Biomedical subjects

Marc-André Delsuc

Publications and source records attributed to Marc-André Delsuc.

7 recordsLinked to original sources

PubMed2004

Measurement of aroma compound self-diffusion in food models by DOSY.

Self-diffusion measurement of solutes in polymer gels has been investigated using pulsed gradient spin echo NMR spectroscopy. However, few data are available on the self-diffusion of small solutes in natural polysaccharide polymers used as thickeners in the food industry. Since aroma diffusion in food matrices could have an impact on flavor release, this is an interesting and economic challenge. Diffusion ordered spectroscopy (DOSY) resolves diffusion data for each component in complex mixtures. We used DOSY with the inverse Laplace transform approach with the maximum entropy algorithm to investigate diffusion of two aroma compounds, ethyl butanoate and linalool, in an iota-carrageenan matrix as the food model. We showed that the self-diffusion coefficient values of small molecules in a polysaccharide matrix could be easily extracted using this method. We then investigated the impact of the gelling state of iota-carrageenan matrices on the self-diffusion of ethyl butanoate.

Acyclic Monoterpenes↗

PubMed2004

From NMR chemical shifts to amino acid types: investigation of the predictive power carried by nuclei.

An approach to automatic prediction of the amino acid type from NMR chemical shift values of its nuclei is presented here, in the frame of a model to calculate the probability of an amino acid type given the set of chemical shifts. The method relies on systematic use of all chemical shift values contained in the BioMagResBank (BMRB). Two programs were designed, one (BMRB stats) for extracting statistical chemical shift parameters from the BMRB and another one (RESCUE2) for computing the probabilities of each amino acid type, given a set of chemical shifts. The Bayesian prediction scheme presented here is compared to other methods already proposed: PROTYP RESCUE and PLATON and is found to be more sensitive and more specific. Using this scheme, we tested various sets of nuclei. The two nuclei carrying the most information are C(beta) and H(beta), in agreement with observations made in Grzesiek and Bax, 1993. Based on four nuclei: H(beta), C(beta), C(alpha) and C', it is possible to increase correct predictions to a rate of more than 75%. Taking into account the correlations between the nuclei chemical shifts has only a slight impact on the percentage of correct predictions: indeed, the largest correlation coefficients display similar features on all amino acids.

Amino Acids↗

PubMed2003

Active peptidic mimics of the second intracellular loop of the V(1A) vasopressin receptor are structurally related to the second intracellular rhodopsin loop: a combined 1H NMR and biochemical study.

Vasopressin (VP) receptors belong to the widespread G protein-coupled receptor family. The crucial role of VP receptor intracellular loops in the coupling with the heterotrimeric G proteins was previously demonstrated by construction of a vasopressin receptor chimera. Yet, no fine structural data are available concerning the receptor molecular determinants involved in their interactions with G proteins. In this study, we synthesized both a linear and a cyclic form of the second intracellular loop (i2) of the human V(1a) vasopressin receptor isoform that is important for the interaction between the alphaq/alpha11 G protein and the receptor. These two peptides are biologically active. They specifically inhibit vasopressin binding to the V(1a) receptor, suggesting that the corresponding endogenous peptides contribute to the structure of the vasopressin binding site via intra- or intermolecular interactions with the core of the V(1a) receptor. The i2 peptide structures were determined by (1)H NMR. Both exhibit a helix and helical elements in their N- and C-terminal parts, respectively, separated by a turn imposed by a proline residue. More interestingly, the central Pro-Leu motif conserved in many GPCRs and thought to be important for coupling to G proteins can adopt different conformations. The "U" shape structure of the i2 loop is compatible with its anchoring to transmembrane domains III and IV and is very similar to the shape of bovine rhodopsin i2. Altogether, these data contribute to a better understanding of the structure of a not yet crystallized GPCR using the mimetic peptide approach.

Amino Acid Sequence↗

PubMed2003

Refined solution structure of a liganded type 2 wheat nonspecific lipid transfer protein.

