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Academic literature on the topic 'Conformational analysis'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 August 2024

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Journal articles on the topic "Conformational analysis"

1

Yaoita, Yasunori, and Koichi Machida. "Conformational Assignments of Thujopsene and Related Compounds." Natural Product Communications 14, no. 9 (September 2019): 1934578X1987893. http://dx.doi.org/10.1177/1934578x19878936.

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Conformational analysis suggests that thujopsene (1) can exist as 2 possible conformations, steroidal and nonsteroidal. The conformation of 1 has been investigated using a NMR spectroscopic method. Analyses of the 1H NMR, ROESY, and long-range 1H-1H COSY spectra indicate that 1 exists in a steroidal conformation. Although the conformations of related compounds 2 and 3 were originally assigned as nonsteroidal, careful reexamination of the published NMR data indicates that both compounds exist in a steroidal conformation.

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Thach, Trung Thanh, Donghyuk Shin, Seungsu Han, and Sangho Lee. "New conformations of linear polyubiquitin chains from crystallographic and solution-scattering studies expand the conformational space of polyubiquitin." Acta Crystallographica Section D Structural Biology 72, no. 4 (March 30, 2016): 524–35. http://dx.doi.org/10.1107/s2059798316001510.

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The conformational flexibility of linkage-specific polyubiquitin chains enables ubiquitylated proteins and their receptors to be involved in a variety of cellular processes. Linear or Met1-linked polyubiquitin chains, associated with nondegradational cellular signalling pathways, have been known to adopt multiple conformations from compact to extended conformations. However, the extent of such conformational flexibility remains open. Here, the crystal structure of linear Ub2was determined in a more compact conformation than that of the previously known structure (PDB entry 3axc). The two structures differ significantly from each other, as shown by an r.m.s.d. between Cαatoms of 3.1 Å. The compactness of the linear Ub2structure in comparison with PDB entry 3axc is supported by smaller values of the radius of gyration (Rg; 18versus18.9 Å) and the maximum interatomic distance (Dmax; 55.5versus57.8 Å). Extra intramolecular hydrogen bonds formed among polar residues between the distal and proximal ubiquitin moieties seem to contribute to stabilization of the compact conformation of linear Ub2. An ensemble of three semi-extended and extended conformations of linear Ub2was also observed by small-angle X-ray scattering (SAXS) analysis in solution. In addition, the conformational heterogeneity in linear polyubiquitin chains is clearly manifested by SAXS analyses of linear Ub3and Ub4: at least three distinct solution conformations are observed in each chain, with the linear Ub3conformations being compact. The results expand the extent of conformational space of linear polyubiquitin chains and suggest that changes in the conformational ensemble may be pivotal in mediating multiple signalling pathways.

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Wu, Shanshan, Tam T. T. N. Nguyen, Olga V. Moroz, Johan P. Turkenburg, Jens E. Nielsen, Keith S. Wilson, Kasper D. Rand, and Kaare Teilum. "Conformational heterogeneity of Savinase from NMR, HDX-MS and X-ray diffraction analysis." PeerJ 8 (June 26, 2020): e9408. http://dx.doi.org/10.7717/peerj.9408.

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Background Several examples have emerged of enzymes where slow conformational changes are of key importance for function and where low populated conformations in the resting enzyme resemble the conformations of intermediate states in the catalytic process. Previous work on the subtilisin protease, Savinase, from Bacillus lentus by NMR spectroscopy suggested that this enzyme undergoes slow conformational dynamics around the substrate binding site. However, the functional importance of such dynamics is unknown. Methods Here we have probed the conformational heterogeneity in Savinase by following the temperature dependent chemical shift changes. In addition, we have measured changes in the local stability of the enzyme when the inhibitor phenylmethylsulfonyl fluoride is bound using hydrogen-deuterium exchange mass spectrometry (HDX-MS). Finally, we have used X-ray crystallography to compare electron densities collected at cryogenic and ambient temperatures and searched for possible low populated alternative conformations in the crystals. Results The NMR temperature titration shows that Savinase is most flexible around the active site, but no distinct alternative states could be identified. The HDX shows that modification of Savinase with inhibitor has very little impact on the stability of hydrogen bonds and solvent accessibility of the backbone. The most pronounced structural heterogeneities detected in the diffraction data are limited to alternative side-chain rotamers and a short peptide segment that has an alternative main-chain conformation in the crystal at cryo conditions. Collectively, our data show that there is very little structural heterogeneity in the resting state of Savinase and hence that Savinase does not rely on conformational selection to drive the catalytic process.

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Frydenvang, K., and B. Jensen. "Conformational analysis of acetylcholine and related choline esters." Acta Crystallographica Section B Structural Science 52, no. 1 (February 1, 1996): 184–93. http://dx.doi.org/10.1107/s0108768195007567.

