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PubMed2004

Unified model to predict self-assembly of nonionic surfactants in solution and adsorption on solid or fluid hydrophobic surfaces: effect of molecular structure.

We have developed a pseudo-phase model to predict the self-assembly of nonionic surfactants on hydrophobic solid or fluid interfaces and in bulk solution. The uniqueness of this model is that it provides the relationship between molecular structure and self-assembly in solution and on interfaces. This model requires the input of minimal new experimental data. The remaining model parameters may be calculated on the basis of the surfactant molecular structure. The validity of the model has been established by comparing predictions with a wide array of experimental data for nonionic surfactant adsorption at the hydrophobic solid-water interface and at the air-water interface. The same model is then used to predict the self-assembly in bulk solution. The model predictions for critical aggregation concentration, aggregate shapes, and adsorption isotherms of various surfactants are in good agreement with the experimental data available in the literature.

Journal Article↗
PubMed1985

Molecular structure, stereochemistry and interactions of steffimycin B, and DNA binding anthracycline antibiotic.

The crystal and molecular structure of anthracycline antibiotic steffimycin B(C29H32O13) has been determined by X-ray diffraction and the stereochemistry revealed. The orthorhombic crystals belong to space group P2(1)2(1)2(1), with the dimensions; a = 8.253 (2), b = 8.198 (2), c = 40.850 (8) A and Z = 4. Intensity data were collected for 2518 independent reflections. The structure was solved by direct methods and refined to an R value of 0.066 for 1410 reflections. The configuration in ring A is 7R,8S,9S. Ring A adopts half chair conformation, while the sugar ring has the regular chair conformation. The molecule most probably binds to double helical DNA through intercalation and hydrogen bonding.

Anthracyclines↗
PubMed1990

Molecular structure of a major insulin/mitogen-activated 70-kDa S6 protein kinase.

The molecular structure of a rat hepatoma 70-kDa insulin/mitogen-stimulated S6 protein kinase, obtained by molecular cloning, is compared to that of a rat homolog of the 85-kDa Xenopus S6 protein kinase alpha; both kinases were cloned from H4 hepatoma cDNA libraries. The 70-kDa S6 kinase (calculated molecular mass of 59,186 Da) exhibits a single catalytic domain that is most closely related in amino acid sequence (56% identity) to the amino-terminal, kinase C-like domain of the rat p85 S6 kinase (calculated molecular mass of 82,695 Da); strong similarity extends through a further 67 residues carboxyl-terminal to the catalytic domain (40% identity), corresponding to a region also conserved among the kinase C family. Outside of this segment of approximately 330 amino acids, the structures of the p70 and p85 S6 kinases diverge substantially. The p70 S6 kinase is known to be activated through serine/threonine phosphorylation by unidentified insulin/mitogen-activated protein kinases. A model for the regulation of p70 S6 protein kinase activity is proposed wherein the low activity of the unphosphorylated enzyme results from the binding of a basic, inhibitory pseudosubstrate site (located carboxyl-terminal to the extended catalytic domain) to an acidic substrate binding region (located amino-terminal to the catalytic domain); substrate binding is thereby prevented. S6 kinase activation requires displacement of this inhibitory segment, which is proposed to occur consequent to its multiple phosphorylation. The putative autoinhibitory segment contains several serine and threonine residues, each followed directly by a proline residue. This motif may prevent autophosphorylation but permit transphosphorylation; two of these serine residues reside in a maturation promoting factor (MPF)/cdc-2 consensus motif. Thus, hormonal regulation of S6 kinase may involve the action of MPF/cdc-2 or protein kinases with related substrate specificity.

Amino Acid Sequence↗
PubMed2006

Cytoskeletal polymer networks: the molecular structure of cross-linkers determines macroscopic properties.