The refined structure of a wheat type 2 nonspecific lipid transfer protein (ns-LTP2) liganded with l-alpha-palmitoylphosphatidylglycerol has been determined by NMR. The (15)N-labeled protein was produced in Pichia pastoris. Physicochemical conditions and ligandation were intensively screened to obtain the best NMR spectra quality. This ns-LTP2 is a 67-residue globular protein with a diameter of about 30 A. The structure is composed of five helices forming a right superhelix. The protein presents an inner cavity, which has been measured at 341 A(3). All of the helices display hydrophobic side chains oriented toward the cavity. The phospholipid is found in this cavity. Its fatty acid chain is completely inserted in the protein, the l-alpha-palmitoylphosphatidylglycerol glycerol moiety being located on a positively charged pocket on the surface of the protein. The superhelix structure of the protein is coiled around the fatty acid chain. The overall structure shows similarities with ns-LTP1. Nevertheless, large three-dimensional structural discrepancies are observed for the H3 and H4 alpha-helices, the C-terminal region, and the last turn of the H2 helix. The lipid is orthogonal to the orientation observed in ns-LTP1. The volume of the hydrophobic cavity appears to be in the same range as the one of ns-LTP1, despite the fact that ns-LTP2 is shorter by 24 residues.

Amino Acid Sequence↗

PubMed2002

Different qualitative and quantitative regulation of V beta TCR transcripts during early acute allograft rejection and tolerance induction.

Recently, using a global method of T cell repertoire analysis, we showed that purified naive T cells confronted in vitro with allogeneic APCs in a direct pathway-restricted MLR up-regulate their Vbeta mRNAs without exhibiting skewing of complementarity-determining region 3 (CDR3) length distribution. In this report, using this approach, we show in vivo that Vbeta transcript regulation and CDR3 length distribution follow the same pattern during acute rejection of MHC-incompatible heart allografts. In contrast, in tolerance induction by priming of recipients with donor cells, the vigorous Vbeta mRNA accumulation with Gaussian CDR3 length distribution is abolished, providing a possible explanation for the down-regulation of activated T cells in tolerant animals. In addition, tolerated grafts harbor T cells with a highly altered repertoire, suggestive of self-restricted presentation with some patterns corresponding to previously identified regulatory cells.

Acute Disease↗

PubMed2002

Structure refinement of flexible proteins using dipolar couplings: application to the protein p8MTCP1.

The present study deals with the relevance of using mobility-averaged dipolar couplings for the structure refinement of flexible proteins. The 68-residue protein p8MTCP1 has been chosen as model for this study. Its solution state consists mainly of three alpha-helices. The two N-terminal helices are strapped in a well-determined alpha-hairpin, whereas, due to an intrinsic mobility, the position of the third helix is less well defined in the NMR structure. To further characterize the degrees of freedom of this helix, we have measured the dipolar coupling constants in the backbone of p8MTCP1 in a bicellar medium. We show here that including D(dip)HN dipolar couplings in the structure calculation protocol improves the structure of the alpha-hairpin but not the positioning of the third helix. This is due to the motional averaging of the dipolar couplings measured in the last helix. Performing two calculations with different force constants for the dipolar restraints highlights the inconstancy of these mobility-averaged dipolar couplings. Alternatively, prior to any structure calculations, comparing the values of the dipolar couplings measured in helix III to values back-calculated from an ideal helix demonstrates that they are atypical for a helix. This can be partly attributed to mobility effects since the inclusion of the 15N relaxation derived order parameter allows for a better fit.

Animals↗

PubMedDate not supplied

CRAACK: consensus program for NMR amino acid type assignment.

Protein peak spectrum assignment is a prerequisite of the nuclear magnetic resonance study of a molecule. We present here a computer tool which proposes the determination of the amino acid type from the values of the chemical shifts. This tool is based on two consensus algorithms based on several published typing algorithms and was trained and extensively tested against the Biological Magnetic Resonance Bank chemical shift data bank. The first one accomplishes the analysis with support vector machine technology, grouping related amino acids together, and presents a mean rate of success above 90% on the test set. The second one uses a classical consensus algorithm of vote. Furthermore, secondary structural prediction is available. This tool can be used for assisting manual assignment of peptides and proteins and can also be used as a step in an automated approach to assignment. This program has been called CRAACK and is publicly available at the following URL: http://abcis.cbs.cnrs.fr/craack.

Algorithms↗