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The crystal structures of carbamoylcholine [2-(carbamoyloxy)-N,N,N-trimethylethanaminium] chloride, bromide and iodide, methoxycarbonylcholine [2-(methoxycarbonyloxy)-N,N,N-trimethylethanaminium] iodide, acetylcholine [2-(acetyloxy)-N,N,N-trimethylethanaminium] chloride and succinylcholine { 2,2′-[(1,4-dioxo-1,4-butanediyl)bis(oxy)]bis(N,N,N-trimethylethanaminium)} iodide have been redetermined at 105 K in order to obtain detailed and accurate information on the geometry of choline esters and to elucidate the conformationally dependent changes of geometry. The conformational flexibility and the preferred conformations are elucidated based on results obtained from X-ray crystallographic studies and molecular mechanics (MM2) calculations. The usefulness of molecular mechanics calculations for quaternary ammonium ions is discussed.

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5

Boldyrev, I. A. "Conformational Diversity of Lipids." JETP Letters 119, no. 7 (April 2024): 549–55. http://dx.doi.org/10.1134/s0021364023603573.

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The conformational diversity of hydrophobic lipid chains has been studied. The number of possible conformations of a lipid chain, as well as the number of these conformations that can be realized in a real system, has been determined. A set theory approach to the analysis of conformations of lipid molecules has been proposed, and a relation of the sets of conformations realized in a lipid structure to the energy of the system has been introduced. Using the set theory, it has been considered which conformations of hydrophobic lipid chains can be realized in the real system. The notion of the key conformation has been formulated to estimate the correlation between the structural characteristics of lipids and the energy characteristics of membranes.

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6

Kecel, Serda, Aysen E. Ozel, Sevim Akyuz, and Sefa Celik. "Conformational analysis and vibrational spectroscopic investigation of L-alanyl-L-glutamine dipeptide." Spectroscopy 24, no. 3-4 (2010): 219–32. http://dx.doi.org/10.1155/2010/917414.

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In this study conformational behavior of anticancer chemotherapy dipeptide Ala-Gln and its dimers have been investigated by molecular mechanic and ab-initio calculations. The calculations on Ala-Gln dipeptide as a function of side chain torsion angles, enable us to determine their energetically preferred conformations. The relative positions of the side chain residues of the stable conformations of dipeptide were obtained, depending on the obtained conformational analysis results. The lowest energy conformation of the dipeptide has been determined by using the Ramachandran maps (Biopolymers6(1963), 1494;J. Mol. Biol.7(1963), 95) and compared with the quantum chemical ab-initio results. The geometry optimization, vibrational wavenumbers and intensity calculations of Ala-Gln dipeptide were carried out with theGaussian03program by using DFT with B3LYP functional and 6-31++G(d,p) basis set. The IR (4000–400 cm−1) and Raman spectra of the Ala-Gln dipeptide have been reported in solid phase, and compared with the theoretical vibrational data.

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Horta-López, Perla H., Jan Rícny, Benjamín Florán-Garduño, and Francisco Garcia-Sierra. "Association of Conformationally Altered Tau with α-1-antichymotrypsin in the Nuclei of Neurons in the Alzheimer's Disease Brain." Journal of Experimental Neurology 4, no. 3 (November 24, 2023): 109–14. http://dx.doi.org/10.33696/neurol.4.080.

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Conformational changes of Tau have been described to occur during its fibrillary and non-fibrillary aggregation inside neurons affected in the brain of Alzheimer’s disease (AD) patients. Two consecutive conformations have been described during the progression of the disease: an early conformation detected with the Alz-50 antibody, recognizing Tau molecules folding its amino terminus over its third repeated domain, and a later conformation involving the bending of the proline-rich region over the third repeated domain. α-1-antichymotrypsin (ACT) is an acute phase serum glycoprotein that is overexpressed in the brain of AD cases and associated with extracellular amyloid-ß aggregates. We have recently reported that in a large population of neurons affected in AD brains, Tau protein undergoing the conformational change detected by Tau-66 antibody accumulates as non-fibrillary aggregates and colocalizes with extensive accumulations of granular diffuse intracellular deposits of ACT. In this report, we further analyzed Tau-ACT interactions in the neurons from the hippocampus of AD brains. By using superresolution confocal microscopy and quantitative colocalization analysis, we corroborated the mutual association and mislocalization of conformationally altered Tau protein and ACT to the nuclear compartment. These results suggest that ACT can play an abnormal pathological role in AD by contributing to the abnormal transport of truncated and conformationally altered Tau protein to the nucleus.

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Gaalswyk, Kari, and Christopher N. Rowley. "An explicit-solvent conformation search method using open software." PeerJ 4 (May 31, 2016): e2088. http://dx.doi.org/10.7717/peerj.2088.

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Computer modeling is a popular tool to identify the most-probable conformers of a molecule. Although the solvent can have a large effect on the stability of a conformation, many popular conformational search methods are only capable of describing molecules in the gas phase or with an implicit solvent model. We have developed a work-flow for performing a conformation search on explicitly-solvated molecules using open source software. This method uses replica exchange molecular dynamics (REMD) to sample the conformational states of the molecule efficiently. Cluster analysis is used to identify the most probable conformations from the simulated trajectory. This work-flow was tested on drug molecules α-amanitin and cabergoline to illustrate its capabilities and effectiveness. The preferred conformations of these molecules in gas phase, implicit solvent, and explicit solvent are significantly different.

