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[Optical properties and molecular structure of nucleic acids and their components. X. Infrared spectra and molecular structure of denatured DNA with different water content and degree of protonation].

IR-spectra (4000-900 cm-minus-1) of heat denatured DNA (d-DNA) of calf thymus have been obtained in the range of relative humidity of 0-93% and of the guota of protoned bases alpha of 0-0,5. fron these spectra the diagram of d-DNA states is plotted as the relationships of intensities and the location of some bands with and relative humidity. At alpha approximately 0,2 a compact structure S2-1 with firm hydrogen bonds between protoned and unprotoned bases which is similar to those observed earlier while protoning homopolynucleotides poly-A and poly-C. At G1'-large values of alpha S2-1-conformation destroyed and a loose structure (alpha approximately 0,35) appears. the latter is characterized by a minimum H-binding of the base and increased hydration. Further increase of alpha brings about the formation of sufficiently compact G2-1-STRUCTURE WHICH IS CHARACTERIZED BY SOLID H-bonds between PO2-groups and protoned bases. A specific effect of the structures found on the state of absorbed water and the structure of hydrate envelope is revealed.

Animals↗
PubMed2005

Managing the solvent water polarization to obtain improved NMR spectra of large molecular structures.

In large molecular structures, the magnetization of all hydrogen atoms in the solute is strongly coupled to the water magnetization through chemical exchange between solvent water and labile protons of macromolecular components, and through dipole-dipole interactions and the associated "spin diffusion" due to slow molecular tumbling. In NMR experiments with such systems, the extent of the water polarization is thus of utmost importance. This paper presents a formalism that describes the propagation of the water polarization during the course of different NMR experiments, and then compares the results of model calculations for optimized water polarization with experimental data. It thus demonstrates that NMR spectra of large molecular structures can be improved with the use of paramagnetic spin relaxation agents which selectively enhance the relaxation of water protons, so that a substantial gain in signal-to-noise can be achieved. The presently proposed use of a relaxation agent can also replace the water flip-back pulses when working with structures larger than about 30 kDa. This may be a valid alternative in situations where flip-back pulses are difficult to introduce into the overall experimental scheme, or where they would interfere with other requirements of the NMR experiment.

Chaperonin 60↗
PubMed1993

Refined 1.8 A X-ray crystal structure of astacin, a zinc-endopeptidase from the crayfish Astacus astacus L. Structure determination, refinement, molecular structure and comparison with thermolysin.

Astacin, a 200 residue digestive zinc-endopeptidase from the crayfish Astacus astacus L., is the prototype of the "astacin family", which comprises several membrane-bound mammalian endopeptidases and developmentally implicated regulatory proteins. Large trigonal crystals of astacin were grown, and X-ray reflection data to 1.8 A resolution were collected. The astacin structure has been solved by multiple isomorphous replacement using six heavy-atom derivatives, and refined to a crystallographic R-value of 0.158 applying stringent constraints. All 200 residues are clearly defined by electron density; 181 solvent molecules have been localized. Besides the native structure, the structures of Hg-astacin (with a mercury ion replacing the zinc) and of the apoenzyme were also refined. The astacin molecule exhibits a kidney-like shape. It consists of an amino-terminal and a carboxy-terminal domain, with a deep active-site cleft in between. The zinc ion, located at the bottom of this cleft, is co-ordinated in a novel trigonal-bipyramidal geometry by three histidine residues, a tyrosine and by a water molecule, which is also bound to the carboxylate side-chain of Glu93. The amino-terminal domain of astacin consists mainly of two long alpha-helices, one centrally located and one more peripheral, and of a five-stranded pleated beta-sheet. The amino terminus protrudes into an internal, water-filled cavity of the lower domain and forms a buried salt bridge with Glu103; amino-terminally extended pro-forms of astacin are thus not compatible with this structure. The carboxy-terminal domain of astacin is mainly organized in several turns and irregular structures. Because they share sequence identity of about 35%, the structures of the proteolytic domains of the other "astacin" members must be quite similar to astacin. Only a few very short deletions and insertions quite distant from the active-site distinguish their structures from astacin. The five-stranded beta-sheet and the two helices of the amino-terminal domain of astacin are topologically similar to the structure observed in the archetypal zinc-endopeptidase thermolysin; the rest of the structures are, in contrast, completely unrelated in astacin and thermolysin. The zinc ion, the central alpha-helix and the zinc-liganding residues His92, Glu93 and His96 of astacin are nearly superimposable with the respective groups of thermolysin, namely with the zinc ion, the "active-site helix", and His142TL, Glu143TL and His146TL of the zinc-binding consensus motif His-Glu-Xaa-Xaa-His (where Xaa is any amino acid residue).(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1983

Correlation of structure and activity in ansamycins. Molecular structure of sodium rifamycin SV.

