We wish to determine the full energy landscapes for RNA tertiary structure formation and protein secondary structures. We wish to develop theory as close to analytic as possible, that gives partition functions of biomolecules. We will use the energy landscapes to predict stable non-native states, conformational switching, cooperative transitions, and folding transitions. Ultimately we aim to predict biological function. As well, energy landscapes will have applications in determining the stability of proteins. This can be used in determining for which amino acid sequence of the beta-amyloid protein are aggregates most stable. We are in the preliminary stages of testing a new method for enumerating conformations of polymers with given contact constraints. The polymer is modeled as a network of self avoiding walks. The approach can be completely generalized to handle complex non-local polymer interactions and works in 3 dimensional lattice models. We hope to use this method to handle non-local protein interactions during folding.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Postdoctoral Individual National Research Service Award (F32)
Project #
5F32GM020460-02
Application #
6385158
Study Section
Physical Biochemistry Study Section (PB)
Program Officer
Cassatt, James
Project Start
2000-05-01
Project End
Budget Start
2001-05-01
Budget End
2001-08-31
Support Year
2
Fiscal Year
2001
Total Cost
$12,444
Indirect Cost
Name
University of California San Francisco
Department
Pharmacology
Type
Schools of Pharmacy
DUNS #
073133571
City
San Francisco
State
CA
Country
United States
Zip Code
94143