Mechanism of interaction of PITPalpha with membranes: conformational changes in the C-terminus associated with membrane binding

Eukaryotic phosphatidylinositol transfer proteins (PITPs) are composed predominantly of small ( approximately 32 kDa) soluble proteins that bind and transfer a single phospholipid, normally phosphatidylinositol or phosphatidycholine. Two forms, PITPalpha and PITPbeta, which share approximately 80% amino acid sequence similarity, are known. Rat PITPalpha was labeled at specific single reactive Cys residues with I-AEDANS and used to examine PITP-membrane interactions. Upon binding to phospholipid vesicles, PITP labeled with AEDANS at the C-terminus, a region postulated to be involved in membrane binding, shows significant decreases in both steady-state and dynamic fluorescence anisotropy. In contrast, PITPs labeled with AEDANS at sites located distal to the C-terminus show increases in both steady-state and dynamic anisotropy. These results suggest that interaction of PITP with membrane surfaces leads to significant alterations in conformation and perhaps melting of the C-terminal helix.     

Allele effects in MHC-peptide interactions: a theoretical analysis of HLA-DRbeta1*0101-HA and HLA-DRbeta1*0401-HA complexes

HLA-DRbeta1*0101-HA and HLA-DRbeta1*0401-HA complexes are studied and compared by means of their computationally derived multipolar moments and electrostatic potentials. Changes in electrostatic potential are associated with definite pocket interaction profiles. Thus, Pocket 1 projects itself as an anchoring pocket for both complexes, in accordance with experimental results. While Pocket 4 has an anchoring profile in the HLA-DRbeta1*0101 allele, it presents itself as modulating pocket-peptide interactions in HLA-DRbeta1*0401. Pockets 6 and 7 both strongly contribute to allele specificity, with Pocket 7 being very important for HLA-DRbeta1*0401-HA. Pocket 9 acts as a "double purpose" interaction site for both alleles. It both projects itself as an anchoring pocket as well as modulating pocket-peptide interactions.     

Structural elucidation of type III group B Streptococcus capsular polysaccharide using molecular dynamics simulations: the role of sialic acid

The conformational properties of the capsular polysaccharide (CPS) from group B Streptococcus serotype III (GBS III) are derived from 50 ns explicitly solvated molecular dynamics simulations of a 25-residue fragment of the CPS. The results from the simulations are shown to be consistent with experimental NMR homo- and heteronuclear J-coupling and NOE data for both the sialylated native CPS and for the chemically desialylated polysaccharide. A helical structure is predicted with a diameter of 29.3 A and a pitch 89.5 A, in which the sialylated side chains are arrayed on the exterior surface of the helix. The results provide an explanation for the observation that CPS antigenicity varies with carbohydrate chain length up to approximately 4 pentasaccharide repeat units. The conformation of the immunodominant region is established and shown to be independent of the presence of sialic acid. The data provide an explanation for the observation that the specificity of the determinant, associated with the major population of antibodies raised upon immunization of rabbits with GBS III, is dependent on the presence of sialic acid. In the sialylated native CPS, the antibody response is largely directed against the immunodominant core of the helix. From simulations of the desialylated CPS, a model emerges which suggests that the minor population of antibodies, whose determinant is not sialic acid dependent, recognizes the same immunodominant region, but that in the disordered CPS this region is not presented in a regular repeating motif.     

The alpha-(1-->6) glycosidic linkage as a novel conformational entropic regulator in osmoregulated periplasmic alpha-cyclosophorohexadecaose

Molecular dynamics simulations were performed to explain the conformational effect of an alpha-(1-->6)-glycosidic linkage upon the cyclic osmoregulated periplasmic glucan (OPG) produced by Xanthomonas campestris pv. citri. We suggest that a single alpha-(1-->6)-glycosidic linkage in cyclic OPG functions as a novel entropic regulator, which reduces the conformational entropy of cyclic OPG and increases the motional entropy of solvent water molecules.     

Conformational folding of xyloglucan side chains in aqueous solution from molecular dynamics simulation

Molecular dynamics simulation was carried out on xyloglucan with explicit water molecules to investigate the folding mechanism of side chains onto a main chain in aqueous solution. The model xyloglucan was composed of 12 beta-D-glucopyranoses as a main chain substituted with six galactoses and three xyloses as side chains. Two conditions were set for the ribbon-like main chain; one is restricted to be 'flat' and the other is without restriction. The free main chain of xyloglucan has a 'twisted' conformation as the major one. Conformational folding of side chains onto the main chain was analyzed with dihedral angles at each glycosidic linkage. In a 5-ns calculation, the xyloglucan has a tendency to contract in both the restricted and the free systems, but the mode of contraction is different. Side chains tend to stick onto the flat surface of the main chain in the restricted system, while they do not tightly do so in the free one; instead the main chain takes a twisted and sometimes embowed conformation. This result indicates that the main chain has greater attractive forces to bind side chains when it is flat, while it loses the ability as it is twisted.     