The crystal and molecular structure of the sodium salt of rifamycin SV (clinically known as rifacin) as the monohydrate ethanol solvate has been determined to study the conformation of the ansa chain in unsubstituted rifamycins and also to clarify the metal complexation with rifamycins. The crystals belong to the space group P2(1)2(1)2(1) with cell dimensions (estimated standard deviations in parentheses) of a = 12.061 (2), b = 13.936 (2), and c = 24.731 (4) A. The structure was solved by direct methods and refined to an R factor of 0.069. The conformation of the ansa chain differs from that of other active rifamycins, e.g., rifampcin and rifamycin B at the joining point of the ansa chain to the naphthohydroquinone chromophore. The conformation of the middle part of the ansa chain, which is essential for activity against DNA-dependent RNA polymerase, remains the same. The sodium ion is penta-coordinated and has a trigonal bipyramidal geometry. The intermolecular hydrogen bonding involves O(9), O(10), O(5), and O(6) through water and ethanol molecules. A two-step mode of action of rifamycins has been postulated, and the conformations of antibiotics suitable for penetration of the membrane barrier and that for antibiotic-enzyme complex formation have been suggested.

Anti-Bacterial Agents↗
PubMed2004

How delocalized is N,N,N',N'-tetraphenylphenylenediamine radical cation? An experimental and theoretical study on the electronic and molecular structure.

The electronic and molecular structure of N,N,N',N'-tetraphenylphenylenediamine radical cation 1(+) is in focus of this study. Resonance Raman experiments showed that at least eight vibrational modes are strongly coupled to the optical charge resonance band which is seen in the NIR. With the help of a DFT-based vibrational analysis, these eight modes were assigned to symmetric vibrations. The contribution of these symmetric modes to the total vibrational reorganization energy is dominant. These findings are in agreement with the conclusions from a simple two-state two-mode Marcus-Hush analysis which yields a tiny electron-transfer barrier. The excellent agreement of the X-ray crystal structure analysis and the DFT computed molecular structure of 1(+) on one hand as well as the solvent and solid-state IR spectra and the DFT-calculated IR active vibrations on the other hand prove 1(+) adopts a symmetrical delocalized Robin-Day class III structure both in the solid state and in solution.

Journal Article↗
PubMed2005

Investigation of anticancer activity of macrocyclic Schiff bases by means of 4D-QSAR based on simplex representation of molecular structure.

Influence of the molecular structure of macrocyclic pyridinophanes, their analogues and some other compounds on anticancer activity (Leukemia, central nervous system (CNS) cancer, prostate cancer, breast cancer, melanoma, non-small cell lung cancer, colon cancer, ovarian cancer, renal cancer) was investigated by means of a new 4D-QSAR approach based on the simplex representation of molecular structures (SiRMS). For all the investigated molecules, the 3D structural models were first created and the set of conformers (fourth dimension) was used. Each conformer was represented as a system of different simplexes (tetratomic fragments of fixed structure, chirality and symmetry). Statistic characteristics of the QSAR partial least squares (PLS) models were satisfactory (correlation coefficient r=0.990-0.861; cross-validation coefficient CVR=0.914-0.633). The molecular fragments increasing and decreasing anticancer activity were defined. This information may be useful for the design and direct synthesis of novel anticancer agents.

Antineoplastic Agents↗
PubMed1997

Synthesis, Molecular Structure, and Reactivity of the Tetranuclear Complex [NBu(4)](2)[Pd(4)(&mgr;-PPh(2))(2)(&mgr;-Cl)(4)(C(6)F(5))(4)]. Molecular Structure of [Pd(2)(&mgr;-PPh(2))(C(6)F(5))(2)(bipy)(2)]ClO(4).C(6)H(14).

