Molecular Biophysics Faculty

Timothy Baker
Department of Chemistry and Biochemistry
The Baker Research Group
tsb@ucsd.edu
Biochemistry, macromolecular, cryoelectron microscopy and three-dimensional, image-reconstruction technique.

Philip E. Bourne
Department of Pharmacology
bourne@sdsc.edu
Bioinformatics with interests that are both biological and engineering based. Biological interests include apoptosis, signal transduction, and protein structure prediction. Engineering interests include data models, query languages, and scientific visualization.

Senyon Choe
Dept. of Chemistry and Biochemistry
Dr. Senyon Choe Research Group
choe@salk.edu
Structural studies of molecular assembly and recognition of biological macromolecules. Current focus is to understand the mechanisms of potassium channels and transmembrane signaling receptors.

Seth Cohen
Department of Chemistry and Biochemistry
The Cohen Research Group
scohen@ucsd.edu
Bioinorganic and coordination chemistry. Metalloregulatory proteins, zinc proteinase inhibitors, and supramolecular materials.

Olga Dudko
Department of Physics
dudko@physics.ucsd.edu

Gourisankar Ghosh
Department of Chemistry and Biochemistry
gghosh@ucsd.edu
1) Understanding the mechanisms of the activation of a transcription factor known as nuclear factor kappa B (NF-kB) to know how activated NF-kB in turn regulate the expression of a variety of gene essential for cellular defense mechanism and apoptosis.
2) Understanding the nucleo-cytoplasmic shuttling of a yeast protein Np13 and Np13-mediated transport of mRNA to the cytoplasm.

Partho Ghosh
Department of Chemistry and Biochemistry
Partho Ghosh Research Group
pghosh@ucsd.edu
Structural and functional nature of macromolecular interactions between bacterial or protozoan pathogens and their mammalian hosts. Using techniques of biochemistry and X-ray crystallography to understand the mechanism of action of pathogen proteins on host cell targets.

Tracy Handel
Department of Pharmacology
thandel@ucsd.edu
Molecular biophysics: Structure and function of chemokines, cytokines, and viral proteins that interfre with the host immune system. Compuational protein design and engineering.

Jeff Hasty
Department of Bioengineering
Systems Biodynamics Lab
jmhasty@ucsd.edu
Computational genomics and the dynamics of gene regulatory networks; dissection and analysis of the complex dynamical interactions involved in the gene regulation.

Terence Hwa
Department of Physics
Laboratory for Statistical Biophysics
thwa@ucsd.edu
Quantitative biology: connecting molecular aspects of transcription and signaling to functional properties of enzymatic and genetic networks; directed evolution of molecular control systems.

Patricia A. Jennings
Department of Chemistry and Biochemistry
pajennings@ucsd.edu
Protein folding, structure and dynamics intimately linked with the biological activity of a system; utilizing a battery of biophysical techniques including optical and NMR spectroscopies to address the factors involved in receptor binding, kinase anchoring and organization of active sites.

Jack Johnson
The Scripps Research Institute
Structural Virology Lab
jjackj@scripps.edu
Structure and mechanism of virus assembly, maturation and infection. Using x-ray crystallography, cryo electron microscopy, a variety of spectroscopic and physical methods as well as molecular and cell biology to relate the genotype (which we can readily manipulate in many viruses) to phenotypes that are readily characterized by biophysical methods.

Tracy Johnson
Division of Biological Sciences
tljohnson@ucsd.edu
Biochemistry: The dynamics of macromolecular machines in gene expression (pre-mRNA splicing, transcription, chromatin modification).

Elizabeth A. Komives
Department of Chemistry and Biochemistry
The Komives Lab
ekomives@ucsd.edu
The biophysical parameters that govern extracellular protein-protein interactions are studied using NMR, Surface plasmon resonance, and amide H/D exchange mass spectrometry. Systems of particular interest include the thrombin-thrombomodulin interaction and the LDL receptor-related protein.