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Li, Xin, Na Wang, Jinyue Yang, Yunhai Huang, Xiongtao Ji, Xin Huang, Ting Wang, Honghai Wang, and Hongxun Hao. "Molecular conformational evolution mechanism during nucleation of crystals in solution." IUCrJ 7, no. 3 (April 24, 2020): 542–56. http://dx.doi.org/10.1107/s2052252520004959.

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Nucleation of crystals from solution is fundamental to many natural and industrial processes. In this work, the molecular mechanism of conformational polymorphism nucleation and the links between the molecular conformation in solutions and in crystals were investigated in detail by using 5-nitrofurazone as the model compound. Different polymorphs were prepared, and the conformations in solutions obtained by dissolving different polymorphs were analysed and compared. The solutions of 5-nitrofurazone were proven to contain multiple conformers through quantum chemical computation, Raman spectra analysis, 2D nuclear Overhauser effect spectroscopy spectra analysis and molecular dynamics simulation. The conformational evolution and desolvation path was illustrated according to the 1H NMR spectra of solutions with different concentrations. Finally, based on all the above analysis, the molecular conformational evolution path during nucleation of 5-nitrofurazone was illustrated. The results presented in this work shed a new light on the molecular mechanism of conformational polymorphism nucleation in solution.

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Merski, Matthew, Marcus Fischer, Trent E. Balius, Oliv Eidam, and Brian K. Shoichet. "Homologous ligands accommodated by discrete conformations of a buried cavity." Proceedings of the National Academy of Sciences 112, no. 16 (April 6, 2015): 5039–44. http://dx.doi.org/10.1073/pnas.1500806112.

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Conformational change in protein–ligand complexes is widely modeled, but the protein accommodation expected on binding a congeneric series of ligands has received less attention. Given their use in medicinal chemistry, there are surprisingly few substantial series of congeneric ligand complexes in the Protein Data Bank (PDB). Here we determine the structures of eight alkyl benzenes, in single-methylene increases from benzene to n-hexylbenzene, bound to an enclosed cavity in T4 lysozyme. The volume of the apo cavity suffices to accommodate benzene but, even with toluene, larger cavity conformations become observable in the electron density, and over the series two other major conformations are observed. These involve discrete changes in main-chain conformation, expanding the site; few continuous changes in the site are observed. In most structures, two discrete protein conformations are observed simultaneously, and energetic considerations suggest that these conformations are low in energy relative to the ground state. An analysis of 121 lysozyme cavity structures in the PDB finds that these three conformations dominate the previously determined structures, largely modeled in a single conformation. An investigation of the few congeneric series in the PDB suggests that discrete changes are common adaptations to a series of growing ligands. The discrete, but relatively few, conformational states observed here, and their energetic accessibility, may have implications for anticipating protein conformational change in ligand design.

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Dissertations / Theses on the topic "Conformational analysis"

1

Smith, Timothy Andrew David. "Conformational analysis studies in NMR spectroscopy." Thesis, University of Liverpool, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.243220.

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Howe, T. J. "Conformational interactions involving aromatic rings." Thesis, University of East Anglia, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.383728.

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3

Bacon, John. "Conformational analysis of cyclohexandiols and related compounds." Thesis, University of South Wales, 1987. https://pure.southwales.ac.uk/en/studentthesis/conformational-analysis-of-cyclohexandiols-and-related-compounds(d78175ac-be32-45a5-907a-892feb68c54d).html.

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The conformational equilibria in disubstituted cyclohexanes containing polar groups lead to a diversity of conformational forms. In solution, the conformational preference is shown to be highly dependent upon the nature of the solvent. In the cyclohexandiol series, the formation of intramolecular and intermolecular hydrogen bonds determines the conformational preference with regard to the molecule as a whole and with respect to the rotamer conformation of the hydroxyl groups. Polar solvents capable of hydrogen bonding to the hydroxyl group have been shown to influence the position of equilibrium between the alternative chair conformations. In cyclohexanol, the equilibrium is always shifted towards the equatorial conformation. 13C nmr, 1H nmr, solution i.r. and matrix isolation i.r. techniques have been used to determine the conformational structures in the cyclohexandiol series and the nature of the solvent interactions. Two types of solvent interaction have been identified, a hydrogen bonded interaction and a non-bonded dipole interaction. A Computer Graphic Simulation has been used to' quantify the conformational energy differences and to rationalize the experimental results in terms of the Van der Waals repulsion energy. The experimental results give strong evidence that in cis cyclohexan-1,3-diol, two types of internal hydrogen bond exist in the diaxial conformation. The Computer Graphic simulation supports this reasoning on thermodynamic grounds.

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Mistry, Jinesh. "Synthesis and conformational analysis of polyarene dendrimers." Thesis, University of Manchester, 2016. https://www.research.manchester.ac.uk/portal/en/theses/synthesis-and-conformational-analysis-of-polyarene-dendrimers(650b10eb-6afd-471c-b688-5f86ee65f42c).html.

