Log in

Relevant bibliographies by topics / Conformational analysis / Journal articles

To see the other types of publications on this topic, follow the link: Conformational analysis.

Journal articles on the topic 'Conformational analysis'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles

Select a source type:

Consult the top 50 journal articles for your research on the topic 'Conformational analysis.'

Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.

You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.

Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.

1

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

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

2

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 (2016): 524–35. http://dx.doi.org/10.1107/s2059798316001510.

Full text

Abstract:

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 struc

APA, Harvard, Vancouver, ISO, and other styles

3

Wu, Shanshan, Tam T. T. N. Nguyen, Olga V. Moroz, et al. "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.

Full text

Abstract:

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

APA, Harvard, Vancouver, ISO, and other styles

4

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

Full text

Abstract:

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 ke

APA, Harvard, Vancouver, ISO, and other styles

5

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

Full text

Abstract:

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 th

APA, Harvard, Vancouver, ISO, and other styles

6

Horta-López, Perla H., Jan Rícny, Benjamín Florán-Garduño та 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, № 3 (2023): 109–14. http://dx.doi.org/10.33696/neurol.4.080.

Full text

Abstract:

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 over

APA, Harvard, Vancouver, ISO, and other styles

7

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.

Full text

Abstract:

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(1

APA, Harvard, Vancouver, ISO, and other styles

8

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.

Full text

Abstract:

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 t

APA, Harvard, Vancouver, ISO, and other styles

9

Li, Xin, Na Wang, Jinyue Yang, et al. "Molecular conformational evolution mechanism during nucleation of crystals in solution." IUCrJ 7, no. 3 (2020): 542–56. http://dx.doi.org/10.1107/s2052252520004959.

Full text

Abstract:

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 a

APA, Harvard, Vancouver, ISO, and other styles

10

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 (2015): 5039–44. http://dx.doi.org/10.1073/pnas.1500806112.

Full text

Abstract:

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 conformat

APA, Harvard, Vancouver, ISO, and other styles

11

Joshi, Arpita, Nurit Haspel, and Eduardo González. "Characterizing Protein Conformational Spaces using Efficient Data Reduction and Algebraic Topology." Journal of Human, Earth, and Future 3 (May 31, 2022): 1–21. http://dx.doi.org/10.28991/hef-sp2022-01-01.

Full text

Abstract:

Datasets representing the conformational landscapes of protein structures are high-dimensional and hence present computational challenges. Efficient and effective dimensionality reduction of these datasets is therefore paramount to our ability to analyze the conformational landscapes of proteins and extract important information regarding protein folding, conformational changes, and binding. Representing the structures with fewer attributes that capture the most variance in the data makes for a quicker and more precise analysis of these structures. In this study, we make use of dimensionality

APA, Harvard, Vancouver, ISO, and other styles

12

Ohhashi, Yumiko, Yoshiki Yamaguchi, Hiroshi Kurahashi, et al. "Molecular basis for diversification of yeast prion strain conformation." Proceedings of the National Academy of Sciences 115, no. 10 (2018): 2389–94. http://dx.doi.org/10.1073/pnas.1715483115.

Full text

Abstract:

Self-propagating β-sheet–rich fibrillar protein aggregates, amyloid fibers, are often associated with cellular dysfunction and disease. Distinct amyloid conformations dictate different physiological consequences, such as cellular toxicity. However, the origin of the diversity of amyloid conformation remains unknown. Here, we suggest that altered conformational equilibrium in natively disordered monomeric proteins leads to the adaptation of alternate amyloid conformations that have different phenotypic effects. We performed a comprehensive high-resolution structural analysis of Sup35NM, an N-te

APA, Harvard, Vancouver, ISO, and other styles

13

Ohno, Shiho, Noriyoshi Manabe, Jun Uzawa, and Yoshiki Yamaguchi. "Comparative Conformational Analysis of Acyclic Sugar Alcohols Ribitol, Xylitol and d-Arabitol by Solution NMR and Molecular Dynamics Simulations." Molecules 29, no. 5 (2024): 1072. http://dx.doi.org/10.3390/molecules29051072.

Full text

Abstract:

Ribitol (C5H12O5) is an acyclic sugar alcohol that was recently identified in O-mannose glycan on mammalian α-dystroglycan. The conformation and dynamics of acyclic sugar alcohols such as ribitol are dependent on the stereochemistry of the hydroxyl groups; however, the dynamics are not fully understood. To gain insights into the conformation and dynamics of sugar alcohols, we carried out comparative analyses of ribitol, d-arabitol and xylitol by a crystal structure database search, solution NMR analysis and molecular dynamics (MD) simulations. The crystal structures of the sugar alcohols showe

APA, Harvard, Vancouver, ISO, and other styles

14

Collins, A., A. Parkin, G. Barr, W. Dong, C. J. Gilmore, and C. C. Wilson. "Configurational and conformational classification of pyranose sugars." Acta Crystallographica Section B Structural Science 64, no. 1 (2008): 57–65. http://dx.doi.org/10.1107/s0108768107067341.

Full text

Abstract:

Automated cluster analysis is used to examine the conformation and configuration of pyranose sugars. Previous findings on this issue are confirmed, importantly from an analysis that requires no prior knowledge of the significant factors determining the conformational classification. The findings on the conformations adopted in the crystalline solid state are found to be different to existing quantum chemical calculations performed for D-glucose in the gas phase, but consistent with empirically determined conformations in the solution state. The use of this clustering analysis in studying chira

APA, Harvard, Vancouver, ISO, and other styles

15

Parvez, Masood, Ted S. Sorensen, and Fang Sun. "Conformational analysis of the bicyclo - [4.4.1]undecan-11-one ring system." Canadian Journal of Chemistry 80, no. 3 (2002): 245–49. http://dx.doi.org/10.1139/v02-022.

Full text

Abstract:

The first conformational analysis of a bicyclo[4.4.1]undecan-11-one system (1) is presented. Based on low-temperature 13C NMR line-broadening measurements and an X-ray structure of the 1,6-dibromo derivative (2), this ketone adopts a chiral conformation with approximate C2 symmetry about an axis containing the >C=0 bond. The observed NMR line-broadening results are consistent with a dynamic interchange of M and P enantiomeric C2 conformations, or expressed another way, the "effective" development of an additional Cs symmetry plane bisecting the molecule at right angles to the plane containi

APA, Harvard, Vancouver, ISO, and other styles

16

Lamichhane, Rajan, Jeffrey J. Liu, Goran Pljevaljcic та ін. "Single-molecule view of basal activity and activation mechanisms of the G protein-coupled receptor β2AR". Proceedings of the National Academy of Sciences 112, № 46 (2015): 14254–59. http://dx.doi.org/10.1073/pnas.1519626112.

Full text

Abstract:

Binding of extracellular ligands to G protein-coupled receptors (GPCRs) initiates transmembrane signaling by inducing conformational changes on the cytoplasmic receptor surface. Knowledge of this process provides a platform for the development of GPCR-targeting drugs. Here, using a site-specific Cy3 fluorescence probe in the human β2-adrenergic receptor (β2AR), we observed that individual receptor molecules in the native-like environment of phospholipid nanodiscs undergo spontaneous transitions between two distinct conformational states. These states are assigned to inactive and active-like re

APA, Harvard, Vancouver, ISO, and other styles

17

Valimehr, Sepideh, Rémi Vuillemot, Mohsen Kazemi, Slavica Jonic, and Isabelle Rouiller. "Analysis of the Conformational Landscape of the N-Domains of the AAA ATPase p97: Disentangling the Continuous Conformational Variability in Partially Symmetrical Complexes." International Journal of Molecular Sciences 25, no. 6 (2024): 3371. http://dx.doi.org/10.3390/ijms25063371.

Full text

Abstract:

Single-particle cryo-electron microscopy (cryo-EM) has been shown to be effective in defining the structure of macromolecules, including protein complexes. Complexes adopt different conformations and compositions to perform their biological functions. In cryo-EM, the protein complexes are observed in solution, enabling the recording of images of the protein in multiple conformations. Various methods exist for capturing the conformational variability through analysis of cryo-EM data. Here, we analyzed the conformational variability in the hexameric AAA + ATPase p97, a complex with a six-fold ro

APA, Harvard, Vancouver, ISO, and other styles

18

Futamata, Ryota, Fumihiko Ogasawara, Takafumi Ichikawa, et al. "In vivo FRET analyses reveal a role of ATP hydrolysis–associated conformational changes in human P-glycoprotein." Journal of Biological Chemistry 295, no. 15 (2020): 5002–11. http://dx.doi.org/10.1074/jbc.ra119.012042.

Full text

Abstract:

P-glycoprotein (P-gp; also known as MDR1 or ABCB1) is an ATP-driven multidrug transporter that extrudes various hydrophobic toxic compounds to the extracellular space. P-gp consists of two transmembrane domains (TMDs) that form the substrate translocation pathway and two nucleotide-binding domains (NBDs) that bind and hydrolyze ATP. At least two P-gp states are required for transport. In the inward-facing (pre-drug transport) conformation, the two NBDs are separated, and the two TMDs are open to the intracellular side; in the outward-facing (post-drug transport) conformation, the NBDs are dime

APA, Harvard, Vancouver, ISO, and other styles

19

Raich, Ivan, Karel Pauk, Ales Imramovsky, and Josef Jampílek. "Conformational and Chiroptical Properties of Salicylamide-Based Peptidomimetics." Symmetry 16, no. 2 (2024): 138. http://dx.doi.org/10.3390/sym16020138.

Full text

Abstract:

Optical rotation (OR), the most frequently used chiroptical method, is used for the characterization of newly synthesized or isolated compounds. Computational predictions of OR are, however, mainly used for the determination of the absolute configurations of chiral compounds, but they may also be used for the verification of conformational analysis results if the experimental values are known. Our computational study deals with the conformational analysis of flexible salicylamide-based peptidomimetics, starting with a conformation search, then a low-level ab initio preoptimization of the hundr

APA, Harvard, Vancouver, ISO, and other styles

20

Kotovych, George, John R. Cann, John M. Stewart, and Hitoshi Yamamoto. "NMR and CD conformational studies of bradykinin and its agonists and antagonists: application to receptor binding." Biochemistry and Cell Biology 76, no. 2-3 (1998): 257–66. http://dx.doi.org/10.1139/o98-028.

Full text

Abstract:

Most physiological processes are regulated by peptides that perform their functions by interacting with specific receptors on cells. Specific conformations of the peptides are required for correct interactions to take place, and a knowledge of the biologically important conformation is vital for the understanding of biological function. Over the last few years extensive studies using nuclear magnetic resonance and circular dichroism have been carried out on bradykinin (Arg1-Pro2-Pro3-Gly4-Phe5-Ser6-Pro7-Phe8-Arg9) and its antagonists with the objective of developing new drugs to combat severe

APA, Harvard, Vancouver, ISO, and other styles

21

Moore, Alexander F., David J. Newman, Shoba Ranganathan, and Fei Liu. "Imaginative Order from Reasonable Chaos: Conformation-Driven Activity and Reactivity in Exploring Protein–Ligand Interactions." Australian Journal of Chemistry 71, no. 12 (2018): 917. http://dx.doi.org/10.1071/ch18416.

Full text

Abstract:

Sir Derek Barton’s seminal work on steroid conformational analysis opened up a new era of enquiry into how the preferred conformation of any molecule could have profound effects on its physical–chemical properties and activities. Conformation-based effects on molecular activity and reactivity continue to manifest, with one key area of investigation currently focussed on conformational entropy in driving protein–ligand interactions. Carrying on from Barton’s initial insight on natural product conformational properties, new questions now address how conformational flexibility within a bioactive

APA, Harvard, Vancouver, ISO, and other styles

22

Weng, Ze F., W. D. Sam Motherwell, Frank H. Allen, and Jacqueline M. Cole. "Conformational variability of molecules in different crystal environments: a database study." Acta Crystallographica Section B Structural Science 64, no. 3 (2008): 348–62. http://dx.doi.org/10.1107/s0108768108005442.

Full text

Abstract:

A methodology is described for analysing the Cambridge Structural Database (CSD) in terms of molecular conformations. Molecular species that have more than a single occurrence across the complete CSD are identified, either as the sole crystal component or co-crystallized with other components. Cluster analysis, based on a root-mean-square fit of coordinates and chemical connectivity, is performed to identify conformational variance for each molecule. Results are analysed in terms of the number of discrete conformations observed versus the number of crystal environments and number of acyclic to

APA, Harvard, Vancouver, ISO, and other styles

23

Garrido-Rodríguez, Pedro, Miguel Carmena-Bargueño, María Eugenia de la Morena-Barrio, et al. "Analysis of AlphaFold and molecular dynamics structure predictions of mutations in serpins." PLOS ONE 19, no. 7 (2024): e0304451. http://dx.doi.org/10.1371/journal.pone.0304451.

Full text

Abstract:

Serine protease inhibitors (serpins) include thousands of structurally conserved proteins playing key roles in many organisms. Mutations affecting serpins may disturb their conformation, leading to inactive forms. Unfortunately, conformational consequences of serpin mutations are difficult to predict. In this study, we integrate experimental data of patients with mutations affecting one serpin with the predictions obtained by AlphaFold and molecular dynamics. Five SERPINC1 mutations causing antithrombin deficiency, the strongest congenital thrombophilia were selected from a cohort of 350 unrel

APA, Harvard, Vancouver, ISO, and other styles

24

Jin, Albert Y., Lisbeth A. Benesch, and Donald F. Weaver. "Computational conformational analysis of neural membrane lipids:development of force field parameters for phospholipids using semi-empirical molecular orbital calculations." Canadian Journal of Chemistry 72, no. 6 (1994): 1596–604. http://dx.doi.org/10.1139/v94-199.

Full text

Abstract:

MM2 force field parameters for phospholipids were developed. These parameters — MM2(Lipid) — were employed in energy-minimization calculations (using crystal structures as starting conformations) on four phospholipids: dimyristoylphosphatidylglycerol, dilauroylphosphatidyl-N,N-dimethylamine, 1,2-dilauroyl-dl-phosphatidylethanolamine, and deoxylysophosphatidylcholine. After minimization, slight conformational changes were seen in the hydrocarbon chains, while greater change was seen at the head group. The diacylglycerol backbone of the energy-minimized structures exhibited conformations corresp

APA, Harvard, Vancouver, ISO, and other styles

25

Conklin, D., S. Fortier, J. I. Glasgow, and F. H. Allen. "Conformational analysis from crystallographic data using conceptual clustering." Acta Crystallographica Section B Structural Science 52, no. 3 (1996): 535–49. http://dx.doi.org/10.1107/s010876819501696x.

Full text

Abstract:

The rapid growth of crystallographic databases has created a demand for novel and efficient techniques for the analysis of molecular conformations, in order to derive new concepts and rules and to generate useful classifications of the available data. This paper presents a conceptual clustering approach, termed IMEM (image memory), which discovers the conformational diversity present in a dataset of crystal structures. In contrast to numerical clustering methods, IMEM views a molecular structure as comprising qualitative relationships among its parts, i.e. the structure is viewed as a molecula

APA, Harvard, Vancouver, ISO, and other styles

26

Alvarez, Maria, Edgardo Saavedra, Mónica Olivella, Fernando Suvire, Miguel Zamora, and Ricardo Enriz. "Theoretical study of the conformational energy hypersurface of cyclotrisarcosyl." Open Chemistry 10, no. 1 (2012): 248–55. http://dx.doi.org/10.2478/s11532-011-0136-1.

Full text

Abstract:

AbstractThe multidimensional Conformational Potential Energy Hypersurface (PEHS) of cyclotrisarcosyl was comprehensively investigated at the DFT (B3LYP/6-31G(d), B3LYP/6-31G(d,p) and B3LYP/6-311++G(d,p)), levels of theory. The equilibrium structures, their relative stability, and the Transition State (TS) structures involved in the conformational interconversion pathways were analyzed. Aug-cc-pVTZ//B3LYP/6-311++G(d,p) and MP2/6-31G(d)//B3LYP/6-311++G(d,p) single point calculations predict a symmetric cis-cis-cis crown conformation as the energetically preferred form for this compound, which is

APA, Harvard, Vancouver, ISO, and other styles

27

Haghdadi, Mina, and Nahid Farokhi. "Density functional theory (DFT) calculations of conformational energies and interconversion pathways in 1,2,7-thiadiazepane." Journal of the Serbian Chemical Society 76, no. 3 (2011): 395–406. http://dx.doi.org/10.2298/jsc100812040h.

Full text

Abstract:

The molecular structure and conformational analysis of 1,2,7-thiadiazapane conformers were investigated by density functional theory (DFT) calculations at the B3LYP/cc-pVDZ level of theory. Four twist-chair (TC), six twist-boat (TB), two boat (B), two chair (C) and four twist (T) conformers were identified as minima and transition states for 1,2,7-thiadiazepane. The TC1 conformer is the most stable conformer and the twist-chair conformers are predicted to be lower in energy than their corresponding boat and chair conformations. DFT predicts a small barrier to pseudo-rotation and a remarkable a

APA, Harvard, Vancouver, ISO, and other styles

28

Everaert, D. H., O. M. Peeters, C. J. De Ranter, N. M. Blaton, A. van Aerschot, and P. Herdewijn. "Conformational Analysis of Substituent Effects on the Sugar Puckering Mode and the anti-HIV Activity of 2′,3′-Dideoxypyrimidine Nucleosides." Antiviral Chemistry and Chemotherapy 4, no. 5 (1993): 289–99. http://dx.doi.org/10.1177/095632029300400505.

Full text

Abstract:

A comparison between the conformational parameters of eleven active and inactive anti-HIV 2′,3′-dideoxypyrimidine nucleosides and a series of 73 uridine and thymidine structures, revealed that our compounds, all having N-glycosidic bond torsion angles χ in the anti range, have pseudorotation phase angles P well distributed over both N (C3′- endo) and S [C2′- endo and C3′- exo) type sugar conformations and have both + sc and ap C4′-C5′ conformations. This means that solid state conformations characterized by P, χ and γ do not provide decisive information for predicting possible anti-HIV activit

APA, Harvard, Vancouver, ISO, and other styles

29

Dubovskii, Peter V., Kira M. Dubova, Gleb Bourenkov, et al. "Variability in the Spatial Structure of the Central Loop in Cobra Cytotoxins Revealed by X-ray Analysis and Molecular Modeling." Toxins 14, no. 2 (2022): 149. http://dx.doi.org/10.3390/toxins14020149.

Full text

Abstract:

Cobra cytotoxins (CTs) belong to the three-fingered protein family and possess membrane activity. Here, we studied cytotoxin 13 from Naja naja cobra venom (CT13Nn). For the first time, a spatial model of CT13Nn with both “water” and “membrane” conformations of the central loop (loop-2) were determined by X-ray crystallography. The “water” conformation of the loop was frequently observed. It was similar to the structure of loop-2 of numerous CTs, determined by either NMR spectroscopy in aqueous solution, or the X-ray method. The “membrane” conformation is rare one and, to date has only been obs

APA, Harvard, Vancouver, ISO, and other styles

30

Bishayee, Anupam, Laura Beguinot, and Subal Bishayee. "Conformational Analysis of the Phosphorylated Epidermal Growth Factor Receptor." Bioscience Reports 19, no. 5 (1999): 397–402. http://dx.doi.org/10.1023/a:1020260105524.

Full text

Abstract:

Phosphorylation-induced conformational changes have been well documented with different receptor tyrosine kinases. However, the susceptible epitopes and the tyrosine residue(s) involved in particular structural alteration mostly remain to be determined. Using a conformation-specific anti-peptide antibody, we have not only identified one such domain in the C-terminal tail of the EGF receptor but also identified the phosphate acceptor sites that are involved in the conformational change.

APA, Harvard, Vancouver, ISO, and other styles

31

Trapp, Melissa L., John F. Wojcik, Walter W. Zajac, Jr., and B. Mario Pinto. "Ab initio DFT calculations of the configurational and conformational preferences of 2-phenylsulfinylcyclohexanones Evidence for "exo-anomeric" interactions." Canadian Journal of Chemistry 84, no. 4 (2006): 685–91. http://dx.doi.org/10.1139/v06-040.

Full text

Abstract:

The conformational analysis of 2-phenylsulfinylcyclohexanone by ab initio density functional calculations is described. Six conformations corresponding to axial/equatorial isomers and rotation about the exocyclic C2S bond in each of the RR or RS diastereomers were calculated and the results were examined in terms of relative energies, electrostatic interactions, orbital interactions, and geometrical variations. The global minimum conformation was the RS isomer that positioned the phenylsulfinyl moiety in an equatorial orientation and the sulfinyl oxygen in an anti orientation with respect to

APA, Harvard, Vancouver, ISO, and other styles

32

Elgeti, Matthias, and Wayne L. Hubbell. "DEER Analysis of GPCR Conformational Heterogeneity." Biomolecules 11, no. 6 (2021): 778. http://dx.doi.org/10.3390/biom11060778.

Full text

Abstract:

G protein-coupled receptors (GPCRs) represent a large class of transmembrane helical proteins which are involved in numerous physiological signaling pathways and therefore represent crucial pharmacological targets. GPCR function and the action of therapeutic molecules are defined by only a few parameters, including receptor basal activity, ligand affinity, intrinsic efficacy and signal bias. These parameters are encoded in characteristic receptor conformations existing in equilibrium and their populations, which are thus of paramount interest for the understanding of receptor (mal-)functions a

APA, Harvard, Vancouver, ISO, and other styles

33

Guerrini, Giuditta, Dora Mehn, Francesco Fumagalli, et al. "Analytical Ultracentrifugation Detects Quaternary Rearrangements and Antibody-Induced Conformational Selection of the SARS-CoV-2 Spike Trimer." International Journal of Molecular Sciences 24, no. 19 (2023): 14875. http://dx.doi.org/10.3390/ijms241914875.

Full text

Abstract:

Analytical ultracentrifugation (AUC) analysis shows that the SARS-CoV-2 trimeric Spike (S) protein adopts different quaternary conformations in solution. The relative abundance of the “open” and “close” conformations is temperature-dependent, and samples with different storage temperature history have different open/close distributions. Neutralizing antibodies (NAbs) targeting the S receptor binding domain (RBD) do not alter the conformer populations; by contrast, a NAb targeting a cryptic conformational epitope skews the Spike trimer toward an open conformation. The results highlight AUC, whi

APA, Harvard, Vancouver, ISO, and other styles

34

Abraham, Raymond J., Rodothea Koniotou, and Fernando Sancassan. "Conformational analysis." Journal of the Chemical Society, Perkin Transactions 2, no. 12 (October 25, 2002): 2025–30. http://dx.doi.org/10.1039/b207841b.

Full text

APA, Harvard, Vancouver, ISO, and other styles

35

Berman, Andrea J., Anne R. Gooding, and Thomas R. Cech. "Tetrahymena Telomerase Protein p65 Induces Conformational Changes throughout Telomerase RNA (TER) and Rescues Telomerase Reverse Transcriptase and TER Assembly Mutants." Molecular and Cellular Biology 30, no. 20 (2010): 4965–76. http://dx.doi.org/10.1128/mcb.00827-10.

Full text

Abstract:

ABSTRACT The biogenesis of the Tetrahymena telomerase ribonucleoprotein particle (RNP) is enhanced by p65, a La family protein. Single-molecule and biochemical studies have uncovered a hierarchical assembly of the RNP, wherein the binding of p65 to stems I and IV of telomerase RNA (TER) causes a conformational change that facilitates the subsequent binding of telomerase reverse transcriptase (TERT) to TER. We used purified p65 and variants of TERT and TER to investigate the conformational rearrangements that occur during RNP assembly. Nuclease protection assays and mutational analysis revealed

APA, Harvard, Vancouver, ISO, and other styles

36

Brewer, Dyanne, Howard Hunter, and Gilles Lajoie. "NMR studies of the antimicrobial salivary peptides histatin 3 and histatin 5 in aqueous and nonaqueous solutions." Biochemistry and Cell Biology 76, no. 2-3 (1998): 247–56. http://dx.doi.org/10.1139/o98-066.

Full text

Abstract:

Conformational studies of the salivary peptides histatin 3 (H3) and histatin 5 (H5) were performed by NMR and circular dichroism (CD) in aqueous and nonaqueous solutions. Histatin 5 has no defined structure in H2O but adopts a more helical conformation in dimethyl sulfoxide and aqueous trifluoroethanol. This is in agreement with the CD analysis, which shows no secondary structure in H2O but increasing helical content in the presence of trifluoroethanol. CD analysis shows that H3 has less propensity to form a helical structure than H5 in similar conditions. The NMR analysis of H3 in H2O at pH 7

APA, Harvard, Vancouver, ISO, and other styles

37

Martynov, Alexander G., Marina A. Polovkova, Yulia G. Gorbunova, and Aslan Yu Tsivadze. "Redox-Triggered Switching of Conformational State in Triple-Decker Lanthanide Phthalocyaninates." Molecules 27, no. 19 (2022): 6498. http://dx.doi.org/10.3390/molecules27196498.

Full text

Abstract:

Double- and triple-decker lanthanide phthalocyaninates exhibit unique physical-chemical properties, particularly single-molecule magnetism. Among other factors, the magnetic properties of these sandwiches depend on their conformational state, which is determined via the skew angle of the phthalocyanine ligands. Thus, in the present work we report the comprehensive conformational study of substituted terbium(III) and yttrium(III) trisphthalocyaninates in solution depending on the substituents at the periphery of molecules, redox-states and nature of solvents. Conjunction of UV-vis-NIR spectrosc

APA, Harvard, Vancouver, ISO, and other styles

38

Deslongchamps, Pierre, and Normand Pothier. "Conformational analysis of 1-oxaspiro[5.5]undecanes. A powerful probe for the endo and the exo anomeric effects in acetals." Canadian Journal of Chemistry 68, no. 4 (1990): 597–603. http://dx.doi.org/10.1139/v90-092.

Full text

Abstract:

A 13C nuclear magnetic resonance spectroscopy study of 1-oxaspiro[5.5]undecanes 1, 4, and 5 as a function of temperature is reported. Compound 1 exists as a rapidly equilibrating mixture of a major and a minor conformer (1a and 1b) at room temperature that can be observed at low temperature. By comparison, 1,7-dioxaspiro[5.5]undecane 2 is conformationally rigid in a single conformation (2a) at room temperature. This completely different behavior demonstrates the importance of the endo and the exo anomeric effects in the acetal function. Keywords: spiro ethers, conformational analysis, 13C NMR.

APA, Harvard, Vancouver, ISO, and other styles

39

Freitas, Matheus Puggina de, and Teodorico de Castro Ramalho. "Employing conformational analysis in the molecular modeling of agrochemicals: insights on QSAR parameters of 2,4-D." Ciência e Agrotecnologia 37, no. 6 (2013): 485–94. http://dx.doi.org/10.1590/s1413-70542013000600001.

Full text

Abstract:

A common practice to compute ligand conformations of compounds with various degrees of freedom to be used in molecular modeling (QSAR and docking studies) is to perform a conformational distribution based on repeated random sampling, such as Monte-Carlo methods. Further calculations are often required. This short review describes some methods used for conformational analysis and the implications of using selected conformations in QSAR. A case study is developed for 2,4-dichlorophenoxyacetic acid (2,4-D), a widely used herbicide which binds to TIR1 ubiquitin ligase enzyme. The use of such an ap

APA, Harvard, Vancouver, ISO, and other styles

40

Ismailova, Larisa Ismail, and Namiq Abdulavval Akhmedov. "SPATIAL STRUCTURE OF THE HEPTAPEPTIDE ANALOGUE OF NOCICEPTIN MOLECULE." Mediterranean Journal of Chemistry 14, no. 2 (2024): 105. http://dx.doi.org/10.13171/mjc02407111782ismailova.

Full text

Abstract:

<p>It is known that nociceptins are a new type of regulatory peptide. Knowledge of these peptide molecules' structural and functional properties is of great practical importance for medicine and pharmacology. Their mechanisms of action are considered anti-opioid. This scientific work is devoted to studying the spatial structure of the heptapeptide H-Phe1-Gly2-Gly3-Phe4-Val5-Gly6-Pro7-OH. It examines the conformational capabilities of this heptapeptide molecule. This neuropeptide molecule is a stable analog of the nociceptin. The biologically active conformation of the peptide molecule, w

APA, Harvard, Vancouver, ISO, and other styles

41

Xue, Yanyan, Yi Sun, Yichun Xia, Xiuming Liu, and Hua Dai. "Observation of SAM-VI Riboswitch Dynamics Using Single-Molecule FRET." Biomolecules 15, no. 6 (2025): 841. https://doi.org/10.3390/biom15060841.

Full text

Abstract:

Riboswitches regulate gene expression through intricate dynamic conformational transitions, with divalent cation Mg2+ and their ligands playing pivotal roles in this process. The dynamic structural mechanism by which the S-adenosyl-L-methionine (SAM) responsive SAM-VI riboswitch (riboSAM) regulates the downstream SAM synthase gene translation remains unclear. In this study, we employed position-selective labeling of RNA (PLOR) to incorporate Cy3-Cy5 into designated positions of riboSAM, applying single-molecule Förster resonance energy transfer (smFRET) method to track its conformational switc

APA, Harvard, Vancouver, ISO, and other styles

42

Durham, Natasha D., Angela R. Howard, Ramesh Govindan, et al. "Real-Time Analysis of Individual Ebola Virus Glycoproteins Reveals Pre-Fusion, Entry-Relevant Conformational Dynamics." Viruses 12, no. 1 (2020): 103. http://dx.doi.org/10.3390/v12010103.

Full text

Abstract:

The Ebola virus (EBOV) envelope glycoprotein (GP) mediates the fusion of the virion membrane with the membrane of susceptible target cells during infection. While proteolytic cleavage of GP by endosomal cathepsins and binding of the cellular receptor Niemann-Pick C1 protein (NPC1) are essential steps for virus entry, the detailed mechanisms by which these events promote membrane fusion remain unknown. Here, we applied single-molecule Förster resonance energy transfer (smFRET) imaging to investigate the structural dynamics of the EBOV GP trimeric ectodomain, and the functional transmembrane pro

APA, Harvard, Vancouver, ISO, and other styles

43

Pérez, J., K. Nolsøe, M. Kessler, L. García, E. Pérez, and J. L. Serrano. "Bayesian methods for the conformational classification of eight-membered rings." Acta Crystallographica Section B Structural Science 61, no. 5 (2005): 585–94. http://dx.doi.org/10.1107/s0108768105023931.

Full text

Abstract:

Two methods for the classification of eight-membered rings based on a Bayesian analysis are presented. The two methods share the same probabilistic model for the measurement of torsion angles, but while the first method uses the canonical forms of cyclooctane and, given an empirical sequence of eight torsion angles, yields the probability that the associated structure corresponds to each of the ten canonical conformations, the second method does not assume previous knowledge of existing conformations and yields a clustering classification of a data set, allowing new conformations to be detecte

APA, Harvard, Vancouver, ISO, and other styles

44

Lubell, William D., Yousra Hamdane, and Julien Poupart. "N-Amino-imidazol-2-one (Nai) Residues as Tools for Peptide Mimicry: Synthesis, Conformational Analysis and Biomedical Applications." Synthesis 54, no. 06 (2022): 1518–26. http://dx.doi.org/10.1055/s-0040-1719862.

Full text

Abstract:

Abstract N-Amino-imidazol-2-one (Nai) residues are tools for studying peptide-backbone and side-chain conformation and function. Recent methods for substituted Nai residue synthesis, conformational analysis by X-ray crystallography and computation, and biomedical applications are reviewed, demonstrating the utility of this constrained residue to favor biologically active turn conformers with defined χ-dihedral angle orientations.1 Introduction2 Synthetic Methods3 Conformational Analysis4 Biomedical Applications5 Conclusions

APA, Harvard, Vancouver, ISO, and other styles

45

Kim, Meewhi, and Ilya Bezprozvanny. "Conformational Models of APP Processing by Gamma Secretase Based on Analysis of Pathogenic Mutations." International Journal of Molecular Sciences 22, no. 24 (2021): 13600. http://dx.doi.org/10.3390/ijms222413600.

Full text

Abstract:

Proteolytic processing of amyloid precursor protein (APP) plays a critical role in the pathogenesis of Alzheimer’s disease (AD). Sequential cleavage of APP by β and γ secretases leads to the generation of Aβ40 (non-amyloidogenic) and Aβ42 (amyloidogenic) peptides. Presenilin-1 (PS1) or presenilin-2 (PS2) play the role of a catalytic subunit of γ-secretase. Multiple familial AD (FAD) mutations in APP, PS1, or PS2 result in an increased Aβ42:Aβ40 ratio and the accumulation of toxic Aβ42 oligomers and plaques in patient brains. In this study, we perform molecular modeling of the APP complex with

APA, Harvard, Vancouver, ISO, and other styles

46

Spooner, Jacob, Heather Wiebe, Miranda Louwerse, Brandon Reader, and Noham Weinberg. "Theoretical analysis of high-pressure effects on conformational equilibria." Canadian Journal of Chemistry 96, no. 2 (2018): 178–89. http://dx.doi.org/10.1139/cjc-2017-0411.

Full text

Abstract:

Along with temperature, pressure is the most important physical parameter determining the thermodynamic properties and reactivity of chemical systems. In this work, we discuss the effects of high pressure on conformational properties of organic molecules and propose an approach toward calculation of conformational volume changes based on molecular dynamics simulations. The results agree well with the experimental data. Furthermore, we demonstrate that pressure can be used as an instrument for fine-tuning of molecular conformations and to propel a properly constructed molecular rotor possessing

APA, Harvard, Vancouver, ISO, and other styles

47

Allman, Tim, and R. E. Lenkinski. "A conformational analysis of adriamycin based upon its 1H nuclear magnetic resonance spectrum in various solvents." Canadian Journal of Chemistry 65, no. 10 (1987): 2405–10. http://dx.doi.org/10.1139/v87-401.

Full text

Abstract:

The solution conformation of adriamycin was studied by 1H nuclear magnetic resonance spectroscopy. The hydrochloride was found to be rigid on the nmr time scale in each of CDCl3, DMF-d7, and DMSO-d6. The sugar and D rings were found to have the same conformations as were found previously by X-ray crystallography. Similar results were found for the free base in DMF-d7 and CDCl3 solutions although the free base was found to be conformationally mobile in acetone-d6 and CD3OD solutions.

APA, Harvard, Vancouver, ISO, and other styles

48

Gerbst, Alexey G., Vadim B. Krylov, and Nikolay E. Nifantiev. "Conformational changes in common monosaccharides caused by per-O-sulfation." Pure and Applied Chemistry 91, no. 7 (2019): 1223–29. http://dx.doi.org/10.1515/pac-2018-1212.

Full text

Abstract:

Abstract Polysulfated carbohydrates play an important role in many biological processes because of their ability to bind to various protein receptors such as different growth factors, blood coagulation factors, adhesion lectins etc. Precise information about spatial organization of sulfated derivatives is of high demand for molecular modelling of such interactions as well as for understanding of the mechanism of pyranoside-into-furanoside rearrangement. In this review we summarize the changes recently revealed for the conformations of common pyranosides and furanosides upon total O-sulfation w

APA, Harvard, Vancouver, ISO, and other styles

49

Agaeva, G., G. Safarli, and N. Godjaev. "MOLECULAR MODELLİNG OF CONFORMATİONAL FLEXİBİLİTY OF HYLAMBATİN MOLECULE." Russian Journal of Biological Physics and Chemisrty 7, no. 2 (2022): 194–98. http://dx.doi.org/10.29039/rusjbpc.2022.0502.

Full text

Abstract:

The features of the spatial organization of the hylambatin molecule were investigated by methods of molecular mechanics and molecular dynamics. Hylambatin consists of twelve amino acid residues in the sequence: Asp-Pro-Pro-Asp-Pro-Asn-Arg-Phe-Tyr-Gly-Met-Met-NH2. Unlike all other tachykinins, hylambatin has a Met residue replacing the usual Leu at penultimate position. The tachykinin peptide hylambatin has been isolated and chemically characterized from methanol extracts of the skin of Hylambates maculatus, an African rhacophorid frog. It has been shown that intravenously administered hylambat

APA, Harvard, Vancouver, ISO, and other styles

50

A., EL Guerdaoui, Tijar R., El Merbouh B., et al. "Conformational analysis of diamide system HCO-L-Phenylalanine-NH2 by genetic algorithm." Chemistry International 2, no. 1 (2016): 47–58. https://doi.org/10.5281/zenodo.1470540.

Full text

Abstract:

Present work reports a detailed conformational and energy study of diamide system HCO-L-Phenylalanine-NH2 using genetic algorithm based on multi-Niche crowding technique (MNC) coupled with semi-empirical method AM1. Analysis showed the existence of 28 conformations covering 6 folds among 9 predicted with multi-dimensional conformational analysis MDCA. The relative stabilities are discussed in terms of hydrogen bonding established within the main chains, and various other types of electrostatic interactions between the main chain and the side one.

APA, Harvard, Vancouver, ISO, and other styles

We offer discounts on all premium plans for authors whose works are included in thematic literature selections. Contact us to get a unique promo code!