Electron Microscopy reconstruction of the yeast vacuolar ATPase. Ribbon models for individual protein subunits have been fit to the electron density.
From the lab of Stephan Wilkens, PhD.
Edward A Berry, PhD
- Sr. Research Scientist of Biochemistry and Molecular Biology
Research Programs and Affiliations
- Biochemistry and Molecular Biology
- Biomedical Sciences Program
Education & Fellowships
- PhD: Cornell University, 1981, Biochemistry
- BS: College of Charleston, S.C., 1974, Biology
- Biological energy transduction by membrane protein complexes, with emphasis on oxidative phosphorylation and photosynthesis.
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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. Maturation and Assembly of Respiratory Complex II (succinate:ubiquinone oxidoreductase).
This mitochondrial membrane protein complex consists of four subunits which are translated on cytoplasmic ribosomes, imported into mitochondria, processed, have co-factors inserted, and assembled to form the mature complex. The largest subunit (flavoprotein) contains covalently bound FAD cofactor, the second subunit has three iron-sulfur clusters, and the two smallest are membrane proteins that ligate a heme between them. Now we are studying the mechanism by which the flavoprotein becomes competent to bind flavin and gets flavin inserted and covalently bound
Exciting new projects:
NEDD9 is a scaffolding protein of the Focal Adhesion, involved in bi-directional signalling between the cell and the extracellular matrix contact point. Over-expression of NEDD9 in breast cancer tumors has been associated with anti-estrogen resistance and increased propensity for metastasis. We are using X-ray crystallography to determine the structure of NEDD9, alone and in complexes with its signaling partners. This information will be useful for understanding the mechanism of signaling and developing drugs to modulate it. Funded by CAROL BALDWIN FOUNDATION.
NOD1 and NOD2 are intracellular receptors of the innate immune system that respond to components of bacterial cell wall by activating NFkB transcription among other things. Loss-of-Function mutations in NOD1 and NOD2 have been linked to Asthma and Crohn's disease, respectively. These proteins consist of three domains: A receptor domain, nucleotide binding/oligomerization domain, and one or two protein-protein interaction domains of the CARD (caspase recruitment and activation domain) type. The latter two domains have homology with those of the Apoptosis Proteas Activating Factor APAF1, while the receptor domains are a kind of leucine-rich repeat (LRR) domain. Disease causing mutations in NOD2 are located in the receptor domain. We are trying to crystallize NOD1, NOD2, and their subdomains, as well as complexes with agonist, nucleotide, and down-stream CARD domains. We recently determined the structure of the CARD domain of NOD1 (PDB ID 4E9M)
De Bari, H. and Berry, E.A. (2013) Structure of Vibrio cholerae ribosome hibernation promoting factor
Acta Crystallographica Section F (in press)
Oot RA, Huang LS, Berry EA, Wilkens S. (2012) Crystal structure of the yeast vacuolar ATPase heterotrimeric EGC(head) peripheral stalk complex Structure. 20:1881-92. doi: 10.1016/j.str.2012.08.020. Epub 2012 Sep 20.PMID: 23000382
Hao GF, Wang F, Li H, Zhu XL, Yang WC, Huang LS, Wu JW, Berry EA, Yang GF. (2012) Computational discovery of picomolar Q(o) site inhibitors of cytochrome bc1 complex. J Am Chem Soc. 134(27):11168-76. doi: 10.1021/ja3001908. PMID: 22690928
Ha JH, Karchin JM, Walker-Kopp N, Huang LS, Berry EA, Loh SN. (2012) Engineering domain-swapped binding interfaces by mutually exclusive folding. J Mol Biol. 416(4):495-502. doi: 10.1016/j.jmb.2011.12.050. PMID: 22245575
Berry EA, Huang LS. (2011) Conformationally linked interaction in the cytochrome bc(1) complex between inhibitors of the Q(o) site and the Rieske iron-sulfur protein. Biochim Biophys Acta. 1807: 1349-63. doi: 10.1016/j.bbabio.2011.04.005. PMID: 21575592
Berry EA, Huang LS, Lee DW, Daldal F, Nagai K, Minagawa N (2010) Ascochlorin is a novel, specific inhibitor of the mitochondrial cytochrome bc1 complex. Biochim Biophys Acta. 1797:360-70. doi: 10.1016/j.bbabio.2009.12.003. PMID: 20025846
Crowley PJ, Berry EA, Cromartie T, Daldal F, Godfrey CR, Lee DW, Phillips JE, Taylor A, Viner R. (2008) The role of molecular modeling in the design of analogues of the fungicidal natural products crocacins A and D. Bioorg Med Chem. 16:10345-55. Epub 2008 Oct 17.
Berry EA, Walker FA. (2008) 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.;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. (2007) X-Ray absorption studies of Zn2+ binding sites in bacterial, avian, and bovine cytochrome bc1 complexes. Biophys J. 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.
SUNY Distinguished Professor Emeritus
- Richard Cross, PhD
- David Turner, PhD