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PubMed1989

Crystallographic resolution and crystal and molecular structures of stereoisomers of 1,3,5-triglycidyl-s-triazinetrione.

The crystal and molecular structures of alpha and beta isomers of the antineoplastic alkylating agent 1,3,5-triglycidyl-s-triazinetrione (TGT) have been determined by X-ray diffraction. Although the isomers differ chemically only in the order of a carbon and an oxygen atom in one of the glycidyl epoxide rings, the molecular conformations and crystal packing arrangements are very different. The different physical and biological properties of the two stereoisomers can be explained on the basis of the structures. The sample of alpha-TGT was found to be a mixture of alpha and beta forms, and it is suggested that use of pure alpha-TGT may lead to better therapeutic results.

Chemical Phenomena↗
PubMed2000

Schiff bases or glycosylamines: crystal and molecular structures of four derivatives of D-mannose.

Crystal and molecular structures of four derivatives of D-mannose are described. Each could exist as either an open-chain Schiff base or as a glycosylamine in the solid state. The derivative formed upon reaction of D-mannose with hydroxylamine is an open-chain oxime, but those formed upon reaction with semicarbazide, aniline, and p-chloroaniline are glycosylamines. The oxime, which crystallizes as the syn-(E) isomer, has a fully extended carbon chain. The glycosylamines are all beta-pyranoses. The packing arrangement of the oxime involves 'head-to-tail' hydrogen bonding. The semicarbazide derivative, which crystallizes as a dihydrate, features a hydrogen-bonded intramolecular bridge formed by the two water molecules and linking O-6 to the carbonyl oxygen atom. The packing arrangements of the aniline and p-chloroaniline derivatives differ from each other but are nevertheless closely related by similar hydrogen-bonding interactions.

Amines↗
PubMed1992

The crystal and molecular structure of the Rhizomucor miehei triacylglyceride lipase at 1.9 A resolution.

The crystal and molecular structure of a triacylglyceride lipase (EC 3.1.1.3) from the fungus Rhizomucor miehei was analyzed using X-ray single crystal diffraction data to 1.9 A resolution. The structure was refined to an R-factor of 0.169 for all available data. The details of the molecular architecture and the crystal structure of the enzyme are described. A single polypeptide chain of 269 residues is folded into a rather unusual singly wound beta-sheet domain with predominantly parallel strands, connected by a variety of hairpins, loops and helical segments. All the loops are right-handed, creating an uncommon situation in which the central sheet is asymmetric in that all the connecting fragments are located on one side of the sheet. A single N-terminal alpha-helix provides the support for the other, distal, side of the sheet. Three disulfide bonds (residues 29-268, 40-43, 235-244) stabilize the molecule. There are four cis peptide bonds, all of which precede proline residues. In all, 230 ordered water molecules have been identified; 12 of them have a distinct internal character. The catalytic center of the enzyme is made up of a constellation of three residues (His257, Asp203 and Ser144) similar in structure and function to the analogous (but not homologous) triad found in both of the known families of serine proteinases. The fourth residue in this system equivalent to Thr/Ser in proteinases), hydrogen bonded to Asp, is Tyr260. The catalytic site is concealed under a short amphipatic helix (residues 85 to 91), which acts as "lid", opening the active site when the enzyme is adsorbed at the oil-water interface. In the native enzyme the "lid" is held in place by hydrophobic interactions.

Amino Acid Sequence↗
PubMed1974

The molecular structure of yeast phenylalanine transfer RNA in monoclinic crystals.

The molecular structure of monoclinic crystals of yeast phenylalanine tRNA is analyzed by comparing it to the orthorhombic crystals of the same material whose structure has been determined. Changing the packing of the molecule from the head-to-head, tail-to-tail arrangement in the orthorhombic lattice to a head-to-tail packing makes it possible to generate a proposed structure for the monoclinic unit cell. The structure factors for the proposed arrangement have been calculated and compared with those experimentally observed from monoclinic crystals. The residuals from this comparison are low enough to conclude that at 4-A resolution, the three-dimensional structure of the molecule in the monoclinic crystal is essentially the same as that in the orthorhombic crystal. In addition, a correlation coefficient calculated from intensities based on a skeletal model of the molecule also confirmed the structure in the monoclinic cell. Electron density difference maps, as well as the presence of close contacts in the anticodon loop region of the monoclinic crystal, suggest that the anticodon loop may have a slightly different conformation than that observed in the orthorhombic crystals.

