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PubMed1991

Structure and conformation of peptides containing the sulphonamide junction. III. Synthesis, crystal and molecular structure of a taurine containing peptidic oxa-cyclol.

The insertion of the (S)-lactyl residue into the cyclodipeptide cyclo (-Tau-Pro-) 3 leads in good yields to the first example of a stable tetrahedral adduct (oxa-cyclol) 5 containing the sulphonamide junction. Compound 5 does not show a significant tendency towards tautomeric equilibria and possesses an unexpected syn-orientation involving the hydroxyl group and the Pro-H alpha. The crystal structure and molecular conformation of 5 has been determined. Crystals are orthorhombic, s.g. P2(1)2(1)2(1), with a = 6.607, b = 12.297, c = 16.622 A. The cisoidal conformation around the S-N bond is very similar to that found in the previously studied linear and cyclic peptides containing a sulphonamide junction. The taurine nitrogen is practically planar whereas the proline nitrogen, bound to the SO2 group, is highly pyramidal. In the tricyclic system of 5 the seven-membered ring adopts a twist-chair conformation while the pyrrolidine and oxazolidinone rings show an envelope conformation. The crystal packing is characterized by three hydrogen bonds all formed by means of a water molecule.

Amino Acid Sequence↗
PubMed1993

[The effect of molecular structure of hydroxyethyl starch on the elimination kinetics and fluidity of blood in human volunteers].

Influence of the Molecular Structure of Hydroxyethyl Starch on Elimination Kinetics and Blood Fluidity in Voluntary Subjects In a cross-over study 6 volunteers received an infusion of 500 ml hydroxyethyl starch of a batch with a high C2/C6-substitution ratio (10.8), or after a washout period of 3 months they received a batch with a low C2/C6-substitution ratio (5.8). The infusion solution was administered at random. The batches were identical as regards their physicochemical characteristics (HES 200/0.5 10%). The concentration and molecular weight distribution of the intravascular hydroxyethyl starch molecules were determined after infusion up to 24 h, the blood fluidity before and after infusion. The substitution ratio of the C2- or C6-atoms in the glucose ring has an effect on the degradation of the hydroxyethyl starch molecule: the molecules with a high C2/C6-substitution ratio appear to be degraded within the same period of time, the resulting degradation products, however, have a higher molecular weight. This influences the blood fluidity. While the haematocrit decrease occurring 1 h after end of infusion is comparable, it keeps up for a longer time in case of a higher C2/C6-substitution ratio. The increase of plasma viscosity is more pronounced in case of a high C2/C6-substitution ratio. Clinical consequences are discussed.

Adult↗
PubMed2006

Molecular structures and electronic transitions of 3,6-diphenyl-1,2-dithiin and its radical cation: a spectroelectrochemical and DFT study.

One-electron oxidation of 3,6-diphenyl-1,2-dithiin yields the corresponding radical cation. The product is stable at low temperatures and can be distinguished by a triplet EPR signal. Cyclic voltammetric, UV-vis spectroelectrochemical, and DFT studies were performed to elucidate its molecular structure and electronic properties. Time-dependent DFT calculations reproduce appreciably well the UV-vis spectral changes observed during the oxidation. The results reveal a moderately twisted structure of the 1,2-dithiin heterocycle in the radical cation.

Cations↗
PubMed1994

Effect of molecular structure of poly(glycidyl ether) reagents on crosslinking and mechanical properties of bovine pericardial xenograft materials.

With the identification of the exacerbating effect of glutaraldehyde on calcification of heart valve materials, there exists a renewed interest in both alternative reagents and the effects of crosslinking on connective tissues. One potentially useful class of reagents are poly(glycidyl ether) compounds. We have examined 5 of these reagents with different molecular sizes and functionalities for their effects on mechanical properties and collagen denaturation (shrinkage) temperature. Samples of bovine pericardium were tested fresh or after 48 h fixation in one of the five compounds for denaturation temperature, stress-strain response, stress relaxation, plastic deformation, and fracture properties. Of the compounds tested, those with intermediate length backbones and 4 or 5 epoxide groups were most effective in producing intrahelical crosslinking and increased denaturation temperature over 48 h. However, in samples examined after 17 months of fixation, all reagents had equivalently increased the denaturation temperature. Examination of mechanical results revealed two distinct mechanisms for mechanical change. Observed shifting of the stress-strain curve to the right (due to shrinkage), increased plastic deformation, and some reduction of stress relaxation are all unrelated to denaturation temperature (and hence to changes in intrahelical crosslinking). An alternate mechanism, perhaps formation of intermolecular crosslinks may be responsible. Intrahelical crosslinking produces only lesser reductions in stress relaxation. Cross-comparison of reagents of differing molecular structure provides a useful tool toward increased understanding of the mechanical consequences of tissue crosslinking.