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Polyarene dendrimers with rigid aromatic regions are of interest due to their shape persistent nature. A novel series of G1 dendrimers containing a substituted 1,3-phenyl core are reported and were found to exhibit atropisomerism. This was investigated in the solid state (X ray), in solution (NMR), and via computational studies. The synthesis of fluorinated G1 dendrimers allowed for the analysis of interconversion between conformations via 19F-19F EXSY NMR (exchange spectroscopy). These were shown to exist as two distinct sets of three interconverting atropisomers. Each atropisomer was identified as well as their respective interconversion pathway. By increasing the size of the core of the G1 dendrimers resulted in physical separation of atropisomers by preparative HPLC. Results suggest certain conformers are energetically unfavourable reducing the total number of atropisomers observed.

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5

Wodtke, Robert, Gloria Ruiz-Gómez, Manuela Kuchar, M. Teresa Pisabarro, Pavlina Novotná, Marie Urbanová, Jörg Steinbach, Jens Pietzsch, and Reik Löser. "Cyclopeptides containing the DEKS motif as conformationally restricted collagen telopeptide analogues: synthesis and conformational analysis." Royal Society of Chemistry, 2015. https://tud.qucosa.de/id/qucosa%3A36280.

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The collagen telopeptides play an important role for lysyl oxidase-mediated crosslinking, a process which is deregulated during tumour progression. The DEKS motif which is located within the N-terminal telopeptide of the α1 chain of type I collagen has been suggested to adopt a βI-turn conformation upon docking to its triple-helical receptor domain, which seems to be critical for lysyl oxidase-catalysed deamination and subsequent crosslinking by Schiff-base formation. Herein, the design and synthesis of cyclic peptides which constrain the DEKS sequence in a β-turn conformation will be described. Lysine-side chain attachment to 2-chlorotrityl chloride-modified polystyrene resin followed by microwave-assisted solid-phase peptide synthesis and on-resin cyclisation allowed for an efficient access to head-to-tail cyclised DEKS-derived cyclic penta- and hexapeptides. An Nε-(4-fluorobenzoyl)lysine residue was included in the cyclopeptides to allow their potential radiolabelling with fluorine-18 for PET imaging of lysyl oxidase. Conformational analysis by ¹H NMR and chiroptical (electronic and vibrational CD) spectroscopy together with MD simulations demonstrated that the concomitant incorporation of a D-proline and an additional lysine for potential radiolabel attachment accounts for a reliable induction of the desired βI-turn structure in the DEKS motif in both DMSO and water as solvents. The stabilised conformation of the cyclohexapeptide is further reflected by its resistance to trypsin-mediated degradation. In addition, the deaminated analogue containing allysine in place of lysine has been synthesised via the corresponding ε-hydroxynorleucine containing cyclohexapeptide. Both ε-hydroxynorleucine and allysine containing cyclic hexapeptides have been subjected to conformational analysis in the same manner as the lysine-based parent structure. Thus, both a conformationally restricted lysyl oxidase substrate and product have been synthetically accessed, which will enable their potential use for molecular imaging of these important enzymes.

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Marchesi, Chiara. "Conformational analysis and absolute configuration of Spiropyrazolones." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2017. http://amslaurea.unibo.it/13968/.

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The relative configuration of the four stereocenters of spiropyrazolones 1, epi-1 and 2 was determined by NMR-NOE analysis. It turned out that while compound 1 has the 1R*, 2S*, 3R*, 4S* relative configuration, epi-1 is the diastereoisomer at the C-4 (1R*, 2S*, 3R*, 4R* relative configuration). A full conformational analysis was performed by Molecular Mechanics (MMFF field) scan of the potential energy surface, and the best conformations were optimized by DFT calculations, including the effect of the solvent in the calculations. The absolute configuration of the three compounds was then determined by the comparison of the Electronic CD spectra with the simulated spectra obtained by TD-DFT calculations. Four different functionals were used to achieve data redundancy and a more reliable assignment. The 1R, 2S, 3R, 4S absolute configuration was determined for 1, the 1R, 2S, 3R, 4R for epi-1 and the 1S, 2R, 3S, 4R for compound 2.

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Genov, Daniel G. "Conformational analysis of 2-hydroxyalkyl phosphoryl compounds." Thesis, Staffordshire University, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.306955.

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Edwards, Wayne Robert. "Conformational analysis of thylakoid lumen precursor proteins." Thesis, University of Warwick, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.367106.

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Combettes, Lorraine Eugenie Aurelie. "Synthesis and conformational analysis of fluorinated pyrrolidines." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:e0fa50a1-5f18-41d5-8cee-d0cb2e0a80de.

