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At least 487 records · Page 27Linked to original sources
PubMed1997

The crystal and molecular structure of a valinomycin analogue cyclo[(D-Val-L-Lac-L-Ala-D-Hyi)2(D-Val-L-Lac-L-Val-D-Hyi)]. H2O(C50H82N6 O18.H2O).

The crystal and molecular structure of the valinomycin analogue, cyclo[(D-Val-L-Lac-L-Ala-D-Hyi)2(D-Val-L-Lac-L-Val-D-Hyi)] has been solved by x-ray direct methods using the "Shake and Bake" procedure. The crystals, grown from a mixture of octane/CH2Cl2, belong to space group P2(1) (Z = 4) with cell parameters a = 10.29, b = 32.08, c = 18.73 A, beta = 97.05 degrees, and contain two molecules per asymmetric unit. After anisotropic refinement the standard reliability factor was Rl = 0.058. The conformations of both independent molecules is similar to that observed for isoleucinomycin, cyclo[-(D-Ile-L-Lac-L-Ile-D-Hyi)3] [V. Z. Pletnev et al. (1980) Biopolymers, Vol. 19, pp. 1517-1534]. The structure has an asymmetric conformation stabilized by six intramolecular H bonds, five bonds being of the 4-->1 type and one bond being of the 5-->1 type. One water molecule is caged in the internal cavity of each cyclodepsipeptide. This conformation could represent an intermediate state between free and complexed forms of valinomycin.

Crystallography, X-Ray↗
PubMed1997

Molecular structure of a functional Drosophila centromere.

Centromeres play a critical role in chromosome inheritance but are among the most difficult genomic components to analyze in multicellular eukaryotes. Here, we present a highly detailed molecular structure of a functional centromere in a multicellular organism. The centromere of the Drosophila minichromosome Dp1187 is contained within a 420 kb region of centric heterochromatin. We have used a new approach to characterize the detailed structure of this centromere and found that it is primarily composed of satellites and single, complete transposable elements. In the rest of the Drosophila genome, these satellites and transposable elements are neither unique to the centromeres nor present at all centromeres. We discuss the impact of these results on our understanding of heterochromatin structure and on the determinants of centromere identity and function.

Animals↗
PubMed1999

Molecular structure and functional role of vascular tight junctions.

Interendothelial tight junctions regulate paracellular permeability and maintain cell polarity. The assembly and remodeling of tight junctions are examined, focusing on the molecular interactions between tight junction components and their functional role in endothelial biology. The molecular structures of two subcellular organelles related to tight junctions, the intercalated disks in cardiomyocytes and the slit diaphragms in glomerular podocytes, are discussed.

Cardiovascular Physiological Phenomena↗
PubMed2006

[The characteristic of vocal fold molecular structure].

INTRODUCTION: The authors present the layer structure of the vocal fold (by Hirano) indicating at the same time its clinical usefulness in laser chordectomy. MATERIALS AND METHODS: The authors describe the structure of the basement membrane sphere, i.e. the connection between the epithelium and the superficial layer of lamina propria, and the molecular structure of the extracellular matrix of mucosa. RESULTS: The biomechanical significance of fibre proteins and the extracellular matrix is emphasized with special attention paid to hialuronic acid and fibronectin. CONCLUSIONS: Knowing the ultra-structure of the epithelium mucosa connection helps in understanding the mechanism of F0 production. The disorders in cooperation of the biomolecules of lamina propria of the vocal folds can influence the biomechanics of phonation.

Basement Membrane↗
PubMed2005

Three-dimensional computation of atom depth in complex molecular structures.

MOTIVATION: For a complex molecular system the delineation of atom-atom contacts, exposed surface and binding sites represents a fundamental step to predict its interaction with solvent, ligands and other molecules. Recently, atom depth has been also considered as an additional structural descriptor to correlate protein structure with folding and functional properties. The distance between an atom and the nearest water molecule or the closest surface dot has been proposed as a measure of the atom depth, but, in both cases, the 3D character of depth is largely lost. In the present study, a new approach is proposed to calculate atom depths in a way that the molecular shape can be taken into account. RESULTS: An algorithm has been developed to calculate intersections between the molecular volume and spheres centered on the atoms whose depth has to be quantified. Many proteins with different size and shape have been chosen to compare the results obtained from distance-based and volume-based depth calculations. From the wealth of experimental data available for hen egg white lysozyme, H/D exchange rates and TEMPOL induced paramagnetic perturbations have been analyzed both in terms of depth indexes and of atom distances to the solvent accessible surface. The algorithm here proposed yields better correlations between experimental data and atom depth, particularly for those atoms which are located near to the protein surface. AVAILABILITY: Instructions to obtain source code and the executable program are available either from http://sienabiografix.com or http://sadic.sourceforge.net CONTACT: niccolai@unisi.it SUPPLEMENTARY INFORMATION: http://www.Sienabiogzefix.com/publication.

