Thérèse E. Malliavin

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

SummaryThe 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 users 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.

An NMR assignment module implemented in the Gifa NMR processing program.

MOTIVATION Peptide and protein structures are determined daily using NMR spectroscopy. Assignment of the NMR spectra is an important step within the procedure and is usually the limiting one. Computer-aided assignment tools should be user friendly with open architecture to communicate with other programs involved in the structure determination. RESULTS Here we present an interactive NMR assignment module which provides numerous graphic tools for the user. The module is composed of a database management system-handling peaks, spins and spin-systems. The assignment information is maintained as a set of interrelated associative arrays, which serve as generic high-level data structures. The module is developed in the macro language embedded in the Gifa NMR processing program (Pons et al. , J. Biomol. NMR, 8 , 445-452, 1996). This provides the user with a consistent interface, a set of sophisticated tools, and an easily extendible and customizable environment. AVAILABILITY The program is available on request from the authors. The Gifa package can be accessed at: ((http://www.cbs. univ-montp1.fr/GIFA)) CONTACT: Marc-Andre.Delsuc@cbs.univ-montp1.fr

Use of the Cadzow procedure in 2D NMR for the reduction of t1 noise

SummaryA data processing approach is proposed for reducing the t1 noise observed in multidimensional NMR spectra. This method is based on the use of the Cadzow procedure [Cadzow, J.A. (1988) IEEE Trans. Acous. Speech Signal Proc., 36, 49–62], and is demonstrated to be efficient for simulated cases as well as real experiments.

Lobeline Docking on AChBP and Nicotinic Receptors: Discriminating Importance of the Pocket Geometry and of the Ligand Configuration

Docking of lobeline, a partial agonist of nicotinic acetylcholine receptors (nAChRs), was investigated at once into crystallographic structures of acetylcholine binding proteins (AChBP) and into 7 and 42 nAChRs homology models, and compared to behavior of full agonists, nicotine and epibatidine. The homology models were built using as templates the different pocket geometries established in crystallographic AChBP structures. Systematic cross-docking of each ligand into binding pockets of the two other ligands as well as its self-docking into its own pocket were performed in order to better understand the structural features determining the binding of these three ligands chosen for their molecular diversity. In AChBPs, epibatidine and nicotine display similar docking scores in their own pocket and in other ligands pockets: in particular, they also dock favorably into the lobeline pocket. In opposite, lobeline displays different features: it only binds favorably to its own pocket in AChBPs. Furthermore, the docking poses observed starting from lobeline stereoisomers support the importance of the intramolecular hydrogen bond between the alcohol function of the-phenyl-hydroxyethyl arm and the piperidinium proton for the lobeline binding to AChBP. For homology models, cross-dockings are still discriminating and the specificity of lobeline for its binding pocket is conserved.

Grid computing for improving conformational sampling in NMR structure calculation

MOTIVATION Methods for automatic nuclear magnetic resonance (NMR) structure determination need to face a high level of ambiguity encountered in NMR spectra recorded by solid-state NMR and by solution NMR of partially unfolded proteins, leading to time-consuming calculations. The software package Ambiguous Restraints for Iterative Assignment (ARIA) allows for straightforward parallelization of the calculation, as the conformers can be generated in parallel on many nodes. RESULTS Due to its architecture, the adaptation of ARIA to grid computing can be easily achieved by using the middleware glite and JDL (Job Description Language) scripts. This adaptation makes it possible to address highly ambiguous datasets, because of the much larger conformational sampling that can be generated by use of the grid computational power. AVAILABILITY The version 2.3.1 of ARIA implemented on the grid is freely available from the ARIA web site: aria.pasteur.fr/downloads.