Animals↗
PubMedDate not supplied

Molecular structure of BRCA1-estrogen receptor alpha-estrogen complex: relevance to breast cancer?

Recent studies indicate that BRCA1, the first breast cancer susceptibility gene to be identified and cloned, interacts with and regulates the activity of estrogen receptor alpha. The availability of genetic tests for BRCA gene mutations has prompted cancer geneticists to generate information about genetic risk and inform women with a personal or family history of breast or ovarian cancer of preventive measures. However, knowledge on the human BRCA1-estrogen receptor alpha-estrogen complex is limited. Here, the author focuses on its 3D molecular structure and properties.

BRCA1 Protein↗
PubMed2005

Ultrafast electron diffraction: oriented molecular structures in space and time.

The technique of ultrafast electron diffraction allows direct measurement of changes which occur in the molecular structures of isolated molecules upon excitation by femtosecond laser pulses. The vectorial nature of the molecule-radiation interaction also ensures that the orientation of the transient populations created by the laser excitation is not isotropic. Here, we examine the influence on electron diffraction measurements--on the femtosecond and picosecond timescales--of this induced initial anisotropy and subsequent inertial (collision-free) molecular reorientation, accounting for the geometry and dynamics of a laser-induced reaction (dissociation). The orientations of both the residual ground-state population and the excited- or product-state populations evolve in time, with different characteristic rotational dephasing and recurrence times due to differing moments of inertia. This purely orientational evolution imposes a corresponding evolution on the electron scattering pattern, which we show may be similar to evolution due to intrinsic structural changes in the molecule, and thus potentially subject to misinterpretation. The contribution of each internuclear separation is shown to depend on its orientation in the molecular frame relative to the transition dipole for the photoexcitation; thus not only bond lengths, but also bond angles leave a characteristic imprint on the diffraction. Of particular note is the fact that the influence of anisotropy persists at all times, producing distinct differences between the asymptotic "static" diffraction image and the predictions of isotropic diffraction theory.

Journal Article↗
PubMed2004

Study of the relationship of small variations of the molecular structure and the iron state in iron containing proteins by Mössbauer spectroscopy: biomedical approach.

This review considers the results of experimental Mössbauer studies and theoretical calculations of the effect of small variations of protein molecular structure on the iron electronic structure and stereochemistry in order to understand the proteins structural heterogeneity and functional variety. Structural changes in iron containing proteins during various diseases are also considered. These results show the relationship of the small structural variations and Mössbauer parameters of iron containing proteins and demonstrate the possibilities of Mössbauer spectroscopy to obtain new information at the molecular level in biomedical research.

Animals↗
PubMed1997

Molecular structure and dynamics at liquid-liquid interfaces.

The structural, dynamical, and electrical properties of the interface between two immiscible liquids are described. The adsorption of solute molecules and the processes of ion transfer across the interface and of electron transfer at the interface are discussed. The microscopic perspective is emphasized by focusing on selected recent experimental results and on results obtained from molecular dynamics and Monte Carlo computer simulations. The validity of some of the existing models of the interface is examined. A proper account of the molecular structure of the interface is important for understanding solvation and charge transfer processes at the interface.

Adsorption↗
PubMedDate not supplied

Human response to dioxin: aryl hydrocarbon receptor (AhR) molecular structure, function, and dose-response data for enzyme induction indicate an impaired human AhR.

The aryl hydrocarbon receptor (AhR) mediates nearly all studied adverse effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and many related compounds. Binding of TCDD or related ligands to AhR is the key initiating event in downstream biochemical responses. The binding affinity of AhR for TCDD is specific to species and strain, and studies of human AhR demonstrate binding affinities approximately an order of magnitude or more lower than those observed in the most sensitive laboratory strains and species. Molecular genetic studies confirmed that human AhR shares key mutations with the DBA mouse strain that result in an "impaired" AhR (with respect to TCDD binding and responsiveness). Despite a number of polymorphisms in human AhR, the key "DBA-type" mutations appear to be a constant feature of the human AhR, and no polymorphisms have been identified that compensate for the impaired binding function conferred by these mutations. Consistent with the impaired binding status of the human AhR, human cells have consistently required approximately 10-fold higher concentrations of TCDD in vitro than rodent cells to respond with enzyme induction. Recent studies of in vivo enzyme induction-related endpoints in human populations with moderately and highly increased TCDD body burdens detected no relationship between these endpoints and TCDD body burdens at body-burden levels up to 250 ng TEQ/kg body weight, or approximately 25 times above the upper range of current general population background body burdens, while marked elevations in enzyme activity were observed in persons with body burdens above 750 ng TEQ/kg. In contrast, the more sensitive laboratory rodent strains and species exposed to TCDD exhibit significant enzyme induction at body burdens below 50 ng/kg. These interspecies data on the most sensitive and best understood response to binding of TCDD and related compounds to the AhR are consistent with the binding affinity and molecular structure data and support the hypothesis that the human AhR is less functional than the AhR of the more sensitive laboratory animals at a molecular level. Quantitative risk assessments involving interspecies extrapolation from sensitive laboratory species and strains should take these fundamental differences into account when margins of exposure and safety factors are considered.