J. Andrew McCammon
Department of Chemistry and Biochemistry
The McCammon Research Group
jmccammon@ucsd.edu
Statistical mechanics of macromolecules and liquids; theory of protein and nucleic acid structure and function; development and application of computer models and simulation methods for molecular systems.

Ulrich Müller
Department of Chemistry and Biochemistry
ufmuller@ucsd.edu
Design and in vitro evolution of catalytic RNAs, to understand and improve their function. Two types of reactions are studied: RNA polymerization and RNA splicing. RNA polymerization is studied with the aim of learning about possible origins of life, an RNA world. RNA splicing is studied with the aim of developing a therapeutic RNA that can repair mutated mRNAs.

Joseph P. Noel
The Salk Institute
noel@salk.edu
Structural and Functional Analysis of Natural Product Biosynthetic Enzymes and Signal Transduction Cascades.

Melvin Y. Okamura
Department of Physics
mokamura@physics.ucsd.edu
Structure and function of the bacterial reaction center (RC), the membrane protein responsible for conversion of light energy into chemical energy in photosynthetic bacteria. The coupling of electron transfer to proton pumping by a quinone molecule in the RC and the docking and electron transfer reactions of a cytochrome c2 molecule on to the suface of RC using site directed mutagenesis, kinetics, magnetic resonance spectroscopy, x-ray crystallography and computational methods.

Jose N. Onuchic
Department of Physics
jonuchic@ucsd.edu
Theoretical and computational aspects of molecular biophysics. Focusing on electron transfer in proteins and on the protein folding problem.

Stanley J. Opella
Department of Chemistry and Biochemistry
Center for NMR Spectroscopy and Imaging of Proteins
sopella@ucsd.edu
We develop and apply NMR spectroscopy for structural studies of proteins. We are particularly interested in membrane proteins; the approach we are developing as part of our investigations of Vpu from HIV-1 and other channel-forming proteins is generally applicable to membrane proteins in erythrocytes and other mammalian systems. Further, the heme group offers a mechanism for weakly or completely aligning proteins in magnetic fields, an important area of spectroscopic research.

Julian I. Schroeder
Division of Biological Sciences
Julian Schroder's Laboratory
julian@biomail.ucsd.edu
Structure function, regulation and physiology of Arabidopsis guard cell ion channels. Arabidopsis metal transporters are being analyzed using mutant selection in yeast followed by biophysical characterizations in heterolous expression systems and in vivo.

Douglas E. Smith
Department of Physics
des@physics.ucsd.edu
Manipulation and visualization of single DNA molecules using optical tweezers and fluorescence microscopy. Study molecular motors involved in viral DNA packaging and ATP dependent chromatin assembly. Single molecule confocal microscopy and FRET applied to study polypeptide conformation and aggregation. Polymer physics experiments with single DNA molecules.

Palmer Taylor
Department of Pharmacology
Dr. Palmer Taylor's Research Group
pwtaylor@ucsd.edu
Structure and function of receptors and enzymes involved in neurotransmission. The study of functional coupling of receptors to cellular responses specificity of ligand recognition by acetylcholine receptors and acetylcholinesterase, and the structures of cholinesterases and nicotine acetylcholine receptors, as well as, the regulation of expression of the genes encoding these proteins during differentiation and synaptogenesis in neurons, skeletal muscle, and hematopoietic cells.

Lynn F. Ten Eyck
Department of Pharmacology, San Diego Supercomputer Center
teneyckl@sdsc.edu
Macromolecular structure and interactions, with a particular emphasis on new methods for x-ray crystallography, molecular docking and the analysis of conformational changes.

Akif F. Tezcan
Department of Chemistry and Biochemistry
tezcan@ucsd.edu
Bioinorgnic and biophysical chemistry; structural and mechanistic studies of enzymes involved in redox chemistry and mtallocofactor biosynthesis.

