Biomolecular Structure Analysis by Nuclear Magnetic Resonance

David E. Wemmer, Lawrence Berkeley National Laboratory

Research Objectives

The focus of our work is to understand structure-function relationships in biomolecules and their complexes by applying methods of modern multidimensional nuclear magnetic resonance (NMR).

Computational Approach

There are two major stages in the analysis of NMR data which rely heavily on computation. The first is optimized transformation of the time domain NMR data into frequency dimensions. To extend resolution, this transformation uses linear prediction or maximum entropy analysis, followed by Fourier transformation. Artifacts are removed from the data using iterative modeling of various sorts. The second stage of the analysis is in conversion of NMR-derived structural restraints, together with knowledge of the covalent structure of the molecule, into sets of coordinates (models) that are consistent with all experimental observations. This can be done through molecular-dynamics calculations in either Cartesian or internal angle spaces. These models are analyzed to determine the structure-function relationships of interest.

Accomplishments

Time allocated in the past year was used to explore both the data analysis and structure refinement steps. Unfortunately, the analysis program PROSA, though functional on other supercomputers, could not load experimental data when run on the Cray C90. However, the real-space refinement program AMBER was run to analyze the structure of an aptamer DNA (one found through an in vitro selection for arginine binding) in complex with its target. The results indicate a complex folded structure and demonstrate clear structural changes upon binding.

Structures were also calculated for the receiver domain of nitrogen-regulatory protein C (NTRC) from bacteria. This protein is regulated by phosphorylation, and we are trying to determine the structural changes that occur upon phosphorylation. The program DYANA (an angle space dynamics program) was used for refinement of some of the structures. The regions where changes occur were clearly identified, and iterative refinement of the structure is continuing.

Significance

The systems under study are of fundamental interest, as they are examples of regulatory interactions that occur in complex biological systems. Resulting data aid in understanding regulatory interactions and how they can fail under specific circumstances. The insight gained will also be valuable in future efforts to design new regulatory pathways from the principles used in nature.

Publications

S. A. Robertson and D. E. Wemmer, "Structural changes in a DNA aptamer upon arginine binding" (in preparation, 1998).