Tue/Thu 9:30-10:45    LGRT 1020     http://www.chem.umass.edu/~cmartin/Courses/BioStruct/F2000

Craig T. Martin, Chemistry, Univ of Mass        Useful links     Sample Structures   Presentations

News:

• Click here to view your colleagues' presentations (if yours isn't clickable, get your files to Craig and he'll post them).

• A preliminary answer key for the 2nd exam is available. Click here for answers to question 3.
• Take a tour of the large ribosomal subunit
• Click here for the molecules necessary for Question 3 of the 2nd exam. The exam itself can be downloaded here, if you need a fresh copy.
• To any of you using Windows PC's to develop your projects, if you're having trouble with my CHIMEShell package, please do the following:
  • Right-click here and select the menu option that says to download the file to disk (do not do a simple click). Then move the downloaded file into the "Support" folder in "CHIMEShell," replacing the file of the same name there. This new version includes a fix which will make your project work...
• Exam answer key is available, as are graphics supplements for Question 1 and Question 2 are available.
• A big transmembrane protein: cytochrome c oxidase. Check out the "Load all of the subunits" section in "Story." Also look at Maltoporin, a sheet-based transmembrane protein (pore).
• Please check out the Design Guidelines for your presentations.
• As you can see from the revised schedule below, student presentations will begin on Dec 5. I'm looking for volunteers who want to get it over with quickly. There will be 3 presentations per class. You should aim for a 15-20 min presentation, with 5-10 min for questions following.
• A PDF copy of the exam is available for download.
• As a prelude to the assignment I had promised, please read Multiple Alignment, Sequence Motifs and Structure Inference, a chapter in an in-prep book by Cold Spring Harbor Press, and also read Comparative Prot Struct Modeling - Genes & Genomes. This is now for Thursday, Nov 9th's class.
• Material for the exam, due next Thursday, Nov 16 in class), is available here.
• Recent presentations from class are available.
• Whoops!! My apologies. I mis-read my own calendar and didn't show up for lecture last Tuesday. We will begin regular Tuesday sessions next Tuesday (and I will remember!). Tomorrow (Thursday) we will discuss protein-nucleic acid interactions, so read Chapters 8 and 9.
• Atlhough we're not scheduled for the Eric Martz slot this Thursday, if you would like to consider using his presentation-writing shell, you ought to show up to class Thursday afternoon in Stockbridge. His should be easier to use than mine, but since he is just now finishing it, I haven't been able to try it yet.
• Still more news. CHIMEShell can now support TWO different proteins in parallel panels. For those of you considering that for your presentations, Look in the "CHIME2" subdirectory of the downloaded package. Everyone else should stay with the :CHIME1" files, as before.
• Hooray (I hope)! The CHIMEShell should now be working correctly on Macs and PCs. Please test it from here, download it, and test it locally. Please advise me immediately if you find any problems!
• Rasmol Refcard available and FIXED!
• Craig's CHIMEShell is available for download in either a PC format, or a Mac format (only the packaging is different, the file contents are identical in either case), or as a .sit file. This (or an alternate from Eric, not yet ready) is what you will use to put together your macromolecular structure presentation for the end of class. We'll discuss this in Friday afternoon's class. Check it over before you get to class, if you can.
• Remember RNA reading assignments (see schedule below). Also remember that some of the molecules discussed have WEB presentations on our site, including the hammerhead ribozyme, the Pseudoknot, and the Group I ribozyme. Check them out as you read! See also Various DNA structures.
• New Links
  • Proteins
    • Greek Key
    • Alpha Beta
    • Beta Helix
  • Nucleic Acids
    • Various DNA structures
• Supplement for lecture 9/28 is available
• Presentations from Spring 99 are available
• Folding at Home is a massively-distributed project, modeled on SETI at Home (search for extraterresterial intelligence), in which desktop computers can contribute to calculation-intensive attempts to break the protein folding problem. A Mac client is under development. (Thanks to Eric for tipping me on to this one).
• New Homework: Look at AraC. Prepare a topology diagram for it (sheets, helices, and connectivities). Find the motif(s) in the beta sheet structure.
• Homework: Please check out a CHIME tutorial focusing on horseradish peroxidase. Browsing through it, look specifically for blow-ups of peptide backbone interactions (helix, sheet, turn). This is an example of the kind of presentation you will be preparing for the end of the course.

The overall goal of this course is understanding macromolecular structures in biology. "Understand" in this case, means to understand the chemical basis for why the sequence forms the indicated structure (to the extent that this is known - the holy grail for structural biology!). We will learn to analyze structures critically and to think about issues related to protein-engineering and re-design.

