A topical issue: NMR investigations of molecular dynamics

Abstract

The 20 papers in this topical issue of the Journal of Biomolecular NMR reflect the multitude of NMR techniques and approaches used to investigate conformational dynamics critical for folding and stability, molecular recognition, and catalysis of proteins, nucleic acids, and other biological molecules. Of course, any single issue of a journal cannot include a selection of papers comprehensive enough to truly encompass the diversity of developments and applications in a field that continues to expand as rapidly and creatively as NMR spectroscopy. Many alternative selections of papers could have been made equally well and no doubt, indeed one hopes, the work described in this topical issue will inspire developments of increasingly powerful techniques and applications to increasingly deeper questions in biology. New experimental methods drive biological investigations by NMR spectroscopy and several papers in this topical issue present new techniques or novel combinations of existing methods in solution NMR spectroscopy. The Carr-Purcell-Meiboom-Gill (CPMG) pulse sequence has emerged as a critical method for investigating conformational dynamics in biological macromolecules. Most investigations of conformational dynamics of protein backbones have used IS spin systems, such as H–N or methine H–C, as probes, for example, see the paper by Raleigh, Palmer and coworkers described below. To overcome this limitation, Kay and coworkers introduce new CPMG relaxation dispersion experiments for H and C spins in Gly residues (Vallurupalli et al. 2009). The new methods are applied to a mutant of T4 lysozyme that binds hydrophobic ligands in an internal cavity in the protein. Existing theoretical analyses of relaxation during CPMG pulse trains were derived assuming infinitely short ideal refocusing pulses. Myint and Ishima provide a critical assessment of the effects of evolution and relaxation during real finite-length refocusing pulses of the CPMG pulse train (Myint and Ishima 2009). Field cycling enables measurements site-specific relaxation rate constants at low static magnetic fields with the resolution and sensitivity of a high field NMR spectrometer. Redfield, Kern, and coworkers obtain R1 relaxation rate constants at fields as low as 4 T for the nucleocapsid protein of the SARS coronavirus using a home-built field cycling instrument (Clarkson et al. 2009). Together with conventional high field measurements, these data suggest correlated rigid body motions of structural motifs of the protein. Skrynnikov and coworkers use glycerol to increase solution viscosity and thereby increase the rotational diffusion correlation time of the a-spectrin SH3 domain. The longer rotational correlation time extends the time window to which NMR relaxation methods are sensitive to internal motional processes (Xu et al. 2009). Hydrogen exchange between amide moieties and solvent is a longstanding and powerful approach for studying folding and thermodynamics of proteins. However, for large molecules, even the resolution in H–N two-dimensional correlation spectra becomes limiting and three-dimensional spectra cannot be acquired rapidly enough using conventional Cartesian sampling schemes. Wand and coworkers introduce a new method, called AMORE-HX, that uses radial sampling of a three-dimensional HNCO experiment to determine amide hydrogen exchange rates in real time (Gledhill et al. 2009). They show that radial sampling with four angles (69 , 81 , 10 , 27 ) can resolve 328 of the 334 cross peaks that remain A. G. Palmer III (&) Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA e-mail: agp6@columbia.edu