Yitzhak Tor
Department of Chemistry and Biochemistry
The Tor Research Group
ytor@chem.ucsd.edu
RNA-small molecule interactions, RNA-protein recognition, photophysical processes in modified nucleic acids and metal-containing biopolymers.

Roger Y. Tsien
Department of Chemistry and Biochemistry
Tsien Research Group
rtsien@ucsd.edu
Cellular and neurobiological signal transduction using small molecules and macromolecules designed to monitor or perturb key biochemical processes.

Peter G. Wolynes
Department of Chemistry and Biochemistry
Wolynes Research Group
pwolynes@ucsd.edu
A major interest of my group is the energy landscape theory of protein folding and its application to developing structure prediction algorithms. I am also interested in the statistical mechanics of gene regulatory networks.



	Steering Committee Dr. Susan S. Taylor -- Co-P.I. Dr. J. Andrew McCammon -- Co-P.I. Dr. Partho Ghosh -- Member Dr. Elizabeth A. Komives -- Member Dr. Jose Onuchic -- Member Dr. Tracy Johnson – Member Byron Hetrick – Student Member
	Participating Faculty Members The participating faculty are drawn from the Departments of Chemistry and Biochemistry, Biology, Physics, Pharmacology, Cellular & Molecular Medicine, and Bioengineering as well as from The Scripps Research Institute as well as the Salk Institute, and reflect a wide diversity of research interests and expertise. Brief descriptions of the research areas represented by individual faculty members are summarized below.
	Guarav Arya Department of Nanoengineering garya@ucsd.edu Timothy Baker Department of Chemistry and Biochemistry The Baker Research Group tsb@ucsd.edu Biochemistry, macromolecular, cryoelectron microscopy and three-dimensional, image-reconstruction technique. Philip E. Bourne Department of Pharmacology bourne@sdsc.edu Bioinformatics with interests that are both biological and engineering based. Biological interests include apoptosis, signal transduction, and protein structure prediction. Engineering interests include data models, query languages, and scientific visualization. Senyon Choe Dept. of Chemistry and Biochemistry Dr. Senyon Choe Research Group choe@salk.edu Structural studies of molecular assembly and recognition of biological macromolecules. Current focus is to understand the mechanisms of potassium channels and transmembrane signaling receptors. Seth Cohen Department of Chemistry and Biochemistry The Cohen Research Group scohen@ucsd.edu Bioinorganic and coordination chemistry. Metalloregulatory proteins, zinc proteinase inhibitors, and supramolecular materials. Jack Dixon Department of Pharmacology The Dixon Research Group jedixon@ucsd.edu Protein Tyrosine Phosphatases (PTPases). Pieter Dorrestein Department of Chemistry and Biochemistry The Dorrestein Lab pdorrestein@ucsd.edu Olga Dudko Department of Physics dudko@physics.ucsd.edu Gourisankar Ghosh Department of Chemistry and Biochemistry gghosh@ucsd.edu 1) Understanding the mechanisms of the activation of a transcription factor known as nuclear factor kappa B (NF-kB) to know how activated NF-kB in turn regulate the expression of a variety of gene essential for cellular defense mechanism and apoptosis. 2) Understanding the nucleo-cytoplasmic shuttling of a yeast protein Np13 and Np13-mediated transport of mRNA to the cytoplasm. Partho Ghosh Department of Chemistry and Biochemistry Partho Ghosh Research Group pghosh@ucsd.edu Structural and functional nature of macromolecular interactions between bacterial or protozoan pathogens and their mammalian hosts. Using techniques of biochemistry and X-ray crystallography to understand the mechanism of action of pathogen proteins on host cell targets. Tracy Handel Department of Pharmacology thandel@ucsd.edu Molecular biophysics: Structure and function of chemokines, cytokines, and viral proteins that interfre with the host immune system. Compuational protein design and engineering. Jeff Hasty Department of Bioengineering Systems Biodynamics Lab jmhasty@ucsd.edu Computational genomics and the dynamics of gene regulatory networks; dissection and analysis of the complex dynamical interactions involved in the gene