The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks.

NMRPipe: a multidimensional spectral processing system based on UNIX pipes

A novel approach to tailored selective excitation for the measurement of NMR spectra in non-deuterated aqueous solutions (WATERGATE, WATER suppression by GraAdient-Tailored Excitation) is described. The gradient echo sequence, which effectively combines one selective 180° radiofrequency pulse and two field gradient pulses, achieves highly selective and effective water suppression. This technique is ideally suited for the rapid collection of multi-dimensional data since a single-scan acquisition produces a pure phase NMR spectrum with a perfectly flat baseline, at the highest possible sensitivity. Application to the fast measurement of 2D NOE data of a 2.2. mM solution of a double-stranded DNA fragment in 90% H2O at 5 °C is presented.

Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions.

A new program package, XEASY, was written for interactive computer support of the analysis of NMR spectra for three-dimensional structure determination of biological macromolecules. XEASY was developed for work with 2D, 3D and 4D NMR data sets. It includes all the functions performed by the precursor program EASY, which was designed for the analysis of 2D NMR spectra, i.e., peak picking and support of sequence-specific resonance assignments, cross-peak assignments, cross-peak integration and rate constant determination for dynamic processes. Since the program utilizes the X-window system and the Motif widget set, it is portable on a wide range of UNIX workstations. The design objective was to provide maximal computer support for the analysis of spectra, while providing the user with complete control over the final resonance assignments. Technically important features of XEASY are the use and flexible visual display of ‘strips’, i.e., two-dimensional spectral regions that contain the relevant parts of 3D or 4D NMR spectra, automated sorting routines to narrow down the selection of strips that need to be interactively considered in a particular assignment step, a protocol of resonance assignments that can be used for reliable bookkeeping, independent of the assignment strategy used, and capabilities for proper treatment of spectral folding and efficient transfer of resonance assignments between spectra of different types and different dimensionality, including projected, reduced-dimensionality triple-resonance experiments.

The program XEASY for computer-supported NMR spectral analysis of biological macromolecules.

NMR spectroscopy in the structural elucidation of oligosaccharides and glycosides.

The three-dimensional solution structure of the complex between calcium-bound calmodulin (Ca(2+)-CaM) and a 26-residue synthetic peptide comprising the CaM binding domain (residues 577 to 602) of skeletal muscle myosin light chain kinase, has been determined using multidimensional heteronuclear filtered and separated nuclear magnetic resonance spectroscopy. The two domains of CaM (residues 6 to 73 and 83 to 146) remain essentially unchanged upon complexation. The long central helix (residues 65 to 93), however, which connects the two domains in the crystal structure of Ca(2+)-CaM, is disrupted into two helices connected by a long flexible loop (residues 74 to 82), thereby enabling the two domains to clamp residues 3 to 21 of the bound peptide, which adopt a helical conformation. The overall structure of the complex is globular, approximating an ellipsoid of dimensions 47 by 32 by 30 angstroms. The helical peptide is located in a hydrophobic channel that passes through the center of the ellipsoid at an angle of approximately 45 degrees with its long axis. The complex is mainly stabilized by hydrophobic interactions which, from the CaM side, involve an unusually large number of methionines. Key residues of the peptide are Trp4 and Phe17, which serve to anchor the amino- and carboxyl-terminal halves of the peptide to the carboxyl- and amino-terminal domains of CaM, respectively. Sequence comparisons indicate that a number of peptides that bind CaM with high affinity share this common feature containing either aromatic residues or long-chain hydrophobic ones separated by a stretch of 12 residues, suggesting that they interact with CaM in a similar manner.

https://science.sciencemag.org/content/sci/256/5057/632.full.pdf

Solution structure of a calmodulin-target peptide complex by multidimensional NMR.

Rapid recording of 2D NMR spectra without phase cycling. Application to the study of hydrogen exchange in proteins

https://spin.niddk.nih.gov/bax/lit/508/139.pdf

Three-dimensional triple-resonance NMR Spectroscopy of isotopically enriched proteins

https://spin.niddk.nih.gov/bax/lit/508/121.pdf

Comparison of different modes of two-dimensional reverse-correlation NMR for the study of proteins

Publisher Summary This chapter discusses a third method, referred to as quantitative “ J correlation.” In this approach, the J coupling is obtained from the fraction of magnetization that is transferred from a nucleus to its J -coupled partner. Quantitative J correlation is a useful and general approach for measuring a large variety of two- and three-bond homo- and heteronuclear J couplings, providing access to the study of a large number of dihedral angles in proteins. The approach is not limited to isotopically enriched proteins and has also been used to measure a large number of heteronuclear 1 H- 13 C J couplings in the cyclic decapeptide gramicidin S. The quantitative J correlation experiments are particularly useful for defining the X∼ angle, as a substantial number of J couplings defined by this angle can now be measured. The large number of J couplings overdetermines χ l if there exist only a single rotametric state. In cases of rotamer averaging, however, this large number of independent J measurements provides a unique opportunity to characterize the motional averaging process.

Measurement of homo- and heteronuclear J couplings from quantitative J correlation

https://spin.niddk.nih.gov/bax/lit/508/125.pdf

Rolf Tschudin

Papers

Rapid recording of 2D NMR spectra without phase cycling. Application to the study of hydrogen exchange in proteins

Three-dimensional triple-resonance NMR Spectroscopy of isotopically enriched proteins

Comparison of different modes of two-dimensional reverse-correlation NMR for the study of proteins

Measurement of homo- and heteronuclear J couplings from quantitative J correlation

Three-dimensional NOESY-HMQC spectroscopy of a 13C-labeled protein