UNIVERSITY OF CALIFORNIA, SAN DIEGO
UNIVERSITY OF CALIFORNIA, SAN DIEGO
UNIVERSITY OF CALIFORNIA, SAN DIEGO
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14 <strong>CALIFORNIA</strong>, <strong>SAN</strong> <strong>DIEGO</strong><br />
moment dependence on HOOC torsion, J. Chem. Phys, 129, Sergiy Markutsya, Shankar Subramaniam, R. Dennis Vigil Dynamics Revealed by Dye-Triggered Aggregation and DA-<br />
074316/1-074316/16 (2008). and Rodney O. Fox, On Brownian Dynamics Simulation of KAP1�-Mediated Localization in Living Cells, Chem. Biol.<br />
Jamie Matthews, Juliane L. Fry, Coleen M. Roehl, Paul O. Nanoparticle Aggregation, Ind. Eng. Chem. Res, 47, 3338- (Cambridge, MA, U. S.), 14, 1031-1042 (2007).<br />
Wennberg and Amitabha Sinha, Vibrational overtone initiated<br />
unimolecular dissociation of HOCH2OOH and<br />
HOCD2OOH: Evidence for mode selective behavior, J.<br />
Chem. Phys, 128, 184306/1-184306/12 (2008).<br />
Shuping Li, Jamie Matthews and Amitabha Sinha, Atmo-<br />
3345 (2008).<br />
Brian Saunders, Stephen Lyon, Matthew Day, Brenda Riley,<br />
Emily Chenette and Shankar Subramaniam, The Molecule<br />
Pages database, Nucleic Acids Res, 36, D700-D706<br />
(2008).<br />
Natarajan Kannan, Jian Wu, Ganesh S. Anand, Shibu Yooseph,<br />
Andrew F. Neuwald, J. Craig Venter and Susan S. Tay-<br />
lor, Evolution of allostery in the cyclic nucleotide binding<br />
module, GenomeBiology, 8, No pp. given (2007).<br />
Sharmin Schauble, Charles C. King, Manjula Darshi, Anspheric<br />
Hydroxyl Radical Production from Electronically Ex- tonius Koller, Kavita Shah and Susan S. Taylor, Identificacited<br />
NO2 and H2O, Science (Washington, DC, U. S.), 319,<br />
1657-1660 (2008).<br />
Jamie Matthews, State-resolved photochemistry and spectroscopic<br />
charecterization of atmospherically relevant hydroperoxides.<br />
(D)<br />
SUBRAMANIAM, SHANKAR (b.1953) Professor.<br />
B.Sc, 1972, Osmania University; M.A.Sc, 1974, Osmania<br />
University; Ph.D, 1982, Indian Institute of Technology<br />
Kanpur. His present research focuses several important<br />
aspects of computational biology. These include<br />
web-based approaches to bioinformatics, going from<br />
protein sequence to structure and function and studying<br />
protein recognition and function. TEL: (858) 822-0986<br />
FAX: (858) 534-5722<br />
Web: www.chem.ucsd.edu/Faculty/bios/subramaniam.<br />
html<br />
TAUBER, MICHAEL J. Assistant Professor. B.A,<br />
1992, Cornell University; Ph.D, 2002, University of California,<br />
Berkeley. Postdoctoral researcher, 2002-2003,<br />
University of California, Berkeley; ACS-PRF Research<br />
Associate, 2003-2006, Northwestern University. Physi-<br />
cal Chemistry. Our group investigates charge sharing and<br />
excited state dynamics in organic molecular assemblies,<br />
including self-assembled systems, by a variety of spectroscopic<br />
techniques including pump-probe Raman &<br />
resonance Raman, EPR, and transient absorption. Other<br />
topics of current research are new 3-dimensional architectures<br />
for dye-sensitized solar cells, and solvation<br />
structure/dynamics. TEL: (858) 534-7334 FAX: (858)<br />
000-0000<br />
Email: mtauber@ucsd.edu<br />
