BIOL 6312

Proteins: Structure, Function, and Design

Spring 2018


Instructor: Steven Vik (214) 768-4228

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



Course Links


Tentative Schedule (some topics might change)(Lectures at

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:
Some course materials will be hosted at the website:

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 ( Version 14.4 is now available for downloading (  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 (  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

Copyright 2018, Steven B. Vik, Southern Methodist University