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The aim of this thesis was to investigate the synthesis and the conformational analysis of fluorinated pyrrolidines. We focused on two strategies namely, the iodoamination and fluoroamination of fluorinated precursors. Iodoamination Our first approach for the synthesis of fluorinated pyrrolidines relied on the iodocyclisation of allylic fluorides bearing pendant nitrogen nucleophiles. These allylic fluorides were obtained by fluorodesilylation of suitably functionalised allylsilanes. After validation of this methodology, the scope and limitations of the iodoamination were investigated. Furthermore, we were able to probe the influence of the fluorine moiety on the level of diastereocontrol of the cyclisation. Fluoroamination The second route focused on a key reaction: an unprecedented electrophilic fluoroamination of an aminated allylsilane. From a mechanistic point of view, the presence of the silyl group act as a 1,2-dipole and activate the double bond towards electrophilic fluorination. This methodology required the initial screening of a silyl directing group that would promote electrophilic addition, without subsequent desilylation. Finally, we investigated the level of diastereocontrol displayed by these cyclisations as a function of the E/Z geometry of the starting aminated allylsilane. Conformational analysis Moreover the 3-fluoropyrrolidines obtained via iodoamination served to investigate the stereoelectronic influence of the fluorine gauche effect on ring conformations. Solid state single crystal X-ray analysis and solution phase NMR spectroscopy were used for this purpose. Due to complicated conformational analysis of saturated five-membered rings in solution, 1D 19F-1H heteronuclear nOe (HOESY) experiments have been optimised for applications to this type of small molecules. These have been employed to estimate 19F-1H internuclear distances and were combined with vicinal 3JFH and 3JHH scalar coupling constants in order to analyse the ring conformations.

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Wong, Lilly. "Conformational analysis of C-terminal Src kinase /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2004. http://wwwlib.umi.com/cr/ucsd/fullcit?p3153687.

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Books on the topic "Conformational analysis"

1

Polozov, R. V. (Robert Valentinovich), Konoplev, G. G. (Gennadiĭ Grigorʹevich), and Institut biologicheskoĭ fiziki (Akademii͡a nauk SSSR), eds. Neploskoe stroenie aminozameshchennykh azotistykh osnovaniĭ, PCILO konformat͡sionnoe issledovanie. Pushchino: Nauch. t͡sentr biologicheskikh issledovaniĭ AN SSSR, 1989.

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Rasmussen, Kjeld. Potential Energy Functions in Conformational Analysis. Berlin, Heidelberg: Springer Berlin Heidelberg, 1985. http://dx.doi.org/10.1007/978-3-642-45591-9.

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S, Glass Richard, ed. Conformational analysis of medium-sized heterocycles. New York, N.Y: VCH Publishers, 1988.

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Juaristi, Eusebio. Introduction to stereochemistry and conformational analysis. New York: Wiley, 1991.

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1903-, Arbuzov Boris Aleksandrovich, Vereshchagin A. N. 1938-, and Institut organicheskoĭ i fizicheskoĭ khimii im. A.E. Arbuzova., eds. Konformat͡s︡ionnyĭ analiz uglevodorodov i ikh proizvodnykh. Moskva: "Nauka", 1990.

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Shevchenko, S. M. Molekula v prostranstve. Leningrad: "Khimii͡a︡," Leningradskoe otd-nie, 1986.

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Skazka, V. S. Sedimentat͡s︡ionno-diffuzionnyĭ analiz polimerov v rastvore: Problemy konformat͡s︡ionnogo analiza makromolekul. Leningrad: Izd-vo Leningradskogo universiteta, 1985.

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Dodziuk, Helena. Modern conformational analysis: Elucidating novel exciting molecular structures. New York: VCH, 1995.

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W, Rabideau Peter, ed. Conformational analysis of cyclohexenes, cyclohexadienes, and related hydroaromatic compounds. New York, N.Y: VCH, 1989.

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Keresü, G. M. Molecular mechanics and conformational analysis in drug design. Oxford: Blackwell Science, 1999.

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Book chapters on the topic "Conformational analysis"

1

Klebe, Gerhard. "Conformational Analysis." In Drug Design, 335–46. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-17907-5_16.

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Eliel, Ernest L. "Conformational Analysis." In Pioneering Ideas for the Physical and Chemical Sciences, 25–39. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4899-0268-9_3.

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Shimizu, Ryo, Ken-ichi Nunami, Hitoshi Kubota, Akio Kinumaki, and Kazuo Matsumoto. "Conformational analysis of Imidapril." In Peptide Chemistry 1992, 227–30. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1474-5_66.

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Schwab, Christof H. "Conformational Analysis and Searching." In Handbook of Chemoinformatics, 262–301. Weinheim, Germany: Wiley-VCH Verlag GmbH, 2008. http://dx.doi.org/10.1002/9783527618279.ch9b.

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Eliel, Ernest L. "Erratum to: Conformational Analysis." In Pioneering Ideas for the Physical and Chemical Sciences, 321. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4899-0268-9_35.

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Carver, J. P., D. Mandel, S. W. Michnick, A. Imberty, and J. W. Brady. "Conformational Analysis of Oligosaccharides." In ACS Symposium Series, 266–80. Washington, DC: American Chemical Society, 1990. http://dx.doi.org/10.1021/bk-1990-0430.ch016.

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Miljković, Momcilo. "Conformational Analysis of Monosaccharides." In Carbohydrates, 27–56. New York, NY: Springer New York, 2009. http://dx.doi.org/10.1007/978-0-387-92265-2_2.

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Pratt, David W. "Conformational Analysis by Laser Spectroscopy." In Low Temperature Molecular Spectroscopy, 351–69. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-0281-7_14.

