A method for correlations analysis of coordinates: applications for molecular conformations

We describe a new method to analyze multiple correlations between subsets of coordinates that represent a sample. The correlation is established only between specific regions of interest at the coordinates. First, the region(s) of interest are selected at each molecular coordinate. Next, a correlation matrix is constructed for the selected regions. The matrix is subject to further analysis, illuminating the multidimensional structural characteristics that exist in the conformational space. The method's abilities are demonstrated in several examples: it is used to analyze the conformational space of complex molecules, it is successfully applied to compare related conformational spaces, and it is used to analyze a diverse set of protein folding trajectories.     

NMR studies of molecular conformations in alpha-cyclodextrin

A new approach for analysis of NMR parameters is proposed. The experimental data set includes scalar couplings, NOEs, and residual dipolar couplings. The method, which aims at construction of the conformational distribution function, is applied to alpha-cyclodextrin in isotropic solution and dissolved in a dilute liquid crystal. An attempt to analyze the experimental data using an average molecular conformation resulted in unacceptable errors. Our approach rests on the maximum entropy method (ME), which gives the flattest possible distribution, consistent with the experimental data. Very good agreement between experimental and calculated NMR parameters was observed. In fact, two conformational states were required in order to obtain a satisfactory agreement between calculated and experimental data. In addition, good agreement with Langevin dynamics computer simulations was obtained.     

Conformational analysis of bradykinin by annealed molecular dynamics and comparison to NMR-derived conformations

Conformational analysis of bradykinin (BK), a nonapeptide of the sequence RPPGFSPFR, was accomplished using annealed molecular dynamics (AMD) at 1000 K in BIOGRAF 2.2. One hundred anneal cycles produced 100 conformations over approximately 2000 ps. These conformations were compared to structures derived by nuclear magnetic resonance (NMR) methods for similar shape and energy. Energy minimization of relevant conformations using both BIOGRAF 2.2 and AMBER 3.0a revealed that the AMD-determined conformations are in the same energy range as the NMR-determined structures. Also, the shape of the relevant conformations appeared similar, suggesting that AMD is a good tool for the conformational analysis of small peptide ligands. © 1993 John Wiley & Sons, Inc.     

Dipole moments and molecular conformations of acetylpyrimidines

By comparing experimentally determined dipole moments with those derived from vector-addition and semiempirical computation using MNDO and AM 1 approximations the conformations of 4- and 5-acetylpyrimidines were found to be close to planar, while that of 2-acetylpyrimidine exhibited a torsion angle of 90°.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 10, pp. 1387–1390, October, 1992.     

Calculation of alcohol conformations by molecular mechanics

The geometries and energies of simple alcohols were calculated with a molecular mechanics force field. The force field requires the application of the charge interaction model with charges calculated by the CNDO/2 method, the importance of electrostatic interactions for the equilibrium of rotamers about the C-O bond exceeds that of van der Waals interactions. The calculated rotamer populations are discussed with regard to the value of ¹H NMR coupling constants ³JHCOH and other experimental data.     

Sialyldisaccharide conformations: a molecular dynamics perspective

Sialyldisaccharides are significant terminal components of glycoconjugates and their negative charge and conformation are extensively utilized in molecular recognition processes. The conformation and flexibility of four biologically important sialyldisaccharides [Neu5Acα(2-3)Gal, Neu5Acα(2-6)Gal, Neu5Acα(2-8)Neu5Ac and Neu5Acα(2-9)Neu5Ac] are studied using Molecular Dynamics simulations of 20 ns duration to deduce the conformational preferences of the sialyldisaccharides and the interactions which stabilize the conformations. This study clearly describes the possible conformational models of sialyldisaccharides deduced from 20 ns Molecular Dynamics simulations and our results confirm the role of water in the structural stabilization of sialyldisaccharides. An extensive analysis on the sialyldisaccharide structures available in PDB also confirms the conformational regions found by experiments are detected in MD simulations of 20 ns duration. The three dimensional structural coordinates for all the MD derived sialyldisaccharide conformations are deposited in the 3DSDSCAR database and these conformational models will be useful for glycobiologists and biotechnologists to understand the biological functions of sialic acid containing glycoconjugates.     