Models, Structural↗
PubMed2004

Dynamic molecular structure of DPPC-DLPC-cholesterol ternary lipid system by spin-label electron spin resonance.

The hydrated ternary lamellar lipid mixture of dipalmitoyl-PC/dilauroyl-PC/cholesterol (DPPC/DLPC/Chol) has been studied by electron spin resonance (ESR) to reveal the dynamic structure on a molecular level of the different phases that exist and coexist over virtually the full range of composition. The spectra for more than 100 different compositions at room temperature were analyzed by nonlinear least-squares fitting to provide the rotational diffusion rates and order parameters of the end-chain labeled phospholipid 16-PC. The ESR spectra exhibit substantial variation as a function of composition, even though the respective phases generally differ rather modestly from each other. The Lalpha and Lbeta phases are clearly distinguished, with the former exhibiting substantially lower ordering and greater motional rates, whereas the well-defined Lo phase exhibits the greatest ordering and relatively fast motional rates. Typically, smaller variations occur within a given phase. The ESR spectral analysis also yields phase boundaries and coexistence regions which are found to be consistent with previous results from fluorescence methods, although new features are found. Phase coexistence regions were in some cases confirmed by observing the existence of isosbestic points in the absorption mode ESR spectra from the phases. The dynamic structural properties of the DPPC-rich Lbeta and DLPC-rich Lalpha phases, within their two-phase coexistence region do not change with composition along a tie-line, but the ratio of the two phases follows the lever rule in accordance with thermodynamic principles. The analysis shows that 16-PC spin-label partitions nearly equally between the Lalpha and Lbeta phases, making it a useful probe for studying such coexisting phases. Extensive study of two-phase coexistence regions requires the determination of tie-lines, which were approximated in this study. However, a method is suggested to accurately determine the tie-lines by ESR.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1992

Photorealistic image generation of molecular structure on PC screen using the ray-tracing technique.

A PC version of three-dimensional molecular graphics package has been developed to run under MS-DOS environment on IBM PC-compatible computers equipped with a VGA graphics board. The program consists of two parts: a menu-driven interactive system module in EGA mode, and a ray-tracing module in VGA mode. In the 256-color VGA mode, ray-tracing images are represented with a 4-color map, with 64 levels for each color: 32 levels of illuminance and 32 levels of saturation. Molecular structure can be analyzed along various directions with various light sources. Ray-tracing images are also represented in a 16-color EGA mode with the half-toning method, which can display 76 gray levels for each color. To obtain good photo-realistic images in an efficient way, we have used two light sources, with an intensity ratio of 7:3, which are located in front of the top right and bottom left corners of the screen.

Carboxypeptidases↗
PubMed2001

Molecular structure of the peritrophic membrane (PM): identification of potential PM target sites for insect control.

Peritrophic membranes (PMs) are an invertebrate-unique structure that lines the digestive tract, playing important roles in facilitating food digestion and providing protection to the gut epithelium. The importance of PMs in insects has been recognized ever since its presence was identified 200 years ago. In the last 5 years, significant progress towards understanding the PM molecular structure and the mechanism for PM formation has been made. Recent studies on Type 1 PMs from lepidopteran larvae have suggested a model for the PM molecular structure and formation. The important physiological functions of the PM suggest that PMs can be a significant structural target for insect control and the current understanding of the structure of lepidopteran larval PMs has provided us with potential opportunities for targeting the PM by various mechanisms.

Animals↗
PubMed1989

Crystal and molecular structure of methyl O-alpha-D-manno-pyranosyl-(1----2)-alpha-D-mannopyranoside.

