Biomolecular Structure Chem 791B
Tue/Thu 9:30-10:45 LGRT 114 Craig T. Martin, Chemistry, Univ of Mass Useful links in macromolecular modeling
The overall theme of this course is understanding macromolecular structures in biology. Traditional lectures will present concepts in structure, including the physical basis for structure and stability, molecular interactions, and design. The course will also make extensive use of public domain structural databases and software tools for obtaining and viewing structures, including the WEB. Workshop will include hands-on tutorials in the use of publicly available software.
As the course progresses, students will choose their favorite protein, and will develop oral and WEB-based presentations, which illustrate principles learned throughout the course.
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Text: "Introduction to Protein Structure, 2nd Edition," C Branden and J. Tooze, and selected readings from the literature.
Date | Topic | Reading | |||||||||||||||||||||||||
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Jan 26 | Tu | Organizational, fundamental principles | Chapter 1 on your own | ||||||||||||||||||||||||
Jan 28 | Th | Forces and basics of structure | Chpt 4, Creighton | ||||||||||||||||||||||||
Feb 2 | Tu | Motifs of Protein Structure | Chapter 2 | ||||||||||||||||||||||||
Feb 4 | Th | More on motifs | Chapters 3 & 4 | ||||||||||||||||||||||||
Feb 9 | Tu | Motifs, determining structures | Chapt 5 & 18 | ||||||||||||||||||||||||
Feb 11 | Th | Motifs, determining structures | Chapt 5 & 18 | ||||||||||||||||||||||||
Feb 16 | Tu | No class - Monday class sched | |||||||||||||||||||||||||
Feb 18 | Th | Struct Analysis Workshop (SwissPDBViewer)* | |||||||||||||||||||||||||
Feb 23 | Tu | Homologous structures | |||||||||||||||||||||||||
Feb 25 | Th | Homology modeling Workshop* | |||||||||||||||||||||||||
Mar 2 | Tu | Protein Engineering | Chapter 17 | ||||||||||||||||||||||||
Mar 4 | Th | Biomaterials | Chapter 14 | ||||||||||||||||||||||||
Mar 9 | Tu | Membrane proteins | Chapter 12 | ||||||||||||||||||||||||
Mar 11 | Th | Metalloproteins | |||||||||||||||||||||||||
Mar 16 | Tu | No class - Spring Break | |||||||||||||||||||||||||
Mar 18 | Th | No class - Spring Break | |||||||||||||||||||||||||
Mar 23 | Tu | Nucleic acids - basics | Chapter 7 | ||||||||||||||||||||||||
Mar 25 | Th | Nucleic acids - more | |||||||||||||||||||||||||
Mar 30 | Tu | DNA-protein interactions | Chapter 8 & 9 | ||||||||||||||||||||||||
Apr 1 | Th | Authoring Workshop* | |||||||||||||||||||||||||
Apr 6 | Tu | RNA structures, ribozymes | |||||||||||||||||||||||||
Apr 8 | Th | Aptamers et al. - engineering RNA | |||||||||||||||||||||||||
Apr 13 | Tu | Protein/RNA folding | Chapter 6 | ||||||||||||||||||||||||
Apr 15 | Th | Protein Folding - Steve Eyles | |||||||||||||||||||||||||
Apr 20 | Tu | Final Workshop - meet in CRC | Apr 22
| Th
| Student presentations
| Catherine McIntosh | Carlotta Cancelliere Greg Gallagher Apr 27
| Tu
| Student presentations
| Binu James | Robert Chou Matthias Ober Hordur Kristinsson Apr 29
| Th
| No class
| May 4
| Tu
| Student presentations
| George DeBusk | Charu Taneja Eddie Esposito May 6
| Th
| Student presentations
| Vivek Prabhu | Jesse Charette Jenny Habink Renuka Sivendran May 11
| Tu
| Student presentations
| Irina Alimov | Sarah Carpenter Shujun Chen Anton Manuilov |
Note that the student presentations will be in the Chemistry Resource Center in Goessmann
More information at: http://www.chem.umass.edu/~cmartin/Courses/BioStruct/S99