Algorithms↗
PubMed1992

The molecular structure of UDP-galactose 4-epimerase from Escherichia coli determined at 2.5 A resolution.

UDP-galactose 4-epimerase catalyzes the conversion of UDP-galactose to UDP-glucose during normal galactose metabolism. The molecular structure of UDP-galactose 4-epimerase from Escherichia coli has now been solved to a nominal resolution of 2.5 A. As isolated from E. coli, the molecule is a dimer of chemically identical subunits with a total molecular weight of 79,000. Crystals of the enzyme used for this investigation were grown as a complex with the substrate analogue, UDP-benzene, and belonged to the space group P2(1)2(1)2(1) with unit cell dimensions of a = 76.3 A, b = 83.1 A, c = 132.1 A, and one dimer per asymmetric unit. An interpretable electron density map calculated to 2.5 A resolution was obtained by a combination of multiple isomorphous replacement with six heavy atom derivatives, molecular averaging, and solvent flattening. Each subunit of epimerase is divided into two domains. The larger N-terminal domain, composed of amino acid residues 1-180, shows a classic NAD+ binding motif with seven strands of parallel beta-pleated sheet flanked on either side of alpha-helices. The seventh strand of the beta-pleated sheet is contributed by amino acid residues from the smaller domain. In addition, this smaller C-terminal domain, consisting of amino acid residues 181-338, contains three strands of beta-pleated sheet, two major alpha-helices and one helical turn. The substrate analogue, UDP-benzene, binds in the cleft located between the two domains with its phenyl ring in close proximity to the nicotinamide ring of NAD+. Contrary to the extensive biochemical literature suggesting that epimerase binds only one NAD+ per functional dimer, the map clearly shows electron density for two nicotinamide cofactors binding in symmetry-related positions in the dimer. Likewise, each subunit in the dimer also binds one substrate analogue.

Computer Simulation↗
PubMedDate not supplied

[Relationship between the molecular structure of aqueous solutions of polyethylene glycol and the compactness of double-stranded DNA molecules].

The dependence of viscosity of the water solutions of poly(ethylene glycol) (PEG) on the molecular weight has been studied. It has been shown that there is a "transitional" region in PEG properties which accounts for the formation of fluctuation polymer network of the PEG molecules. It has been shown that the "transitional" region in properties of PEG which appears at a certain concentration of PEG (CtrPEG) is characteristic of the PEG preparations with molecular weights exceeding 600 and dependence of the value of CtrPEG on the molecular weight of PEG was obtained. Compactization of double-stranded DNA molecules in PEG-containing water-salt solutions has been studied and the dependence of the value of CcrPEG, . i.e. the concentration of PEG at which the compact particles of DNA appear in the solution, on the molecular weight of PEG was obtained. The correlation between these two dependences reflecting quite different physico-chemical processes shows that the double-stranded DNA molecules are constrained within the polymer network of the PEG molecules. The influence of ionic strength and ionic composition of the solution on the formation of a compact form was investigated. The transition of the DNA molecules from a linear to a compact state may occur only at a definite value of ionic strength of the solution. This transition may occur at the change of K+ for Na+ cations (at a constant value of CPEG). The extent of compactization of the DNA molecules in PEG-containing water-salt solutions is monitored by the molecular structure and by the ionic strength of the solvent. It is supposed that the peculiarities of compactization of the DNA molecules in PEG-containing water-salt solutions reflect some characteristics of conformational transitions of the DNA molecules which occur in vivo.

Circular Dichroism↗
PubMed1981

Molecular structures of packageable ColE1 hybrids and the generation of deletion mutants from one of the hybrids.

