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Scientific Report 2005


Molecular Biology





Chairman's Overview

Staff


Peter E. Wright, Ph.D.*
Professor and Chairman
Cecil H. and Ida M. Green Investigator in Medical Research

Ruben Abagyan, Ph.D.
Professor

Carlos F. Barbas III, Ph.D.*
Professor
Janet and W. Keith Kellogg II Chair, Molecular Biology

Michael N. Boddy, Ph.D.
Assistant Professor

Charles L. Brooks III, Ph.D.
Professor

Monica J. Carson, Ph.D.**
Associate Professor
University of California
Riverside, California

David A. Case, Ph.D.
Professor

Geoffrey Chang, Ph.D.*
Associate Professor

Jerold Chun, M.D., Ph.D.
Professor

Lisa Craig, Ph.D.**
Assistant Professor
Simon Fraser University
Burnaby, British Columbia

Valerie De Crecy Lagard, Ph.D.**
Assistant Professor
University of Florida
Gainesville, Florida

Luis De Lecea, Ph.D.
Associate Professor

Lluis Ribas De Pouplana, Ph.D.
Adjunct Assistant Professor

Ashok Deniz, Ph.D.
Assistant Professor

H. Jane Dyson, Ph.D.
Professor

John H. Elder, Ph.D.
Professor

Martha J. Fedor, Ph.D.*
Associate Professor

James Arthur Fee, Ph.D.
Professor of Research

Elizabeth D. Getzoff, Ph.D.****
Professor

David B. Goodin, Ph.D.
Associate Professor

David S. Goodsell Jr., Ph.D.
Associate Professor

Joel M. Gottesfeld, Ph.D.
Professor

Robert Hallewell, D.Phil.
Adjunct Associate Professor

Jennifer Harris, Ph.D.
Assistant Professor of Biochemistry

Christian A. Hassig, Ph.D.
Adjunct Assistant Professor

Mirko Hennig, Ph.D.
Assistant Professor

John E. Johnson, Ph.D.
Professor

Gerald F. Joyce, M.D., Ph.D.*****
Professor

Ehud Keinan, Ph.D.
Adjunct Professor

Richard A. Lerner, M.D., Ph.D.*****
President, Scripps Research
Lita Annenberg Hazen Professor of Immunochemistry
Cecil H. and Ida M. Green Chair in Chemistry

Scott Lesley, Ph.D.
Assistant Professor of Biochemistry

Tianwei Lin, Ph.D.
Assistant Professor

Clare McGowan, Ph.D.
Associate Professor

Duncan E. McRee, Ph.D.
Adjunct Associate Professor

David P. Millar, Ph.D.
Associate Professor

Louis Noodleman, Ph.D.
Associate Professor

Arthur J. Olson, Ph.D.
Professor

James C. Paulson, Ph.D.††
Professor

Vijay Reddy, Ph.D.
Assistant Professor

Steven I. Reed, Ph.D.
Professor

Victoria A. Roberts, Ph.D.**
Associate Professor
University of California
San Diego, California

Paul Russell, Ph.D.
Professor

Michel Sanner, Ph.D.
Associate Professor

Harold Scheraga, Ph.D.
Adjunct Professor

Paul R. Schimmel, Ph.D.*****
Ernest and Jean Hahn Professor of Molecular Biology and Chemistry

Anette Schneemann, Ph.D.
Associate Professor

Subhash C. Sinha, Ph.D.*
Associate Professor

Gary Siuzdak, Ph.D.
Adjunct Associate Professor

Robyn L. Stanfield, Ph.D.
Assistant Professor

James Steven, Ph.D.
Assistant Professor

Raymond C. Stevens, Ph.D.†††
Professor

Charles D. Stout, Ph.D.
Associate Professor

Peiqing Sun, Ph.D.
Assistant Professor

J. Gregor Sutcliffe, Ph.D.
Professor

John A. Tainer, Ph.D.*
Professor

Fujie Tanaka, Ph.D.
Assistant Professor

Elizabeth Anne Thomas, Ph.D.
Assistant Professor

James R. Williamson, Ph.D.*****
Professor
Associate Dean, Kellogg School of Science and Technology