In living cells the mechanical properties of the actin cytoskeleton are defined by the local activation of different actin cross-linking proteins. These proteins consist of actin-binding domains that are separated and geometrically organized by different numbers of rod domains. The detailed molecular structure of the cross-linking molecules determines the structural and mechanical properties of actin networks in vivo. In this study, we systematically investigate the impact of the length of the spacing unit between two actin-binding domains on in vitro actin networks. Such synthetic cross-linkers reveal that the shorter the constructs are, the greater the elastic modulus changes in the linear response regime. Because the same binding domains are used in all constructs, only the differences in the number of rod domains determine their mechanical effectiveness. Structural rearrangements of the networks show that bundling propensity is highest for the shortest construct. The nonlinear mechanical response is affected by the molecular structure of the cross-linker molecules, and the observed critical strains and fracture stress increase proportional to the length of the spacing unit.

Actins↗
PubMed2001

Self-assembled molecular structures as ultrasonically-responsive barrier membranes for pulsatile drug delivery.

Noninvasive ultrasound has been shown to increase the release rate on demand from drug delivery systems; however, such systems generally suffer from background drug leaching. To address this issue, a drug-containing polymeric monolith coated with a novel ultrasound-responsive coating was developed. A self-assembled molecular structure coating based on relatively impermeable, ordered methylene chains forms an ultrasound-activated on-off switch in controlling drug release on demand, while keeping the drug inside the polymer carrier in the absence of ultrasound. The orderly structure and molecular orientation of these C12 n-alkyl methylene chains on polymeric surfaces resemble self-assembled monolayers on gold. Their preparation and characterization have been published recently (Kwok et al. [Biomacromolecules 2000;1(1):139-148]). Ultrasound release studies showed that a copolymer of 2-hydroxyethyl methacrylate and ethylene glycol dimethacrylate (MW 400) coated with such an ultrasound-responsive membrane maintained sufficient insulin for multiple insulin delivery, compared with a substantial burst release during the first 2 h from uncoated samples. With appropriate surface coating coverage, the background leach rate can be precisely controlled. The biological activity of the insulin releasate was tested by assessing its ability to regulate [C14]-deoxyglucose uptake in 3T3-L1 adipocyte cells in a controlled cell culture environment. Uptake triggered by released insulin was comparable to that of the positive insulin control. The data demonstrate that the released insulin remains active even after the insulin had been exposed to matrix synthesis and the methylene chain coating process.

Adipocytes↗
PubMed1997

ALTER: eclectic management of molecular structure data.

ALTER is a computer program written to facilitate easy conversion between different representations of molecular structure data. The program functions as a file converter, data generation engine, and through the creation of control or input files, as an interface to other programs. The main aspects of program function--the reading and writing of files; coordinate transformation; data reorganization: structure building; data abstraction, including the generation of a wide variety of topological indices and constitutional descriptors; and display--are described in appropriate detail.

Computer Graphics↗
PubMed2003

Capturing time-resolved changes in molecular structure by negative staining.

Imaging structural intermediates of biological processes is a key step in understanding biological function. Because intermediates are commonly short-lived, lasting only milliseconds, the main methods used to capture them have been conventional imaging of analog or inhibited states, having extended lifetimes, or rapid (millisecond timescale) freezing of intermediates with subsequent observation by cryo-EM. We have developed a simpler method that fixes structure on the millisecond timescale. The procedure consists of briefly (milliseconds) exposing the macromolecular structure of interest on an EM grid to conditions that initiate the structural change, then immediately fixing with uranyl acetate or tannic acid. Specimens are then observed by negative staining. The key finding that validates this approach is our demonstration that uranyl acetate, and in some cases tannic acid, fixes protein molecular structure on the millisecond timescale. This is demonstrated by our observation that exposure of actin and myosin filaments to these fixatives for as little as 10 ms is sufficient to fully preserve them against changes that normally induce rapid and major alteration in their molecular structure. Fixation appears to stabilize both ionic and hydrophobic bonds. This approach should be of general utility for studying transient molecular changes in many systems.