regulation. Alexander Hoffmann Department of Chemistry and Biochemistry Signaling Systems Laboratory ahoffmann@ucsd.edu Biochemistry: signaling, transcription, computational network, stress and immune responses, apoptosis, proliferation. Terence Hwa Department of Physics Laboratory for Statistical Biophysics thwa@ucsd.edu Quantitative biology: connecting molecular aspects of transcription and signaling to functional properties of enzymatic and genetic networks; directed evolution of molecular control systems. Trey Ideker Department of Bioengineering Laboratoryfor Integrative Network Biology tideker@ucsd.edu Develop large-scale, computer-aided models of biological signaling and regulatory pathways. Patricia A. Jennings Department of Chemistry and Biochemistry pajennings@ucsd.edu Protein folding, structure and dynamics intimately linked with the biological activity of a system; utilizing a battery of biophysical techniques including optical and NMR spectroscopies to address the factors involved in receptor binding, kinase anchoring and organization of active sites. Jack Johnson The Scripps Research Institute Structural Virology Lab jjackj@scripps.edu Structure and mechanism of virus assembly, maturation and infection. Using x-ray crystallography, cryo electron microscopy, a variety of spectroscopic and physical methods as well as molecular and cell biology to relate the genotype (which we can readily manipulate in many viruses) to phenotypes that are readily characterized by biophysical methods. Tracy Johnson Division of Biological Sciences tljohnson@ucsd.edu Biochemistry: The dynamics of macromolecular machines in gene expression (pre-mRNA splicing, transcription, chromatin modification). Simpson Joseph Department of Chemistry and Biochemistry The Simpson Joseph Research Group sjoseph@chem.ucsd.edu Understanding the molecular mechanism of protein synthesis and the effect of antibiotics that inhibit this process. Judy Kim Department of Chemistry and Biochemistry Kim Research Group judyk@chem.ucsd.edu Biophysical chemistry; spectroscopic studies of membrane protein folding and dynamics. Elizabeth A. Komives Department of Chemistry and Biochemistry The Komives Lab ekomives@ucsd.edu The biophysical parameters that govern extracellular protein-protein interactions are studied using NMR, Surface plasmon resonance, and amide H/D exchange mass spectrometry. Systems of particular interest include the thrombin-thrombomodulin interaction and the LDL receptor-related protein. J. Andrew McCammon Department of Chemistry and Biochemistry The McCammon Research Group jmccammon@ucsd.edu Statistical mechanics of macromolecules and liquids; theory of protein and nucleic acid structure and function; development and application of computer models and simulation methods for molecular systems. Mauricio Montal Division of Biological Sciences montal@biomail.ucsd.edu Structure and function of channel proteins. Ulrich Müller Department of Chemistry and Biochemistry ufmuller@ucsd.edu Design and in vitro evolution of catalytic RNAs, to understand and improve their function. Two types of reactions are studied: RNA polymerization and RNA splicing. RNA polymerization is studied with the aim of learning about possible origins of life, an RNA world. RNA splicing is studied with the aim of developing a therapeutic RNA that can repair mutated mRNAs. Terunaga Nakagawa Department of Chemistry and Biochemistry nakagawa@ucsd.edu Molecular mechanism of synaptic plasticity. Alexandra C. Newton Department of Pharmacology The Newton Lab anewton@ucsd.edu Structure, function, and regulation of protein kinase C, a key signal transducer. Joseph P. Noel The Salk Institute noel@salk.edu Structural and Functional Analysis of Natural Product Biosynthetic Enzymes and Signal Transduction Cascades. Melvin Y. Okamura Department of Physics mokamura@physics.ucsd.edu Structure and function of the bacterial reaction center (RC), the membrane protein responsible for conversion of light energy into chemical energy in photosynthetic bacteria. The coupling of electron transfer to proton pumping by a quinone molecule in the RC and the docking and electron