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Journal articles on the topic 'Changing the Conformation of Molecules'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Abou-Hadeed, Khaled, Petr Nesvadba, and Albert Gossauer. "Bilindionostilbenoparacyclophanes Mimic the Spectroscopic Properties of Photoreceptors for Bacterial Oxygenic Photosynthesis." CHIMIA 42, no. 7-8 (1988): 282. https://doi.org/10.2533/chimia.1988.282.

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Bilindionostilbenoparacyclophanes are a new type of photodynamic molecules capable of stabilizing, at convenience, helical-shaped or «stretched» conformations of bile pigment chromophores without changing the structure of the latter. – Why do «native» phycobiliproteins intensively fluoresce, but they do not after denaturation? Which is the reason for the enhanced absorption of visible light of biliprotein chromophores when compared with free bile pigment molecules? These and other related questions have to be answered by the study of the spectroscopic properties of bilindionostilbenoparacyclop

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Imanbayev, Ye, Ye Tileuberdi, Ye Ongarbayev, et al. "Changing the Structure of Resin-Asphaltenes Molecules in Cracking." Eurasian Chemico-Technological Journal 19, no. 2 (2017): 147. http://dx.doi.org/10.18321/ectj645.

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In the paper, structural changing of resin-asphaltene molecules in cracking process of oil sand bitumen are investigated. Cracking process to natural bitumen carried out in an open-to-air reactor, which extracted from oil sand by organic solvent. Reaction temperature was 450 °С and process duration was 60 min. The reactor was heated at a rate of 10 °C/min up to the desired temperature. Di-tert-butyl peroxide was used as radical formation additive. When limiting oxygen, it can be used catalyst molecule supplies as the oxidizer. The thermal destruction processes of heavy hydrocarbons with the ca

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3

Sakane, Ayuko, Shin Yoshizawa, Masaomi Nishimura, et al. "Conformational plasticity of JRAB/MICAL-L2 provides “law and order” in collective cell migration." Molecular Biology of the Cell 27, no. 20 (2016): 3095–108. http://dx.doi.org/10.1091/mbc.e16-05-0332.

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In fundamental biological processes, cells often move in groups, a process termed collective cell migration. Collectively migrating cells are much better organized than a random assemblage of individual cells. Many molecules have been identified as factors involved in collective cell migration, and no one molecule is adequate to explain the whole picture. Here we show that JRAB/MICAL-L2, an effector protein of Rab13 GTPase, provides the “law and order” allowing myriad cells to behave as a single unit just by changing its conformation. First, we generated a structural model of JRAB/MICAL-L2 by

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4

Lu, Dan, Aihua Chai, Xiuxia Hu, et al. "Conformational Transition of Semiflexible Ring Polyelectrolyte in Tetravalent Salt Solutions: A Simple Numerical Modeling without the Effect of Twisting." International Journal of Molecular Sciences 25, no. 15 (2024): 8268. http://dx.doi.org/10.3390/ijms25158268.

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In this work, the conformational behaviors of ring polyelectrolyte in tetravalent salt solutions are discussed in detail through molecular dynamics simulation. For simplification, here we have neglected the effect of the twisting interaction, although it has been well known that both bending and twisting interactions play a deterministic in the steric conformation of a semiflexible ring polymer. The salt concentration CS and the bending energy b take a decisive role in the conformation of the ring polyelectrolyte (PE). Throughout our calculations, the b varies from b = 0 (freely joint chain) t

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Zhang, Xing-Xing, Jian Li, and Yun-Yin Niu. "A Review of Crystalline Multibridged Cyclophane Cages: Synthesis, Their Conformational Behavior, and Properties." Molecules 27, no. 20 (2022): 7083. http://dx.doi.org/10.3390/molecules27207083.

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This paper reviews the most stable conformation of crystalline three-dimensional cyclophane (CP) achieved by self-assembling based on changing the type of aromatic compound or regulating the type and number of bridging groups. [3n]cyclophanes (CPs) were reported to form supramolecular compounds with bind organic, inorganic anions, or neutral molecules selectively. [3n]cyclophanes ([3n]CPs) have stronger donor capability relative to compound [2n]cyclophanes ([2n]CPs), and it is expected to be a new type of electron donor for the progress of fresh electron conductive materials. The synthesis, co

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Barbier, Thibaut, Oana Dumitrescu, Gérard Lina, Yves Queneau, and Laurent Soulère. "Importance of the 2,6-Difluorobenzamide Motif for FtsZ Allosteric Inhibition: Insights from Conformational Analysis, Molecular Docking and Structural Modifications." Molecules 28, no. 5 (2023): 2055. http://dx.doi.org/10.3390/molecules28052055.