The crystal and molecular structure of a synthetic mannosyl disaccharide, methyl O-alpha-D-mannopyranosyl-(1----2)-alpha-D-mannopyranoside, has been determined from X-ray diffractometer data by direct methods by use of the Multan programs. The crystals are monoclinic, space group P2 with unit cell dimensions, a 8.086(1), b 9.775(1), c 9.975(2) A, beta 104.58(1) degrees, Z 2, and Dm 1.54 g/cm3. The structure was refined to an R-value of 0.033 for 1359 reflections measured with CuK alpha radiation. The mannopyranose units have the chair conformations 4C(D) with C-5' and C-2' deviating from the best plane through the other four atoms of the ring by -0.68 and +0.53 A in the nonreducing group, and C-3 and O-5 deviating from the mean plane through the other four atoms by +0.57 and -0.66 A, respectively, in the "potentially" reducing residue. The ring-to-ring conformation can be described as (phi, psi) = (-64.5, 105.5 degrees). The conformation across the C-5--C-6 bond is gauche-gauche in both the sugars. The crystal structure is stabilized by a network of intermolecular O-H...O hydrogen bonds.

Carbohydrate Conformation↗
PubMed1991

Characterization of benzodiazepinooxazoles: crystal and molecular structure of trans and cis isomers of oxazolam.

The stereochemistry of the trans and cis isomers of 2(S)- and 2(R)-oxazolam is described. A total of four molecular structures of the 11b(R) and 11b(S) diastereomers of 2(S)- and 2(R)-oxazolam have been revealed by X-ray diffraction techniques. 2(S)-Oxazolam crystallizes in space group P2(1)/c, with cell dimensions a = 16.180(2) A, b = 8.791(2) A, c = 13.574(2) A, and beta = 102.07(1) degrees. The molecule in an asymmetric unit exhibited disorder at the 2-carbon (C2) atom, and the structures for trans and cis isomers have been resolved crystallographically. 2(S)-Oxazolam forms polymeric chains with intermediation of ethanol through hydrogen bonding. 2(R)-Oxazolam crystallizes in space group P1, with cell dimensions a = 7.754(1) A, b = 8.654(1) A, c = 15.795(2) A, alpha = 104.09(1) degrees, beta = 91.19(1) degrees, and gamma = 114.00(1) degrees. A similar disorder at the C2 position has been elucidated by a mixture of trans- and cis-2(R)-oxazolams. The two 2(R)-oxazolam molecules form a dimer with a hydrogen bond net. The structural details, focusing on the conformation and molecular complex formation of both oxazolams, have been discussed in connection with the oxazolidine ring stability and the crystal polymorph.

Anti-Anxiety Agents↗
PubMed2006

Molecular structure and conformation of chloronitromethane as determined by gas-phase electron diffraction and theoretical calculations.

The molecular structure of chloronitromethane was studied in the gas phase at a nozzle-tip temperature of 373 K. The experimental data were interpreted using a dynamic model where the molecules are undergoing torsional motion governed by a potential function: V = V2/2x(1 - cos 2tau) + V4/2x(1 - cos 4tau) with V2 = 0.81(30) and V4 = 0.12(40) kcal/mol (tau is the dihedral angle between the C-Cl and N-O bond). The conformer with a zero degree dihedral angle is the most stable conformer. Comparison with results from HF/MP2/B3LYP 6-311G(d,p) calculations were made. The important geometrical parameter values (for the eclipsed form) obtained from least-squares refinements are the following: r(C-H) = 1.061(18)A, r(C-N) = 1.509 (5)A, r(N-O) = 1.223(1)A, r(C-Cl) = 1.742(2)A, angleClCN = 115.2(7) degrees, angleO4NC = 118.9(10) degrees, angleO5NC = 114.9(16) degrees, and angleClCH 115(4) degrees.

Computer Simulation↗
PubMed2004

Molecular structure of human geminin.

The origin licensing repressor geminin is a unique bifunctional protein providing a molecular link between cellular proliferation, differentiation and genomic stability. Here we report the first molecular structure of human geminin, determined by EM and image processing at a resolution of 17.5 A. The geminin molecule is a tetramer formed by two dimers with monomers interacting via coiled-coil domains. The unusual structural organization of geminin provides molecular insight into its bifunctional nature.

Cell Cycle Proteins↗
PubMed1995

Phase transition behavior and molecular structures of monounsaturated phosphatidylcholines. Calorimetric studies and molecular mechanics simulations.

