Refinement of Three-Dimensional Protein and DNA Structures in Solution from NMR Data

Abstract

Two-dimensional NMR, in particular two-dimensional nuclear Overhauser effect (2D NOE) spectra, when used in conjunction with distance geometry and energy refinement calculations can be used to determine the high-resolution structure of DNA fragments and small proteins. To understand functional interactions of proteins and nucleic acids, it is important to know their solution structures to high-resolution. Problems addressed with DNA structure and with protein structure studies are often of a different nature. In general, we are interested in fairly subtle structural changes in the DNA helix which are sequence-dependent and, consequently, guide protein, mutagen or drug recognition. These subtle variations demand detailed knowledge of the structure and, therefore, accurate internuclear distance and perhaps torsion angle constraints. But one can define a protein tertiary structure with moderate accuracy using distance geometry or restrained molecular dynamics calculations without accurately determining interproton distances; a qualitative assessment of 2D NOE intensities is often all that is needed. However, in proteins possessing less common structural features, it may be especially valuable to have additional structural constraints and more accurate constraints for use with the computational techniques. And, even more importantly, we will want better defined structures at ligand binding sites (with and without ligand bound).