, 46, 291-305
Zhuang, J.; Reddi, A.R.; Wang, Z.; Khodaverdian, B.; Hegg, E.L.; Gibney, B.R. Evaluating the Roles of the Heme a Sidechains in Cytochrome c Oxidase Using Designed Heme Proteins, Biochemistry, 2006, 45, 12530-12538
Zhuang, J.; Amoroso, J.H.; Kinloch, R.; Dawson, J.H.; Baldwin, M.J.; Gibney, B.R. "Evaluation of electron-withdrawing groups effects on heme binding in designed proteins: Implications for heme a in cytochrome c oxidase". Inorg. Chem. 2006, 45, 4685-4694.
Yu, B.; Edstrom, W.C.; Benach, J.; Hamuro, Y.; Weber, P.C.; Gibney, B.R.; Hunt, J. F. "Substrate Recognition and Redox Chemistry of AlkB Repair Enzyme Revealed by Crystal Structures" Nature, 2006, 439, 879-884.
Gibney, B.R.; Tommos, C.T. "De novo Design of Photosynthetic Biomimetics", Adv. in Photosynthesis and Respiration, T. Wydrzynski and K. Satoh, eds., Springer, New York, 2005, 22, 729-751.
Zhuang, J.; Kinloch, R.; Dawson, J.H.; Baldwin, M.J.; Gibney, B.R. "Design of a Five-Coordinate Heme Protein Maquette: A Spectroscopic Model of Deoxymyoglobin", Inorg. Chem., 2004, 43, 8218-8220.
Reedy, C.J.; Gibney, B.R. "Heme-Protein Assemblies", Chem. Rev. 2004, 101, 617-649 (Thematic Issue on Biomimetic Inorganic Chemistry).
"Nonnatural Amino Acid Ligands in Heme Protein Design" H.K. Privett, C.J. Reedy, M.L. Kennedy and B.R. Gibney, J. Am. Chem. Soc., 2002, 124, 6828-6829.
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