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A conformational analysis and molecular docking study comparing 2,6-difluoro-3-methoxybenzamide (DFMBA) with 3-methoxybenzamide (3-MBA) has been undertaken for investigating the known increase of FtsZ inhibition related anti S. aureus activity due to fluorination. For the isolated molecules, the calculations reveal that the presence of the fluorine atoms in DFMBA is responsible for its non-planarity, with a dihedral angle of −27° between the carboxamide and the aromatic ring. When interacting with the protein, the fluorinated ligand can thus more easily adopt the non-planar conformation found

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Kong, Yi, Shiyu Fu, Xuedi Yang, Shao-Yuan Leu та Chuanshuang Hu. "Cellulose Iβ behaviors in non-solvent liquid media: Molecular dynamic simulations". BioResources 18, № 4 (2023): 8223–48. http://dx.doi.org/10.15376/biores.18.4.8223-8248.

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The structural changes of cellulose in non-solvent liquid media can provide insights into the high-value utilization of cellulose. This study includes molecular dynamics simulations of 36-chain cellulose Iβ microfibril model (Iβ-MF) behavior in 16 non-solvent liquids with different polarities at room temperature using two carbohydrate force fields (CHARMM36, GLYCAM06). Iβ-MF in CHARMM36 retains more than 70% of the tg conformation in 16 liquids, and the retention of the tg conformation increased with decreasing liquid polarity. Liquid polarity can affect the hydroxymethyl conformation of cellu

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8

Iwasaki, Koki, and Yutaka Matsuo. "Fabrication of Elastic Color-Changing Films—Elastomer Films Incorporating Mechanochromic Fluorenylidene–Acridane." Molecules 30, no. 8 (2025): 1761. https://doi.org/10.3390/molecules30081761.

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A pressure-sensitive elastomer film incorporating fluorenylidene–acridane (FA) in its folded conformation was successfully developed for use in pressure-sensitive applications. The elastomer network was swollen with acetone, creating space to accommodate FA molecules. Although FA dissolved in acetone and adopted a twisted conformer, a solvent exchange process with methanol facilitated the reprecipitation of FA in its yellow folded conformation within the elastomer matrix. Confocal and scanning electron microscopy confirmed the incorporation of FA in its folded form within the matrix, while fil

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Knauf, P. A., L. J. Spinelli, and N. A. Mann. "Flufenamic acid senses conformation and asymmetry of human erythrocyte band 3 anion transport protein." American Journal of Physiology-Cell Physiology 257, no. 2 (1989): C277—C289. http://dx.doi.org/10.1152/ajpcell.1989.257.2.c277.

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With Cl as substrate, the human red blood cell anion transport (band 3) protein can exist in four conformations: Ei, with the transport site facing the cytoplasm; Eo, with the transport site facing the external medium; and ECli and EClo, the corresponding forms loaded with Cl. Flufenamic acid (FA), an inhibitor that binds to an external site different from the transport site, binds to Eo with a dissociation constant of 0.0826 +/- 0.0049 (SE) microM. Binding of iodide or sulfate to the external-facing transport site reduces the affinity by 1.66 or 14.3-fold, respectively. Changing from Eo to Ei

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Benesch, Matthew G. K., David A. Mannock, and Ronald N. McElhaney. "Sterol Chemical Structure and Conformation Influence the Thermotropic Phase Behaviour of Dipalmitoylphosphatidylcholine Bilayers." Eureka 2, no. 1 (2011): 11–23. http://dx.doi.org/10.29173/eureka10294.

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Studying the nature of interactions between the sterol ring system and neigbouring phospholipid molecules is important for our understanding of the properties of sterols in biological molecules and the role of such interactions in many disease processes. In this project, the thermotropic phase behaviour of binary dipalmitoylphosphatidylcholine (DPPC)/sterol mixtures with different sterol ring configurations (C5,6 double bond, 5α-H and 5β-H orientation and either 3α-OH, 3β-OH, 3-ketone functional groups) was investigated using differential scanning calorimetry (DSC) and was compared to earlier

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Data, Przemyslaw, Masato Okazaki, Satoshi Minakata, and Youhei Takeda. "Thermally activated delayed fluorescence vs. room temperature phosphorescence by conformation control of organic single molecules." Journal of Materials Chemistry C 7, no. 22 (2019): 6616–21. http://dx.doi.org/10.1039/c9tc00909d.

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The time-resolved photophysical analysis of a multi-color-changing mechanochromic luminescent compound has been disclosed, which reveals distinct different emission paths to boost TADF and RTP of the emitter depending on its molecular conformations.

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12

Perczel, Andrås, Raymond Daudel, Jånos G. Ångyån, and Imre G. Csizmadia. "A study on the backbone/side-chain interaction in N-formyl-(L)serineamide." Canadian Journal of Chemistry 68, no. 10 (1990): 1882–88. http://dx.doi.org/10.1139/v90-291.