E. A. Weiss, M. J. Tauber, R. F. Kelley, M. J. Ahrens, M.<br />
A. Ratner and M. R. Wasielewski, Conformationally gated<br />
tion of ChChd3 as a Novel Substrate of the cAMP-dependent<br />
Protein Kinase (PKA) Using an Analog-sensitive Catalytic<br />
Subunit, J. Biol. Chem, 282, 14952-14959 (2007).<br />
Kenneth M. Humphries, Juniper K. Pennypacker and Susan<br />
S. Taylor, Redox Regulation of cAMP-dependent Protein<br />
Kinase Signaling: kinase versus phosphatase inactivation, J.<br />
Biol. Chem, 282, 22072-22079 (2007).<br />
Neal M. Alto, Andrew W. Weflen, Matthew J. Rardin,<br />
Defne Yarar, Cheri S. Lazar, Raffi Tonikian, Antonius Koller,<br />
Susan S. Taylor, Charles Boone, Sachdev S. Sidhu, San-<br />
dra L. Schmid, Gail A. Hecht and Jack E. Dixon, The type III<br />
effector EspF coordinates membrane trafficking by the spa-<br />
tiotemporal activation of two eukaryotic signaling pathways,<br />
J. Cell Biol, 178, 1265-1278 (2007).<br />
Ganesh S. Anand, Matthew Hotchko, Simon H. J. Brown,<br />
Lynn F. Ten Eyck, Elizabeth A. Komives and Susan S. Taylor,<br />
R-subunit Isoform Specificity in Protein Kinase A: Distinct<br />
Features of Protein Interfaces in PKA Types I and II by<br />
Amide H/ 2 Email: shsubramaniam@ucsd.edu<br />
Publication list has not been verified by the department.<br />
Jayesh Pandey, Mehmet Koyutuerk, Yohan Kim, Wojciech<br />
Szpankowski, Shankar Subramaniam and Ananth Grama,<br />
Functional annotation of regulatory pathways,<br />
Bioinformatics, 23, i377-i386 (2007).<br />
Mano Ram Maurya and Shankar Subramaniam, A kinetic<br />
switching between superexchange and hopping within oligop-phenylene-based<br />
molecular wires, J. Am. Chem. Soc, 127,<br />
11842-11850 (2005).<br />
E. A. Weiss, M. J. Tauber, M. A. Ratner and M. R. Wasie-<br />
lewski, Electron spin dynamics as a probe of molecular dynamics:<br />
Temperature-dependent magnetic field effects on<br />
charge recombination within a covalent radical ion pair, J.<br />
Am. Chem. Soc, 127, 6052-6061 (2005).<br />
R. F. Kelley, M. J. Tauber and M. R. Wasielewski, Linker-<br />
H Exchange Mass Spectrometry, J. Mol. Biol, 374,<br />
487-499 (2007).<br />
Marat Valiev, Jie Yang, Joseph A. Adams, Susan S. Taylor<br />
and John H. Weare, Phosphorylation Reaction in cAPK Protein<br />
Kinase-Free Energy Quantum Mechanical/Molecular<br />
Mechanics Simulations, J. Phys. Chem. B, 111, 13455-13464<br />
(2007).<br />
Chinten James Lim, Jaewon Han, Nima Yousefi, Yuliang<br />
Ma, Paul S. Amieux, G. Stanley McKnight, Susan S. Taylor<br />
model for calcium dynamics in RAW 264.7 cells: 1. Mecha- controlled energy and charge transfer within chlorophyll treand Mark H. Ginsberg, �4 Integrins are type I cAMP-depen-<br />
nisms, parameters, and subpopulational variability, Biophys. foils, Angew. Chem. Int. Ed, 45, 7979-7982 (2006).<br />
dent protein kinase-anchoring proteins, Nat. Cell Biol, 9,<br />
J, 93, 709-728 (2007).<br />
M. J. Tauber, R. F. Kelley, J. M. Giaimo, B. Rybtchinski 415-421 (2007).<br />
Mano Ram Maurya and Shankar Subramaniam, A kinetic and M. R. Wasielewski, Electron hopping in pi-stacked cova- Shibu Yooseph, Granger Sutton, Douglas B. Rusch, Aaron<br />
