Working at the interface of biophysics and structural biology, MCB faculty seek to understand the fundamental principles governing protein and cellular functions as well as design principles that can be exploited for synthetic biology and next generation therapeutics.
Area Directors
Area Directors help advise students about classes and rotations in their interest area. They also provide a listing of suggested courses for those interested in Biophysical and Structural Biology.
Faculty Area Directors
- Yasuhiro Arimura, Fred Hutch Basic Sciences (yarimura@fredhutch.org)
- Gaurav Bhardwaj, UW Medical Chemistry (gauravb@uw.edu)
Student Area Directors
- Elizabeth Martinez, Lee Lab (ejm45@uw.edu)
- Juliana Young, Stoddard Lab (jyoung6@uw.edu)
Suggested Curriculum
The suggested curriculum outlined below is meant to guide you in choosing classes, they are not requirements. We highly encourage you to take the Foundational courses, while the Electives are more specialized and often cross between Areas of Interest. Remember to review the UW Time Schedule for the most accurate and up-to-date information regarding whether a course is currently being offered.
2024-2025 Suggested Curriculum (document download)
BIOC 530 – Introduction to Structural Biology
Graduate-level discussion of the structure, function, and chemistry of proteins, control of enzymatic reactions. Prerequisite:a comprehensive course in biochemistry and permission.
Offered AUT, 3.0 credits, Weeks 1-10. Course not currently being offered
MCB 536 – Tools for Computational Biology
Introduction to established best practices in computational biology. Learn to organize unstructured data into standard formats, transform data for statistical analyses, and visualize the transformed data. Learn workflows for reproducible research such as version control, project organization, and code documentation. Gain basic experience with Linux command line tools and the Python and R programming languages. Classes will involve hands-on learning through coding exercises, collaborative problem solving, and extensive use of online learning resources.
Offered AUT, 3.0 credits, Weeks 1-10, every year. Will be offered in AUT 2025
BIOEN 588 – Computational Protein Design
Explores methods in protein engineering, emphasizing biomedical and biotechnological applications. Includes molecular visualization, homology modeling, molecular dynamics, computational protein design, and evaluation of designs. Introduces current research in subject area. Students learn to use and apply computational tools to investigate design problems.
Offered WIN, 4.0 credits, Weeks 1-10, every year. Will be offered in WIN 2025
CONJ 544 – Protein Structure, Modification and Regulation
Overview of general principles of protein structure, including forces that contribute to folding and stabilization, followed by an extended coverage of the means by which protein structure and function are modified and regulated. Examples from recent developments in protein folding, processing, and allosteric regulation. Prerequisite: Introductory biochemistry and cell biology.
Offered WIN, 1.5 credits, Weeks 1-5. Will be offered in WIN 2025
MEDCH 553 – Structure and Function of Macromolecular Protein Assemblies
Discussion of research strategies, methods, and current literature concerning macromolecular self-assembly processes and protein-protein interactions as they relate to biological specificity. Emphasis on experimental approaches used in current literature. Prerequisite: permission of instructor.
Offered AUT/WIN/SPR/SUM, 3.0 credits. Will be offered in WIN 2025
MEDCH 554 – Biophysical & Structural Virology
Discusses current topics in virus research and literature. Weekly sessions led by all participating members of the research group. Prerequisite: permission of instructor. Credit/no-credit only.
Offered AUT/WIN/SPR/SUM, 1.0 credits. Will be offered in WIN 2025
MEDCH 555 – Biophysics and Pharmacology of Dynamic Proteins
Discusses current topics in protein dynamics, focusing on intrinsically disordered proteins and drug-metabolizing enzymes. Weekly sessions led by all participating members of the research group. Prerequisite: permission of instructor.
Offered AUT/WIN/SPR/SUM, 1.0 credits. Will be offered in WIN 2025
PBIO 545 – Quantitative Methods in Neuroscience
Discusses quantitative methods applicable to the study of the nervous system. Revolves around computer exercises/discussion of journal papers. May include linear systems theory, Fourier analysis, ordinary differential equations, stochastic processes, signal detection, and information theory. Offered jointly with NEURO 545.
Offered WIN, 3.0 credits, Weeks 1-10. Will be offered in WIN 2025
PHCOL 501 – Drug Discovery and Emerging Therapeutics
Consideration of the general principles and current approaches involved in modern drug discovery and development, with an emphasis on basic concepts in drug action, delivery, and metabolism. Discussion of novel drug discovery techniques and emerging non-standard therapeutics.
Offered AUT, 2.0 credits. Course not currently being offered
Spotlight
Modeling in Seattle
Seattle is a major center for protein structure/design and structural biology. Seattle MCB faculty are leaders in x-ray crystallography, nuclear magnetic resonance (NMR), electron microscopy (EM), and small angle x-ray scattering (SAXS). Seattle MCB faculty are also at the forefront in computational design to enhance or create new protein function, and computational methods to analyze complex data sets or model single cell behavior. Visit the Institute of Protein Design to learn more about 3D protein modeling from Dr. David Baker.