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Approaches to the Determination of More Accurate Cross-Relaxation Rates and the Effects of Improved Distance Constraints on Protein Solution Structures

  • Chapter
Dynamics and the Problem of Recognition in Biological Macromolecules

Part of the book series: NATO ASI Series ((NSSA,volume 288))

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Abstract

In the past decade, nuclear magnetic resonance (NMR) has become an accepted and widely-used technique for studying the structure and dynamics of small- to moderate-sized proteins, nucleic acids, oligosaccharides, and molecular complexes (Wüthrich, 1986; Clore and Gronenborn, 1991). The fundamental phenomenon that allows the extraction of three-dimensional structural information from NMR studies is cross relaxation between protons (Neuhaus and Williamson, 1989). While other NMR parameters such as chemical shifts and J-coupling constants also contain structural information (Case et al., 1994), cross relaxation as manifested in the nuclear Overhauser effect (NOE) is unique in providing pairwise information: each cross peak in a two-dimensional NOESY (Nuclear Overhauser Effect SpectroscopY) spectrum provides evidence of a short-range through-space interaction between two identified protons, and a macromolecular NOESY dataset may contain thousands of such peaks. Typically, each assigned cross peak is used to derive a distance “constraint,” or pair of bounds between which the distance is assumed to lie, and the dataset of bounds (perhaps along with additional information) is fed into one of several complex computer algorithms for conversion to a set of three-dimensional coordinates. Thus, the accuracy and precision of distances derived from NOESY spectra, and the effect of such accuracy and precision on the derived macromolecular structures, are key considerations in NMR structure determinations. In this Chapter, we review the development of experimental and calculational NMR techniques that allow improved accuracy in the determination of cross-relaxation rates and assess the usefulness of these techniques in structure determinations in proteins and nucleic acids.

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Author notes

  1. John L. Markley

    Present address: Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 215, Boulder, CO, 80309-0215, USA

Authors and Affiliations

  1. Department of Biochemistry, University of Wisconsin, Madison, Madison, Wisconsin, 53706, USA

    Charles G. Hoogstraten & John L. Markley

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  1. Charles G. Hoogstraten
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  2. John L. Markley
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  1. Stanford University, Stanford, California, USA

    Oleg Jardetzky

  2. ESBS, Université Louis Pasteur, Illkirch Graffenstaden, France

    Jean-François Lefèvre

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© 1996 Springer Science+Business Media New York

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Hoogstraten, C.G., Markley, J.L. (1996). Approaches to the Determination of More Accurate Cross-Relaxation Rates and the Effects of Improved Distance Constraints on Protein Solution Structures. In: Jardetzky, O., Lefèvre, JF. (eds) Dynamics and the Problem of Recognition in Biological Macromolecules. NATO ASI Series, vol 288. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-5839-2_8

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  • DOI: https://doi.org/10.1007/978-1-4615-5839-2_8

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4613-7677-4

  • Online ISBN: 978-1-4615-5839-2

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