Computational Biology & Bioinformatics Discussion Group
Posted March 13, 2010
Isaiah Arkin and his research colleagues at the Hebrew University will stop at nothing to understand just what makes diseases like influenza and SARS so dangerous. Coupling computational modeling with classic biochemical experimentation and bioinformatic analysis, Arkin has achieved a great deal of insight into the inner workings of these bugs at the molecular level. Here he describes his work to the Computational Biology & Bioinformatics Discussion Group and other meeting attendees.
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D. E. Shaw & Co.
A specialized investment and technology development firm whose activities range from computer-based quantitative investment management to the development and financing of technology-oriented business ventures.
Arbely, E., Z. Granot, I. Kass, et al. 2006. A trimerizing GxxxG motif is uniquely inserted in the Severe Acute Respiratory Syndrome (SARS) coronavirus spike protein transmembrane domain. Biochemistry 45: 11349-11356.
Arbely, E., Z. Khattari, G. Brotons, et al. 2004. A highly unusual palindromic transmembrane helical hairpin formed by SARS coronavirus E protein. J. Mol. Biol. 341: 769-779.
Astrahan, P., I. Kass, M. A. Cooper & I. T. Arkin. 2004. A novel method of resistance for influenza against a channel-blocking antiviral drug. Proteins 55: 251-257.Hay, A. J., A. J. Wolstenholme, J. J. Skehel & M. H. Smith. 1985. The molecular basis of the specific anti-influenza action of amantadine. EMBO J. 4: 3021–3024. (PDF, 747 KB) FULL TEXT
Kass, I. & I. T. Arkin. 2005. How pH opens a H+ channel: the gating mechanism of influenza A M2. Structure 13: 1789-1798.
Lehnert, U., Y. Xia, T. E. Royce, et al. 2004. Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions. Q. Rev. Biophys. 37: 121-146.
Leonov, H. & I. T. Arkin. 2005. A periodicity analysis of transmembrane helices.Bioinformatics 21: 2604-2610. Epub 2005 Mar 3.
Pinto, L. H. & R. A. Lamb. 2006. The M2 proton channels of influenza A and B viruses. J. Biol. Chem. 281: 8997-9000. Epub 2005 Dec 30.
Pinto, L. H. & R. A. Lamb. 2004. Viral ion channels as models for ion transport and targets for antiviral drug action. FEBS Lett. 560: 1-2.
Russ, W. P. & D. M. Engelman. 1999. TOXCAT: a measure of transmembrane helix association in a biological membrane. Proc. Natl. Acad. Sci. USA 96: 863-868. FULL TEXT
Senes, A., D. E. Engel & W. F. DeGrado. 2004. Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs. Curr. Opin. Struct. Biol. 14: 465-479.
Spaar, A., C. Munster & T. Salditt. 2004. Conformation of peptides in lipid membranes studied by x-ray grazing incidence scattering. Biophys. J. 87: 396-407. FULL TEXT
Tian, C., P. F. Gao, L. H. Pinto, et al. 2003. Initial structural and dynamic characterization of the M2 protein transmembrane and amphipathic helices in lipid bilayers. Protein Sci. 12: 2597-2605. FULL TEXT
Venkataraman, P., R. A. Lamb & L. H. Pinto. 2005. Chemical rescue of histidine selectivity filter mutants of the M2 ion channel of influenza A virus. J. Biol. Chem. 280: 21463-21472. Epub 2005 Mar 22.
Isaiah Arkin, PhD
The Hebrew University
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Isaiah Arkin earned his PhD at Yale University, where he also went on to conduct postdoctoral research in the area of molecular biophysics. He later became a lecturer in biochemistry at Cambridge University before joining the Department of Biological Chemistry at the Hebrew University in Jerusalem as an Associate Professor. He is currently on sabbatical as a visiting scientist at D. E. Shaw Research in New York, where his research is focused on experimental and computational structural biology of membrane proteins. Arkin is specifically interested in elucidating membrane protein structure, focusing on viral ion channels.
Kiryn Haslinger is a science writer and editor with a masters in theoretical chemistry. Since working with James D. Watson on his book DNA: The Secret of Life as a research and editorial assistant, she has written freelance articles on science and scientific history.