Graduate Programs

Our laboratory is associated with several graduate education and research programs leading to doctoral degrees in the biomolecular and biochemical sciences. We are part of the Division of Basic Sciences at the Fred Hutchinson Cancer Research Center, which jointly administrates the Graduate Program in Molecular and Cellular Biology (MCB) with the University of Washington. Additionally, our laboratory (and four others at the Hutchinson Center) are members of the Graduate Program in Biomolecular Structure and Design, which is a relatively new program administrated by the University of Washington and supported by the Hutchinson Center. Dr. Stoddard is also an affiliate faculty member of the Department of Biochemistry at the University of Washington. For more information on these graduate programs, proceed to the pages shown below.

• Molecular and Cellular Biology Program
• Biomolecular Structure and Design Program
• Department of Biochemistry

Course Descriptions

ConJoint/MCB 544: Protein Structure, Diversification and Regulation

Drs. Roland Strong and Barry Stoddard take turns teachning a graduate level course on Protein Structure-Function studies, intended for any interested students in the molecular and cellular life sciences.  The course is co-listed as ConJoint 544/MCB544.  It is taught at the Fred Hutchinson Cancer Research Center on tuesday and thursday afternoons.  The course is taught the first five weeks of each winter quarter. 

The following link (CLICK HERE), or Click on 'View Syllabus' below) will take you to the detailed course description, including the topics and readings for each session.

Syllabus and Schedule

View syllabus

Meets Tues/Thurs 3:20 to 4:40 at FHCRC rooms B1-072/074. 1.5 credits.

Survey level core course primarily for first year graduate students. 

Description

While life likely arose from an RNA-centric origin, and many of the fundamental processes comprising the flow of genetic information and expression of biomolecules are governed by nucleic acids, proteins have evolved to carry out many of the core biochemical and biophysical processes required for life, such as generation of force and motion, creation of physical structures, transmission of material and information, and catalysis of most biological reactions.  Over the past 25 years, the development and use of proteins as therapeutic agents has increased dramatically, an advance that can be attributed to the enormous number of protein structures and mechanisms that have been elucidated, and  especially  the recent development of powerful methods for protein structural prediction and protein designa nd engineering

This course will provide a graduate-level survey of many of the fundamental properties of proteins that govern and define their folding, structures and function, and at the same time will introduce students to some of the most commonly used tools (and best practices) for modeling, analyzing and modifying protein structures and properties.  The class will provide detailed discussion and examples of how protein chemistry and structure/function analyses are employed, while also offering a survey of questions, approaches, results and 'greatest hits' from the past 25 years of protein-structure function analyses.

Over the course of the class, we will discuss all sorts of protein questions and topics, including:

(1) Examples of analyses of protein structure-function relationships via NMR, Crystallography, CryoEM and Computational Prediction and Design

(2) Basic principles governing protein folding and protein shape-shifting and moonlighting and the analysis of protein evolution, divergence and specialization via ancestral reconstructions

(3) Functional and structural consequences of protein alternative splicing.

(5) Functional and structural consequences of protein quaternary assemblage and multimerization, cooperativity and allostery.

(6) Protein design then and now: atomistic force-based design in 2003 and data-driven machine learning design in 2024

The course will assume knowledge at the level of an advanced undergraduate biochemistry course, and will be heavily skewed towards the use of structural information to understand the physical basis of protein behavior.  Emphasis will be placed upon the use and visualization of protein structural models as an essential component of fully appreciating protein behavior and function.  Background and understanding in the areas we will discuss at the level of Stryer, Biochemistry or Alberts, Molecular Biology of the Cell will be assumed.

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