Structural Biology & Molecular Biophysics Graduate Training Program
The UCI Structural Biology & Molecular
Biophysics Graduate Training Program is part of a large, multidisciplinary
Graduate Program in Molecular Biology, Genetics, and Biochemistry in the
Available state-of-the-art instrumentation for structural biology and molecular biophysics includes a Rigaku R-Axis IV imaging plate area detector with mirror optics, a Siemens X-1000 multi-wire detector with mirror optics, 800 MHz NMR spectrometer, SGI 3D-graphics workstations and servers, DEC Alpha workstations and servers, access to a local HP/Convex Exemplar SPP2000 with 16 CPUs (HP PA-8000) with 2 GB main memory, as well as other computational resources. Further instrumentation includes atomic force microscopy (AFM), dynamic light scattering (DLS), a Jasco J-720 circular dichroism spectropolarimeter, MSC titration calorimeter, and Microcal VP-DSC scanning calorimeter.
Structural Biology & Molecular Biophysics Curriculum
Required Concentration Core Courses (4):
|
MB 204 |
Structure and Function of Proteins |
|
MB 203 |
Structure and Biosynthesis of Nucleic Acids |
|
DB 231B |
Cell Biology OR |
|
DB 231D |
Molecular, Cellular, and Developmental Neurobiology |
|
MB 206 |
Regulation of Gene Expression OR |
|
MB 207 |
Advanced Molecular Genetics OR |
|
DB 210 |
Advanced Developmental Genetics |
Elective Courses:
|
CHM218 |
Metallobiochemistry |
|
MBB211 |
Magnetic Resonance in Biology |
|
MBB223 |
Introduction to Computational Biology |
|
MBB240 |
Macromolecular Structure, Function, and Interaction |
|
MBB254 / PB211 |
Protein Crystallography |
|
PHY147 |
Physics Principles in Biology and Medicine |
|
PB204 |
Concepts of Biophysics |
|
PB205 |
Electronics for Biologists |
|
PB232 |
Physiology of Ion Channels |
|
PB261 |
Protein Stability and Structure |
|
PB271 A, B |
Molecular Physiology and Disease |
|
|
plus various "journal club" literature classes |
For descriptions of elective courses, see below.
Structural Biology & Molecular Biophysics Faculty
Track coordinator - Melanie Cocco, +
Molecular Biophysics:
Agnes
Henschen-Edman, + M.D./Ph.D.,
Professor of Molecular Biology & Biochemistry
Protein structure and function studies on fibrinogen, a
blood coagulation protein
Lan
Huang, + Ph.D., Assistant Professor of
Physiology & Biophysics and Developmental & Cell Biology
Proteomics analysis using mass spectrometry and
bioinformatics to elucidate protein structure and function, with initial
emphasis on the 26S proteasome functional spcificity
Paul Gershon, + Ph.D., Professor of Molecular
Biology & Biochemistry
Mechanistic and structural characterization of vaccinia viral proteins, with an emphasis on specific mRNA
synthetic and modification enzymes, using mass spectroscopy, atomic force
microscopy and crystallography
Ray
Luo, + Ph.D., Assistant Professor of Molecular
Biology & Biochemistry
Computational biochemistry; protein structure prediction
and folding mechanisms, protein-protein and protein-ligand
interactions; simulation methodologies for computational biology and chemistry
Hamid
M. Said , + Ph.D., Professor of Medicine and
Physiology & Biophysics
Cellular and molecular aspects of intestinal transport of
water-soluble vitamins
Donald
F. Senear, + Ph.D., Professor of Molecular
Biology & Biochemistry
Interactions of proteins and DNA in transcriptional
regulation using biophysical, chemical and molecular biological approaches
Structural Biology:
Melanie
Cocco, + Ph.D., Assistant Professor of
Molecular Biology & Biochemistry
Conformations and dynamics of soluble DNA-binding
proteins and development of new strategies to study membrane protein structures
using NMR spectroscopy and other biophysical techniques; projects involve
understanding cancer and repair of CNS damage
Celia
Goulding, + Ph.D., Professor of Molecular
Biology & Biochemistry
Structural and biochemical studies of
molecular assemblies in Mycobacterium tuberculosis
Frances
A. Jurnak, + Ph.D., Professor of Physiology &
Biophysics
Macromolecular crystallography of cancer-related
proteins, EF-Tu-antibiotics, and pectate
lyases; rational drug design and development of micro
devices for gene cloning and expression
Janos K. Lanyi, + Ph.D., Professor of Physiology &
Biophysics and Microbiology & Molecular Genetics
Structure and function in rhodopsins
using structural, spectroscopic, and genetic engineering techniques
Hartmut "Hudel"
Luecke, + Ph.D., Professor of Molecular Biology
& Biochemistry, Physiology & Biophysics and Chemistry
Biochemistry and macromolecular crystallography of
membrane proteins, structure-based drug design on cancer; angiogenesis and
immunological targets
Rachel
Martin, + Ph.D., Professor of Molecular
Biology & Biochemistry
Solid state NMR spectroscopy of proteins
Alexander
McPherson, + Ph.D., Professor of Molecular
Biology & Biochemistry and Physiology & Biophysics
Microgravity research on macromolecular crystal growth;
x-ray diffraction analysis of protein, nucleic acid, and virus crystals; atomic
force microscopy studies of biological structures
Thomas
L. Poulos, + Ph.D., Professor of Molecular Biology
& Biochemistry and Physiology & Biophysics
Protein engineering and crystallography on heme containing enzymes and related redox
proteins, including nitric oxide synthase, cytochrome P450 and peroxidases
Markus
Ribbe, + Ph.D., Professor of Molecular Biology
& Biochemistry
Assembly & function of Metalloproteins
Sheryl
Tsai, + Ph.D., Assistant Professor of
Molecular Biology & Biochemistry
Structure, function and drug design of protein complexes
that (1) make pharmaceutically important natural products and (2) are targeted
as therapeutics for cancer, obesity and infectious disease
Larry E.
