Faculty

Edward A Berry, Ph.D. Assistant Professor of Biochemistry and Molecular Biology 4281 Weiskotten Hall Upstate Medical University 750 East Adams Street Syracuse, NY 13210 (315) 464-8751 Lab/Professional Web Site

Education and Clinical Training

Research Program and Department Affiliations

Research Interests

Research Abstract

1. Oxidative Phosphorylation/ Redox Enzymes / Biological Energy Conservation

Mitochondria are the "Powerhouses" of the cell, oxidizing fuel molecules to generate energy for cellular processes. This oxidation is accomplished by the respiratory electron transfer chain, which transfers electrons from strongly reducing substrates to oxygen by a series of intermediate steps, with energy conserved at each step. The respiratory chain consists of multi-subunit trans¬membrane protein complexes, and energy is conserved in the form of a transmembrane gradient in electrochemical potential of the hydrogen ion, ΔμH+. Similar electron transfer chains function in photosynthesis and in respiratory and photosynthetic metabolism of bacteria. We are involved in structural and functional investigations aimed at elucidating the mechanism of energy conservation by these electron transfer chains.

2. Structural Biology of Membrane Proteins / X-ray Crystallography.

A significant fraction of the genes of any organism code for proteins that carry out their function embedded in the lipid bilayer of a biological membrane. These proteins include transporters which move solute molecules across the membrane, transmembrane receptors which respond to conditions outside the cell to bring about a response inside, and bioenergetic enzymes "plugged into" the electro¬chemical gradient. The importance of this class of proteins is emphasized by the fact that a disproportionate number of therapeutic drugs, in fact something like 50%, have membrane proteins as their targets. Functional and structural studies are complicated by the fact that these proteins are not soluble in aqueous solutions, however they can be extracted from the membranes, purified, maintained in a mono disperse state, and even crystallized using detergents or other amphiphilic molecules. Because the respiratory complexes described above are membrane proteins, we have accumulated a lot of experience working with this class of proteins.

3. Macromolecules as Nano-devices / Electron Transfer coupled to catalysis at the single molecule level.

It is predicted that one of the next technological revolutions will be the development of techniques for production of incredibly tiny machines, on the scale of a few tens of nanometers. This is the scale of protein or DNA molecules, and it is likely that genetically engineered macromolecules will play an important role. Together with a group of scientists centered at the "Molecular Foundry" in Berkeley, we are proposing a large scale investigation of techniques for engineering systems involving electron transfer from photoexcitable nanoparticles to redox enzymes catalyzing useful chemistry. If this proposal is funded it will open a new direction of research in our laboratory.

Selected Publications:

Crowley PJ, Berry EA, Cromartie T, Daldal F, Godfrey CR, Lee DW, Phillips JE, Taylor A, Viner R. The role of molecular modeling in the design of analogues of the fungicidal natural products crocacins A and D. Bioorg Med Chem. 2008 Dec 15;16(24):10345-55. Epub 2008 Oct 17.

Berry EA, Walker FA. Bis-histidine-coordinated hemes in four-helix bundles: how the geometry of the bundle controls the axial imidazole plane orientations in transmembrane cytochromes of mitochondrial complexes II and III and related proteins. J Biol Inorg Chem. 2008 May;13(4):481-98. Review.

Giachini L, Francia F, Veronesi G, Lee DW, Daldal F, Huang LS, Berry EA, Cocco T, Papa S, Boscherini F, Venturoli G. X-Ray absorption studies of Zn2+ binding sites in bacterial, avian, and bovine cytochrome bc1 complexes. Biophys J. 2007 Oct 15;93(8):2934-51. Epub 2007 Jun 15.

Devanathan S, Salamon Z, Tollin G, Fitch JC, Meyer TE, Berry EA, Cusanovich MA. Plasmon waveguide resonance spectroscopic evidence for differential binding of oxidized and reduced Rhodobacter capsulatus cytochrome c2 to the cytochrome bc1 complex mediated by the conformation of the Rieske iron-sulfur protein. Biochemistry. 2007 Jun 19;46(24):7138-45. Epub 2007 May 22.

Huang LS, Shen JT, Wang AC, Berry EA. Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the "oxaloacetate-inhibited" state. Biochim Biophys Acta. 2006 Sep-Oct;1757(9-10):1073-83. Epub 2006 Jul 12.

Huang LS, Sun G, Cobessi D, Wang AC, Shen JT, Tung EY, Anderson VE, Berry EA. 3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme. J Biol Chem. 2006 Mar 3;281(9):5965-72. Epub 2005 Dec 21.

Publications - link to PubMed

This profile was last updated on 10/22/2009

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http://www.upstate.edu/biochem/faculty.php?ID=berrye

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