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Heifer, Carin A., and Wayne L. Mattice. "Conformational Analysis of Profisetinidin Dimers." In Plant Polyphenols, 479–85. Boston, MA: Springer US, 1992. http://dx.doi.org/10.1007/978-1-4615-3476-1_27.

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Aulabaugh, A., J. J. Leban, R. Crouch, F. C. Kull, A. Landavazo, and J. McDermed. "Conformational analysis of bombesin analogues." In Peptides 1990, 526–28. Dordrecht: Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-011-3034-9_221.

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Conference papers on the topic "Conformational analysis"

1

Lin, Wei, Shervin Fatehi, Michael Carrillo, Stephen Kukolich, Zunwu Zhou, G. Grubbs II, Nicole Moon, Joshua Isert, and Karla Salazar. "CONFORMATIONAL ANALYSIS OF CYCLOBUTANECARBOXYLIC ACID." In 2022 International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2022. http://dx.doi.org/10.15278/isms.2022.mi10.

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Plessow, Regina, K. Lotte, and A. Brockhinke. "Detection of conformational changes in proteins with FRET." In Laser Applications to Chemical and Environmental Analysis. Washington, D.C.: OSA, 2002. http://dx.doi.org/10.1364/lacea.2002.sac6.

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Takimoto, Takahiro, Yoshiyuki Kawashima, and Nobuhiko Kuze. "CONFORMATIONAL ANALYSIS OF _-HEXANOLACTONE BY MICROWAVE SPECTROSCOPY." In 74th International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2019. http://dx.doi.org/10.15278/isms.2019.wi04.

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Biczysko, Malgorzata. "CHALLENGES IN CONFORMATIONAL ANALYSIS OF FLEXIBLE MOLECULES." In 2020 International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2020. http://dx.doi.org/10.15278/isms.2020.wg08.

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Biczysko, Malgorzata. "CHALLENGES IN CONFORMATIONAL ANALYSIS OF FLEXIBLE MOLECULES." In 2021 International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2021. http://dx.doi.org/10.15278/isms.2021.wa02.

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Bowen, A. D., and Yue Shi. "Probing the Effect of Conformational Constraints on Binding." In 2012 SC Companion: High Performance Computing, Networking, Storage and Analysis (SCC). IEEE, 2012. http://dx.doi.org/10.1109/sc.companion.2012.334.

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Yang, Xi, and Hong Yan. "Principal component analysis of nucleosome DNA conformational data." In 2010 International Conference on Machine Learning and Cybernetics (ICMLC). IEEE, 2010. http://dx.doi.org/10.1109/icmlc.2010.5580721.

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Zinn, Sabrina, Melanie Schnell, and Thomas Betz. "CONFORMATIONAL ANALYSIS OF IBUPROFEN USING BROADBAND MICROWAVE SPECTROSCOPY." In 69th International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2014. http://dx.doi.org/10.15278/isms.2014.fd05.

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Bruijnes, Chris, Ron Bosman, Peter Bareman, and Arie Besemer. "Conformational Analysis Of Starch Derivatives By FTIR Spectroscopy." In Intl Conf on Fourier and Computerized Infrared Spectroscopy, edited by David G. Cameron. SPIE, 1989. http://dx.doi.org/10.1117/12.969491.

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Bernardi, Anna, and Laura Raimondi. "Conformational analysis of GM1 oligosaccharide in water solution." In The first European conference on computational chemistry (E.C.C.C.1). AIP, 1995. http://dx.doi.org/10.1063/1.47679.

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Reports on the topic "Conformational analysis"

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Katz, Christopher E., and Jeffrey Aube. Synthesis, Conformational Analysis, and Biological Activity of Proposed Vitronectin Antagonists. Fort Belvoir, VA: Defense Technical Information Center, April 2001. http://dx.doi.org/10.21236/ada395699.

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George. PR-015-08610-R01 Laboratory Conformation of the Effect of Methanol on Gas Chromatograph Performance. Chantilly, Virginia: Pipeline Research Council International, Inc. (PRCI), November 2010. http://dx.doi.org/10.55274/r0010717.

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In natural gas production and processing applications, methanol is commonly injected into natural gas streams containing water to prevent the formation of hydrates in gas lines and subsequent equipment damage. However, gas chromatographs (GCs) at field sites are typically not equipped to identify or measure methanol, and unless excess methanol is expected to carry over into a gas stream, samples sent to a laboratory are not likely to be analyzed for methanol. As a result, the potential exists for errors in gas property determination, particularly in heating value and sound speed. A previous PRCI project investigated the potential for GCs to quantify methanol as a hydrocarbon, and estimated the resulting errors on heating value and other properties. This theoretical study used assumptions about where methanol would elute on GC columns, but experimental data on GC performance in streams with methanol was unavailable to verify these assumptions. To verify the estimates of the theoretical study, this project collected experimental data on methanol elution behavior in a series of field and laboratory GCs, and established the errors in computed natural gas properties caused by methanol behavior. Three GCs used by the laboratory of a PRCI member company were nominated for testing: ABB NGC 8206 C7+ field GC, Agilent Model 7890A laboratory GC, configured for extended natural gas analysis, and Daniel Model 575 C6+ field GC. The separation columns, valve configurations, and other design features of these GCs that could influence methanol elution were reviewed. Since each GC was predicted to respond differently to methanol, the nominated units were accepted for testing. A fourth GC, a Varian CP-4900 Quad MicroGC outfitted to quantify methanol, was provided to the lab to serve as a reference unit. Hydrocarbon base gas compositions were chosen to represent production and transmission gases and a gas blender was consulted to identify an effective method of stabilizing the methanol content of the test gases delivered to the GCs. Lab personnel and the gas blender then provided the required hardware and the test and calibration gases, with the gas blend compositions traceable to NIST.