ColE1 derivatives carrying cohesive end sites of lambda phage genome (= cos lambda) can be packaged within lambda phage particles. The DNA structure of the prototype ColE1-cos lambda derivative named pKY2257 was studied because of its potential usefulness in various fields in molecular biology. pKY2257, which carries an intact galactose operon of E. coli, is a convenient replicon to detect Tn3 translocation. It was found that one of the PK2257::Tn3 derivatives, pKY2113, generated various small plasmids in E. coli. The molecular structures of some of these deletion mutants were compared with each other and with those of parental plasmid DNAs by heteroduplex analysis and restriction enzyme digestion. A possible mechanism, which seems to be unique to this kind of deletions, is discussed on the basis of the present results.

Bacteriocin Plasmids↗
PubMed2001

Rational design of lipid molecular structure: a case study involving the C19:1c10 monoacylglycerol.

The phase properties of lipids have far-reaching consequences in membrane biology. Their influence ranges from domain formation in intact biomembranes to membrane protein reconstitution and crystallization. To exploit phase behavior in the spirit of rational design, it is imperative that the rules relating lipid molecular structure and liquid crystal or mesophase behavior be established. Phase behavior is quantitatively and concisely represented in the form of temperature-composition phase diagrams. A somewhat limited number of phase diagrams exists for the monoacylglycerols. The objective of the current study was to determine the quality of phase behavior prediction for a specific monoacylglycerol based on an analysis of the existing phase diagrams for related chain homologs. To this end, a phase diagram for the monononadecenoin (19:1c10)/water system was predicted in the temperature range from -15 degrees C to 120 degrees C and from 0% to 80% (w/w) water. The prediction was tested by constructing the corresponding phase diagram using low- and wide-angle x-ray diffraction, differential scanning calorimetry, and polarized light microscopy. The results show that the predicted and experimental phase diagrams agree remarkably well. They also highlight the need for additional phase studies of the type described to enlarge the data bank of phase diagrams and to strengthen the foundations of the rational design approach.

Calorimetry, Differential Scanning↗
PubMed1988

Crotoxin, a phospholipase A2 neurotoxin from the South American rattlesnake Crotalus durissus terrificus: purification of several isoforms and comparison of their molecular structure and of their biological activities.

Crotoxin, the major toxin of the venom of the South American rattlesnake Crotalus durissus terrificus is a mixture of several isoforms that differ slightly in their molecular structure. The toxin consists of two nonidentical subunits: a basic and weakly toxic phospholipase A2, component B, and an acidic and nontoxic subunit, component A. In the present investigation, we have used fast-performance liquid chromatography (FPLC) on anionic and cationic exchange columns to purify isoforms of both crotoxin subunits. Two component A isoforms and four component B isoforms were obtained in a homogeneous state, and their purity was verified by isoelectric focusing in polyacrylamide gels. The amino acid composition of the purified component A and component B isoforms was in good agreement with the protein sequences determined previously with mixtures of isoforms. The amino acid compositions indicated that for both crotoxin components the isoforms differed only by the replacement of few amino acid residues. Eight crotoxin complexes have been prepared in a homogeneous state by reassociation of pure component A and component B isoforms. The quantitative comparison of enzymatic and pharmacological properties of the reconstituted crotoxins indicated that the two component A isoforms had identical properties, whereas the four component B isoforms fell in two classes: crotoxin complexes formed with component B isoforms of the first class were enzymatically less active and pharmacologically more potent than those obtained with component B isoforms of the second class.

Amino Acids↗
PubMedDate not supplied

Effective descriptions of molecular structures and the quantitative structure-activity relationship studies.

In this research, we found CoMFA alone could not obtain sufficiently a strong equation to allow confident prediction for aminobenzenes. When some other parameter, such as heat of molecular formation of the compounds, was introduced into the CoMFA model, the results were improved greatly. It gives us a hint that a better description for molecular structures will yield a better prediction model, and this hint challenged us to look for another method--the projection areas of molecules in 3D space for 3D-QSAR. It is surprising that much better results than that obtained by using CoMFA were achieved. Besides the CoMFA analysis, multiregression analysis and neural network methods for building the models were used in this paper.

Journal Article↗
PubMed2002

Molecular structures and excited states of CpM(CO)(2) (Cp = eta(5)-C(5)H(5); M = Rh, Ir) and [Cl(2)Rh(CO)(2)](-). Theoretical evidence for a competitive charge transfer mechanism.