Vickery, + Ph.D., Professor of Physiology
& Biophysics
Molecular chaperones in protein folding and assembly
using structural and genetic engineering techniques
Ion Channels:
Michael
D. Cahalan, + Ph.D., Professor of Physiology
& Biophysics
Calcium and potassium channels in the immune system
K. George Chandy, + M.D./Ph.D.,
Professor of Physiology & Biophysics and Microbiology & Molecular Genetics
Molecular biology and structure of potassium ion channels
in T-lymphocytes and other ion channels which serve as targets for the design
of novel immunosuppressive agents
Harry T. Haigler, + Ph.D., Professor of Physiology
& Biophysics
Mechanisms of growth factor signal transduction and annexin calcium-binding proteins
James E. Hall,
+
Ph.D., Professor of Physiology & Biophysics
Biophysics of membrane channels, including gap junctions,
water channels and junctional channels
Janos K. Lanyi, + Ph.D., Professor of Physiology &
Biophysics and Microbiology & Molecular Genetics
Structure and function in rhodopsins
using structural, spectroscopic, and genetic engineering techniques
Hartmut "Hudel"
Luecke, + Ph.D., Assistant Professor of
Molecular Biology & Biochemistry, Physiology & Biophysics, and Computer
Science
Biochemistry and macromolecular crystallography of
membrane-associated proteins; structure-based drug design on cancer,
angiogenesis and immunological targets
Stephen H. White, +
Ph.D., Professor of Physiology & Biophysics
Membrane protein folding and stability; energetics of protein-bilayer
interactions; structure of fluid lipid bilayers;
experimental hydrophobicity scales; antimicrobial
peptides; global statistics of protein sequences
Elective Course Descriptions
CHM218 - Metallobiochemistry
A review of the biochemistry of metallic elements emphasizing methods for
studying metals in biological systems; the chemical basis for nature's exploitation
of specific elements; structures of active sites' mechanisms; solid-state
structures and devices' metals in medicine.
MBB211 - Magnetic Resonance in Biology
Basic principles of magnetic resonance. Survey of applications in biology
including: protein and nucleic acid structure determination and dynamics,
electron paramagnetic resonance and magnetic resonance imaging.
MBB223
- Introduction to Computational Biology
The use of theories and methods based on computer science, mathematics, and
physics in molecular biology and biochemistry. Basics in biomolecular modeling. Analysis of
sequence, structural data and function of biomolecules.
MBB240 -
Macromolecular Structure, Function, and Interaction
Chemistry of macromolecules with emphasis on proteins. Properties of
proteins, forces that maintain protein structure, structure/function
relationships, interactions with ligands and other
macromolecules, and experimental methods to study structure, function, and
interactions.
MBB254 / PB211 - Protein Crystallography
Course introduces students to the theory and practice of macromolecular
crystallography. Course covers all aspects, including protein crystallization,
space groups, phasing methods, electron density map interpretation, refinement
and preparation of results for publication.
PHY147 - Physics
Principles in Biology and Medicine
Physical principles in biology and medicine with examples from physiology and
medical diagnostics and therapeutics. A: Principles of imaging. B:
Ionizing radiation, radiology and nuclear medicine, magnetism and MRI,
acoustics and ultrasound. C: Biophysics of light, thermal and microwave
radiations, hydrodynamics, bioelectricity, biomagnetism
and electrophysiology.
PB204 - Concepts of
Biophysics
Crystallography; introduction to time-resolved absorption and fluorescence
spectroscopy; concepts of kinetic order and kinetic rate theory.
PB205 - Electronics for Biologists
Basic principles of electricity; properties and use of discrete components and
integrated circuits; circuit analysis and design. Intended
for advanced students in the life sciences.
PB232 - Physiology of Ion Channels
An introductory course on the roles ion channels play
in important cellular processes such as nerve conduction, synaptic
transmission, cell signaling, gene regulation and cell-cell communication.
Demonstrations include patch clamp recording, reconstitution of channels in
lipid bilayers and analysis of single channel
properties. Intended for students interested in cell biology,
protein structure and neurophysiology.
PB261 - Protein
Stability and Structure
Fundamental biophysical principles of the folding and structure of proteins in
aqueous and membrane environments. Analysis of key papers concerned with
general structural features of proteins, protein folding, and protein structure
prediction.
PB271 A, B - Molecular Physiology and
Disease
Introduces students to concepts of molecular physiology and pharmacology
related directly to human diseases.
Examples of Interdisciplinary Research Opportunities
- Cancer-related proteins
- Mn/CAIX antigen overexpressed in cervical and renal cancer and hypoxic tumors
- Soluble type II TGF beta receptor overexpressed in pancreatic cancer
- Wnt signaling pathway proteins in colon cancer
- Glypican I protein overexpressed in pancreatic and breast cancer
- Nitric oxide synthase
Virology Organized Research Unit and Viral Structural Genomics:
- Vaccinia viral proteins
- HIV integrase
- Poliovirus polypeptide 3 CD
- Jaagsiekte sheep retrovirus proteins as model for lung cancer
- Herpes simplex ICP27, an inhibitor of host cell splicing of RNA transcripts
- Viral capsid proteins for particle assembly
Center for Interdisciplinary Chemical Synthesis:
- Inhibitors of iNOS
- Phage display selection of polypeptide inhibitors
Center for Proteomics Technology (In Development):
- Miniaturized integrated devices for single cell proteomics
- Microchips for protein crystallization
- Microplatforms for gene cloning and expression