Ian A. Wilson, D.Phil.*
Professor

Curt Wittenberg, Ph.D.
Professor

Kurt Wüthrich, Ph.D.
Cecil H. and Ida M. Green Professor of Structural Biology

Todd O. Yeates, Ph.D.
Adjunct Professor

Qinghai Zhang, Ph.D.
Assistant Professor

Guo Fu Zhong, Ph.D.**
Fudan University
Shanghai, China

SERVICE FACILITIES


Ola Blixt, Ph.D.
Core Manager, Consortium for Functional Glycomics

John Chung, Ph.D.
Manager, Nuclear Magnetic Resonance Facilities

Gerard Kroon
Assistant Manager, Nuclear Magnetic Resonance Facilities

Michael E. Pique
Director, Graphics Development

Nahid Razi, Ph.D.
Assistant Core Manager, Consortium for Functional Glycomics

Peter Sobieszcsuk, Ph.D.
Core Manager, Consortium for Functional Glycomics

SENIOR STAFF SCIENTIST


Wayne A. Fenton, Ph.D.

Aymeric Pierre De Parseval, Ph.D.

Karla Ewalt, Ph.D.**
Princeton University
Princeton, New Jersey

Brian M. Lee, Ph.D.

Maria Martinez-Yamout, Ph.D.

Garrett M. Morris, Ph.D.

Chiaki Nishimura, Ph.D.

Jeffrey Speir, Ph.D.

Manal Swairjo, Ph.D.

Mutsuo Yamaguchi, Ph.D.

Xueyong Zhu, Ph.D.
 

SENIOR RESEARCH ASSOCIATES


David Barondeau, Ph.D.

Kirk Beebe, Ph.D.

Ryan Burnett, Ph.D.

Brian Collins, Ph.D.

Adrienne Elizabeth Dubin, Ph.D.

Maria Alejandra Gamez-Abascal, Ph.D.

Peter B. Hedlund, M.D., Ph.D.

Ying Chuan Lin, Ph.D.

Rebecca Page, Ph.D.**
Brown University
Providence, Rhode Island

Mikhail Popkov, Ph.D.

Richard R. Rivera, Ph.D.

Lincoln Scott, Ph.D.

Koji Tamura, Ph.D.Liang Tang, Ph.D.**
Burnham Institute
La Jolla, California

Ellie Tzima, Ph.D.**
University of North Carolina
Chapel Hill, North Carolina

Xiang-Lei Yang, Ph.D.

Dirk M. Zajonc, Ph.D.
 

RESEARCH ASSOCIATES


Sunny Abraham, Ph.D.

Fabio Agnelli, Ph.D.

Moballigh Ahmad, Ph.D.

Alexander Ivanov Alexandrov, Ph.D.

Marcius Da Silva Almeida, Ph.D.

Beatriz Gonzalez Alonso, Ph.D.

David Alvarez-Carbonell, Ph.D.

Jianghong An, Ph.D.**
British Columbia Cancer Agency
Vancouver, British Columbia

Yu An, Ph.D.

Crystal Stacy Anglen, Ph.D.**
Neurome, Inc.
La Jolla, California

Brigitte Anliker, Ph.D.

Roger Armen, Ph.D.

Joseph W. Arndt, Ph.D.

Mabelle Ashe, Ph.D.

Jamie Mitchell Bacher, Ph.D.

Michael F. Bailey, Ph.D.**
Bio21 Institute
Parkville, Victoria, Australia

Manidipa Banerjee, Ph.D.

Christopher Baskerville, Ph.D.

Lipika Basummalick, Ph.D.

Konstantinos Beis, Ph.D.

Per Bengston, Ph.D.