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The N-formyl-serineamide (For-Ser-NH2), a model diamide for the conformational behaviour of the protein backbone at serine residue, has been gradient optimized for selected conformations at the abinitio 3-21G level. Previous molecular mechanics ECEPP/2 calculations suggested that the optimal side-chain (χ1, χ2) and backbone [Formula: see text] conformations are strongly coupled, due to intramolecular H-bonding formed between the side-chain hydroxyl group and the amide moiety. Four different side-chain geometries (I–IV) were considered at each of the four backbone conformations (α, β, β′, γ) gi

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13

Zheng, Dong, Xiang-Ai Yuan, Haibo Ma, et al. "Unexpected solvent effects on the UV/Vis absorption spectra of o -cresol in toluene and benzene: in contrast with non-aromatic solvents." Royal Society Open Science 5, no. 3 (2018): 171928. http://dx.doi.org/10.1098/rsos.171928.

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Cresol is a prototype molecule in understanding intermolecular interactions in material and biological systems, because it offers different binding sites with various solvents and protonation states under different pH values. It is found that the UV/Vis absorption spectra of o -cresol in aromatic solvents (benzene, toluene) are characterized by a sharp peak, unlike the broad double-peaks in 11 non-aromatic solvents. Both molecular dynamics simulations and electronic structure calculations revealed the formation of intermolecular π-complexation between o -cresol and aromatic solvents. The therm

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14

Hurdax, Philipp, Michael Hollerer, Larissa Egger, et al. "Controlling the electronic and physical coupling on dielectric thin films." Beilstein Journal of Nanotechnology 11 (October 1, 2020): 1492–503. http://dx.doi.org/10.3762/bjnano.11.132.

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Ultrathin dielectric/insulating films on metals are often used as decoupling layers to allow for the study of the electronic properties of adsorbed molecules without electronic interference from the underlying metal substrate. However, the presence of such decoupling layers may effectively change the electron donating properties of the substrate, for example, by lowering its work function and thus enhancing the charging of the molecular adsorbate layer through electron tunneling. Here, an experimental study of the charging of para-sexiphenyl (6P) on ultrathin MgO(100) films supported on Ag(100

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15

Chen, Yu, Ravin Seepersaud, Barbara A. Bensing, Paul M. Sullam, and Tom A. Rapoport. "Mechanism of a cytosolic O-glycosyltransferase essential for the synthesis of a bacterial adhesion protein." Proceedings of the National Academy of Sciences 113, no. 9 (2016): E1190—E1199. http://dx.doi.org/10.1073/pnas.1600494113.

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O-glycosylation of Ser and Thr residues is an important process in all organisms, which is only poorly understood. Such modification is required for the export and function of adhesin proteins that mediate the attachment of pathogenic Gram-positive bacteria to host cells. Here, we have analyzed the mechanism by which the cytosolic O-glycosyltransferase GtfA/B of Streptococcus gordonii modifies the Ser/Thr-rich repeats of adhesin. The enzyme is a tetramer containing two molecules each of GtfA and GtfB. The two subunits have the same fold, but only GtfA contains an active site, whereas GtfB prov

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16

Zhao, Ying, Qinghua Fang, and Manfred Lindau. "The number of SNAP25 molecules changing conformation preceding a fusion event increases with vesicle size." Biophysical Journal 122, no. 3 (2023): 461a—462a. http://dx.doi.org/10.1016/j.bpj.2022.11.2478.

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17

Merigeau, Karine, Bernadette Arnoux, David Perahia, Kjeld Norris, Fanny Norris та Arnaud Ducruix. "1.2 Å Refinement of the Kunitz-Type Domain from the α3 Chain of Human Type VI Collagen". Acta Crystallographica Section D Biological Crystallography 54, № 3 (1998): 306–12. http://dx.doi.org/10.1107/s0907444997010846.

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The recombinant Kunitz-type domain (C5) of human collagen α3(VI) chain was previously described at 1.6 Å resolution at room temperature. By changing the crystallization conditions and using synchrotron radiation, we are able to record diffraction data to 1.2 Å resolution for crystals of the same space group at 291 K. The protein–water–ion model has been refined anisotropically against these new data using the program SHELXL93; the results converged to an R factor of 15.0%, with all data between 7 and 1.2 Å. The final electron-density map reveals a clear chain tracing with a few disordered resi

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18

Perrott, Allyson L., and Donald R. Arnold. "The importance of conformation in the reactivity of radical cations. Changing configuration at saturated carbon centres." Canadian Journal of Chemistry 70, no. 1 (1992): 272–79. http://dx.doi.org/10.1139/v92-037.

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Irradiation of an acetonitrile solution of cis 1-methyl-2-phenylcyclopentane (1bcis); 1,4-dicyanobenzene (2), an electron-accepting photosensitizer; and 2,4,6-collidine (3), a nonnucleophilic base, leads to configurational isomerization of the cyclopentane; the photostationary state lies > 99% in favour of the trans isomer. The mechanism proposed for this reaction involves formation of the radical cation of 1bcis by photoinduced electron transfer to the singlet excited state of 2, deprotonation of the radical cation assisted by the base 3, reduction of the resulting benzylic radical by the

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19

Lunkad, Raju, Anastasiia Murmiliuk, Zdeněk Tošner, Miroslav Štěpánek, and Peter Košovan. "Role of pKA in Charge Regulation and Conformation of Various Peptide Sequences." Polymers 13, no. 2 (2021): 214. http://dx.doi.org/10.3390/polym13020214.