Anionic tetranuclear complexes with the molecular formula [NBu(4)](2)[Pd(4)(&mgr;-PPh(2))(2)(&mgr;-X)(4)(C(6)F(5))(4)] [X = Cl (1), Br (2)] were obtained by reaction of [NBu(4)](2)[Pd(2)(&mgr;-PPh(2))(2)(C(6)F(5))(4)] and PdCl(2) (or K(2)[PdCl(4)]) in acetone, followed by reaction with KBr for 2. The reactions of 1 with neutral monodentate (L) or bidentate (L-L) ligands afford the dinuclear derivatives [Pd(2)(&mgr;-PPh(2))(&mgr;-Cl)(C(6)F(5))(2)L(2)] [L = PPh(3) (3), py (4)] or [Pd(2)(&mgr;-PPh(2))(C(6)F(5))(2)(L-L)(2)](n)() [n = 1-, L-L = acac (6); n = 1+, L-L = bipy (7) or phen (8)]. The structures of complexes 1 and 7 were determined by single-crystal X-ray diffraction studies. The bis(acetone) solvate of complex 1, [NBu(4)](2)[Pd(4)(&mgr;-PPh(2))(2)(&mgr;-Cl)(4)(C(6)F(5))(4)].2C(3)H(6)O, crystallizes in the monoclinic system, space group P2(1)/c, with a = 11.679(5) Å, b = 16.552(7) Å, c = 23.868(8) Å, beta = 101.10(3) degrees, V = 4527.6(15) Å(3), and Z = 2. The central core of the anion has the shape of a rectangle with the four Pd atoms in the corners. The hexane solvate of complex 7, [Pd(2)(&mgr;-PPh(2))(C(6)F(5))(2)(bipy)(2)][ClO(4)].C(6)H(14), crystallizes in the monoclinic system, space group P2(1)/n, with a = 16.214(3) Å, b = 10.311(2) Å, c = 28.380(6) Å, beta = 100.82(3) degrees, V = 4660(2) Å(3), and Z = 4. In both complexes, the long Pd.Pd distances (>3.1 Å) clearly point to the absence of any Pd-Pd interaction.

Journal Article↗
PubMed2005

Crystalline molecular machines: encoding supramolecular dynamics into molecular structure.

Crystalline molecular machines represent an exciting new branch of crystal engineering and materials science with important implications to nanotechnology. Crystalline molecular machines are crystals built with molecules that are structurally programmed to respond collectively to mechanic, electric, magnetic, or photonic stimuli to fulfill specific functions. One of the main challenges in their construction derives from the picometric precision required for their mechanic operation within the close-packed, self-assembled environment of crystalline solids. In this article, we outline some of the general guidelines for their design and apply them for the construction of molecular crystals with units intended to emulate macroscopic gyroscopes and compasses. Recent advances in the preparation, crystallization, and dynamic characterization of these interesting systems offer a foothold to the possibilities and help highlight some avenues for future experimentation.

Journal Article↗
PubMed2003

MOLVIE: an interactive visualization environment for molecular structures.

A Molecular visualization interactive environment (MOLVIE), is designed to display three-dimensional (3D) structures of molecules and support the structural analysis and research on proteins. The paper presents the features, design considerations and applications of MOLVIE, especially the new functions used to compare the structures of two molecules and view the partial fragment of a molecule. Being developed in JAVA, MOLVIE is platform-independent. Moreover, it may run on a webpage as an applet for remote users. MOLVIE is available at http://www.cs.ucsb.edu/~mli/Bioinf/software/index.html.

Amino Acid Sequence↗
PubMed2004

Molecular structure of proline.