Svitlana Berezhna, Ph.D.

William Henry Bisson, Ph.D.

Pilar Blancafort, Ph.D.**
University of North Carolina
Chapel Hill, North Carolina

David Boehr, Ph.D.

David Bostick, Ph.D.

Ronald M. Brudler, Ph.D.

Lintao Bu, Ph.D.

Rosa Maria Cardoso, Ph.D.

Justin E. Carlson, Ph.D.

Andrew Barry Carmel, Ph.D.

Qing Chai, M.D., Ph.D.

Brian Chapados, Ph.D.

Eli Chapman, Ph.D.

Anju Chatterji, Ph.D.

Anton Vladislavovich Cheltsov, Ph.D.

Jianhan Chen, Ph.D.

Yen-Ju Chen, Ph.D.

Zhiyong Chen, Ph.D.

Jaeyoung Cho, Ph.D.**
Hallym University
Kangwon, South Korea

Jungwoo Choe, Ph.D.

Chung Jen Chou, Ph.D.

Li-Chiou Chuang, Ph.D.

Jean-Pierre Clamme, Ph.D.

Linda Maria Columbus, Ph.D.

Adam Corper, Ph.D.

Qizhi Cui, Ph.D.

Carla P. Da Costa, Ph.D.

Douglas Daniels, Ph.D.**
Yale University
New Haven, Connecticut

Sanjib Das, Ph.D.

Paramita Dasgupta, Ph.D.**
Mayo Clinic
Rochester, Minnesota

Robert De Bruin, Ph.D.

Roberto N. De Guzman, Ph.D.**
University of Kansas
Lawrence, Kansas

Sohela De Rozieres, Ph.D.

Qingdong Deng, Ph.D.

Paula Desplats, Ph.D.

Buchi Ramachary Dhevalapally, Ph.D.**
University of Hyderabad
Hyderabad, India

Claire Louise Dovey, Ph.D.

Zhanna Druzina, Ph.D.

Li-Lin Du, Ph.D.

Theresia Dunzendorfer-Matt, Ph.D.**
Leopold Franzens Universität
Innsbruck, Austria

Scott Eberhardy, Ph.D.

Marc-Olivier Ebert, Ph.D.**
Leopold Franzens Universität
Innsbruck, Austria

Stephen Edgcomb, Ph.D.

Susanna V. Ekholm-Reed, Ph.D.Reza Mobini Farahani, Ph.D.**
Sahlgrenska University Hospital
Göteborg, Sweden

Daniel Felitsky, Ph.D.

Allan Chris Merrera Ferreon, Ph.D.

Josephine Chu Ferreon, Ph.D.

Pierre Henri Gaillard, Ph.D.

Hui Gao, Ph.D.

Elsa D. Garcin, Ph.D.

Shannon E. Gardell, Ph.D.

Edith Caroline Glazer, Ph.D.

Bettina Groschel, Ph.D.

Björn Grünenfelder, Ph.D.**
Novartis Institutes for BioMedical Research
Cambridge, Massachusetts

Fang Guo, Ph.D.

Gye Won Han, Ph.D.

Hongna Han, Ph.D.**
American BioScience, Inc.
Santa Monica, California

Shoufa Han, Ph.D.

Wenge Han, Ph.D.

Jason W. Harger, Ph.D.

Brian Henriksen, Ph.D.**
Eurogentec North America, Inc.
San Diego, California

David M. Herman, Ph.D.

Deron Herr, Ph.D.

Kenichi Hitomi, Ph.D.

Reto Horst, Ph.D.

Yunfeng Hu, Ph.D.Joy Huffman, Ph.D.**
McKinsey & Company
Los Angeles, California

Laura M. Hunsicker, Ph.D.**
Trinity University
San Antonio, Texas

Kwan Hoon Hyun, Ph.D.

Wonpil Im, Ph.D.

