Application of NMR, molecular simulation, and hydrodynamics to conformational analysis of trisaccharides

The preferred conformations and conformational flexibilities of the trisaccharides alpha-D-Glcp-(1-->2)-beta-D-Glcp-(1-->3)-alpha-D-Glcp-OMe (I) and alpha-D-Glcp-(1-->3)[beta-D-Glcp-(1-->4)]-alpha-D-Glcp-OMe (II) in aqueous solution were determined using nuclear magnetic resonance (NMR) spectroscopy, molecular dynamics (MD) and Langevin dynamics (LD) simulations, and hydrodynamics calculations. Both trisaccharides have a vicinal substitution pattern in which long range (nonsequential) interactions may play an important role. LD simulation at 600 K indicated that the all-syn conformation predominated, though other conformations were apparent. NOE data and MD and LD simulations at 298 K all indicated that trisaccharide I is a single all-syn conformer in solution. Given that previous studies showed evidence of anti-conformers in beta-D-Glcp-(1-->2)-beta-D-Glcp-(1-->3)-alpha-D-Glcp-OMe, this result provides an example of how changing the anomeric configuration of one residue from beta to alpha can make an oligosaccharide more rigid. Discrepancies in inter-ring distances obtained by experiment and by simulation of the all-syn conformer suggest the presence of an anti-psi conformation at the beta-(1-->4)-linkage for II. A combined analysis of measured and calculated translational diffusion constants and (13)C T(1) relaxation times yield order parameters of 0.9 for each trisaccharide. This implies that any interconversion among conformations is significantly slower than tumbling. Anisotropies of approximately 1.6 and 1.3 calculated for I and II, respectively, are consistent with the observed relatively flat T(1) profiles because the tumbling is not in the motional narrowing regime.

Micelle-bound conformation of a hairpin-forming peptide: combined NMR and molecular dynamics study

A peptide fragment from a protein hairpin turn region was modified by addition of isoleucine residues to both ends to enhance binding to lipid micelles; the resulting peptide (I(1)-I(2)-C(3)-N(4)-N(5)-P(6)-H(7)-I(8)-I(9)) contains the core sequence I-C-N-N-P-H from an antibody-binding region of hemagglutinin A. Nuclear magnetic resonance (NMR) diffusion measurements indicated partial binding (43-65%) of the peptide to micelles of n-octylglucoside and significantly stronger binding (85%) to dodecylphosphocholine (DPC) micelles. Simulated annealing and conformational analysis using nuclear Overhauser enhancement restraints revealed a type I or III hairpin turn between residues N(5) and I(8) of the DPC-bound peptide. Amide exchange experiments support the possibility that a hydrogen bond forms between N(5) and I(8), stabilizing the turn. In contrast, no discernable structure was observed for the peptide in aqueous solution by either NMR or circular dichroism. Molecular dynamics simulations of DPC micelles and peptide-micelle complexes suggested that the peptide lies flat on the micelle surface and showed rapid rearrangement of the lipids to accommodate the bound peptide. According to a search performed using the basic local alignment search tool (BLAST), the sequences N-P-H-I and N-P-H-V are present as hairpin turns in eight of the nine proteins whose crystal structures were available. The addition of isoleucine residues and the use of lipid micelles to stabilize hairpin conformations equivalent to those found in proteins generates new possibilities for reproducing biologically important hairpin turns from short, linear peptides.

Modified GOESY in the analysis of disaccharide conformation

One-dimensional nuclear magnetic resonance techniques were applied to the conformational investigation of a disaccharide. More specifically, nuclear Overhauser enhancements (NOEs) of protons on either side of the glycosidic bond have been used to determine the conformation of the disaccharide alpha-l-Rhap-(1 --> 2)-alpha-l-Rhap-OMe. A modified GOESY sequence, incorporating selective excitation and pulsed field gradient enhancement, was developed and used to accurately measure small NOE signals of interest. These experiments were named M-GOESY, for modified GOESY, and the data they provided were used to calculate internuclear distances in the disaccharide molecule. The accuracy of the M-GOESY measurements was enhanced by elimination of indirect effects, or spin diffusion, by selective inversion(s) of either the intermediate magnetization or the source and target magnetization during the mixing time. Results of this study indicate that the alpha-l-Rhap-(1 --> 2)-alpha-l-Rhap-OMe disaccharide molecule exists primarily in one conformation, with the glycosidic torsion angle psi approximately -30 degrees based on past molecular dynamics simulations.

CD4-IgG binding threshold for inactivation of human immunodeficiency virus type 1

The stoichiometry of human immunodeficiency virus type 1 (HIV-1) inactivation by soluble receptor CD4-IgG hybrid dimers (CD4-IgG) was examined. The extent of HIV-1 inactivation was measured in a sensitive plaque-forming assay, and the corresponding level of CD4-IgG binding was determined by immunofluorescence of infected cells. Ninety percent virus inactivation occurred at relatively low levels of CD4-IgG binding (10% of the saturating level). At even lower binding levels (1.4% of maximum binding), virus survival was 44%. Over a broad range of binding conditions, the survival curve followed a model in which viruses binding more than a threshold level of CD4-IgG were completely inactivated, while viruses binding less remained infectious. The data indicate that CD4-IgG binding to 1.4% of gp120 binding sites equals the threshold for inactivation. Thus, virus inactivation can begin when 3 CD4-IgG (of approximately 216 gp120 sites) bind per virion.

Binding of Au(CN)2- and Pt(CN)4-2- to horse liver alcohol dehydrogenase. A 35C1NMR relaxation study

The binding of Au(CN)2- and Pt(CN)4-2- ions to the coenzyme binding site of horse liver alcohol dehydrogenase (alcohol : NAD+ oxidoreductase EC 1.1.1.1) has been studied by 35C1 nuclear magnetic relaxation. Longitudinal relaxation rates were analyzed in terms of a simple model and binding constants for Au(CN)2-, Pt(CN)4-2- and C1- were estimated. From a comparison between transverse and longitudinal relaxation rates the correlation time and the quadrupole coupling constant of bound chloride ion were obtained. The quadrupole coupling constant estimated from a simple electrostatic model for chloride ion interacting with an arginine group agrees with the experimental value.