Dipole moments and molecular conformations of some thioanhydrides

Electric dipole moments of methyl thiobenzoate (1.70 D), thiophthalic anhydride (3.92 D) and dibenzoyl sulphide (3.88 D) have been measured in benzene at 25° C. The predicted moments of these compounds were calculated and the results interpreted in terms of their conformations.     

Cluster analysis from molecular similarity matrices using a non-linear neural network

A non-linear neural network model to perform cluster analysis is presented. It provides an efficient parallel algorithm for solving this pattern recognition task, consisting, from the mathematical point of view, of a combinatorial optimization problem. A new classification technique is discussed in order to visualize clustering patterns within a molecular set, by means of numerical analysis of the similarity matrix. As an example of the application of the reported neural network model, a quantum molecular similarity study in the field of structure-activity relationships is reported. A molecular set made of eighteen quinolones is used as an example. The resultant cluster distribution showed a good qualitative correlation between similarity data and biological activity.     

Unusual molecular conformations in fluorinated, contorted hexabenzocoronenes

Fluorinated, contorted hexabenzocoronenes (HBCs) have been synthesized in a facile manner via Suzuki-Miyaura coupling of fluorinated phenyl boronic acids followed by photocyclization and Scholl cyclization. In addition to the molecular conformation observed in previous HBC derivatives, close-contact fluorine-fluorine intramolecular interactions result in a metastable conformation not previously observed. Heating the metastable HBCs above 100 °C irreversibly converts them to the stable conformation, suggesting that the metastable conformation arises from a kinetically arrested state during cyclization.     

Mapping molecular conformations with multiple-mode two-dimensional infrared spectroscopy

The multiple-mode two-dimensional infrared (2D-IR) spectrum in a broad frequency range from 1000 to 3200 cm(-1) of a 1-cyanovinyl acetate solution in CCl(4) is reported. By analyzing its relative orientations of the transition dipole moments of normal modes that cover vibrations of all chemical bonds, the three-dimensional molecular conformations and their population distributions of 1-cyanovinyl acetate are obtained, with the aid of quantum chemistry calculations that translate the experimental transition dipole moment cross angles into the cross angles among chemical bonds.     

Vibrational spectra and molecular conformations of unbranched dialkyl selenides

The IR and Raman spectra of six unbranched dialkyl selenides, namely ethylmethyl selenide, methylpropyl selenide, butylmethyl selenide, diethyl selenide, ethylpropyl selenide and dipropyl selenide, have been systematically investigated. The spectra are analysed on the basis of the spectral examination and the normal coordinate treatment. The CH₂-Se stretching wavenumbers of the dialkyl selenides correlate well with the conformation about the CSe-C-C bond axes. The molecular conformation in the solid and liquid states is studied by utilizing this correlation in conjunction with the wave-numbers of the CH₂ rocking and skeletal deformation vibrations. The conformational stability in the liquid state is also examined and the enthalpy difference between the trans and gauche forms of ethylmethyl selenide is obtained as 0.22 ± 0.05 kcal mol^?1, the gauche form being more stable. The conformational stability of dialkyl ethers, sulphides and selenides are comparatively discussed.     

Computational study on the molecular conformations of phenolic compounds

The study of the conformation of eight phenolic compounds (i.e. phenol, guaiacol, syringol, pyrocatechol, o-, m-, p-cresol and vanillin) was carried out using B3LYP (Becke, 3-parameter, Lee-Yan-Parr) method and cc-pVTZ (correlation consistent polarized polarisation Valence triple zêta) basis set. Potential energy surfaces were plotted in order to identify the minimum energy structures and the transition states. For the first time, structures of vanillin and syringol were completely determined. Moreover, our work also confirms that the most stable conformations of m-cresol and p-cresol are obtained when the methyl group presents a hydrogen atom at the perpendicular of the benzene ring. The possibility of intramolecular hydrogen bonding was also investigated. Guaiacol, pyrocatechol, syringol and vanillin present a structure stabilized by the presence of a moderate hydrogen bond. Finally, potential energy barriers and rotational potential functions were calculated. The comparison of the rotational potential parameters for each molecule highlights the presence of similarities specific to each substituent and their neighbours.     