Traditional lectures will present concepts in structure, including the physical basis for structure and stability, molecular interactions, and design. Workshops will include hands-on tutorials in the use of publicly available software. Early in the course, we will join Professor Eric Martz's course on the use of Protein Explorer, for hands-on experience. Students will choose their favorite protein, and will develop oral and WEB-based presentations which illustrate principles learned throughout the course.

Text: "Introduction to Protein Structure, 2nd Edition," C Branden and J. Tooze, and selected readings from the literature.

Date		Time	Room	Topic	Reading
Sep 7	Thu	9:30-11:00	Hsbrk 136	Organization, Introduction	Chapter 1
Sep 7	Thu	3:00-6:00	Stkbrg 301	Protein Explorer Tutorial
Sep 14	Thu	9:30-11:00	LGRT 1020	Forces and basics of structure	Chpt 4, Creighton
Sep 14	Thu	3:00-6:00	Stkbrg 301	Protein Explorer Tutorial
Sep 21	Thu	9:30-11:00	LGRT 1020	Why do proteins fold?
Sep 21	Thu	3:00-6:00	Stkbrg 301	Protein Explorer Tutorial
Sep 28	Thu	9:30-11:00	LGRT 1020	Motifs of Protein Structure	Chapters 2, 3, & 4
Sep 28	Thu	3:00-6:00	Stkbrg 301	Protein Explorer Tutorial
Oct 5	Thu	9:30-11:00	LGRT 1020	Determining/analyzing structures	Crystallography Made Crystal Clear, Gale Rhodes
Oct 5	Thu	3:00-6:00	Stkbrg 301	Protein Explorer Tutorial
Oct 12	Thu	9:30-11:00	LGRT 1020	Nucleic acids - principles	Chapter 7
Oct 12	Thu	3:00-6:00	Stkbrg 301	Beyond Protein Explorer
Oct 19	Thu	9:30-11:00	LGRT 1020	Nucleic acids - examples	Ribozyme Structure and Function
Oct 19	Thu	3:00-6:00	Stkbrg 301	Beyond Protein Explorer	RNA Folds: Insights from Recent Crystal Structures
Oct 26	Thu	9:30-11:00	LGRT 1020	Ribozymes, riboproteins, the Ribosome
Oct 26	Thu	3:00-6:00	Stkbrg 301	Beyond Protein Explorer
Oct 31	Tue	9:30-11:00	LGRT 1020	Protein-Nucleic Acid Interactions	Chapters 8 & 9
Nov 2	Thu	9:30-11:00	LGRT 1020	Protein-Nucleic Acid Interactions
Nov 7	Tue	9:30-11:00	LGRT 1020	Homology Modeling /CHIME	Comparative Prot Struct Modeling - Genes & Genomes
Nov 9	Thu	9:30-11:00	LGRT 1020	Homology Modeling	1st exam distributed in class
Nov 14	Tue	9:30-11:00	LGRT 1020	SwissPDBViewer - aligning structures
Nov 16	Thu	9:30-11:00	CRC?	CHIMEShell Authoring Workshop	1st exam due back in class
Nov 21	Tue	9:30-11:00	LGRT 1020	Membrane Proteins	Membrane Protein Folding and Stability Helical Membrane Protein Folding, Stability, and Evolution
Nov 23	Thu			Thanksgiving - no class
Nov 28	Tue	9:30-11:00	LGRT 1020	Protein Folding Dynamics	Intrinsically Unstructured Proteins: Re-assessing ... Paradigm or try here
Nov 30	Thu	9:30-11:00	LGRT 1020	Structure, Unstructure, Dynamics
Dec 5	Tue	9:30-11:00	LGRT 1020	Student Presentations   1. Sherri - DNaK (1DKX)   2. Cherry - Hemocyanin (1HC6)   3. Angelo - Cytosolic Phospholipase A2 (1CJY)	2nd Exam distributed in class
Dec 7	Thu	9:30-11:00	LGRT 1020	Student Presentations   4. Gizem   5. Frances - Monomeric Hb & Mb (1MOH and 1A6M)   6. Ahmet - Chymotrypsin inhibitor 2 Mutants (1YPC)
Dec 12	Tue	9:30-11:00	LGRT 1020	Student Presentations   7. Ray - T7 DNA polymerase (1T7P)   8. Tony - CheR - methyltransferase (1AF7 or 1BC5)   9. Anas - Ser Chemotaxis Receptor (1QU7)   10. Thomas - Isocitrate lyase (1F61 (apo), 1F8M 1F8I)	2nd Exam Due back in class
Dec 14	Thu			No class

Presentations