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Peptides containing amino acids with ionisable side chains represent a typical example of weak ampholytes, that is, molecules with multiple titratable acid and base groups, which generally exhibit charge regulating properties upon changes in pH. Charged groups on an ampholyte interact electrostatically with each other, and their interaction is coupled to conformation of the (macro)molecule, resulting in a complex feedback loop. Their charge-regulating properties are primarily determined by the pKA of individual ionisable side-chains, modulated by electrostatic interactions between the charged

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Lunkad, Raju, Anastasiia Murmiliuk, Zdeněk Tošner, Miroslav Štěpánek, and Peter Košovan. "Role of pKA in Charge Regulation and Conformation of Various Peptide Sequences." Polymers 13, no. 2 (2021): 214. http://dx.doi.org/10.3390/polym13020214.

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Peptides containing amino acids with ionisable side chains represent a typical example of weak ampholytes, that is, molecules with multiple titratable acid and base groups, which generally exhibit charge regulating properties upon changes in pH. Charged groups on an ampholyte interact electrostatically with each other, and their interaction is coupled to conformation of the (macro)molecule, resulting in a complex feedback loop. Their charge-regulating properties are primarily determined by the pKA of individual ionisable side-chains, modulated by electrostatic interactions between the charged

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21

Cui, Lin Lin, and Hua Nan Guan. "Computer Simulation on Conformation Properties of Polymer Chain." Applied Mechanics and Materials 341-342 (July 2013): 195–98. http://dx.doi.org/10.4028/www.scientific.net/amm.341-342.195.

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The author adopts Monte Carlo compute method to simulate the linear polymer chain lattice model in multiple chain systems of chain lengthn=20, 50, 100 while the volume fraction Φ=0.125, and makes a research on the variational situation of the size (measured with the mean-square end-to-end distance <R2> and the mean-square radius of gyration <S2>), shape (measured with the mean asphericity factor <A>) with changing of the interaction energy between solvent molecule and polymer chain segment molecule εPS. Results indicate <R2>, <S2> and <A> have the changing r

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XIAO, JUNWU, YINGCHUN ZHU, JIANHUI YUAN, et al. "POLYMORPH SELECTION OF CALCIUM CARBONATE BY THE MORPHOLOGY OF BIOMACROMOLECULES: FROM ARAGONITE, VATERITE TO CALCITE." Modern Physics Letters B 23, no. 31n32 (2009): 3695–706. http://dx.doi.org/10.1142/s0217984909022083.

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The selective polymorph synthesis of aragonite, vaterite and calcite was done by changing the conformation of chitosan molecules. Aragonite crystals in hexagonal prism-like shape were obtained in chitosan precipitates, vaterite crystals in hexagonal symmetrical plate-like shape were prepared in chitosan gel, and calcite nanoparticles were obtained in chitosan sol. The phenomenon of polymorph selection of biominerals by the morphology of biomacromolecules indicates that the studies on the relation between biominerals and biomacromelecules have general interest not only in bionics, but also in b

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Salin, Mikko, Evangelia G. Kapetaniou, Matti Vaismaa, et al. "Crystallographic binding studies with an engineered monomeric variant of triosephosphate isomerase." Acta Crystallographica Section D Biological Crystallography 66, no. 8 (2010): 934–44. http://dx.doi.org/10.1107/s0907444910025710.

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Crystallographic binding studies have been carried out to probe the active-site binding properties of a monomeric variant (A-TIM) of triosephosphate isomerase (TIM). These binding studies are part of a structure-based directed-evolution project aimed towards changing the substrate specificity of monomeric TIM and are therefore aimed at finding binders which are substrate-like molecules. A-TIM has a modified more extended binding pocket between loop-7 and loop-8 compared with wild-type TIM. The A-TIM crystals were grown in the presence of citrate, which is bound in the active site of each of th

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Rahayu, Premy Puspitawati, Manik Eirry Sawitri, Dwi Setiawan, and Citra Nurma Yunita. "Interaction of Sambiloto (Andrographis paniculata) Bioactive Compound with Milk Protein (Whey and Casein) Through Molecular Docking and Molecular Dynamics Simulation as a Basis for Encapsulation." Jurnal Penelitian Pendidikan IPA 10, no. 7 (2024): 4129–38. http://dx.doi.org/10.29303/jppipa.v10i7.7696.

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This research aims for developing immune-boosting products necessary. The active ingredient in Andrographis paniculate (AP) acts as an immunostimulant which can improve the work of the immune system. The first stage of research was a collection of bioactive compounds from KnapSack database of Kanaya, Dr. Duke's Phytochemical and Ethnobotanical were compiled and selected based on the online pass results of each bioactive compound as an immunomodulator and 10 active compounds were obtained which will be continued. The second stage of research was a docking molecular between whey proteins (β-lact

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COX, D. L., R. ENDRES, R. V. KULKARNI, M. LABUTE, and R. R. P. SINGH. "ELECTRON CORRELATION EFFECTS IN BIOLOGICAL MOLECULES." International Journal of Modern Physics B 16, no. 20n22 (2002): 3377. http://dx.doi.org/10.1142/s0217979202014462.

