We propose to continue a feasibility study of the determination of the structures of biomacromolecules in noncrystalline environments. We will use two dimensional NMR experiments, in conjunction with distance geometry calculations and computer graphics, to measure the solution structure of peptides, nucleotides and small proteins. High resolution proton NMR spectra contain enough information to determine molecular geometries with an accuracy of a few angstroms. The important steps to obtain this information are: assignment of the proton NMR signals, measurement of NOEs for short distance determinations, use of paramagnetic reagents for long distance measurements, calculation of molecular coordinates from the distances using distance geometry, and refinement of the molecular structure using energy calculations, molecular dynamics, and interactive computer graphics. Experiments are described to improve the spectral assignment procedures and to assess the feasibility of measuring a wide range of distances. The complications introduced by molecular motion are discussed. The effort will be pointed toward structural and dynamic comparisons of engineered proteins and unusual nucleic acid structures. We hope these experiments will identify the quantitative limits of, and prospects for, the emerging NMR technology. It should have a significant impact on questions of molecular design. The project is a large one, requiring access to a high field spectrometer and considerable computational power. Because of the enormous potential of the method and the very significant effort required to bring it to maturity, we propose to continue the project as a Resource-Related Research Project.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Resource-Related Research Projects (R24)
Project #
5R24RR001695-06
Application #
3450552
Study Section
Special Emphasis Panel (SSS (E))
Project Start
1984-06-01
Project End
1990-11-30
Budget Start
1989-12-01
Budget End
1990-11-30
Support Year
6
Fiscal Year
1990
Total Cost
Indirect Cost
Name
University of California San Francisco
Department
Type
Schools of Pharmacy
DUNS #
073133571
City
San Francisco
State
CA
Country
United States
Zip Code
94143
James, T L (1994) Assessment of quality of derived macromolecular structures. Methods Enzymol 239:416-39
Bishop, K D; Blocker, F J; Egan, W et al. (1994) Hepatitis B virus direct repeat sequence: imino proton exchange rates and distance and torsion angle restraints from NMR. Biochemistry 33:427-38
Ulyanov, N B; Schmitz, U; James, T L (1993) Metropolis Monte Carlo calculations of DNA structure using internal coordinates and NMR distance restraints: an alternative method for generating a high-resolution solution structure. J Biomol NMR 3:547-68
Davis, J H; Bradley, E K; Miljanich, G P et al. (1993) Solution structure of omega-conotoxin GVIA using 2-D NMR spectroscopy and relaxation matrix analysis. Biochemistry 32:7396-405
Basus, V J; Song, G; Hawrot, E (1993) NMR solution structure of an alpha-bungarotoxin/nicotinic receptor peptide complex. Biochemistry 32:12290-8
Schmitz, U; Ulyanov, N B; Kumar, A et al. (1993) Molecular dynamics with weighted time-averaged restraints for a DNA octamer. Dynamic interpretation of nuclear magnetic resonance data. J Mol Biol 234:373-89
Oshiro, C M; Kuntz, I D (1993) Application of distance geometry to the proton assignment problem. Biopolymers 33:107-15
Guiles, R D; Basus, V J; Kuntz, I D et al. (1992) Sequence-specific 1H and 15N resonance assignments for both equilibrium forms of the soluble heme binding domain of rat ferrocytochrome b5. Biochemistry 31:11365-75
Hurle, M R; Eads, C D; Pearlman, D A et al. (1992) Comparison of solution structures of mutant bovine pancreatic trypsin inhibitor proteins using two-dimensional nuclear magnetic resonance. Protein Sci 1:91-106
Schmitz, U; Sethson, I; Egan, W M et al. (1992) Solution structure of a DNA octamer containing the Pribnow box via restrained molecular dynamics simulation with distance and torsion angle constraints derived from two-dimensional nuclear magnetic resonance spectral fitting. J Mol Biol 227:510-31

Showing the most recent 10 out of 37 publications