Animals↗
PubMed1987

Crystal and molecular structures of the complex of alpha-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 A resolution.

The molecular structure of the complex between bovine pancreatic alpha-chymotrypsin (EC 3.4.4.5) and the third domain of the Kazal-type ovomucoid from Turkey (OMTKY3) has been determined crystallographically by the molecular replacement method. Restrained-parameter least-squares refinement of the molecular model of the complex has led to a conventional agreement factor R of 0.168 for the 19,466 reflections in the 1.8 A (1 A = 0.1 nm) resolution shell [I greater than or equal to sigma (I)]. The reactive site loop of OMTKY3, from Lys13I to Arg21I (I indicates inhibitor), is highly complementary to the surface of alpha-chymotrypsin in the complex. A total of 13 residues on the inhibitor make 113 contacts of less than 4.0 A with 21 residues of the enzyme. A short contact (2.95 A) from O gamma of Ser195 to the carbonyl-carbon atom of the scissile bond between Leu18I and Glu19I is present; in spite of it, this peptide remains planar and undistorted. Analysis of the interactions of the inhibitor with chymotrypsin explains the enhanced specificity that chymotrypsin has for P'3 arginine residues. There is a water-mediated ion pair between the guanidinium group on this residue and the carboxylate of Asp64. Comparison of the structure of the alpha-chymotrypsin portion of this complex with the several structures of alpha and gamma-chymotrypsin in the uncomplexed form shows a high degree of structural equivalence (root-mean-square deviation of the 234 common alpha-carbon atoms averages 0.38 A). Significant differences occur mainly in two regions Lys36 to Phe39 and Ser75 to Lys79. Among the 21 residues that are in contact with the ovomucoid domain, only Phe39 and Tyr146 change their conformations significantly as a result of forming the complex. Comparison of the structure of the OMTKY3 domain in this complex to that of the same inhibitor bound to a serine proteinase from Streptomyces griseus (SGPB) shows a central core of 44 amino acids (the central alpha-helix and flanking small 3-stranded beta-sheet) that have alpha-carbon atoms fitting to within 1.0 A (root-mean-square deviation of 0.45 A) whereas the residues of the reactive-site loop differ in position by up to 1.9 A (C alpha of Leu18I). The ovomucoid domain has a built-in conformational flexibility that allows it to adapt to the active sites of different enzymes. A comparison of the SGPB and alpha-chymotrypsin molecules is made and the water molecules bound at the inhibitor-enzyme interface in both complexes are analysed for similarities and differences.

Animals↗
PubMed2006

The influence of the molecular structure of lipid membranes on the electric field distribution and energy absorption.

We consider the influence of the molecular structure of phospholipid membranes on their dielectric properties in the radio frequency range. Membranes have a stratified dielectric structure on the submolecular level, with the lipid chains forming a central hydrophobic layer enclosed by the polar headgroups (HGs) and bound water layers. In our numerical model, isotropic permittivities of 2.2 and 48.8 were assigned to the lipid chain and bound water layers, respectively. The HG region was assumed to possess an anisotropic static permittivity with 142.2 and 30.2 in the tangential and normal directions, respectively. The permittivities of the HG and bound water regions have been assumed to disperse at frequencies around 51 and 345 MHz to become 2.2 and 1.8, respectively, in both the normal and tangential directions. Electric field distribution and absorption were calculated for phospholipid vesicles with 75 nm radius as an example. Significant absorption has been obtained in the HG and bound water regions. Averaging the membrane absorption over the layers resulted in a decreased absorption below 1 GHz but a more than 10-fold increase above 1 GHz, compared to a model with a homogeneous membrane of averaged properties. We propose single particle dielectric spectroscopy by AC electrokinetics at low-bulk medium conductivities for an experimental verification of our model.

Absorption↗
PubMed1993

Molecular structural changes in Mallory body proteins in human and mouse livers: an infrared spectroscopy study.

To study the molecular structure of Mallory body (MB) proteins we applied infrared spectroscopy of the isolated MBs from livers obtained from autopsied patients with alcoholic cirrhosis and griseofulvin-fed (GF-fed) mice. Liver frozen sections were extracted with detergent and digested with deoxyribo- and ribonuclease and collagenase. MB-enriched fractions were then separated out using the aqueous two-phase polymer system. Immunohistochemical and electron microscopic examination showed that the MB composition was virtually identical in human and mouse livers. Infrared spectra of both MB samples showed that the MBs had more numerous and stronger intermolecular hydrogen bonding than did the background control fractions as well as the cytoskeletal fraction from control and GF-fed mice. This may explain why the proteins in MBs are aggregated. The relative amount of beta-sheets was increased compared to the alpha-helices in the MBs, indicating that conformational changes in the cytokeratin peptides of the MBs had occurred. This may explain why the antigenic sites observed in MB proteins show changes in affinity for antibodies to cytokeratins as observed by immunohistochemical staining of MBs.

