ABSTRACT
Residual dipolar couplings (RDCs) have recently emerged as a new tool in nuclear magnetic resonance (NMR) with which to study macromolecular structure and function in a solution environment. RDCs are complementary to the more conventional use of NOEs to provide structural information. While NOEs are local-distance restraints, RDCs provide long-range orientational information. RDCs are now widely utilized in structure calculations. Increasingly, they are being used in novel applications to address complex issues in structural biology such as the accurate determination of the global structure of oligonucleotides and the relative orientation of protein domains. This review briefly describes the theory and methods for obtaining RDCs and then describes the range of biological applications where RDCs have been used.
Subject(s)
Algorithms , Crystallography/methods , DNA/chemistry , Magnetic Resonance Spectroscopy/methods , Proteins/chemistry , RNA/chemistry , Macromolecular Substances , Nucleic Acid Conformation , Protein Binding , Protein Folding , Protein Structure, Tertiary , SolutionsABSTRACT
Recent methods of aligning proteins which were developed in order to measure residual dipolar couplings (RDCs) in solution can also be used for additional applications such as measuring the 15N CSA in the form of chemical shift differences, Deltadelta. A new XPLOR-NIH module has been developed and implemented for NMR structure refinement using the 15N Deltadelta data as restraints. The results of this refinement are shown using the protein Bax. This method should be amenable to any protein which can be studied by NMR. An analysis comparing the structural information provided by NH RDCs and the 15N Deltadelta is included.
Subject(s)
Algorithms , Anisotropy , Models, Molecular , Nitrogen Isotopes/chemistry , Nuclear Magnetic Resonance, Biomolecular/methods , Proteins/chemistry , Proto-Oncogene Proteins c-bcl-2 , Computer Simulation , Hydrogen/chemistry , Hydrogen Bonding , Magnetics , Protein Conformation , Proto-Oncogene Proteins/chemistry , Quality Control , Reproducibility of Results , Sensitivity and Specificity , bcl-2-Associated X ProteinABSTRACT
An analysis of backbone hydrogen bonds has been performed on nine high-resolution protein X-ray crystal structures. Backbone hydrogen-bond geometry is compared in the context of X-ray crystal structure resolution. A strong correlation between the hydrogen-bond distance, R(HO), and the hydrogen-bond angle, theta(NHO), is observed when the X-ray crystal structure resolution is <1.00 A. Ab initio calculations were performed to substantiate these results. The angle and distance limits found in our correlation for the backbone hydrogen-bond geometry can be used to evaluate the quality of protein structures and for further NMR structure refinement.
