BIOL 6312

BIOL 6312

Proteins: Structure, Function, and Design

Spring 2018

Instructor: Steven Vik (214) 768-4228

Class: TuTh 9:30-10:50 130 DLS

email: svik@smu.edu

WWW: faculty.smu.edu/svik

Course Links

Syllabus

Tentative Schedule (some topics might change)(Lectures at smu.instructure.com)

Date		Topics	Computer sessions	HW	Readings: Williamson
Tu Jan 23	1	Introduction			Ch 1
Th Jan 25	2	H-bonding, ion pairs, Secondary Structure			Ch 1
Tu Jan 30	3	Prediction of secondary structure, Helix capping	Lesson 1		Ch 1
Th Feb 1	4	Properties of the Amino Acids			Ch 1
Tu Feb 6	5	Protein Folding	Lesson 2	HW#1 due	Ch 1, Ch 4.5
Th Feb 8	6	Structural Motifs			Ch 1.3, Ch 2.1
Tu Feb 13	7	All alpha folds,	Lesson 3		Ch 2
Th Feb 15	8	coiled coils		HW#2 due	Ch 2
Tu Feb 20	9	All beta folds	Lesson 4		Ch 2
Th Feb 22	10	Alpha/beta folds			Ch 1.4, Ch 2.2
Tu Feb 27		No Class
Th Mar 1	11	Fold Databases and Evolution		HW#3 due	Ch 3.1, 2.3
Tu Mar 6	12	Quaternary Structure	Lesson 5		Ch 3
Th Mar 8	13	Oligomers/AllosteryProtein Interactions		HW#4 due	Ch 4.1, 4.2
Mar 13, 15		Spring Break
Tu Mar 20	14	Protein purification	Lesson 6		Ch 11.1, 11.5.1
Th Mar 22	15	X-ray crystallography/Cryo EM			Ch 11.4
Tu Mar 27	16	NMR	Lesson 7	HW#5 due	Ch 11.3
Th Mar 29	17	Protein Interaction Domains, Cooperativity, Diffusion
Tu Apr 3	18	Epistasis, Ancient Proteins Natively unstructured proteins,	Lesson 8	Midterm given out	Ch 4.3, 4.4
Th Apr 5	19	Protein modifications, Folding in vivo,			Ch 4.5
Tu Apr 10	20	Amyloids, Catalysis,	Lesson 9	Midterm due	Ch 5
Th Apr 12	21	Catalysis (part 2), Cofactors Molecular motions		HW#6 due	Ch 5
Tu Apr 17	22	Membrane proteins, Tertiary Structure Predictions	Lesson 10		Ch 1.3.3
Th Apr 19	23	Membrane proteins			Ch 8.3, 8.4
Tu Apr 24		No Class
Th Apr 26	24	Membrane proteins		HW#7 due
Tu May 1	25	Metabolons, Supercomplexes	Lesson 11		Ch 9.4, 10
Th May 3	26	Strategies of Mutagenesis, Thermal Stability		HW#8 due
Th May 10		Student Presentations, (Final exam time)	9:30	Project

The text for the course:

How Proteins Work (2012), available in the SMU Bookstore

Mike Williamson

Publisher's Website

Other reading material will be provided.

The lectures will be posted on Canvas: https://smu.instructure.com
Some course materials will be hosted at the website: http://faculty.smu.edu/svik/6312.6312.html.

The lectures include links to textbook figures, figures from other sources, on-line abstracts and articles, and animated structures using Jmol. To view the the Jmol structures I recommend Firefox, or possibly Chrome. Safari and Internet Explorer are not recommended.

Approximately once per week, we will spend 30 minutes in class to learn how to use the molecular visualization application Jmol. Detailed instructions will be provided in advance. Students should bring laptops to class for these lessons.

Jmol (http://jmol.sourceforge.net/) Version 14.4 is now available for downloading (http://sourceforge.net/projects/jmol/files/latest/download?source=files). This is free, open-source software. It was based on the Java programming language. It runs as a free-standing application, and it can be used to host interactive molecules on web pages as an applet. The application will run under Windows, Mac OS X, and Linux. The web applet comes in two versions, one that requires the user to have Java installed, but this has become increasingly problematic as Java has been by the criminal element. Therefore, I have converted all of my pages to the new "JSmol" format. This version requires only javascript to function in the browser, and is sometimes referred to as HTML5. It also makes it possible to use a tablet or mobile phone to view the lectures.

I will show you how to make web pages using JSMol, that display interactive molecules. I recommend BlueGriffon as a free web page editor (http://bluegriffon.org). I will also show you how to make high-quality images of proteins, and movies.

Grading will be based on one take-home exam, given after midterm, (20%), about 8 homework assignments, primarily involving analysis of proteins by computer (45%), and a final project that includes a review paper with web tutorial using Jmol to describe recent studies of a protein or a group of related proteins, due on Finals week (35%) , split between the presentation (20%) and the paper (15%). The web tutorials will be presented on May 10. The topic should be chosen in consultation with the instructor. Sample topics will be provided. (or check out previous projects, linked below)

Final Project Description-link

Links to previous projects

Last modified April 29, 2018

Comments/questions: email me