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Allosteric (conformation changing) proteins with transition metal atoms are at the heart of much important biological function (e.g., myoglobin hemoglobin used for storing and transporting oxygen in the bloodstream). In the case of myoglobin and hemoglobin, oxygen ligation to the iron center induces a spin crossover (high to low) coupled to a structural change; apart from the role of Hunds' exchange in the spin crossover, electron interaction effects have been ignored. We argue that the spin crossover/structure change observed in the similarly structured but far simpler cobalt valence tautomer

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Berthier, Sylvie, Marie-Hélène Paclet, Sandra Lerouge, et al. "Changing the Conformation State of Cytochromeb558Initiates NADPH Oxidase Activation." Journal of Biological Chemistry 278, no. 28 (2003): 25499–508. http://dx.doi.org/10.1074/jbc.m209755200.

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D’Amelio, Nicola, Benjamin Tanielian, Mourad Sadqi, Pilar López-Navajas, and Victor Muñoz. "Cognate DNA Recognition by Engrailed Homeodomain Involves a Conformational Change Controlled via an Electrostatic-Spring-Loaded Latch." International Journal of Molecular Sciences 23, no. 5 (2022): 2412. http://dx.doi.org/10.3390/ijms23052412.

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Transcription factors must scan genomic DNA, recognize the cognate sequence of their control element(s), and bind tightly to them. The DNA recognition process is primarily carried out by their DNA binding domains (DBD), which interact with the cognate site with high affinity and more weakly with any other DNA sequence. DBDs are generally thought to bind to their cognate DNA without changing conformation (lock-and-key). Here, we used nuclear magnetic resonance and circular dichroism to investigate the interplay between DNA recognition and DBD conformation in the engrailed homeodomain (enHD), as

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Yadav, Malti, Kamalendu Pal, and Udayaditya Sen. "Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication." Biochemical Journal 476, no. 21 (2019): 3333–53. http://dx.doi.org/10.1042/bcj20190399.

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Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca

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Li, Runmei, Cong Cheng, Zhuorui Wang, et al. "Conformational Stability of Poly (N-Isopropylacrylamide) Anchored on the Surface of Gold Nanoparticles." Materials 14, no. 2 (2021): 443. http://dx.doi.org/10.3390/ma14020443.

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To verify the temperature sensitive failure of poly (N-isopropylacrylamide) (PNIPAM) anchored on the surface of gold nanoparticles (AuNPs), the UV-Vis spectra with temperature variations of the following aqueous solutions respectively containing AuNPs-PNIPAM, Au-PNIPAM/PNIPAM, PNIPAM, in different media (including salt, ethanol, HCl and cetyltrimethylammoniumbromide (CTAB)), were systematically determined. The results indicated that the UV-Vis spectrum of AuNPs-PNIPAM suspension hardly changed even above the Lower Critical Solution Temperature (LCST) of PNIPAM, but that of Au-PNIPAM/PNIPAM sha

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Slavicek, Petr, Šárka Paušová, and Karel Bouzek. "From Gas to Solution: The Changing Neutral Structure of Proline upon Solvation." Journal of Physical Chemistry A 128, no. 47 (2024): 10202–12. https://doi.org/10.1021/acs.jpca.4c05628.

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Liquid-jet photoelectron spectroscopy (LJ-PES) and electronic-structure theory were employed to investigate the chemical and structural properties of the amino acid L-proline in aqueous solution for its three ionized states (protonated, zwitterionic, deprotonated). This is the first PES study of this amino acid in its most biologically relevant environment. Proline’s structure in the aqueous phase under neutral conditions is zwitterionic, distinctly different from the non-ionic neutral form in the gas phase. By analyzing the carbon 1s and nitrogen 1s core-levels as well as the valence sp

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Cui, Lin Lin, and Hua Nan Guan. "Monte Carlo Simulation on Conformation Properties of Polymer Multiple Chain System." Advanced Materials Research 734-737 (August 2013): 3141–44. http://dx.doi.org/10.4028/www.scientific.net/amr.734-737.3141.

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The author adopts Monte Carlo compute method to simulate the linear polymer chain lattice model in multiple chain systems of different volume fraction Φ while chain lengthn=50, and makes a research on the variational situation of the size (measured with the mean-square end-to-end distance <R2> and the mean-square radius of gyration <S2>), shape (measured with the mean asphericity factor ) with changing of the interaction energy between solvent molecule and polymer chain segment moleculeεPS. Results indicate <R2>, <S2> and have the changing rules that they become small w

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Chen, Liang, Kefeng Zhao, Xinxiu Cao, Jiangang Liu, Xinhong Yu, and Yanchun Han. "Diketopyrrolopyrrole-based polymer fibrils formation by changing molecular conformation during film formation." Journal of Polymer Science Part B: Polymer Physics 56, no. 15 (2018): 1079–86. http://dx.doi.org/10.1002/polb.24609.