Molecular structures and excited states of CpM(CO)(2) (Cp = eta(5)-C(5)H(5); M = Rh, Ir) and [Cl(2)Rh(CO)(2)](-) complexes have been investigated using the B3LYP and the symmetry-adapted cluster (SAC)/SAC-configuration interaction (SAC-CI) theoretical methods. All the dicarbonyl complexes have singlet ground electronic states with large singlet-triplet separations. Thermal dissociations of CO from the parent dicarbonyls are energetically unfavorable. CO thermal dissociation is an activation process for [Cl(2)Rh(CO)(2)](-) while it is a repulsive potential for CpM(CO)(2). The natures of the main excited states of CpM(CO)(2) and [Cl(2)Rh(CO)(2)](-) are found to be quite different. For [Cl(2)Rh(CO)(2)](-), all the strong transitions are identified to be metal to ligand CO charge transfer (MLCT) excitations. A significant feature of the excited states of CpM(CO)(2) is that both MLCT excitation and a ligand Cp to metal and CO charge transfer excitation are strongly mixed in the higher energy states with the latter having the largest oscillator strength. A competitive charge transfer excited state has therefore been identified theoretically for CpRh(CO)(2) and CpIr(CO)(2). The wavelength dependence of the quantum efficiencies for the photoreactions of CpM(CO)(2) reported by Lees et al. can be explained by the existence of two different types of excited states. The origin of the low quantum efficiencies for the C-H/S-H bond activations of CpM(CO)(2) can be attributed to the smaller proportion of the MLCT excitation in the higher energy states.

Journal Article↗
PubMed1982

Molecular structures of 2,4-diaminopyrimidine antifolates with antineoplastic activity.

2,4-Diamino-5-(1-adamantyl)-6-methylpyrimidine (DAMP) and its ethanesulfonate salt (DAMP-ES) are potent inhibitors of mammalian dihydrofolate reductase and also inhibit the growth of cultured cells as effectively as the drug methotrexate (MTX). DAMP is currently in phase I clinical studies. An analogue of DAMP having 5-(1-naphthyl) in place of the adamantyl group (DNMP) possesses little cytotoxic as well as enzyme inhibitory activity. The crystal and molecular structures of DAMPM-ES and DNMP were determined in order to elucidate the conformational aspects of drug specificity. The molecular conformation of DAMP-ES shows that the C8--C7 bond of the adamantyl ring is nearly coplanar with the pyrimidine ring (C8--C7--C5--C6 = 7.5 degrees) instead of staggered as expected from steric considerations. As a result, the pyrimidine ring and its 4,6-substituents are severely distorted from coplanarity. In DNMP, the 1-naphthalene ring is perpendicular to the pyrimidine ring (C8--C7--C5--C6 = -87.0 degrees) which is itself planar. N1 is protonated in DAMP-ES but not in DNMP. When the two structures are compared, the 5-substituents occupy different regions of space, with the outer ring of the naphthalene group outside of the volume occupied by the adamantyl ring. Therefore, the reduced effectiveness of DNMP may be caused by the inability of the naphthalene to fit the binding site in dihydrofolate reductase. This is the situation when DNMP is placed in the methotrexate binding site of Lactobacillus casei crystal structure.

Antineoplastic Agents↗
PubMed1995

The strength of a calcified tissue depends in part on the molecular structure and organization of its constituent mineral crystals in their organic matrix.

High-voltage electron-microscopic tomographic (3D) studies of the ultrastructural interaction between mineral and organic matrix in a variety of calcified tissues reveal different crystal structural and organizational features in association with their respective organic matrices. In brittle or weak pathologic or ectopic calcifications, including examples of osteogenesis imperfecta, calciphylaxis, calcergy, and dermatomyositis, hydroxyapatite crystals occur in various sizes and shapes and are oriented and aligned with respect to collagen in a manner which is distinct from that found in normal calcified tissues. A model of collagen-mineral interaction is proposed which may account for the observed crystal structures and organization. The results indicate that the ultimate strength, support, and other mechanical properties provided by a calcified tissue are dependent in part upon the molecular structure and arrangement of its constituent mineral crystals within their organic matrix.

Animals↗