Actins↗
PubMed2000

A new thiatriazine isomer: synthesis, tautomerism, and molecular structure of 3,6-diphenyl-4H-1,2,4,5-thiatriazine as a precursor to the 1,2,4,5-thiatriazinyl radical

The diphenyl derivative of 4H-1,2,4,5-thiatriazine (5) was prepared by oxidative cyclization of 9. The molecular structure of 5, obtained by X-ray diffraction [orthorhombic, Pna2(1), a = 9.7746(13) A, b = 21.692(2) A, c = 5.6580(8) A], compares favorably with that predicted with ab initio calculations. The thiatriazine 5 was used as a precursor to the 3,6-diphenyl-1,2,4,5-thiatriazinyl radical (4) through either oxidation with PbO(2), or conversion to and reduction of sulfiminyl chloride 6 with Ph(3)Sb. The weak ESR quintet (a(N) = 1.03 mT, g = 2.0103) observed in the latter case correlates well with the molecular structure of 4, but the results of DFT calculations are ambiguous. Ab initio calculations show that 4H-1,2, 4,5-thiatriazine (I-4H) is the most stable tautomer and is the second most stable isomer among the six possible thiatriazines. All isomeric thiatriazinyl radicals exhibit similar spin distribution patterns. 1,2,4,5-Thiatriazinyl radical (I-R) is calculated to be 23. 1 kcal/mol less stable than the most stable 1,2,4,6 isomer II-R.

Journal Article↗
PubMed2003

Unlocking the molecular structure of fungal melanin using 13C biosynthetic labeling and solid-state NMR.

Melanins are enigmatic pigments found in all biological kingdoms that are associated with a variety of functions, including microbial virulence. Despite being ubiquitous in nature, melanin pigments have long resisted atomic-level structural examination because of their insolubility and amorphous organization. Cryptococcus neoformans is a human pathogenic fungus that melanizes only when provided with exogenous substrate, thus offering a unique system for exploring questions related to melanin structure at the molecular level. We have exploited the requirement for exogenous substrate in melanin synthesis as well as the capabilities of high-resolution solid-state nuclear magnetic resonance (NMR) to establish the predominantly aliphatic composition of l-dopa melanin and to introduce (13)C labels that permit the identification of proximal carbons in the developing biopolymer. By swelling solid melanin samples in organic solvents and using two-dimensional heteronuclear NMR in conjunction with magic-angle spinning, we have identified chemical bonding patterns typical of alkane, alkene, alcohol, ketone, ester, and indole functional groups. These findings demonstrate the feasibility of a novel approach to determining the structure of melanin using metabolic labeling and NMR spectroscopy.

Carbon Radioisotopes↗
PubMed1987

Crystal and molecular structure of aspartame X HCl X 2H2O.

The crystal and molecular structure of the hydrochloride salt of the peptide sweetener aspartame (alpha-L-Asp-L-Phe methyl ester) has been determined at 120 K using 3877 reflections with I greater than 2.5 sigma I. Space group P2(1)2(1)2(1), cell dimensions a = 6.768(1), b = 9.796(1) and c = 26.520(3) A; final R factor 0.033. While the N-terminal L-Asp group in the structure of aspartame itself forms a six-membered ring with an intramolecular hydrogen bond between the carboxylate and the protonated amino terminus, the corresponding group in the hydrochloride adopts a completely different conformation with a weak intramolecular hydrogen bond between the carboxyl group and the N atom of the L-Phe residue. The L-Phe methyl ester moiety is rather similar in the two structures. Of the many possible conformations of aspartame, only one may be expected to function as a substrate at the receptor site for sweet taste, and a proposal is made for this active conformation.

Aspartame↗
PubMed1989

Molecular structure of the netropsin-d(CGCGATATCGCG) complex: DNA conformation in an alternating AT segment.