model for calcium dynamics in RAW 264.7 cells: 2. Knock- lent and self-assembled perylene diimides observed by EN- L. Halpern, Shannon J. Williamson, Karin Remington, Jonadown<br />
response and long-term response, Biophys. J, 93, 729- DOR spectroscopy, J. Am. Chem. Soc, 128, 1782-1783 than A. Eisen, Karla B. Heidelberg, Gerard Manning, Wei-<br />
740 (2007). (2006).<br />
zhong Li, Lukasz Jaroszewski, Piotr Cieplak, Christopher S.<br />
Andrea L. Hevener, Jerrold M. Olefsky, Donna Reichart, R. F. Kelley, M. J. Tauber and M. R. Wasielewski, Intra- Miller, Huiying Li, Susan T. Mashiyama, Marcin P. Joachim-<br />
M. T. Audrey Nguyen, Gautam Bandyopadyhay, Ho-Yin molecular electron transfer through the 20-position of a iak, Christopher van Belle, John-Marc Chandonia, David A.<br />
Leung, Matthew J. Watt, Chris Benner, Mark A. Febbraio, chlorophyll-a derivative: An unexpectedly efficient conduit Soergel, Yufeng Zhai, Kannan Natarajan, Shaun Lee, Benja-<br />
Anh-Khoi Nguyen, Brian Folian, Shankar Subramaniam, for charge transport, J. Am. Chem. Soc, 128, 4779-4791 min J. Raphael, Vineet Bafna, Robert Friedman, Steven E.<br />
Frank J. Gonzalez, Christopher K. Glass and Mercedes Ri- (2006).<br />
Brenner, Adam Godzik, David Eisenberg, Jack E. Dixon, Sucote,<br />
Macrophage PPAR� is required for normal skeletal M. J. Ahrens, M. J. Tauber and M. R. Wasielewski, Bis(n- san S. Taylor, Robert L. Strausberg, Marvin Frazier and J.<br />
muscle and hepatic insulin sensitivity and full antidiabetic ef- octylamino)perylene-3,4:9,10-bis(dicarboximide)s and their Craig Venter, The Sorcerer II global ocean sampling expedi-<br />
fects of thiazolidinediones, J. Clin. Invest, 117, 1658-1669 radical cations: Synthesis, electrochemistry, and ENDOR tion: expanding the universe of protein families, PLoS Biol,<br />
(2007). spectroscopy, J. Org. Chem, 71, 2107-2114 (2006).<br />
5, 432-466 (2007).<br />
Jin Sun, Francine Battaglia and Shankar Subramaniam, Richard F. Kelley, Michael J. Tauber, Thea M. Wilson and Natarajan Kannan, Susan S. Taylor, Yufeng Zhai, J. Craig<br />
Hybrid two-fluid DEM simulation of gas-solid fluidized Michael R. Wasielewski, Controlling energy and charge Venter and Gerard Manning, Structural and functional diverbeds,<br />
J. Fluids Eng, 129, 1394-1403 (2007). transfer in linear chlorophyll dimers, Chem. Commun. (Cam- sity of the microbial kinome, PLoS Biol, 5, 467-478 (2007).<br />
Robert W. Byrnes, Eoin Fahy and Shankar Subramaniam, bridge, U. K.), 42, 4407-4409 (2007).<br />
Natarajan Kannan, Nina Haste, Susan S. Taylor and An-<br />
A laboratory information management system for high- Christina M. Stuart, Michael J. Tauber and Richard A. Ma- drew F. Neuwald, The hallmark of AGC kinase functional dithroughput<br />
experimental lipidomics: Minimal information re- thies, Structure and Dynamics of the Solvated Electron in Al- vergence is its C-terminal tail, a cis-acting regulatory mod-<br />
quired for the analysis of lipidomics experiments (MIALE), cohols from Resonance Raman Spectroscopy, J. Phys. Chem. ule, Proc. Natl. Acad. Sci. U. S. A, 104, 1272-1277 (2007).<br />
JALA, 12, 230-238 (2007). A, 111, 8390-8400 (2007).<br />
Rahul Das, Veronica Esposito, Mona Abu-Abed, Ganesh<br />
Kara Schmelzer, Eoin Fahy, Shankar Subramaniam and S. Anand, Susan S. Taylor and Giuseppe Melacini, cAMP ac-<br />
