Biomolecular Structure   Chem 791B

Tue/Thu 9:30-10:45    LGRT 114

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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.

T7 RNA polymerase docking model

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

Date
Topic Reading
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