CONJOINT 544 “Protein Structure, Modification Diversification and Regulation”

First five weeks of winter quarter, 2023 (Tuesday, January 3 thru Thursday, February 2)
        1.5 credits

Meeting Time and Place:   Tuesdays and Thursdays 3:30 to 4:50 in the Fred Hutch Weintraub Building Room B1-072/074 (first floor, right side, past Thomas Lobby and Espresso Bar, across from Cafeteria and Library)

Shuttle Schedule from UW School of Medicine:   https://transportation.uw.edu/getting-around/shuttles/uw-fred-hutch-south-lake-union#schedule-uwmc-to-slu

Instructor(s):

Barry Stoddard    FHCRC Basic Sciences/UW Biochemistry)  (Weeks 1 to 3

Melody Campbell    FHCRC Basic Sciences/UW Biochemistry) (Week 4)

Phil Bradley         FHCRC Public Health Sciences and Basic Sciences/UW Genome Sciences)  (Week 5)

Class grading

1. Attend  sessions and participate in discussion and Q/A about readings and lectures (vast majority of weighting)

2. Participate in any 'pop quizzes' focused on assigned readings (At instructor's discretion)

3. Complete an assigned Writing Project (to be described in Week 1) and turn in by Friday, March 3

Rationale and Background

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 biological reactions.  Over the past 10 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 over the past 40+ years, and  especially  the recent development of powerful methods for protein 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, covering various aspects of protein structure and function such as:

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

(2) Protein folds and protein shape-shifting and moonlighting

(3) Protein modeling, fold design and structure-based stabilization and optimization

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

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

(6) Ancestral reconstruction analyses.

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.

SYLLABUS:

Week One  (Jan 3 / 5)                                         Protein Structure and Folds: Definitions, Basics and Tools

Tools to check out:

Structure Databases                                                        RCSB

Structure Illustration                                                        PYMOL

Structure Similarity Searches                                        DALI,   FATCAT

Structure Stabilization                                                    PROSS

Readings:

Tuesday:

1.  Burley, S.K. et al. (2022) "RCSB Protein Data Bank (RCSB.org): Delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning"  Nucleic Acids Research Nov 24; gkac1077.  doi: 10.1093/nar/gkac1077.  Online ahead of print.  PubMed 36420884    Publisher Link

Thursday:

2.  Marciano et al. (2022) "Protein quaternary structures in solution are a mixture of multiple forms" Chem Sci 13: 11680 - 11695.  PubMed 36320402   PubMed Central Link    Publisher Link

Week Two     (Jan 10 / 12)                                   Structure-Function Studies via NMR

Readings:

Tuesday:

1. Hu, Y. et al. (2021) "NMR-based methods for protein analysis" Anal. Chem. 93 (4): 1866 - 1879.      PubMed 33439619        Publisher Link

2. Tuinstra RL et al.  and Volkman BF. (2008) “Interconversion between two unrelated protein folds in the lymphotactin native state” Proc Natl Acad Sci 105 (13): 5057-62.     PubMed 18364395       PubMed Central 2278211       Publisher Link

3. Dishman, A. et al. (2021) "Evolution of fold switching in a metamorphic protein" Science 371: 86 - 90.    PubMed  33384377         PubMed Central 8017559         Publisher link

Thursday:

4. Garcia J, Gerber SH, Sugita S, Südhof TC, Rizo J. (2004) “A conformational switch in the Piccolo C2A domain regulated by alternative splicing” Nat Struct Mol Biol. 11 (1): 45-53.   PubMed 14718922        Publisher Link

Week Three     (Jan 17 / 19)                            Structure-Function Studies via Crystallography

Readings:  

Tuesday:

1. Jaskolski, et al. (2014) "A brief history of macromolecular crystallography, illustrated by a family tree and its Nobel Fruits" The FEBS Journal 2891: 3985 - 4009.   PubMed 24698025        PubMed Central: 6309182       Publisher Link

Thursday:

2. Ohto U, Ishida H, Krayukhina E, Uchiyama S, Inoue N, Shimizu T. Structure of IZUMO1-JUNO reveals sperm-oocyte recognition during mammalian fertilization. Nature. 2016 Jun 23;534(7608):566-9.     PubMed 27309808        Publisher Link

-and-

3. Aydin H, Sultana A, Li S, Thavalingam A, Lee JE. Molecular architecture of the human sperm IZUMO1 and egg JUNO fertilization complex. Nature. 2016 Jun 23;534(7608):562-5.     PubMed: 27309818         PubMed Central:  5319863      Publisher Link

Week Four (Jan 24 / 26)                                Structure-Function Studies via CryoEM

Readings:

Tuesday:

1.  Cheng, Y. (2015) "Single Partile CryoEM at crystallographic resolution" Cell 161: 450 - 457.     PubMed 25910205       PubMedCentral 4409662        Publisher Link

Thursday:

2. Gao Y. et al. (2016) "TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action"  Nature 534: 347 - 351.  PubMed 27281200      PubMedCentral 4911334       Publisher Link

Week Five     (JAN 31  / FEB 2)                      Protein structure prediction (AlphaFold)  

Readings:

Tuesday:

1. Tunyasuvunakool, K. et al. (2021) "Highly accurate protein structure prediction for the human proteome" Nature 596: 590 - 596.  PubMed 34293799        PubMed Central 8387240    Publisher Link

Thursday:

2.  Varadi, M. et al. (2022) "ALphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models" Nucleic Acids Research D1: 439- 444.   PubMed  34791371         PubMed Central 8728224         Publisher Link

FINAL WRITING ASSIGNMENT (DUE FRIDAY, MARCH 3)                      FROM STRUCTURE AND/OR MODEL to FUNCTIONAL ANNOTATION

Reading:

1. de Crecy-Lagard, V. et al. (2022) "A roadmap for the functional annotation of protein families: a community perspective" Database  1 - 16 (Meeting report).      PubMed 35961013           PubMed Central 9374478           Publisher Link

Your assignment:  If you go to the AlphaFold Protein modeling database (https://alphafold.ebi.ac.uk) and search on "Unknown Function" you will find that 56,656 proteins  (as of 26-December-2022) come up, spanning all model organisms that have been subjected to AlphaFold structural predictions. That corresponds to between and quarter and a third of all such modeled protein structures. Beyond that, I can guarantee that the functional annotations provided for those that don't come up as 'unknown' are, in many cases, either flat-out wrong or are quite uninformative (i.e. 'kinase' or 'binding protein', etc).

Your assigment is to (1) read the really interesting final assignment above, that describes the problem from the standpoint of a very broad community of molecular, cellular and structural biologists, and then (2) to find an interesting 'unknown function' protein from the AlphaFold database (or if you wish, from the RCSB; a search for 'Unknown Function' at that site generates over 70,000 hits) and to use all the tools, intuition, knowledge, and imagination you have at your disposal to provide a defendable (and hopefully testable) hypothesis regarding potential function.

How will you choose? So many interesting hits to consider. Personally, I'd go after something that flat-out looks really cool and complex.

How will you analyze?  Consider searching for all structural homologous proteins using DALI or FATCAT or the RCSB itself, as well as all sequence homologues, and see what pops up. Then, start looking for conservation patters that might indicate functionally conserved sites. Look at stereochemical features of such areas of the proteins. Look at potential sites of covalent modification. Look to see if there are any publications linking the protein (and its gene) to a biological phenomena or phenotype.

How to impress me?  HAVE FUN, write really clearly and cleanly, make original figures, and dig as deep as you can. 

And again....if you've participated fully in the class to the point where you're now taking this on, you've already done just fine and have nothing to sweat regarding graduate graded credit for it. So, please don't turn this into a 'thing' other than seeing where webservers and your own thought processes take you.

THANKS FOR TAKING CONJOINT 544!

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