Biomolecular Structure - Fall 2004

Chem 791A, SPIRE number 72300 Instructor: Craig Martin CMartin@chem.umass.edu Last updated: 9/8/2004
MW 1:45p-3:00p LGRT 1020 First week only: WF 1:25pm LGRT 202

Note that as of Dec 3, the Jmol package has been updated. A number of things are improved, but in particular, distance and angle measurement is back to working again. You can download the update and simply replace the old files with the new. No changes to your index.html file are required.

Your presentations are available on line


Exam 2 Resources

Exam 1 Resources


Reading for the next class: download it here

Resources

For the Jmol workshop, go directly to the JmolShell Home Page.

For the Nucleic Acids part of the course: go to the CHIME link for Nucleic Acids. Be sure to be read the stuff below about which browser to use.

The program Rasmol runs on both Macintosh and Windows platforms and allows one to display protein and nucleic acid structures. It has a long history and can be downloaded in various versions. It allows one to manipulate structures in the sense that one can change coloring, representation, turn elements on and off, and interogate structures. One cannot in any way change a structure using Rasmol.

Rasmol, in turn, inspired a browser-based plug in, CHIME, with the same functionalities, using almost the identical command set. Thus going back and forth between the two easy.

CHIME allowed the creation of a WEB-based (and CHIME-based) exploration tool called Protein Explorer. This package is widely used and very powerful. A limitation of CHIME (and of Protein Explorer) is that you must install a plug-in into your browser. A more serious limitation is that development of CHIME has stopped and will likely not continue. As a consequence, there are limitations regarding which browsers work on specific platforms.

Most recently, a new browser-based alternative has arisen, inspired by Rasmol and by CHIME This software, Jmol, also runs on both platforms (and Unix, et al.). It exists both as a stand-alone JAVA application and as a browser-based function. Note that for the browser function, you don't need to download anything to your computer - the software is automatically downloaded when you access a Jmol-enabled site (don't worry, it's safe). Again, the command set is based on Rasmol/CHIME, so the transition should be easy.

A different program, available on both platforms, is Swiss PDBViewer, or DeepView. This program is excellent at viewing structures, but also allows for some manipulations. For example, this program will allow homology modeling. There is no browser-based version, so this is not good for preparing presentations of structure.

See the site MolviZ.Org for more detailed descriptions of these and other software.


Finally, various presentations have been prepared for this course using CHIME and some of these will be converted to Jmol format. These are listed below. Also listed is download information for pre-prepared packages for creating presentations in either CHIME or Jmol
  • CHIME-based:
  • Jmol-based:
  • Textbook: "Protein Structure & Function," Gregory A. Petsko & Dagmar Ringe, Sinauer Press, 2004.
    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 little background in protein and nucleic acid structure.


    Brief Syllabus:

    Week Dates Chapters Topics
    1 Sept 8 & 10 1-0 to 1-8 Sequence to Structure: primary, secondary, and tertiary structure
    2 Sept 13 & 15 1-9 to 1-15 Tertiary structure continued. Folding, protein stability, forces guiding structure
    3 Sept 20 & 22 1-16 to 1-22 Quaternary structure. Survey of motifs: alpha, beta, and mixed domains. Protein flexibility
    4 Sept 27 & 29 5-1 to 5-3 Structure Determination:practical aspects of NMR
    5 Oct 4 & 6 5-1 to 5-3 Structure Determination: practical aspects of x-ray crystallography
    6 Oct 13
    Tools: Protein Data Bank. Introduction to Protein Explorer, SwissPDB Viewer, jMol
    2 & 7 Oct 18 & 20 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
    8 Oct 25 & 27
    Nucleic Acid Structure: DNA, RNA, riboproteins, ribozymes, aptamers
    9 Nov 1 & 3 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
    10 Nov 8 & 10
    jMol workshop - Getting ready for presentations
    11 Nov 15 & 17 4-0 to 4-7 From Sequence to Function: Sequence alignment, protein profiling, deriving function from sequence, protein evolution, homology modeling
    12 Nov 24 4-8 to 4-17 Protein superfamilies, strategies for identifying binding sites and catalytic residues. Case studies.
    13 Nov 29

    13 Dec 1
    Student presentations: Rishi Arora, Seyma Keskin, Ming Zhang
    14 Dec 6
    Student presentations: Xiaoqing Liu, Marielle Cajita
    14 Dec 8
    Student presentations: Agya Frimpong, Brian Jordan
    15 Dec 13
    Student presentations: Abigail Guce, Basar Gider, Kate Harris