Dipole moments and molecular conformations ofO-vinyl- andO-ethylacetoximes in solutions

Dipole moments of the molecules ofO-vinyl- andO-ethylacetoximes in octane and THF were measured at different temperatures. In octane, the equilibrium mixture of stableO-vinylacetoxime conformers consists of forms with different polarity. Polarity of these conformers, which are due to rotation about the C−O and N−O bonds, is mainly determined by the relative position of the lone electron pairs of nitrogen and oxygen atoms. The fraction of the polar conformer increases as temperature increases, as well as on going from octane to THF. Saturation of the vinyl group in theO-vinylacetoxime molecule nearly halves the molecular dipole moment in the nonpolar medium, which radically differentiates this compound from vinyl ethers. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1685–1690, September, 1999.     

Extended conformations of isolated molecular bottle-brushes: Influence of side-chain topology

A Monte Carlo study is presented to discuss the influence of the side-chain topology on the enhancement of the persistence length of a molecular bottle-brush in a dilute athermal solution due to the excluded volume interactions between the side chains. The structures investigated consisted of freely jointed backbones of 100 hard spheres (beads) of diameter 1 to which 50 equally flexible side chains were grafted. The diameter of the side-chain beads was varied from 1 to 3 in the same units. For every given size of the side-chain bead, the length of the side chains was varied from 4 to 20 beads. The ratio between the persistence length and the bottle-brush diameter, which is the determining factor for lyotropic behavior of conventional semi-flexible chains, was found to be almost independent of the side-chain length. At the same time, it was found to increase considerably with increasing size of the side-chain beads, suggesting that by a proper choice of the chemistry lyotropic behavior of molecular bottle-brushes due to excluded-volume interactions between the side chains might be achieved. Moreover, relatively short side chains can be used since the side chain length has only a minor influence on the ratio between the persistence length and the diameter. These findings are in a good agreement with recent experimental observations.     

Comprehensive structural analysis of the open and closed conformations of Theileria annulata enolase by molecular modelling and docking

Theileria annulata is an apicomplexan parasite which is responsible for tropical theileriosis in cattle. Due to resistance of T. annulata against commonly used antitheilerial drug, new drug candidates should be identified urgently. Enolase might be a druggable protein candidate which has an important role in glycolysis, and could also be related to several cellular functions as a moonlight protein. In this study; we have described three-dimensional models of open and closed conformations of T. annulata enolase by homology modeling method for the first time with the comprehensive domain, active site and docking analyses. Our results show that the enolase has similar folding patterns within enolase superfamily with conserved catalytic loops and active site residues. We have described specific insertions, possible plasminogen binding sites, electrostatic potential surfaces and positively charged pockets as druggable regions in T. annulata enolase.     

Effect of molecular conformations on the adsorption behavior of gold-binding peptides

Despite extensive recent reports on combinatorially selected inorganic-binding peptides and their bionanotechnological utility as synthesizers and molecular linkers, there is still only limited knowledge about the molecular mechanisms of peptide binding to solid surfaces. There is, therefore, much work that needs to be carried out in terms of both the fundamentals of solid-binding kinetics of peptides and the effects of peptide primary and secondary structures on their recognition and binding to solid materials. Here we discuss the effects of constraints imposed on FliTrx-selected gold-binding peptide molecular structures upon their quantitative gold-binding affinity. We first selected two novel gold-binding peptide (AuBP) sequences using a FliTrx random peptide display library. These were, then, synthesized in two different forms: cyclic (c), reproducing the original FliTrx gold-binding sequence as displayed on bacterial cells, and linear (l) dodecapeptide gold-binding sequences. All four gold-binding peptides were then analyzed for their adsorption behavior using surface plasmon resonance spectroscopy. The peptides exhibit a range of binding affinities to and adsorption kinetics on gold surfaces, with the equilibrium constant, Keq, varying from 2.5x10(6) to 13.5x10(6) M(-1). Both circular dichroism and molecular mechanics/energy minimization studies reveal that each of the four peptides has various degrees of random coil and polyproline type II molecular conformations in solution. We found that AuBP1 retained its molecular conformation in both the c- and l-forms, and this is reflected in having similar adsorption behavior. On the other hand, the c- and l-forms of AuBP2 have different molecular structures, leading to differences in their gold-binding affinities.