The molecular structures of the two lowest-energy conformers of proline, Pro-I and Pro-II, have been characterized by ab initio electronic structure computations. An extensive MP2/6-31G* quartic force field for Pro-I, containing 62,835 unique elements in the internal coordinate space, was computed to account for anharmonic vibrational effects, including total zero-point contributions to isotopomeric rotational constants. New re and improved r0 least-squares structural refinements were performed to determine the heavy-atom framework of Pro-I, based on experimentally measured (A. Lesarri, S. Mata, E. J. Cocinero, S. Blanco, J. C. Lopez, J. L. Alonso, Angew. Chem. 2002, 114, 4867; Angew. Chem. Int. Ed. 2002, 41, 4673) rotational constant sets of nine isotopomers and our ab initio data for structural constraints and zero-point vibrational (ZPV) shifts. Without the ab initio constraints, even the extensive set of empirical rotational constants cannot satisfactorily fix the molecular structure of the most stable conformer of proline, a 17-atom molecule with no symmetry. After imposing the ab initio constraints, excellent agreement between theory and experiment is found for the heavy-atom geometric framework, the root-mean-square (rms) residual of the empirical rotational constant fit being cut in half by adding ZPV corrections. The most significant disparity, about 0.07 A, between the empirical and the best ab initio structures, concerns the r(N...H) distance of the intramolecular hydrogen bond. Some of the experimental quartic centrifugal distortion constants assigned to Pro-II have been corrected based on data obtained from a theoretical force field.

Models, Chemical↗
PubMed1994

WinMGM: a fast CPK molecular graphics program for analyzing molecular structure.

A molecular modeling program is presented which has been written for Microsoft windows 3.1 and Windows NT operating systems. The program permits interactive molecular manipulation and also provides analytical tools such as energy computations and solvent accessible surfaces. An extremely fast algorithm is used which generates realistic space-filling CPK images in addition to wire frame, ribbons, MIDAS, labels, and points. An important feature of this algorithm is a highly optimized Z-buffer, which is described.

Algorithms↗
PubMed1997

Molecular structure of the "low molecular weight antigen" of Toxoplasma gondii: a glucose alpha 1-4 N-acetylgalactosamine makes free glycosyl-phosphatidylinositols highly immunogenic.

Toxoplasma gondii is a ubiquitous parasitic protozoan causing congenital infection and severe encephalitis in the course of the acquired immunodeficiency syndrome. Glycosyl-phosphatidylinositols of T. gondii have been shown to be identical with the low molecular weight antigen which elicits an early immunoglobulin M immune response in humans. A detailed study of the structures of these glycolipid antigens was performed. Radiolabelled glycolipids were extensively analysed by chemical and exoglycosidase treatments in combination with high pH anion-exchange chromatography, gel-filtration and lectin affinity chromatography. In addition, carbohydrate fragments prepared and purified from bulk preparations of unlabelled glycolipids by high performance liquid chromatography were subjected to two-dimensional 1H nuclear magnetic resonance spectroscopy, fast-atom bombardment-mass spectrometry, and methylation linkage analysis in order to elucidate the structure of T. gondii GPIs. The following structures were identified: (ethanolamine-PO4)-Man alpha 1-2Man alpha 1-6(GalNAc beta 1-4)Man alpha 1-4GlcN alpha-inositol-PO4-lipid and the novel structure (ethanolamine-PO4)-Man alpha 1-2Man alpha 1-6(Glc alpha 1-4GalNAc beta 1-4)Man alpha 1-4 GlcN alpha-inositol-PO4-lipid both with and without terminal ethanolamine phosphate. Evidence is provided, that only T. gondii GPIs bearing the unique glucose-N-acetylgalactosamine side branch are immunogenic in humans and that this structure is widely distributed among T. gondii isolates. Monoclonal antibodies have been characterized to recognize structures with different degrees of side-chain modification. We suggest that these reagents in combination with recently devised techniques for insertional mutagenesis in T. gondii should greatly facilitate the cloning of genes essential for GPI side-chain modification.

Acetylgalactosamine↗
PubMed2005

[Quantitative structure-retention relationships of monosubstituted alkanes by dividing its molecular structure into substructure].

In order to investigate the quantitative structure-retention relationship in gas chromatography (GC) , the molecular structure of monosubstituted alkane RX (X = halogen, OH, SH, NH2) is divided into two parts, R and X, to obtain molecular structure parameters, and the retention times in GC for 37 monosubstituted alkanes RX were determined. It was proposed that the retention time in GC is affected by three main factors for RX compounds, alkyl group R, substituted group X, and interaction between R and X. Using four parameters, the eigenvalue of bonding orbital-connection matrix EVM, the polarizability effect index of alkyl group PEI, the mass content for substituted group X, and the partial charge deltaN(H) on hydrogen atom of the group X, a quantitative structure-retention correlation model with correlation coefficient (r) of 0.9948 and standard deviation (S) of 0.0991 was obtained for the 37 RX compounds. The model obtained has good predictive and extrapolation ability. The predicted retention indexes are in good agreement with the experimental ones for alcohols.