Tasneem Islam, Ph.D.**
University of Melbourne
Melbourne, Australia

Shuichiro Ito, Ph.D.**
Sankyo Co., Ltd.
Tokyo, Japan

Kai Jenssen, Ph.D.

Glenn C. Johns, Ph.D.

Eric C. Johnson, Ph.D.

Margaret Alice Johnson, Ph.D.

Hamid Reza Kalhor, Ph.D.††††

Christian Kannemeier, Ph.D.

Mili Kapoor, Ph.D.

Andrey Aleksandrovich Karyakin, Ph.D.

Yang Khandogin, Ph.D.

Ilja V. Khavrutskii, Ph.D.

Reza Khayat, Ph.D.

Dae Hee Kim, Ph.D.

Min Ju Kim, Ph.D.**
Genomics Institute of the Novartis Research Foundation
San Diego, California

Eda Koculi, Ph.D.

Milka Kostic, Ph.D.

Julio Kovacs, Ph.D.

Irina Kufareva, Ph.D.Shantanu Kumar, Ph.D.

Iaroslav Kuzmin, Ph.D.††††

Hugo Alfredo Lago-Zarrilli, Ph.D.††††

Bianca Lam, Ph.D.

Polo Chun Hung Lam, Ph.D.

Emma Langley, Ph.D.

Jason Lanman, Ph.D.

Jonathan C. Lansing, Ph.D.**
Momenta Pharmaceuticals
Cambridge, Massachusetts

Chang-Wook Lee, Ph.D.

Chul Won Lee, Ph.D.

Jinhyuk Lee, Ph.D.

June Hyung Lee, Ph.D.

Kelly Lee, Ph.D.

Katrina Lehmann, Ph.D.††††

Chenglong Li, Ph.D.

Vasco Liberal, Ph.D.

William M. Lindstrom, Ph.D.

Hui-Yue Christine Lo, Ph.D.

Kunheng Luo, Ph.D.

John Gately Luz, Ph.D.**
Harvard University
Boston, Massachusetts

Che Ma, Ph.D.**
Academia Sinica
Taipei, Taiwan

Ann MacLaren, Ph.D.

Laurent Magnenat, Ph.D.**
Serono Pharmaceutical Research Institute SA
Geneva, Switzerland

Darly Joseph Manayani, Ph.D.

Jeff Mandell, Ph.D.

Maria Victoria Martin-Sanchez, Ph.D.

Tsutomu Matsui, Ph.D.

Daniel McElheny, Ph.D.**
University of Chicago
Chicago, Illinois

Benoit Melchior, Ph.D.**
University of California
Riverside, California

David Metzgar, Ph.D.**
Naval Health Research Center
San Diego, California

Jonathan Mikolosko, Ph.D.

Susumu Mitsumori, Ph.D.

Heiko Michael Moeller, Ph.D.**
Universität Konstanz
Konstanz, Germany

Seongho Moon, Ph.D.

Bettina Moser, Ph.D.**
University of Illinois at Chicago
Chicago, Illinois

Samrat Mukhopadhyay, Ph.D.

Christopher Myers, Ph.D.**
Naval Health Research Center
San Diego, California

Sreenivasa Chowdari Naidu, Ph.D.**
MediVas, L.L.C.
San Diego, California

Toru M. Nakamura, Ph.D.**
University of Illinois at Chicago
Chicago, Illinois

Sujatha Narayan, Ph.D.

Hung Nguyen, Ph.D.

Tadateru Nishikawa, Ph.D.

Eishi Noguchi, Ph.D.**
Drexel University
Philadelphia, Pennsylvania

Wataru Nomura, Ph.D.

Brian Nordin, Ph.D.**
ActivX Biosciences, Inc.
La Jolla, California

Karin E. Norgard-Sumnicht, Ph.D.**
San Diego State University
San Diego, California

Brian V. Norledge, Ph.D.

Michael Oberhuber, Ph.D.**
Leopold Franzens Universität
Innsbruck, Austria

Wendy Fernandez Ochoa, Ph.D.