Edward A. Dennis, The lipid maps initiative in lipidomics,<br />
Methods Enzymol, 432, 171-183 (2007).<br />
Eoin Fahy, Dawn Cotter, Robert Byrnes, Manish Sud, Andrea<br />
Maer, Joshua Li, David Nadeau, Yihua Zhau and Shankar<br />
Subramaniam, Bioinformatics for lipidomics, Methods<br />
Enzymol, 432, 247-273 (2007).<br />
Purnima Guda, Shankar Subramaniam and Chittibabu<br />
Guda, Mitoproteome: human heart mitochondrial protein sequence<br />
database, Methods Mol. Biol. (Totowa, NJ, U. S.),<br />
357, 375-383 (2007).<br />
Joelle R. Zavzavadjian, Sam Couture, Wei Sun Park,<br />
James Whalen, Stephen Lyon, Genie Lee, Eileen Fung,<br />
Qingli Mi, Jamie Liu, Estelle Wall, Leah Santat, Kavitha<br />
Dhandapani, Christine Kivork, Adrienne Driver, Xiaocui<br />
Zhu, Mi Sook Chang, Baljinder Randhawa, Elizabeth Gehrig,<br />
Heather Bryan, Mary Verghese, Andreia Maer, Brian Saunders,<br />
Yuhong Ning, Shankar Subramaniam, Tobias Meyer,<br />
Melvin I. Simon, Nancy O’Rourke, Grischa Chandy and Iain<br />
D. C. Fraser, The alliance for cellular signaling plasmid collection:<br />
a flexible resource for protein localization studies<br />
and signaling pathway analysis, Mol. Cell. Proteomics, 6,<br />
413-424 (2007).<br />
Manish Sud, Eoin Fahy, Dawn Cotter, Alex Brown, Edward<br />
A. Dennis, Christopher K. Glass, Alfred H. Merrill, Jr.,<br />
Robert C. Murphy, Christian R. H. Raetz, David W. Russell<br />
and Shankar Subramaniam, LMSD: LIPID MAPS structure<br />
database, Nucleic Acids Res, 35, D527-D532 (2007).<br />
Ying Xu and Shankar Subramaniam, Consistent modeling<br />
TAYLOR, SU<strong>SAN</strong> S. (b.1942) Professor. B.A, 1964,<br />
University of Wisconsin; Ph.D, 1968, The Johns Hopkins<br />
University. Postdoctoral Fellowship, 1969-1971,<br />
Laboratory of Molecular Biology, Cambridge, England;<br />
Postdoctoral Fellowship, 1971-1972, University of California,<br />
San Diego. Biochemistry; Crystallography.<br />
CAMP-dependent Protein Kinase: Dynamics of Structures<br />
and Localization cAMP-dependent protein kinase<br />
(cAPK) serves as a prototype for the entire protein kinase<br />
superfamily. Crystal structures of the RIa and RIIb<br />
cAMP binding domains of the R subunits show clear isoform<br />
differences. From these structures we can more fully<br />
appreciate the conformational versatility of this ancient<br />
signaling module that binds cAMP and mediates a<br />
biological response. This stable module binds with high<br />
affinity to scaffold proteins. The molecular basis for targeting<br />
has been elucidated by solving high-resolution<br />
structures of two D/D domains by hetero nuclear NMR<br />
in collaboration with Dr. Patricia Jennings. Isoform dif-<br />
ferences in PKA targeting are being explored. We have<br />
identified two novel AKAPs that bind to both RIa and<br />
RIIb. Both target cAPK to mitochondria. We are beginning<br />
to elucidate the molecular basis for this targeting.<br />
TEL: (858) 534-3677 FAX: (858) 534-8193<br />
Web: susantaylorlab.ucsd.edu/<br />
Email: staylor@ucsd.edu<br />
tivation of PKA defines an ancient signaling mechanism,<br />
Proc. Natl. Acad. Sci. U. S. A, 104, 93-98 (2007).<br />