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Liu, Ying, Yuqi Cao, Xue Li, Yang Li, and Bowei Wang. "Cyano-Functionalized Diarylethene Derivatives with Aggregation-Induced Emission Enhancement and Piezofluorochromic Behaviours." Australian Journal of Chemistry 72, no. 5 (2019): 369. http://dx.doi.org/10.1071/ch18450.

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Four donor–acceptor (D-A) type phenothiazine derivatives were designed and synthesized and all of them exhibited an aggregation-induced emission enhancement (AIEE) effect and red-shifted piezofluorochromic (PFC) behaviour. Moreover, it was found that the compound containing a shorter alkyl chain displayed more remarkable PFC properties. This result was probably ascribed to highly twisted conformations which can lead to loose solid molecular packing with cavities and weak interactions. After they were pressed, the planarization of the molecular conformation increased and molecular conjugation d

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Zhu, Jieqing, Chuanmei Zhang, Jiafu Liu, Xiuli Jiang, Nada Haydar та Hu Shan. "Long Range Conformational Transmission Of Integrin Activation and Signaling By α1/α1’-Helix Unbending At The Junction". Blood 122, № 21 (2013): 198. http://dx.doi.org/10.1182/blood.v122.21.198.198.

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Abstract Platelet specific integrin αIIbβ3 plays an essential role in hemostasis and thrombosis. It has been used as a prototype for understanding integrin activation and conformational regulation. Crystal structures of αIIbβ3 headpiece composed of the αIIb β-propeller and β3 βI, hybrid, and PSI domains in the absence or presence of RGD-mimetic drugs revealed the headpiece changing from a closed to an open conformation upon ligand binding. A striking change is the swing-out motion of the β3 hybrid domain away from the βI and the αIIb thigh domains. This is accompanied by the changing of the α1

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Chen, Jianzhong, Jian Wang, Wanchun Yang, Lu Zhao, Juan Zhao, and Guodong Hu. "Molecular Mechanism of Phosphorylation-Mediated Impacts on the Conformation Dynamics of GTP-Bound KRAS Probed by GaMD Trajectory-Based Deep Learning." Molecules 29, no. 10 (2024): 2317. http://dx.doi.org/10.3390/molecules29102317.

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The phosphorylation of different sites produces a significant effect on the conformational dynamics of KRAS. Gaussian accelerated molecular dynamics (GaMD) simulations were combined with deep learning (DL) to explore the molecular mechanism of the phosphorylation-mediated effect on conformational dynamics of the GTP-bound KRAS. The DL finds that the switch domains are involved in obvious differences in conformation contacts and suggests that the switch domains play a key role in the function of KRAS. The analyses of free energy landscapes (FELs) reveal that the phosphorylation of pY32, pY64, a

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Anger, F., R. Scholz, A. Gerlach, and F. Schreiber. "Vibrational modes and changing molecular conformation of perfluororubrene in thin films and solution." Journal of Chemical Physics 142, no. 22 (2015): 224703. http://dx.doi.org/10.1063/1.4922052.

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Wang, Lewen, Tengfei He, Hailiang Liao, et al. "A Theoretical Design of Chiral Molecules through Conformational Lock towards Circularly Polarized Luminescence." Photonics 9, no. 8 (2022): 532. http://dx.doi.org/10.3390/photonics9080532.

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Circularly polarized (CP) light has shown great potential in quantum computing, optical communications, and three-dimensional displays. It is still a challenge to produce high-efficiency and high-purity CP light. Herein, we proposed a strategy to design chiral organic small molecules for CP light generation. These kinds of chiral molecules are formed by achiral light-emitting groups and achiral alkyl chains through conformational lock, which indicates that chirality can also be introduced into achiral light-emitting groups through rational molecular design. The chirality of these molecules can

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Steele, Jane C., Stephen P. Young, Jane C. Goodall, and Phillip H. Gallimore. "Structural Aspects of the Interaction Between Heterogeneic Human Papillomavirus Type 1 E4-Specific T Cell Receptors and the Same Peptide/HLA-DQ8 Complex." Journal of Immunology 161, no. 9 (1998): 4745–52. http://dx.doi.org/10.4049/jimmunol.161.9.4745.

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Abstract TCR usage has been studied in a panel of Th cell clones specific for the same peptide epitope (P N S Q D R G R P R R S D), derived from the human papillomavirus type 1 (HPV1) E4 protein, and restricted through HLA-DQ8. After identifying the V, D, and J genes used by the TCRs and sequencing across the V(D)J junctions, five different α-chain sequences and five different β-chain sequences, comprising six independent clones, were identified. A structural model of our E4 peptide/HLA-DQ8 complex predicted that the guanidinyl side chain on the arginine residue at position 6 of the peptide co

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Lee, Jennifer J., Swetha Ramadesikan, Adrianna F. Black, et al. "Heterogeneity in Lowe Syndrome: Mutations Affecting the Phosphatase Domain of OCRL1 Differ in Impact on Enzymatic Activity and Severity of Cellular Phenotypes." Biomolecules 13, no. 4 (2023): 615. http://dx.doi.org/10.3390/biom13040615.

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Lowe Syndrome (LS) is a condition due to mutations in the OCRL1 gene, characterized by congenital cataracts, intellectual disability, and kidney malfunction. Unfortunately, patients succumb to renal failure after adolescence. This study is centered in investigating the biochemical and phenotypic impact of patient’s OCRL1 variants (OCRL1VAR). Specifically, we tested the hypothesis that some OCRL1VAR are stabilized in a non-functional conformation by focusing on missense mutations affecting the phosphatase domain, but not changing residues involved in binding/catalysis. The pathogenic and confor

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ZHAO, TONG-JUN, YONG-HONG WANG, HAI-LONG AN, YONG ZHAN, WEI-LI YAN, and YI-ZHONG ZHUO. "MECHANOCHEMICAL COUPLING OF MOLECULAR MOTORS WITH NONCONSERVATIVE FORCE." International Journal of Modern Physics B 18, no. 17n19 (2004): 2762–65. http://dx.doi.org/10.1142/s0217979204026056.

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The biochemical process for coupling between hydrolysis of ATP and the performance of mechanical work involves a sequence of events. Here we present a two-dimensional ratchet model with a non-conservative impulsive force field. The non-conservative impulsive force that represents the chemical energy consumed in the conformation changing process provides a source of non-equilibrium fluctuation, which is a crucial factor for the Brownian motors and can lead to macroscopic motion.

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Rabiller, Philippe, Bertrand Toudic, Laurent Guérin, Céline Mariette, and Mark Hollingsworth. "Diffuse scattering and phase transitions in aperiodic inclusion compounds." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C621. http://dx.doi.org/10.1107/s2053273314093784.

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Small molecules, such as urea, thiourea, perhydrotriphenylene can be co-crystallised with long-chain hydrocarbon molecules to form inclusion compounds. The guest chains are confined to narrow, approximately cylindrical, channels created by the host small-molecule lattice. The stoichiometry and the conformations of the chains included inside the channels are function of internal interactions such as intra-chain interaction, but also of overall co-operative properties of the resulting three dimensionally ordered single crystal. These intergrowth compounds may form incommensurate composite crysta

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Jang, Yongwoo, Woori Kim, Pierre Leblanc, Chun-Hyung Kim, and Kwang-Soo Kim. "Potent synthetic and endogenous ligands for the adopted orphan nuclear receptor Nurr1." Experimental & Molecular Medicine 53, no. 1 (2021): 19–29. http://dx.doi.org/10.1038/s12276-021-00555-5.

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AbstractUntil recently, Nurr1 (NR4A2) was known as an orphan nuclear receptor without a canonical ligand-binding domain, featuring instead a narrow and tight cavity for small molecular ligands to bind. In-depth characterization of its ligand-binding pocket revealed that it is highly dynamic, with its structural conformation changing more than twice on the microsecond-to-millisecond timescale. This observation suggests the possibility that certain ligands are able to squeeze into this narrow space, inducing a conformational change to create an accessible cavity. The cocrystallographic structure

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Lee, Rachael, Michael Probert, and Jonathon Steed. "The changeable nature of urea inclusion compounds." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1706. http://dx.doi.org/10.1107/s205327331408293x.

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Urea inclusion compounds (UICs), the β-phase of urea, have been known only since 1949 and have revealed various structural and behavioural characteristics of interest, largely influenced by the type of guest molecule present in the crystal. These structures have a hexagonally symmetrical honeycomb structure of a hydrogen-bonded urea network encapsulating the guest molecules, a defining motif of these clathrates. The simplest of this class contains an alkane guest (C7-C20), creating an incommensurate relationship between host and guest and a significantly disordered crystal structure with respe

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Greene, Lois E., Farrin Saba, Rebecca E. Silberman, and Xiaohong Zhao. "Mechanisms for Curing Yeast Prions." International Journal of Molecular Sciences 21, no. 18 (2020): 6536. http://dx.doi.org/10.3390/ijms21186536.

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Prions are infectious proteins that self-propagate by changing from their normal folded conformation to a misfolded conformation. The misfolded conformation, which is typically rich in β-sheet, serves as a template to convert the prion protein into its misfolded conformation. In yeast, the misfolded prion proteins are assembled into amyloid fibers or seeds, which are constantly severed and transmitted to daughter cells. To cure prions in yeast, it is necessary to eliminate all the prion seeds. Multiple mechanisms of curing have been found including inhibiting severing of the prion seeds, gradu

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Harano, Izumi, Chigusa Okano, Yuriko Takayama, Eri Nasuno, Ken-ichi Iimura, and Norihiro Kato. "Color Transition Properties of Water Dispersible Polydiacetylene Particles Conjugated with the Thermosensitive Polymer." Applied Mechanics and Materials 863 (February 2017): 38–43. http://dx.doi.org/10.4028/www.scientific.net/amm.863.38.