Amy Odegard, Ph.D.

Yoshiaki Zenmei Ohkubo, Ph.D.**
Rutgers University
Piscataway, New Jersey

Brian L. Olson, Ph.D.

Brian Paegel, Ph.D.

Covadonga Paneda, Ph.D.**
Molecular and Integrative Neurosciences Department, Scripps Research

Sandeep Patel, Ph.D.

Natasha Paul, Ph.D.**
Stratagene, Inc.
La Jolla, California

Stephanie Pebernard, Ph.D.

Suzanne Peterson, Ph.D.**
University of California
San Diego, California

Wolfgang Stefan Peti, Ph.D.**
Brown University
Providence, Rhode Island

Goran Pljevaljčić, Ph.D.

Corinne Chantal Ploix, Ph.D.**
Novartis International AG
Basel, Switzerland

Stephanie Pond, Ph.D.

Owen Pornillos, Ph.D.

Daniel Joseph Price, Ph.D.

Plachikkat Krishnan Radha, Ph.D.††††

Grazia Daniela Raffa, Ph.D.

John Reader, Ph.D.**
University of North Carolina
Chapel Hill, North Carolina

Stevens Kastrup Rehen, Ph.D.**
Universidade Federal do Rio de Janeiro
Rio de Janeiro, Brazil

Jean-Baptiste Reiser, Ph.D.**
European Synchrotron Radiation Facility
Grenoble, France

Miguel A. Rodriguez-Gabriel, Ph.D.**
Universidad Complutense de Madrid
Madrid, Spain

Stanislav Rudyak, Ph.D.

Sean Ryder, Ph.D.

Sanjay Adrian Saldanha, Ph.D.

Sanjita Sasmal, Ph.D.††††

Mika Aoyagi Scharber, Ph.D.**
Burnham Institute
La Jolla, California

Jennifer S. Scorah, Ph.D.

Pedro Serrano-Navarro, Ph.D.

Craig McLean Shepherd, Ph.D.

William Shih, Ph.D**
Dana Farber Cancer Institute
Boston, Massachusetts

David S. Shin, Ph.D.

Develeena Shivakumar, Ph.D.Holly Heaslet Soutter, Ph.D.

Natalie Spielewoy, Ph.D.**
Weatherall Institute of Molecular Medicine
Oxford, England

Greg Springsteen, Ph.D.

Deborah J. Stauber, Ph.D.**
Novartis Institutes for BioMedical Research
Cambridge, Massachusetts

Derek Steiner, Ph.D.**
Johnson & Johnson
San Diego, California

Gudrun Stengel, Ph.D.

Daniel Stoffler, Ph.D.**
Universität Basel
Basel, Switzerland

Kenji Sugase, Ph.D.

Vidyasankar Sundaresan, Ph.D.**
GE Infrastructure
Trevose, Pennsylvania

Magnus Sundstrom, Ph.D.

Jeff Suri, Ph.D.**
GluMetrics, Inc.
Long Beach, California

Blair R. Szymczyna, Ph.D.

Florence Muriel Tama, Ph.D.

Jinghua Tang, Ph.D.**
University of California
San Diego, California

Nardos Tassew, Ph.D.

Hiroaki Tateno, Ph.D.

Michela Taufer, Ph.D.**
University of Texas
El Paso, Texas

Ewan Richardson Taylor, Ph.D.

Donato Tedesco, Ph.D.**
Berlex Biosciences
Richmond, California

Hua Tian, Ph.D.

Rhonda Torres, Ph.D.**
Merck & Co.
Rahway, New jersey

Megan Wright Trevathan, Ph.D.**
Harvard Medical School
Boston, Massachusetts

Ulrich Ignaz Tschulena, Ph.D.

Julie L. Tubbs, Ph.D.

Naoto Utsumi, Ph.D.

Frank van Drogen, Ph.D.

Philip Arno Venter, Ph.D.