The molecular structure of the complex between a minor groove binding drug (netropsin) and the DNA dodecamer d(CGCGATATCGCG) has been solved and refined by single-crystal X-ray diffraction analysis to a final R factor of 20.0% to 2.4-A resolution. The crystal is similar to that of the other related dodecamers with unit cell dimensions of a = 25.48 A, b = 41.26 A, and c = 66.88 A in the space group P2(1)2(1)2(1). In the complex, netropsin binds to the central ATAT tetranucleotide segment in the narrow minor groove of the dodecamer B-DNA double helix as expected. However, in the structural refinement the drug is found to fit the electron density in two orientations equally well, suggesting the disordered model. This agrees with the results from solution studies (chemical footprinting and NMR) of the interactions between minor groove binding drugs (e.g., netropsin and distamycin A) and DNA. The stabilizing forces between drug and DNA are provided by a combination of ionic, van der Waals, and hydrogen-bonding interactions. No bifurcated hydrogen bond is found between netropsin and DNA in this complex due to the unique dispositions of the hydrogen-bond acceptors (N3 of adenine and O2 of thymine) on the floor of the DNA minor groove. Two of the four AT base pairs in the ATAT stretch have low propeller twist angles, even though the DNA has a narrow minor groove. Alternating helical twist angles are observed in the ATAT stretch with lower twist in the ApT steps than in the TpA step.

Base Composition↗
PubMed2006

Intramolecular hydrogen bond, molecular structure and vibrational assignment of tetra-acetylethane. A density functional study.

The intramolecular hydrogen bond, molecular structure and vibrational frequencies of tetra-acetylethane have been investigated by means of high-level density functional theory (DFT) methods with most popular basis sets. Fourier transform infrared and Fourier transform Raman spectra of this compound and its deuterated analogue were recorded in the regions 400-4000 cm(-1) and 40-4000 cm(-1), respectively. The calculated geometrical parameters of tetra-acetylethane were compared to the experimental results of this compound and its parent molecule (acetylacetone), obtained from X-ray diffraction. The O...O distance in tetra-acetylethane, about 2.424A, suggests that the hydrogen bond in this compound is stronger than acetylacetone. This conclusion is well supported by the NMR proton chemical shifts and O-H stretching mode at 2626 cm(-1). Furthermore, the calculated hydrogen bond energy in the title compound is 17.22 kcal/mol, which is greater than the acetylacetone value. On the other hand, the results of theoretical calculations show that the bulky substitution in alpha-position of acetylacetone results in an increase of the conjugation of pi electrons in the chelate ring. Finally, we applied the atoms in molecules (AIM) theory and natural bond orbital method (NBO) for detail analyzing the hydrogen bond in tetra-acetylethane and acetylacetone. These results are in agreement with the vibrational spectra interpretation and quantum chemical calculation results. Also, the conformations of methyl groups with respect to the plane of the molecule and with respect to each other were investigated.

Acetylene↗
PubMed2005

[Correlation between absorption rates of beta-adrenoreceptor antagonists in rat small intestine and their molecular structures].

OBJECTIVE: To study the correlation between the absorption rate constants of beta-adrenoreceptor antagonists in rat small intestinal segments and their molecular structural parameters. METHODS: The net atomic charges and the molecular volumes of 11 beta-adrenoreceptor antagonists were obtained with the semiempirical self-consistent field molecular orbital calculation CNDO/2 method and Mont Carlo method respectively, using the minimum energy conformation obtained from the optimization of the standard molecular geometry with the molecular mechanics MM+ method. The stepwise multiple regression analysis was used to obtain the correlation equations. RESULTS: The absorption rate constants of beta-adrenoreceptor antagonists in rat jejunum or ileum were well linearly correlated with the sum of the net charges of all hydrogen atoms and the molecular volumes. The beta-adrenoreceptor antagonist with higher lipophilicity, weaker hydrogen-bonding potential,and smaller molecular volume had greater absorption rate constants. CONCLUSION: The absorption rate constants of beta-adrenoreceptor antagonists in rat small intestinal segments are mainly related with their lipophilicity,hydrogen-bonding potential and molecular size.

Adrenergic beta-Antagonists↗
PubMedDate not supplied

[Immunochemical and electron microscopic analysis of the high-molecular structures in the tick-borne encephalitis virus].

High-molecular structures of tick-borne encephalitis virus were sedimented by centrifugation from virus-containing culture fluid and separated by sucrose concentration gradient centrifugation into 3 main fractions: rapidly sedimenting virions, the fraction sedimenting at a moderate rate, represented by "stellate" structures, and the fraction found on the top of the gradient and represented by structures similar in size and shape to virions, designated slowly sedimenting virions. The latter are first described in the paper. In immunodiffusion, the rapidly sedimenting virions form 1 of the 2 precipitation bands closer to the antigen-containing well, and in immunoelectrophoresis give 2 precipitation bands, anodic and cathodic, which fuse, indicating immunological identify of the 2 subpopulations of rapidly sedimenting virions. The slowly sedimenting virions in immunodiffusion form one of the 2 precipitation bands closer to the antigen well, and in immunoelectrophoresis form the cathodic precipitation band. The material sedimenting in the gradient at a moderate rate gives in immunodiffusion one precipitation band, the 3rd from the antigen well, and in immunoelectrophoresis forms a separate anodic precipitation band. This high-molecular non-virion antigen is found in small amounts also in fractions containing the rapidly sedimenting and slowly sedimenting virions. It is at least partially antigenically identical to previously studied low molecular non-virion ("soluble") antigen of tick-borne encephalitis virus.

Centrifugation, Density Gradient↗
PubMed1999

Molecular structure of the amyloid-forming protein kappa I Bre.

The molecular structure of the amyloid-forming Bence-Jones protein kappa I Bre has been determined by X-ray crystallography at 2.0 A resolution. The fragment from the kappa chain of immunoprotein contains 107 amino acid residues, and polymerizes in the crystal form into a giant helical spiral, surrounding a cylinder of water 50 A in diameter with a repeat of 77.56 A, containing 12 kappa molecules, plus another 12 molecules from neighboring parallel spirals. The resulting structure has many features which have been found or suggested from studies on the protein fibrils found in amyloid deposits. From the results of the X-ray crystal structure a hypothesis is presented for the structure and formation of the amyloid fibril.

Amino Acid Sequence↗
PubMed1975

The crystal and molecular structure of delta-9-tetrahydrocannabinolic acid b.

The crystal and molecular structure of the title compound C-22H-30O-4, has been determined by X-ray methods using 1106 reflections above background level collected by counter methods. The crystals are orthorhombic, space group P2-12-12-1 with cell dimensions a equals 16.514(2) A; b equals 14.324(2) A; c equals 8.744(1) A; there are four molecules per unit cell. The structure was refined to an R of 0.084 (weighted R-w equals 0.068). The cyclohexene and the pyran part of the molecule occurs in the half-chair conformation. The bond distances and angles, and a slight twist of the benzene ring, indicate considerable stains in the aromatic system. Both the phenolic and carboxylic group are significantly out of the plane through the aromatig ring. The angle between this plane and a plane through the cyclohexene ring is 37.7 degrees. The pentyl sidechain occurs in an extended gauche conformation, and the thermal parameters of this part of the molecule are very high. The molecules are held together by van der Waals forces in the c-directions, and hydrogen bonds (2.688 A) from phenolic to carboxylic groups in the a-b plane. There is a short ultra-molecular hydrogen bond (2.490 A) from the carboxylic group to the pyran oxygen.

Cannabis↗
PubMed1992

Crystal and molecular structure of RNase Rh, a new class of microbial ribonuclease from Rhizopus niveus.

The crystal structure of RNase Rh, a new class of microbial ribonuclease from Rhizopus niveus, has been determined at 2.5 A resolution by the multiple isomorphous replacement method. The crystal structure was refined by simulated annealing with molecular dynamics. The current crystallographic R-factor is 0.200 in the 10-2.5 A resolution range. The molecular structure which is completely different from the known structures of RNase A and RNase T1 consists of six alpha-helices and seven beta-strands, belonging to the alpha+beta type structure. Two histidine and one glutamic acid residues which were predicted as the most probably functional residues by chemical modification studies are found to be clustered. The steric nature of the active site taken together with the relevant site-directed mutagenesis experiments (Irie et al.) indicates that: (i) the two histidine residues are the general acid and base; and (ii) an aspartic acid residue plays a role of recognizing adenine moiety of the substrate.

Amino Acid Sequence↗