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Seeman, Jeffrey I., Henry V. Secor, P. J. Breen, V. H. Grassian, and E. R. Bernstein. A Study of Non-Rigid Aromatic Molecules by Supersonic Molecular Jet Spectroscopy: Observation and Spectroscopic Analysis of the Stable Conformations of Various Alkylbenzenes. Fort Belvoir, VA: Defense Technical Information Center, July 1988. http://dx.doi.org/10.21236/ada199409.

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Sadot, Einat, Christopher Staiger, and Mohamad Abu-Abied. Studies of Novel Cytoskeletal Regulatory Proteins that are Involved in Abiotic Stress Signaling. United States Department of Agriculture, September 2011. http://dx.doi.org/10.32747/2011.7592652.bard.

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In the original proposal we planned to focus on two proteins related to the actin cytoskeleton: TCH2, a touch-induced calmodulin-like protein which was found by us to interact with the IQ domain of myosin VIII, ATM1; and ERD10, a dehydrin which was found to associate with actin filaments. As reported previously, no other dehydrins were found to interact with actin filaments. In addition so far we were unsuccessful in confirming the interaction of TCH2 with myosin VIII using other methods. In addition, no other myosin light chain candidates were found in a yeast two hybrid survey. Nevertheless we have made a significant progress in our studies of the role of myosins in plant cells. Plant myosins have been implicated in various cellular activities, such as cytoplasmic streaming (1, 2), plasmodesmata function (3-5), organelle movement (6-10), cytokinesis (4, 11, 12), endocytosis (4, 5, 13-15) and targeted RNA transport (16). Plant myosins belong to two main groups of unconventional myosins: myosin XI and myosin VIII, both closely related to myosin V (17-19). The Arabidopsis myosin family contains 17 members: 13 myosin XI and four myosin VIII (19, 20). The data obtained from our research of myosins was published in two papers acknowledging BARD funding. To address whether specific myosins are involved with the motility of specific organelles, we cloned the cDNAs from neck to tail of all 17 Arabidopsis myosins. These were fused to GFP and used as dominant negative mutants that interact with their cargo but are unable to walk along actin filaments. Therefore arrested organelle movement in the presence of such a construct shows that a particular myosin is involved with the movement of that particular organelle. While no mutually exclusive connections between specific myosins and organelles were found, based on overexpression of dominant negative tail constructs, a group of six myosins (XIC, XIE, XIK, XI-I, MYA1 and MYA2) were found to be more important for the motility of Golgi bodies and mitochondria in Nicotiana benthamiana and Nicotiana tabacum (8). Further deep and thorough analysis of myosin XIK revealed a potential regulation by head and tail interaction (Avisar et al., 2011). A similar regulatory mechanism has been reported for animal myosin V and VIIa (21, 22). In was shown that myosin V in the inhibited state is in a folded conformation such that the tail domain interacts with the head domain, inhibiting its ATPase and actinbinding activities. Cargo binding, high Ca2+, and/or phosphorylation may reduce the interaction between the head and tail domains, thus restoring its activity (23). Our collaborative work focuses on the characterization of the head tail interaction of myosin XIK. For this purpose the Israeli group built yeast expression vectors encoding the myosin XIK head. In addition, GST fusions of the wild-type tail as well as a tail mutated in the amino acids that mediate head to tail interaction. These were sent to the US group who is working on the isolation of recombinant proteins and performing the in vitro assays. While stress signals involve changes in Ca2+ levels in plants cells, the cytoplasmic streaming is sensitive to Ca2+. Therefore plant myosin activity is possibly regulated by stress. This finding is directly related to the goal of the original proposal.

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Prusky, Dov, Nancy P. Keller, and Amir Sherman. global regulation of mycotoxin accumulation during pathogenicity of Penicillium expansum in postharvest fruits. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7600012.bard.

