Chem 791A - Biomolecular Structure

Resources:

Class Resource Updates:

The second exam is ready for download. You will need the following links:
- Bleomycin hydrolase
- HIV-1 RNA - neomycin
Want to try the PyMol movie tutorial? Download the files you need in either Windows or Macintosh format.
If you have a PC, download img2avi: documentation and the program itself (right-click each link). This will let you make movies from still images. We'll talk about this in the PyMol workshop.
We're so 21st Century - we now have a Blog. Check it out.
Please note that I have UPDATED the downloadable package for using JmolShell at home. Please use the newer version. It has both a Simple and an Advanced version of the projects. The directory structure also more correctly reflects the documentation. Finally, the beginnings of a control generator have been added to the CMD tab. Try it!
Tools for making JmolShell presentations: Get started; Make controls; Download JmolShell
ConSurf analysis of T7 RNA polymerase
Want to make a more sophisticated morph between two structures? Yale and UMass Morph Servers
Quick Tools: Chimera, Dali server, GROMACS, SURFNET, ConSurf, Robetta/Rosetta
Try JmolShell Generator to quickly pull you protein into JmolShell.
Lecture notes for lecture on membrane proteins (Lynmarie Thompson) - see also a new JMol presentation of some membrane proteins
Movies of protein conformational changes: GroEL - generated by Morph Server (see also Gallery of Morphs)
NMR section:
- Lecture 1 and Lecture 2
- On-line mini NMR course
Crystallography section:
- Lecture 1 and Lecture 2 movies are available for viewing (and hearing!).
- PDF hand-out
- Kevin Cowtan's Book of Fourier
- Karsten's home page. Also background info on the BMB teaching initiative.
Jmol molecular library
- Check out JmolShell, an environment for creating your own presentations in Jmol.
- Explore the structure of CRABP
- and carboxypeptidase and cytochrome c oxidase
See a movie about how RNAi works
Link to membrane simulations

News update:

Thu, Nov 15 - Meet in CRC. Bring you laptop if you have one.
Please check the list of Presentations. Check your entry and see if it needs updating - if so, let Craig know immediately by EMail.
Exam 1 answers are now available on-line.
Campus closure: for scheduling reasons, we went ahead with the second lecture of the crystalography section (the campus had re-opened by that time, but courses did not officially start until 11:00a). If you missed the lecture, please proceed to view the entire lecture, including audio, on-line.
Our first take-home exam is ready for download. Please note that this exam is to be worked on independently. You must not talk, or otherwise communicate, with anyone other than Professor Martin about any aspect of the exam. You may not communicate with your fellow students in the class, nor with any other colleagues, faculty or student.
Everyone should attend the Chemistry Department seminar by Lewis Kay on Thurs (Oct 11, 11:15am in LGRT 1634). Lewis is a pioneer in the application of solution NMR to solve protein structures and his talk will be very appropriate to this class!
Class on Thurs (10-4) will start in the regular room - we'll then move to the CRC
PyMol class #1 material
- Pymol Cheat Sheet
- Download lac repressor coordinates
- Anatomy of a PDB file
Homework - Complete the PyMol tutorial - To begin, download PyMol for your own computer or visit the Chemistry Resource Center (it should be installed already on Macs and PCs). Skip sections 4 and 6, for now. Also play with Jmol and explore its command set.
Please note a new seminar of note to our class: Prof. Katsu Murakami "Structural Biology of RNA Polymerse" Tuesday Oct 2, 4:00pm, OEB Conference Room (319 Morrill III S). Look for insights into the structural evolution of this key enzyme in biology.
Please note a seminar of note to our class: Prof. Heather Desaire "Using Mass Spectrometric Analysis of Glycoproteins to Support HIV Vaccine Development" Thursday Sept 20, 11:15 am, LGRT 1634. Her work aims to answer questions such as:
- What is the carbohydrate composition at each glycosylation site on gp120?
- What is the topology at these sites?
- Where is there a potential for electrostatic interaction, due to negatively charged carbohydrates, on the surface of the protein?

