» Research Group web page		Mark Braiman  Professor Time-resolved vibrational spectroscopy; microbial rhodopsins and G-protein-coupled receptors; miniature IR waveguide sensors mbraiman@syr.edu phone: 315-443-4691 / fax: 315-443-4070 Office: CST 3-006 Education: • B.S., 1977, Harvard University • Ph.D., 1983, University of California at Berkeley • Postdoctoral Fellow, 1983-86, MIT • Postdoctoral Fellow, 1986-1988, Boston University Honors & Awards: • National Science Foundation Predoctoral Fellowship, 1977-1980 • Helen Hay Whitney Postdoctoral Fellowship, 1983-86 • Lucille P. Markey Scholar Award, 1986-1992 Courses: • CHE 106: General Chemistry Lecture • CHE 335*: Chemical and Biochemical Analysis • CHE 346: Physical Chemistry • CHE 467: Introduction to Physical Chemistry Research Laboratory • CHE 474/674: Structural and Physical Biochemistry • CHE 477/677: Biochemistry Structural Laboratory   * denotes current Fall '09 course

Research Interests Interactions of biomolecules with light forms is a unifying theme for research in my group. Step-scan time-resolved FTIR spectra are used to examine dynamics of protein conformational changes, using a variety of biochemical modifications to aid in accounting for the observed spectra. We have also developed 20-micron-thick Ge waveguide biosensors for analyzing the membranes of individual living cells with IR spectroscopy. We are especially interested in membrane proteins that bind derivatives of vitamin A, resulting in a photochemical response to visible or UV light. The majority of our recent effort has been on proteorhodopsin (pR), a solar-energy-transducing protein discovered in oceanic bacteria only in the year 2000. Proteorhodopsin is a distant relative of archaeal membrane proteins that have been known for several decades to pump protons from the cytoplasm to the exterior of the cell. Solar energy transduction by pR throughout the oceans is estimated to approach or exceed total worldwide human energy consumption (∼10 trillion watts). Our recent work has shown that the mechanism of proton pumping in the protein superfamily depends on a transient decrease in the proton affinity of a highly conserved arginine residue, leading to its transient deprotonation, with proton release to the external side of the membrane. We can model the proton releasing group of the microbial rhodopsins with a simple but novel synthetic molecule, consisting of an arginine side chain (guanidine) attached to a tyrosine side chain (phenol) via a long alkane linker. We are also investigating this class of compounds for possible pharmacological properties, since the arginine-tyrosine grouping is also highly conserved and mechanistically important to the visual rhodopsins and entire related superfamily of G-protein-coupled receptors. We are examining the role of retinoic acid, another vitamin A derivative, in mediating the skin's response to ultraviolet light. Up to one-sixth of a person's retinoic acid is converted to the 11-cis form in an hour of exposure to midday sun. This isomer has the greatest ability to halt the growth of keratinocytes in cell culture. Thus 11-cis-retinoic acid might prevent some of the ill effects of sunlight on skin, e.g. by inducing cells to undergo terminal differentiation. We hope to find some therapeutic uses, possibly even an anti-cancer activity, for this only slightly investigated derivative of vitamin A. Ultrathin (<10 micron) planar IR waveguide sensors made of germanium provide the means for extending time-resolved IR spectroscopy of membrane proteins to those triggered by voltage changes, rather than light. Such sensors concentrate and amplify the intensity of the IR energy present in the evanescent wave present within ∼1 micron of the germanium surface, allowing measurement of IR spectra from single cells, e.g. frog oocytes. Selected Publications P. Gourdon, A. Alfredsson, A. Pedersen, E. Malmerberg, M. Nyblom, M. Widell, R. Berntsson, J. Pinhassi, M. Braiman, O. Hansson, N. Bonander G. Karlsson, and Neutze R. "Optimized in vitro and in vivo expression of proteorhodopsin: a seven-transmembrane proton pump." Protein Expr Purif. 58, 103-113 (2008). doi:10.1016/j.pep.2007.10.017 M.S. Braiman and Y. Xiao. "Step-scan time-resolved FTIR spectroscopy of biopolymers," in Vibrational Spectroscopy of Biological and Polymeric Materials, eds. V. Gregoriou and M.S. Braiman, CRC Press, Taylor and Francis group (ISBN 1-57444-539-1), pp. 353-418 (2007). Y. Xiao, R. Partha, R. Krebs, and M. Braiman. "Time-resolved FTIR spectroscopy of the photointermediates involved in fast transient H+ release by proteorhodopsin." J Phys Chem B. 109, 634-641 (2005). DOI: 10.1021/jp046314g Y. Xiao and M. S. Braiman. Modeling amino acid side chains in proteins: 15N NMR spectra of guanidino groups in nonpolar environments. J. Phys. Chem. B, 109:16953-16958. (2005). DOI: 10.1021/jp051279e R. Partha, R. Krebs, T. L. Caterino, and M. S. Braiman. Weakened coupling of conserved arginine to the proteorhodopsin chromophore and its counterion implies structural differences from bacteriorhodopsin. BBA Bioenergetics, 1708, 6-12. (2005). DOI: 10.1016/j.bbabio.2004.12.009 » View all Publications