NMRb: a web-site repository for raw NMR datasets

UNLABELLED The development of NMR in structural proteomics requires the availability of automatic structure determination methods. Many researchers are commonly confronted with the lack of raw datasets during the validation step of such methods. In order to increase test possibilities, the NMRb web-site offers a database of NMR raw datasets, ordered by spectral characteristics. AVAILABILITY NMRb is available from: http://nmrb.cbs.cnrs.fr. SUPPLEMENTARY INFORMATION General organization of NMRb figure, relational model organization, and XML structure files are available from http://nmrb.cbs.cnrs.fr/nmrb-doc.html.

An estimate of spin diffusion in a spin subset: Application to iterative distance calculation from 3D 15N NOESY-HMQC

SummaryA method for quantification of distances between amide hydrogens using only the 3D NOESY-HMQC experiment recorded on a 15N-labelled protein is presented. This method is based on an approximate expression of the NOE intensities between amide hydrogens obtained from continuum modelling of the non-amide spins; this expression is used in a distance calculation algorithm. The algorithm has been named CROWD, standing for Continuum approximation of Relaxati On path Ways between Dilute spins. This approximation as well as the CROWD algorithm are tested on a simulated case; the CROWD algorithm is then applied to experimental data, measured on a fragment of bacteriorhodopsin.

Building Graphs To Describe Dynamics, Kinetics, and Energetics in the d-ALa:d-Lac Ligase VanA.

The d-Ala:d-Lac ligase, VanA, plays a critical role in the resistance of vancomycin. Indeed, it is involved in the synthesis of a peptidoglycan precursor, to which vancomycin cannot bind. The reaction catalyzed by VanA requires the opening of the so-called “ω-loop”, so that the substrates can enter the active site. Here, the conformational landscape of VanA is explored by an enhanced sampling approach: the temperature-accelerated molecular dynamics (TAMD). Analysis of the molecular dynamics (MD) and TAMD trajectories recorded on VanA permits a graphical description of the structural and kinetics aspects of the conformational space of VanA, where the internal mobility and various opening modes of the ω-loop play a major role. The other important feature is the correlation of the ω-loop motion with the movements of the opposite domain, defined as containing the residues A149–Q208. Conformational and kinetic clusters have been determined and a path describing the ω-loop opening was extracted from these clusters. The determination of this opening path, as well as the relative importance of hydrogen bonds along the path, permit one to propose some key residue interactions for the kinetics of the ω-loop opening.

Simultaneous use of solution, solid-state NMR and X-ray crystallography to study the conformational landscape of the Crh protein during oligomerization and crystallization

We explore, using the Crh protein dimer as a model, how information from solution NMR, solid-state NMR and X-ray crystallography can be combined using structural bioinformatics methods, in order to get insights into the transition from solution to crystal. Using solid-state NMR chemical shifts, we filtered intra-monomer NMR distance restraints in order to keep only the restraints valid in the solid state. These filtered restraints were added to solid-state NMR restraints recorded on the dimer state to sample the conformational landscape explored during the oligomerization process. The use of non-crystallographic symmetries then permitted the extraction of converged conformers subsets. Ensembles of NMR and crystallographic conformers calculated independently display similar variability in monomer orientation, which supports a funnel shape for the conformational space explored during the solution-crystal transition. Insights into alternative conformations possibly sampled during oligomerization were obtained by analyzing the relative orientation of the two monomers, according to the restraint precision. Molecular dynamics simulations of Crh confirmed the tendencies observed in NMR conformers, as a paradoxical increase of the distance between the two β1a strands, when the structure gets closer to the crystallographic structure, and the role of water bridges in this context.

A Decomposition of the Noe Intensity Matrix

The protein structure determination by NMR is based on the estimation of the distances between the hydrogens, from the measurement of the nuclear Overhauser effect (nOe). Numerous methods were designed to calculate precise estimates of these distances from the nOe intensities (Borgias and James, 1990; Boelens et al., 1988; Madrid et al., 1991). But, as the exact calculation of the distances requires the knowledge of the entire nOe matrix (Olejniczak et al., 1986), the distance calculation methods are thus limited, not only by the experimental signal-to-noise ratio, but also by the superpositions on the experimental spectra.