Animals↗
PubMed2000

Molecular structure of fagopyritol A1 (O-alpha-D-galactopyranosyl-(1 --> 3)-D-chiro-inositol) by NMR.

The molecular structure of fagopyritol A1, a novel galactopyranosyl cyclitol from buckwheat seeds, was determined to be O-alpha-D-galactopyranosyl-(1 --> 3)-D-chiro-inositol by 1H and 13C NMR. Fagopyritol A1 is a positional isomer of fagopyritol B1 (O-alpha-D-galactopyranosyl-(1 --> 2)-D-chiro-inositol), representing a different series of fagopyritol oligomers. Trimethylsilyl derivatives of both compounds have similar mass spectra, but each may be identified by different abundance ratios of fragments with m/z 305/318 and 318/319.

Carbohydrate Sequence↗
PubMed2001

Molecular structures of carbonyl-linked bis(dioxolene) complexes: can a carbonyl group act as an effective ferromagnetic coupler?

Molecular structures of two bis(ZnIIdioxolene) complexes are described: (TpCum,MeZn)(2)1-H2 (C106H123.50B2N12O10Zn2), tetragonal, P4/ncc, a = 25.1810(2) A, b = 25.1810(2) A, c = 34.7744(2) A, alpha = 90 degrees, beta = 90 degrees, gamma = 90 degrees, Z = 8; (TpCum,MeZn)(2)1-H (C101H120B2N12O6Zn2), triclinic, P1, a = 13.6624(2) A, b = 13.80920(10) A, c = 26.62340(10) A, alpha = 96.6910(10) degrees, beta = 91.8560(10) degrees, gamma = 109.0190(10) degrees, Z = 2. One of the complexes, (TpCum,MeZn)(2)1-H2, has two protonated catecholate ligands, while the other complex, (TpCum,MeZn)(2)1-H, has one protonated catecholate and one semiquinone ligand. When reacted with PbO2, a labile S = 1, bis(ZnIIsemiquinone) complex is formed in which the two semiquinones are attached to a common carbonyl group.

Journal Article↗
PubMed1983

A revised model of the molecular structure of the acetylcholine receptor at the neuromuscular junction.

The recently reported amino acid sequence of the alpha subunit of Electrophorus indicates that a previous hypothesis presented of the molecular structure of the acetylcholine receptor at the neuromuscular junction based on the sequence of the alpha subunit of Torpedo is improbable: an "essential" glu (13) of Torpedo is replaced by ser (13) which cannot subsume the function for glu (13) postulated in the hypothesis. This paper presents a new hypothesis which is applicable to both Electrophorus and Torpedo. A mode of rigorously testing the hypothesis provided by the irreversible blocker, lophotoxin, is described.

Animals↗
PubMedDate not supplied

De novo generation of molecular structures using optimization to select graphs on a given lattice.

A recurrent problem in organic chemistry is the generation of new molecular structures that conform to some predetermined set of structural constraints that are imposed in an endeavor to build certain required properties into the newly generated structure. An example of this is the pharmacophore model, used in medicinal chemistry to guide de novo design or selection of suitable structures from compound databases. We propose here a method that efficiently links up a selected number of required atom positions while at the same time directing the emergent molecular skeleton to avoid forbidden positions. The linkage process takes place on a lattice whose unit step length and overall geometry is designed to match typical architectures of organic molecules. We use an optimization method to select from the many different graphs possible. The approach is demonstrated in an example where crystal structures of the same (in this case rigid) ligand complexed with different proteins are available.

Journal Article↗
PubMed2004

[Study on the relationships between chemiluminescent properties and molecular structures of some biacridine probes].

The chemiluminescent (CL) properties of biacridine probes, such as 10,10'-dimethyl-3,3'-disulfo-9,9'-biacridine (DMDSBA), 3,3'-disulfo-9,9'-biacridine dinitrate (DSBADN), 10,10'-diethcarboxyl-9,9'-biacridine dinitrate (DEBADN), 10,10'-dimethyl-3,3'-diamino-9,9'-biacridine (DMDABA), and 10,10'-di(4-aminobutyl)-9,9-biacridine dinitrate (DABADN), were studied in this paper, and the relationships between properties and molecular structures were obtained. A new theory and some valuable experimental data have been provided for the investigation and exploitation of the new CL probes for biomacromolecules.

Electrochemistry↗