Gifa V. 4: A complete package for NMR data set processing

Abstract

The Gifa program is designed for processing, displaying and analysing 1D, 2D and 3D NMR data sets. It has been constructed in a modular fashion, based on three independent modules: a set of commands that perform all the basic processing operations such as apodisation functions, a complete set of Fourier Transforms, phasing and baseline correction, peak-picking and line fitting, linear prediction and maximum entropy processing; a set of command language primitives that permit the execution of complex macro commands; and a set of graphic commands that permit to build a complete graphic user interface, allowing the user to interact easily with the program. We have tried to create a versatile program that can be easily extended according to the user's requirements and that is adapted to a novice as well as an experienced user. The program runs on any UNIX computer, with or without graphic display, in interactive or batch mode.

The structure of a resuscitation-promoting factor domain from Mycobacterium tuberculosis shows homology to lysozymes

“…The backbone dihedral angle restraints were obtained from chemical shift index analysis using the TALOS program 15 . The two cysteine residues have up-field-shifted 13 Cβ resonances (38.33 and 38.16 ppm, respectively) consistent with a disulfide bond formation 16 which was enforced for structure calculations. Hydrogen bond restraints were incorporated if they were protected from H 2 O-D 2 O exchange as revealed from an HSQC spectrum recorded on a freshly lyophilised sample dissolved in a D 2 O buffer, and were supported by NOE analysis.…”

“…NMR spectra were recorded on samples of 0.5 mM, 15 N or 15 N, 13 C labelled RpfBc domain dissolved in 25 mM Na-acetate pH 4.6, 2 mM β-mercaptoethanol with 5-10% D 2 O for the lock. Some spectra were also collected on sample prepared in D 2 O with the same buffer.…”

“…NMR experiments were carried out at 20°C on Bruker AVANCE 500 and 600 spectrometers equipped with 5 mm z-shielded gradient 1 H-13 C-15 N triple resonance cryogenic probes. NMR data processing and analysis were carried out using GIFA 13 and NMRVIEW 14 . Nucleus resonances ( 1 H, 15 N and 13 C) were assigned using standard three-dimensional (3D) experiments 5 .…”

“…Resonance assignments of RpfBc were carried out with a series of standard 2 and 3D experiments using 15 N-and 15 N, 13 C-labelled protein 5 . The first 22 residues from the N-terminal segment (Asn255-Val276) exhibited negative ratio values in the 1 H-15 N heteronuclear NOE experiment corresponding to highly mobile residues 5 .…”

Differentiating Fragmentation Pathways of Cholesterol by Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

“…Data processing was performed using NPKV2 (NMR Processing Kernel), which was developed independently by the University of Strasbourg and NMRTEC (IllkirchGraffenstaden, France) in 64-bit Python programming language using the commercial platform distributed by Anaconda Continuum Analytics (Austin, TX, USA) [34]. NPKV2 is freely available from the authors.…”