Alkanes↗
PubMed1999

Using imperfect secondary structure predictions to improve molecular structure computations.

MOTIVATION: Until ab initio structure prediction methods are perfected, the estimation of structure for protein molecules will depend on combining multiple sources of experimental and theoretical data. Secondary structure predictions are a particularly useful source of structural information, but are currently only approximately 70% correct, on average. Structure computation algorithms which incorporate secondary structure information must therefore have methods for dealing with predictions that are imperfect. EXPERIMENTS PERFORMED: We have modified our algorithm for probabilistic least squares structural computations to accept 'disjunctive' constraints, in which a constraint is provided as a set of possible values, each weighted with a probability. Thus, when a helix is predicted, the distances associated with a helix are given most of the weight, but some weights can be allocated to the other possibilities (strand and coil). We have tested a variety of strategies for this weighting scheme in conjunction with a baseline synthetic set of sparse distance data, and compared it with strategies which do not use disjunctive constraints. RESULTS: Naive interpretations in which predictions were taken as 100% correct led to poor-quality structures. Interpretations that allow disjunctive constraints are quite robust, and even relatively poor predictions (58% correct) can significantly increase the quality of computed structures (almost halving the RMS error from the known structure). CONCLUSIONS: Secondary structure predictions can be used to improve the quality of three-dimensional structural computations. In fact, when interpreted appropriately, imperfect predictions can provide almost as much improvement as perfect predictions in three-dimensional structure calculations.

Algorithms↗
PubMed2003

Quantitative structure-property relationships for predicting Henry's law constant from molecular structure.

Various models are available for the prediction of Henry's law constant (H) or the air-water partition coefficient (Kaw), its dimensionless counterpart. Incremental methods are based on structural features such as atom types, bond types, and local structural environments; other regression models employ physicochemical properties, structural descriptors such as connectivity indices, and descriptors reflecting the electronic structure. There are also methods to calculate H from the ratio of vapor pressure (p(v)) and water solubility (S(w)) that in turn can be estimated from molecular structure, and quantum chemical continuum-solvation models to predict H via the solvation-free energy (deltaG(s)). This review is confined to methods that calculate H from molecular structure without experimental information and covers more than 40 methods published in the last 26 years. For a subset of eight incremental methods and four continuum-solvation models, a comparative analysis of their prediction performance is made using a test set of 700 compounds that includes a significant number of more complex and drug-like chemical structures. The results reveal substantial differences in the application range as well as in the prediction capability, a general decrease in prediction performance with decreasing H, and surprisingly large individual prediction errors, which are particularly striking for some quantum chemical schemes. The overall best-performing method appears to be the bond contribution method as implemented in the HENRYWIN software package, yielding a predictive squared correlation coefficient (q2) of 0.87 and a standard error of 1.03 log units for the test set.

Chemical Phenomena↗
PubMed2002

A method for the calculation of odor character from molecular structure.

The relationship between molecular structure and odor character is one of the most complex structure-activity problems in biology. Despite over a century of effort, it remains unsolved, and synthesis of new odorants still proceeds largely by trial and error. In previous work, I have argued that the reason for this failure lies in a mistaken assumption, namely that molecular shape determines odor character. Instead, I have taken up and extended an old idea (Dyson, 1938) according to which vertebrate olfactory receptors detect odorants by their molecular vibrations. I propose that the detection mechanism is inelastic electron tunnelling. If this is correct, there should be a correlation between the tunnelling vibrational spectra of odorants and their odor character. Here, using semi-empirical quantum chemistry methods and a simple calculation method for tunnelling mode intensities, I calculate the spectra of structurally diverse odorants belonging to various odor categories. With few exceptions, the calculated spectra of bitter almonds, musks, ambers, woods, sandalwoods and violets strongly correlate with odor character.

Algorithms↗