Hyaluronan chain conformation and dynamics

An overview of the present state of research in the field of hyaluronan chain conformational aspects is presented. The relationship between structure and dynamics are illustrated for a series of hyaluronan oligomers. Conformational characteristics of hyaluronan chains are discussed, together with the dynamic chain patterns, evaluated by using a theoretical approach to diffusive polymer dynamics. The dependence of correlation times and NMR relaxation parameters from the chain dimension are investigated. Topological features and dimensional properties are related to the structural determinants by using classical computational methods of molecular mechanics and Monte Carlo simulation.     

Structural evaluation of conformational transition state responsible for self-assembly of tau microtubule-binding domain

In the brains of Alzheimer's disease patients, the tau protein abnormally aggregates to form an insoluble paired helical filament (PHF). Since the third repeat structure (R3) of the tau microtubule-binding domain plays an essential role in PHF formation and self-aggregates most significantly in an aqueous solution of 20-40% trifluoroethanol (TFE), its possible conformation was estimated from the combination of (i) the TFE-dependent deviations of NH and CalphaH proton chemical shifts from those of the random structure in water and (ii) the TFE-dependent NOE effect connectivity diagrams between the neighboring protons. Consequently, it was indicated that the extended structure of the N-terminal VQIVYK moiety and the alpha-helical-like structure of the LSKVTSKC region provide a structural scaffold for initiating the self-assembled filament formation of the R3 structure. To the best of our knowledge, this is the first study that demonstrated the initial structural moiety and its structural feature necessary for starting the tau PHF formation.     

The structure and function of oxidized albumin in hemodialysis patients: Its role in elevated oxidative stress via neutrophil burst

Oxidized albumin is a reliable marker of oxidative stress in hemodialysis (HD) patients. However, oxidized albumin in vivo and its possible clinical significance has been rarely investigated. In the present study, the qualitative modification of albumin in HD patients (n = 20) was examined and their results were compared with healthy age-matched controls (n = 10). The increase in plasma protein carbonyl levels in HD patients was largely due to an increase in oxidized albumin. Human serum albumin (HSA) of HD patients, HSA of HD patients (HD-HSA) and normal subjects (Normal-HSA) were purified on a blue Sepharose CL-6B column. Spectroscopic analysis confirmed that the HD-HSA samples contained higher levels of carbonyls than Normal-HSA. An HPLC analysis also suggested that the state of the purified HSA used throughout the experiments accurately reflects the redox state of albumin in blood. HD-HSA was found to have a decreased the antioxidant activity, and was able to trigger the oxidative burst of human neutrophils, compared to Normal-HSA. HD-HSA was conformationally altered, with its hydrophobic regions more exposed and to have a negative charge. In binding experiments, HD-HSA showed impaired Site II-ligand binding capabilities. Collectively, the oxidation of plasma proteins, especially HSA, might enhance oxidative stress in HD patients.     

A novel mechanism for the modulation of the Ras-effector interaction by small molecules

When proteins require different conformations for their biological function, all these functional states have to coexist simultaneously in solution. However, the corresponding Gibbs free energy differences are usually rather high and thus the conformation with lowest energy predominates in solution whereas the populations of the states with higher energy (excited states) are very small. A stabilization of these excited states can be used as a novel principle to influence the activity of proteins by small molecules. For a proof of this principle, we selected the Ras protein that was shown by (31)P NMR spectroscopy to exist in solution in at least two different conformational states in its GTP form. One of these states shows a drastically reduced affinity to effectors. With Zn(2+)-cyclen we found a small molecule which selectively stabilizes the weak-binding state. It may serve as lead compound for the development of a new type of Ras-inhibitors.     

NMR spectroscopy: a powerful tool for detecting the conformational features of symmetrical persubstituted mixed cyclomaltoheptaoses (beta-cyclodextrins)

The conformation in solution of exhaustively derivatized mixed cyclomaltooligosaccharides (cyclodextrins) has been defined by NMR spectroscopy. Both tilting of glucopyranose units about the glycosidic linkages and ring deviations from the 4C1 chair conformation are detected, the entities of which are strongly dependent on the nature of the derivatizing groups.