High resolution differential scanning calorimetric studies were performed to investigate the thermotropic phase behavior of 26 molecular species of sn-1 saturated/sn-2 monounsaturated phosphatidylcholines. In parallel with calorimetric studies, the energy-minimized structures and steric energies of the diglyceride moieties of these monoenoic lipids were determined using a molecular mechanics approach. The combined calorimetric and computational studies led to the following results and conclusions. (i) When a single cis-carbon-carbon double bond (delta) is incorporated into a saturated diacylphosphatidylcholine molecule at any position within the central segment of the long sn-2 acyl chain, the resulting monoenoic lipid molecules will, in excess water, exhibit reduced phase transition temperature (Tm) and transition enthalpy (delta H) as they undergo the gel to liquid-crystalline phase transition. The Tm and delta H-lowering effects of the delta bond can be attributed to a decrease in the chain length of the sn-2 acyl chain, a change in the chain length difference between the sn-1 and sn-2 acyl chains, and a local perturbation of the chain-chain van der Waals interaction in the vicinity of the delta bond. (ii) For a series of positional isomers of 1-stearoyl-2-cis-octadecenoylphosphatidylcholine, C(18):C(18:1 delta n)PC, with a delta bond at different positions along the sn-2 acyl chain, the Tm value depends critically on the position of the delta bond. Specifically, the Tm value is minimal as the delta bond is located at the geometric center of the linear segment of the sn-2 acyl chain, and the Tm value is progressively increased as the delta bond migrates toward either end of the sn-2 acyl chain. (iii) The various monoenoic phosphatidylcholines under study can be divided into two groups. The Tm values of most lipids in each group can be correlated in an identical manner with their structural parameters, yielding a common Tm-structure relationship.

Calorimetry, Differential Scanning↗
PubMed1996

Molecular structure and dynamics of some potent 5-HT3 receptor antagonists. Insight into the interaction with the receptor.

The molecular structure and the dynamic behaviour of some potent 5-HT3 antagonists structurally related to quipazine have been investigated by NMR spectroscopy and by computational methods in order to gain insight into the structure-activity relationships at a molecular level. The role of the different dynamic behaviour of these compounds in the binding to 5-HT3 receptors is discussed. A model of ligand-receptor interaction has been developed on the basis of molecular orbital calculations and on the reference ligands quipazine, ondansetron and LY278584. The interaction model proposed herein rationalizes the observed agonist-antagonist shift between quipazine and investigated compounds with the assumption of different but overlapping binding domains for antagonists and agonists at the 5-HT3 receptor.

Affinity Labels↗
PubMed2005

The influence of substrate charge and molecular structure on interphase transfer in cloud point extraction systems.

The specificity of interphase transfer of organic reagents of different types between water and the nonionic-surfactant-rich phases at the cloud point temperature was investigated. In contrast to organic solvents, the ability of the micellar phases to extract highly charged ions of organic reagents was shown. Further evidence of the specificity of interphase transfer in micellar-extraction systems is independent and cooperative influence of substrate molecular structure and hydrophobicity on their distribution. The appearance of host-guest phenomenon in cloud point extraction systems that is inherent in organized systems with molecules of the receptors was established. The possibility of describing reagent distribution using regressions that consider substrate hydrophobicity and molecular structure in the cloud point extraction systems was shown.

Journal Article↗
PubMed2005

LambdaO4 upside down: a new molecular structure for supported VO4 catalysts.