Summary: The purpose of this course is to introduce students to protein and nucleic acid structure, both in the chemical details leading to specific structures and in how structure leads to function. Quoting from the text:

"Two major revolutions have occurred within the last twenty years that have changed the way biologists think about their experiments... The first was the structural revolution. The second is the genomic revolution."

This course will lay the foundations of the former, which in turn is at the heart of the latter. Sequence determines structure determines function.

Prerequisites: The course will assume only a very basic background in protein and nucleic acids.

Grading (tentative):

	Mid-October exam	30 pts
	Mid-Late November exam	30 pts
	Class Presentation	30 pts
	Early December quiz	10 pts

The early December quiz will be comprehensive and may cover topics in student presentations up to that point (date TBA). Those who present early will have the opportunity to submit potential quiz questions (so start thinking now!). The early bird may get a small bonus...

The following minimal cutoffs will be applied:

A = 90-100

B =80-89

C = 70-79

D = 60-69

F = below 60

What does "minimal" mean? As an example, a total score of 90 or better WILL yield an A in the course. In later adjustments, a score of 88 or 89 (for example) may also yield an A for the course.

Brief Syllabus:

Week	Dates (lec notes)	Chapters	Topics
1	Sept 4 & 6	1-0 to 1-8	Sequence to Structure: primary, secondary, and tertiary structure
2	Sept 11 & 13	1-9 to 1-15	Tertiary structure continued. Folding, protein stability, forces guiding structure
3	Sept 18 & 20	1-16 to 1-22	Quaternary structure. Survey of motifs: alpha, beta, and mixed domains. Protein flexibility. Forces that govern structure and stability.
4	Sept 25 & 27	2-0 to 2-16	Structure to Function: Recognition, active sites, binding sites, dynamics, catalysis Active site geometry, how active sites achieve catalysis, redox reactions, cofactors, multi-step enzymes
5	Oct 2 & 4	cont to 2-16	More structure to Function: Redox reactions, cofactors, multi-step enzymes Anatomy of a PDB file. Intro to PyMol.
6	Oct 11		More tools: SwissPDB Viewer, jMol Nucleic Acid Structure: DNA, RNA basics
7	Oct 16 & 18		Nucleic Acid Structure: DNA, RNA, riboproteins, ribozymes, aptamers
8	Oct 23 & 25	5-1 to 5-3	Structure Determination: practical aspects of x-ray crystallography (Guest lecturer: Karsten Theis)
9	Oct 30 & Nov 1	5-1 to 5-3	Structure Determination:practical aspects of NMR (Guest lecturer: Qinghua Wang)
10	Nov 6 & 8	3-0 to 3-20	Control of Protein Function: Protein domains, control by pH and redox, effector ligands, cooperativity, allostery, protein switches, motor proteins, et al. Control by degradation, phosphorylation, two-component signaling, protein splicing, glycosylation Membrane Proteins (Guest lecturer: Lynmarie Thompson) - 11/8/07
11	Nov 13 & 15 Nov 18	4-0 to 4-7	Jmol workshop - Getting ready for presentations From Sequence to Function: Sequence alignment, protein profiling, deriving function from sequence, protein evolution, homology modeling
12	Nov 20 & 27	4-8 to 4-17	Sequence alignment, protein profiling, deriving function from sequence, protein evolution, homology modeling Protein superfamilies, strategies for identifying binding sites and catalytic residues.
13	Nov 29		PyMol Workshop - meet in CRC. Bring your laptop with PyMol installed. Everyone - play with PyMol before class
13	Dec 4		Student presentations: Jon, Carrie, Seena
13	Dec 6		Student presentations: Sam, Yong, Elih
14	Dec 11		Student presentations: Nate, Shayhah, Guanshi
14	Dec 13		Student presentations: Julius, Satamita

Biomolecular Structure - Fall 2007

Brief Syllabus: