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 |
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.
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"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." |
Prerequisites: The course will assume little background in protein and nucleic acid structure.
Week | Dates | Chapters | Topics |
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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 |