Vanadium oxide (1 wt %) supported on gamma-Al(2)O(3) was used to investigate the interface between the catalytically active species and the support oxide. Raman, UV-vis-NIR DRS, ESR, XANES, and EXAFS were used to characterize the sample in great detail. All techniques showed that an isolated VO(4) species was present at the catalyst surface, which implies that no V-O-V moiety is present. Surprisingly, a Raman band was present at 900 cm(-1), which is commonly assigned to a V-O-V vibration. This observation contradicts the current literature assignment. To further elucidate on potential other Raman assignments, the exact molecular structure of the VO(4) entity (1 V=O bond of 1.58 A and 3 V-O bonds of 1.72 A) together with its position relative to the support O anions and Al cation of the Al(2)O(3) support has been investigated with EXAFS. In combination with a structural model of the alumina surface, the arrangement of the support atoms in the proximity of the VO(4) entity could be clarified, leading to a new molecular structure of the interface between VO(4) and Al(2)O(3). It was found that VO(4) is anchored to the support oxide surface, with only one V-O support bond instead of three, which is commonly accepted in the literature. The structural model suggested in this paper leaves three possible assignments for the 900 cm(-1) band: a V-O-Al vibration, a V-O-H vibration, and a V-(O-O) vibration. The pros and cons of these different options will be discussed.

Journal Article↗
PubMed1991

The molecular structure of the high potential iron-sulfur protein isolated from Ectothiorhodospira halophila determined at 2.5-A resolution.

The molecular structure of a high potential iron-sulfur protein (HiPIP) isolated from the purple photosynthetic bacterium, Ectothiorhodospira halophila strain BN9626, has been solved by x-ray diffraction analysis to a nominal resolution of 2.5 A and refined to a crystallographic R value of 18.4% including all measured x-ray data from 30.0- to 2.5-A resolution. Crystals used in the investigation contained two molecules/asymmetric unit and belonged to the space group P21 with unit cell dimensions of a = 60.00 A, b = 31.94 A, c = 40.27 A, and beta = 100.5 degrees. An interpretable electron density map, obtained by combining x-ray data from one isomorphous heavy atom derivative with non-crystallographic symmetry averaging and solvent flattening, clearly showed that this high potential iron-sulfur protein contains 71 amino acid residues, rather than 70 as originally reported. As in other bacterial ferredoxins, the [4Fe-4S] cluster adopts a cubane-like conformation and is ligated to the protein via four cysteinyl sulfur ligands. The overall secondary structure of the E. halophila HiPIP is characterized by a series of Type I and Type II turns allowing the polypeptide chain to wrap around the [4Fe-4S] prosthetic group. The hydrogen bonding pattern around the cluster is nearly identical to that originally observed in the 85-amino acid residue Chromatium vinosum HiPIP and consequently, the 240 mV difference in redox potentials between these two proteins cannot be simply attributed to hydrogen bonding patterns alone.

Amino Acid Sequence↗
PubMed1995

Crystal and molecular structures of human progastricsin at 1.62 A resolution.

The crystal and molecular structures of human progastricsin (hPGC) have been determined using multiple isomorphous replacement methods and anomalous scattering in conjunction with a phased translation function. The structure has been refined to a conventional R-factor (= sigma parallel Fo magnitude of - magnitude of Fc parallel / sigma magnitude of Fo magnitude of) of 0.179 with data to 1.62 A resolution. The first 37 amino acid residues of the prosegment are similar in conformation to the equivalent residues of porcine pepsinogen (pPGN). As in pPGN, the N zeta atom of Lys37p sits between the active-site carboxylate groups of Asp32 and Asp217, thereby preventing catalysis. The side-chains of Tyr38p and Tyr9 sit in the S1' and S1 substrate-binding pockets of hPGC, respectively, in an analogous manner to what is observed in porcine pepsinogen. There are large conformational differences centered around the region containing residues Arg39p to Pro6, relative to the equivalent region in the structure of pPGN. Two surface loops in the vicinity of this segment are also displaced relative to those in pPGN and in mature aspartic proteinases (Phe71 to Thr81 (the "flap"), and Tyr125 to Thr131). In hPGC, Tyr75 O eta does not make its usual hydrogen bond to Trp39 N epsilon 1. Rather, the "flap" containing Tyr75 is excluded from the active site by the polypeptide segment Arg39p to Pro6. However, the conformation of the inhibitory segment, Lys37p to Tyr38p, is virtually identical with that observed in pPGN. Hence the structures of these two proteins indicate that aspartic proteinase zymogens keep themselves inactive at neutral pH by a very similar mechanism in human progastricsin and porcine pepsinogen. This similarity likely carries over to all members of both the pepsinogen A and C families of aspartic proteinase zymogens.

Amino Acid Sequence↗