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An assembly of diacetylene molecules is necessary to progress a topochemical reaction as UV-irradiated polymerization. In this study, we attempt to regularly assemble 10, 12- pentacosadiynoic acid (PCDA) by freezing the solution, followed by lyophilization. Dried PCDA assembly was easily dispersed in aqueous solution by sonication. Irradiation of UV light can promote polymerization reaction of PCDA judging from a color change of the solution into blue. A color transition of the polyPCDA-dispersed solution from blue to red was observed at approximately 56°C due to distortion of its π-conjugated

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Grogan, Catherine, George Amarandei, Shauna Lawless, et al. "Silicon Microcantilever Sensors to Detect the Reversible Conformational Change of a Molecular Switch, Spiropyan." Sensors 20, no. 3 (2020): 854. http://dx.doi.org/10.3390/s20030854.

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The high sensitivity of silicon microcantilever sensors has expanded their use in areas ranging from gas sensing to bio-medical applications. Photochromic molecules also represent promising candidates for a large variety of sensing applications. In this work, the operating principles of these two sensing methods are combined in order to detect the reversible conformational change of a molecular switch, spiropyran. Thus, arrays of silicon microcantilever sensors were functionalized with spiropyran on the gold covered side and used as test microcantilevers. The microcantilever deflection respons

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Padron-Barthe, Laura, Chloé Leprêtre, Elisabeth Martin, Marie-France Counis, and Alicia Torriglia. "Conformational Modification of Serpins Transforms Leukocyte Elastase Inhibitor into an Endonuclease Involved in Apoptosis." Molecular and Cellular Biology 27, no. 11 (2007): 4028–36. http://dx.doi.org/10.1128/mcb.01959-06.

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ABSTRACT The best-characterized biochemical feature of apoptosis is degradation of genomic DNA into oligonucleosomes. The endonuclease responsible for DNA degradation in caspase-dependent apoptosis is caspase-activated DNase. In caspase-independent apoptosis, different endonucleases may be activated according to the cell line and the original insult. Among the known effectors of caspase-independent cell death, L-DNase II (LEI [leukocyte elastase inhibitor]-derived DNase II) has been previously characterized by our laboratory. We have thus shown that this endonuclease derives from the serpin su

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Chinnusamy, Saravanan, Nasrin I. Shaikh, and Milind S. Dangate. "Impact of t-butyl group on the singlet–triplet energy gap via weak orbital overlap of [1,2,5]-thiadiazolo[3,4-C] pyridine-based TADF emitters: Structural modification." Journal of Theoretical and Computational Chemistry 17, no. 07 (2018): 1850048. http://dx.doi.org/10.1142/s0219633618500487.

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We theoretically investigated the combination of D-A and D-spacer (phenyl ring)-A with an electron donating alkyl (t-butyl) group. The strategy of twisting the geometry of the molecule with the alkyl substituents exclusion of strong electron-withdrawing or -donating groups leads to gain efficient deep blue-to-blue thermally activated delayed fluorescence (TADF) emitter through maintaining the band gap while the reduction of singlet-triplet energy gap ([Formula: see text]. The t-butyl group strongly twisted the conformation of molecules by the steric hindrance, which resulted in weak highest oc

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Kilina, Svetlana V., Dinesh Thapa, and Victoria Oas. "Effect of Amino Acids Used As Intercalating Agents on Electro-Magnetic Properties of Montmorillonite Clay Nanostructures." ECS Meeting Abstracts MA2024-01, no. 33 (2024): 1626. http://dx.doi.org/10.1149/ma2024-01331626mtgabs.

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Layered clay minerals, such as montmorillonite (MMT) with a chemical formula (FeMg)0.25Al1.5Si4O10(OH)2.nH2O, belong to non-toxic, natural, low-cost, abundant materials. Usage of unnatural amino acids (AA) with COOH-CH-NH2 moiety as intercalating agents results in formation of clay nanoplatelets of about 1 nm in thickness. Such organically modified MMT nanostructures (nano-MMT) have improved dispersion, mechanical, flame retardancy, thermal, transport, biocompatibility, and biodegradability properties, making them suitable for tissue engineering. Using first-principle calculations based on the

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Zhang, Chao, and Junpo He. "Dendrimer-Like Star-Branched Block Copolymers with Controlled Segment Sequence and their Star-Like Dendrigraft Derivatives." Australian Journal of Chemistry 67, no. 1 (2014): 31. http://dx.doi.org/10.1071/ch13326.

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Star polymers with star-like arms, namely dendrimer-like star-branched block copolymers, were synthesised by anionic polymerisation with 1,3-bis(1-phenylethenyl)benzene (MDDPE) and divinylbenzene (DVB) as the coupling agents. The segment sequence was controlled by changing the polymerisation sequences of different monomers and coupling reactions. Two types of dendrimer-like star-branched block copolymers were prepared with polyisoprene (PI) block incorporated in the interior part or on the periphery. The PI chains in the resulting star copolymers were iteratively grafted through epoxidation an

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