transfer reactions of a cytochrome c2 molecule on to the suface of RC using site directed mutagenesis, kinetics, magnetic resonance spectroscopy, x-ray crystallography and computational methods. Jose N. Onuchic Department of Physics jonuchic@ucsd.edu Theoretical and computational aspects of molecular biophysics. Focusing on electron transfer in proteins and on the protein folding problem. Stanley J. Opella Department of Chemistry and Biochemistry Center for NMR Spectroscopy and Imaging of Proteins sopella@ucsd.edu We develop and apply NMR spectroscopy for structural studies of proteins. We are particularly interested in membrane proteins; the approach we are developing as part of our investigations of Vpu from HIV-1 and other channel-forming proteins is generally applicable to membrane proteins in erythrocytes and other mammalian systems. Further, the heme group offers a mechanism for weakly or completely aligning proteins in magnetic fields, an important area of spectroscopic research. Julian I. Schroeder Division of Biological Sciences Julian Schroder's Laboratory julian@biomail.ucsd.edu Structure function, regulation and physiology of Arabidopsis guard cell ion channels. Arabidopsis metal transporters are being analyzed using mutant selection in yeast followed by biophysical characterizations in heterolous expression systems and in vivo. Douglas E. Smith Department of Physics des@physics.ucsd.edu Manipulation and visualization of single DNA molecules using optical tweezers and fluorescence microscopy. Study molecular motors involved in viral DNA packaging and ATP dependent chromatin assembly. Single molecule confocal microscopy and FRET applied to study polypeptide conformation and aggregation. Polymer physics experiments with single DNA molecules. Palmer Taylor Department of Pharmacology Dr. Palmer Taylor's Research Group pwtaylor@ucsd.edu Structure and function of receptors and enzymes involved in neurotransmission. The study of functional coupling of receptors to cellular responses specificity of ligand recognition by acetylcholine receptors and acetylcholinesterase, and the structures of cholinesterases and nicotine acetylcholine receptors, as well as, the regulation of expression of the genes encoding these proteins during differentiation and synaptogenesis in neurons, skeletal muscle, and hematopoietic cells. Susan S. Taylor Department of Chemistry and Biochemistry Susan Taylor's Lab Homepage staylor@ucsd.edu The structure and function of protein kinases, specifically of cAMP-dependent protein kinase (PKA). Lynn F. Ten Eyck Department of Pharmacology, San Diego Supercomputer Center teneyckl@sdsc.edu Macromolecular structure and interactions, with a particular emphasis on new methods for x-ray crystallography, molecular docking and the analysis of conformational changes. Akif F. Tezcan Department of Chemistry and Biochemistry tezcan@ucsd.edu Bioinorgnic and biophysical chemistry; structural and mechanistic studies of enzymes involved in redox chemistry and mtallocofactor biosynthesis. Yitzhak Tor Department of Chemistry and Biochemistry The Tor Research Group ytor@chem.ucsd.edu RNA-small molecule interactions, RNA-protein recognition, photophysical processes in modified nucleic acids and metal-containing biopolymers. Roger Y. Tsien Department of Chemistry and Biochemistry Tsien Research Group rtsien@ucsd.edu Cellular and neurobiological signal transduction using small molecules and macromolecules designed to monitor or perturb key biochemical processes. Hector Viadu Department of Chemistry and Biochemistry viadiu@ucsd.edu Wei Wang Dept. of Chemistry and Biochemistry Wei Wang Research Group wwang@chem.ucsd.edu Inference of gene regulatory networks and determination of protein specificity. Leor Weinberger Department of Chemistry and Biochemistry lsw@ucsd.edu Peter G. Wolynes Department of Chemistry and Biochemistry Wolynes Research Group pwolynes@ucsd.edu A major interest of my group is the energy landscape theory of protein folding and its application to developing structure prediction algorithms. I am also interested in the statistical mechanics of gene regulatory networks.