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Background to the topic- Penicilliumas a postharvest pathogen and producer of the mycotoxin PAT. Penicilliumspp. are destructive phytopathogens, capable of causing decay in many deciduous fruits, during postharvest handling and storage; and the resulting losses can amount to 10% of the stored produce and the accumulation of large amounts of the mycotoxinpatulin. The overall goal of this proposal is to identify critical host and pathogen factors that modulate P. expansummycotoxin genes and pathways which are required for PAT production and virulence. Our preliminary results indicated that gluconic acid are strongly affecting patulin accumulation during colonization. P. expansumacidifies apple fruit tissue during colonization in part through secretion of gluconic acid (GLA). Several publications suggested that GLA accumulation is an essential factor in P. expansumpathogenicity. Furthermore, down regulation of GOX2 significantly reduced PAT accumulation and pathogenicity. PAT is a polyketide and its biosynthesis pathway includes a 15-gene cluster. LaeA is a global regulator of mycotoxin synthesis. It is now known that patulin synthesis might be subjected to LaeA and sometimes by environmental sensing global regulatory factors including the carbon catabolite repressor CreA as well as the pH regulator factor PacC and nitrogen regulator AreA. The mechanisms by which LaeA regulates patulin synthesis was not fully known and was part of our work. Furthermore, the regulatory system that controls gene expression in accordance with ambient pH was also included in our work. PacC protein is in an inactive conformation and is unable to bind to the promoter sites of the target genes; however, under alkaline growth conditions activated PacC acts as both an activator of alkaline-expressed genes and a repressor of acid-expressed genes. The aims of the project- This project aims to provide new insights on the roles of LaeA and PacC and their signaling pathways that lead to GLA and PAT biosynthesis and pathogenicity on the host. Specifically, our specific aims were: i) To elucidate the mechanism of pH-controlled regulation of GLA and PAT, and their contribution to pathogenesis of P. expansum. We are interested to understanding how pH and/or GLA impact/s under PacC regulation affect PAT production and pathogenesis. ii) To characterize the role of LaeA, the global regulator of mycotoxin production, and its effect on PAT and PacC activity. iii) To identify the signaling pathways leading to GLA and PAT synthesis. Using state- of-the-art RNAseq technologies, we will interrogate the transcriptomes of laeAand pacCmutants, to identify the common signaling pathways regulating synthesis of both GLA and PAT. Major conclusions, solutions, achievements- In our first Aim our results demonstrated that ammonia secreted at the leading edge of the fungal colony induced transcript activation of the global pH modulator PacC and PAT accumulation in the presence of GLA. We assessed these parameters by: (i) direct exogenous treatment of P. expansumgrowing on solid medium; (ii) direct exogenous treatment on colonized apple tissue; (iii) growth under self-ammonia production conditions with limited carbon; and (iv) analysis of the transcriptional response to ammonia of the PAT biosynthesis cluster. Ammonia induced PAT accumulation concurrently with the transcript activation of pacCand PAT biosynthesis cluster genes, indicating the regulatory effect of ammonia on pacCtranscript expression under acidic conditions. Transcriptomic analysis of pH regulated processes showed that important genes and BARD Report - Project 4773 Page 2 of 10 functionalities of P. expansumwere controlled by environmental pH. The differential expression patterns of genes belonging to the same gene family suggest that genes were selectively activated according to their optimal environmental conditions to enable the fungus to cope with varying conditions and to make optimal use of available enzymes. Concerning the second and third Aims, we demonstrated that LaeA regulates several secondary metabolite genes, including the PAT gene cluster and concomitant PAT synthesis invitro. Virulence studies of ΔlaeAmutants of two geographically distant P. expansumisolates (Pe-21 from Israel and Pe-T01 from China) showed differential reduction in disease severity in freshly harvested fruit ranging from no reduction for Ch-Pe-T01 strains in immature fruit to 15–25% reduction for both strains in mature fruit, with the ΔlaeAstrains of Is-Pe-21 always showing a greater loss in virulence. Results suggest the importance of LaeA regulation of PAT and other secondary metabolites on pathogenicity. Our work also characterized for the first time the role of sucrose, a key nutritional factor present in apple fruit, as a negative regulator of laeAexpression and consequent PAT production in vitro. This is the first report of sugar regulation of laeAexpression, suggesting that its expression may be subject to catabolite repression by CreA. Some, but not all of the 54 secondary metabolite backbone genes in the P. expansumgenome, including the PAT polyketide backbone gene, were found to be regulated by LaeA. Together, these findings enable for the first time a straight analysis of a host factor that potentially activates laeAand subsequent PAT synthesis.

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CONFORMATION AND STATIC PERFORMANCE ANALYSIS OF PENTAGONAL THREE-FOUR STRUT HYBRID OPEN-TYPE CABLE DOME. The Hong Kong Institute of Steel Construction, December 2023. http://dx.doi.org/10.18057/ijasc.2023.19.4.9.

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Traditional cable domes exhibit many defects, such as irregular grids and weak circumferential stiffness. This paper proposes a new cable dome and elaborates on the topological form of the new cable dome. Furthermore, the pre-stress state of the structure is deduced by establishing the nodal equilibrium equations. In addition, load states analysis and parametric analysis were conducted using finite element simulations in ANSYS software. The results show that the pre-stress distribution of this structure is reasonable because of the regular grids. Compared to traditional cable domes, the new design shows superior static performance and enhanced circumferential stiffness. As a result, the cables hardly slack under different load conditions. Moreover, it can improve structural stiffness by appropriately adjusting the initial pre-stress, rise-span and thickness-span ratios. Finally, recommended ranges of the above parameters are provided, offering valuable engineering design guidance.

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