Jian Wu, Simon H. J. Brown, Sventja von Daake and Su-<br />
san S. Taylor, PKA Type II� Holoenzyme Reveals a Combinatorial<br />
Strategy for Isoform Diversity, Science (Washington,<br />
DC, U. S.), 318, 274-279 (2007).<br />
Susan S. Taylor, Choel Kim, Cecilia Y. Cheng, Simon H.<br />
J. Brown, Jian Wu and Natarajan Kannan, Signaling through<br />
cAMP and cAMP-dependent protein kinase: Diverse strategies<br />
for drug design, Biochim. Biophys. Acta, Proteins Pro-<br />
teomics, 1784, 16-26 (2008).<br />
Lynn F. Ten Eyck, Susan S. Taylor and Alexandr P. Kornev,<br />
Conserved spatial patterns across the protein kinase<br />
family, Biochim. Biophys. Acta, Proteins Proteomics, 1784,<br />
238-243 (2008).<br />
Natarajan Kannan, Andrew F. Neuwald and Susan S. Tay-<br />
lor, Analogous regulatory sites within the �C-�4 loop re-<br />
gions of ZAP-70 tyrosine kinase and AGC kinases, Biochim.<br />
Biophys. Acta, Proteins Proteomics, 1784, 27-32 (2008).<br />
Natarajan Kannan and Susan S. Taylor, Rethinking pseu-<br />
dokinases, Cell (Cambridge, MA, U. S.), 133, 204-205<br />
(2008).<br />
Yuliang Ma and Susan S. Taylor, A Molecular Switch for<br />
Targeting between Endoplasmic Reticulum (ER) and Mito-<br />
chondria: Conversion of a mitochondria-targeting element<br />
into an er-targeting signal in DAKAP1, J. Biol. Chem, 283,<br />
11743-11751 (2008).<br />
Alexandr P. Kornev, Susan S. Taylor and Lynn F. Ten<br />
of interphase turbulent kinetic energy transfer in particle-laden<br />
turbulent flows, Phys. Fluids, 19, 085101/1-085101/9<br />
Publication list has not been verified by the department. Eyck, A generalized allosteric mechanism for cis-regulated<br />
cyclic nucleotide binding domains, PLoS Comput. Biol, 4,<br />
(2007). Ganesh Anand, Susan S. Taylor and David A. Johnson, No pp. given (2008).<br />
Srinivasan Ramachandran, Lai-Hua Xie, Scott A. John, Cyclic-AMP and Pseudosubstrate Effects on Type-I A-Ki- Alexandr P. Kornev, Susan S. Taylor and Lynn F. Ten<br />
Shankar Subramaniam and Ratnesh Lal, A novel role for nase Regulatory and Catalytic Subunit Binding Kinetics, Bio- Eyck, A helix scaffold for the assembly of active protein kiconnexin<br />
hemichannel in oxidative stress and smoking-in- chemistry, 46, 9283-9291 (2007). nases, Proc. Natl. Acad. Sci. U. S. A, 105, 14377-14382<br />
duced cell injury, PLoS One, 2, No pp. given (2007). Choel Kim, Cecilia Y. Cheng, S. Adrian Saldanha and Su- (2008).<br />
Colin T. Walsh, Julie Radeff-Huang, Rosalia Matteo, Al- san S. Taylor, PKA-I holoenzyme structure reveals a mecha- Larry R. Masterson, Alessandro Mascioni, Nathaniel J.<br />
bert Hsiao, Shankar Subramaniam, Dwayne Stupack and nism for cAMP-dependent activation, Cell (Cambridge, MA, Traaseth, Susan S. Taylor and Gianluigi Veglia, Allosteric<br />
Joan Heller Brown, Thrombin receptor and RhoA mediate U. S.), 130, 1032-1043 (2007). cooperativity in protein kinase A, Proc. Natl. Acad. Sci. U. S.<br />
cell proliferation through integrins and cysteine-rich protein Brent R. Martin, Thomas J. Deerinck, Mark H. Ellisman, A, 105, 506-511 (2008).<br />
61, FASEB J, 22, 4011-4021 (2008). Susan S. Taylor and Roger Y. Tsien, Isoform-Specific PKA Ali Torkamani, Natarajan Kannan, Susan S. Taylor and