Petra Verdino, Ph.D.

Stefan Vetter, Ph.D.**
Florida Atlantic University
Boca Raton, Florida

William Frederick Waas, Ph.D.

Shun-ichi Wada, Ph.D.

Ross Walker, Ph.D.

Robert Scott Williams, Ph.D.

Raphaelle Winsky-Sommerer, Ph.D.**
Universität Zürich
Zürich, Switzerland

Eric L. Wise, Ph.D.

Jonathan Wojciak, Ph.D.

Dennis Wolan, Ph.D.**
Sunesis Pharmaceuticals, Inc.
South San Francisco, California

Hyung Sik Won, Ph.D.**
Konkuk University
Chungju, Korea

Timothy I. Wood, Ph.D.

Eugene Wu, Ph.D.Lan Xu, Ph.D.

Yoshiki Yamada, Ph.D.

Atsushi Yamagata, Ph.D.

Qi Yan, Ph.D.

Yong Yao, Ph.D.

Xiaoqin Ye, M.D., Ph.D.

Yongjun Ye, Ph.D.

Yong Yin, Ph.D.

Veronica Yu, Ph.D.

Yuan Yuan, Ph.D.

Markus Zeeb, Ph.D.

Ying Zeng, Ph.D.

Haile Zhang, Ph.D.

Yong Zhao, Ph.D.

Peizhi Zhu, Ph.D.
 

SCIENTIFIC ASSOCIATES

Enrique Abola, Ph.D.

Andrew S. Arvai, M.S.

Eric Birgbauer, Ph.D.

Ognian V. Bohorov, Ph.D.

Dennis Carlton, B.S.

Ellen Yu-Lin Tsai Chien, Ph.D.

Xiaoping Dai, Ph.D.

Liliane Dickinson, Ph.D.††††

Michael Allen Hanson, Ph.D.

Diane Marie Kubitz, B.A.

Marcy A. Kingsbury, Ph.D.

Rolf Mueller, Ph.D.Padmaja Natarajan, Ph.D.

Marianne Patch, Ph.D.

Gabriela Perez-Alvarado, Ph.D.

Nicholas Preece, Ph.D.

Lin Wang, Ph.D.
 

Visiting Investigators

Stephen J. Benkovic, Ph.D.
Pennsylvania State University
University Park, Pennsylvania

Astrid Graslund, Ph.D.
Stockholm University
Stockholm, Sweden

Arne Holmgren, M.D., Ph.D.
Karolinska Institutet
Stockholm, Sweden

Barry Honig, Ph.D.
Columbia University
New York, New York

Arthur Horwich, M.D.
Yale University
New Haven, Connecticut

Tai-huang Huang, Ph.D.
Academica Sinica
Taipei, Taiwan

Robert D. Rosenstein, Ph.D.
Lawrence Berkeley National Laboratory
Berkeley, California

* Joint appointment in The Skaggs Institute for Chemical Biology
** Appointment completed; new location shown
*** Joint appointment in the Molecular and Integrative Neurosciences Department
**** Joint appointments in the Department of Immunology and The Skaggs Institute for Chemical Biology
***** Joint appointments in the Department of Chemistry and The Skaggs Institute for Chemical Biology
Joint appointment in the Department of Cell Biology
†† Joint appointment in the Department of Molecular and Experimental Medicine
††† Joint appointment in the Department of Chemistry
†††† Appointment completed

 


Toll-like receptors (TLRs) recognize various pathogen-associated molecules and play an important role in innate immune responses. The human TLR3 recognizes double-stranded RNA from viruses and initiates an intracellular signaling pathway through the interaction of TIR domains of TLR3 and the adaptor molecule TRIF. The proposed dimer of the TLR3 ectodomain is displayed on the membrane surface with double-stranded RNA from viruses. The crystal structure was determined by Jungwoo Choe, Ph.D., in the laboratory of Ian A. Wilson, D.Phil.