Journal articles: 'Conformational analysis'

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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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 (February 29, 2024): 1072. http://dx.doi.org/10.3390/molecules29051072.

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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 showed a limited number of conformations, suggesting that only certain stable conformations are prevalent among all possible conformations. The three-bond scholar coupling constants and exchange rates of hydroxyl protons were measured to obtain information on the backbone torsion angle and possible hydrogen bonding of each hydroxyl group. The 100 ns MD simulations indicate that the ribitol backbone has frequent conformational transitions with torsion angles between 180∘ and ±60∘, while d-arabitol and xylitol showed fewer conformational transitions. Taking our experimental and computational data together, it can be concluded that ribitol is more flexible than d-arabitol or xylitol, and the flexibility is at least in part defined by the configuration of the OH groups, which may form intramolecular hydrogen bonds.

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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.

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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 reduction methods for reducing the number of instances and for feature reduction. The reduced dataset that is obtained is then subjected to topological and quantitative analysis. In this step, we perform hierarchical clustering to obtain different sets of conformation clusters that may correspond to intermediate structures. The structures represented by these conformations are then analyzed by studying their high-dimensional topological properties to identify truly distinct conformations and holes in the conformational space that may represent high energy barriers. Our results show that the clusters closely follow known experimental results about intermediate structures as well as binding and folding events. Doi: 10.28991/HEF-SP2022-01-01 Full Text: PDF

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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 (January 17, 2008): 57–65. http://dx.doi.org/10.1107/s0108768107067341.

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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 chirality in the determined structures is discussed, as is the ability of this type of method to examine higher dimensions within the metric multi-dimensional scaling formalism.

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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 (March 1, 2002): 245–49. http://dx.doi.org/10.1139/v02-022.

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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 containing the one carbon bridge (overall average C2v symmetry). This process has a ΔH barrier of 42 kJ mol1 for ketone 1 (43 kJ mol1 for 2).Key words: bicyclo[4.4.1]undecan-11-one, conformational analysis, NMR line broadening, X-ray structure, enantiomers.

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Ohhashi, Yumiko, Yoshiki Yamaguchi, Hiroshi Kurahashi, Yuji O. Kamatari, Shinju Sugiyama, Boran Uluca, Timo Piechatzek, et al. "Molecular basis for diversification of yeast prion strain conformation." Proceedings of the National Academy of Sciences 115, no. 10 (February 21, 2018): 2389–94. http://dx.doi.org/10.1073/pnas.1715483115.

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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-terminal fragment of the Sup35 yeast prion protein, and found that monomeric Sup35NM harbored latent local compact structures despite its overall disordered conformation. When the hidden local microstructures were relaxed by genetic mutations or solvent conditions, Sup35NM adopted a strikingly different amyloid conformation, which redirected chaperone-mediated fiber fragmentation and modulated prion strain phenotypes. Thus, dynamic conformational fluctuations in natively disordered monomeric proteins represent a posttranslational mechanism for diversification of aggregate structures and cellular phenotypes.

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Lamichhane, Rajan, Jeffrey J. Liu, Goran Pljevaljcic, Kate L. White, Edwin van der Schans, Vsevolod Katritch, Raymond C. Stevens, Kurt Wüthrich, and David P. Millar. "Single-molecule view of basal activity and activation mechanisms of the G protein-coupled receptor β2AR." Proceedings of the National Academy of Sciences 112, no. 46 (November 2, 2015): 14254–59. http://dx.doi.org/10.1073/pnas.1519626112.

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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 receptor conformations. Individual receptor molecules in the apo form repeatedly sample both conformations, with a bias toward the inactive conformation. Experiments in the presence of drug ligands show that binding of the full agonist formoterol shifts the conformational distribution in favor of the active-like conformation, whereas binding of the inverse agonist ICI-118,551 favors the inactive conformation. Analysis of single-molecule dwell-time distributions for each state reveals that formoterol increases the frequency of activation transitions, while also reducing the frequency of deactivation events. In contrast, the inverse agonist increases the frequency of deactivation transitions. Our observations account for the high level of basal activity of this receptor and provide insights that help to rationalize, on the molecular level, the widely documented variability of the pharmacological efficacies among GPCR-targeting drugs.

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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 (March 16, 2024): 3371. http://dx.doi.org/10.3390/ijms25063371.

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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 rotational symmetric core surrounded by six flexible N-domains. We compared the performance of discrete classification methods with our recently developed method, MDSPACE, which uses 3D-to-2D flexible fitting of an atomic structure to images based on molecular dynamics (MD) simulations. Our analysis detected a novel conformation adopted by approximately 2% of the particles in the dataset and determined that the N-domains of p97 sway by up to 60° around a central position. This study demonstrates the application of MDSPACE in analyzing the continuous conformational changes in partially symmetrical protein complexes, systems notoriously difficult to analyze due to the alignment errors caused by their partial symmetry.

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Raich, Ivan, Karel Pauk, Ales Imramovsky, and Josef Jampílek. "Conformational and Chiroptical Properties of Salicylamide-Based Peptidomimetics." Symmetry 16, no. 2 (January 24, 2024): 138. http://dx.doi.org/10.3390/sym16020138.

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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 hundreds of conformations found, and, finally, a higher-level DFT optimization. For the resulting minima structures, Boltzmann populations were calculated, followed by OR calculations for all the populated conformers using the DFT method with various basis sets with diffuse functions. Weighted averages of the ORs were compared with experimental values, and the agreement, which ranged from excellent to moderate for various compounds, served as a verification of the conformational analysis results.

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Futamata, Ryota, Fumihiko Ogasawara, Takafumi Ichikawa, Atsushi Kodan, Yasuhisa Kimura, Noriyuki Kioka, and Kazumitsu Ueda. "In vivo FRET analyses reveal a role of ATP hydrolysis–associated conformational changes in human P-glycoprotein." Journal of Biological Chemistry 295, no. 15 (February 28, 2020): 5002–11. http://dx.doi.org/10.1074/jbc.ra119.012042.

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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 dimerized, and the TMDs are slightly open to the extracellular side. ATP binding and hydrolysis cause conformational changes between the inward-facing and the outward-facing conformations, and these changes help translocate substrates across the membrane. However, how ATP hydrolysis is coupled to these conformational changes remains unclear. In this study, we used a new FRET sensor that detects conformational changes in P-gp to investigate the role of ATP binding and hydrolysis during the conformational changes of human P-gp in living HEK293 cells. We show that ATP binding causes the conformational change to the outward-facing state and that ATP hydrolysis and subsequent release of γ-phosphate from both NBDs allow the outward-facing state to return to the original inward-facing state. The findings of our study underscore the utility of using FRET analysis in living cells to elucidate the function of membrane proteins such as multidrug transporters.

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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 (May 1, 1998): 257–66. http://dx.doi.org/10.1139/o98-028.

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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 pathologies associated with its production. In the present review, these techniques for the determination of peptide conformation are reviewed and applied to the study of bradykinin and its antagonists. Modeling of these conformational data in the presence of the B2 receptor or an antibody allows the biologically active conformations to be deduced and these are presented in this review.Key words: bradykinin antagonists, conformational analysis, NMR, CD, B2 receptor binding.

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Garrido-Rodríguez, Pedro, Miguel Carmena-Bargueño, María Eugenia de la Morena-Barrio, Carlos Bravo-Pérez, Belén de la Morena-Barrio, Rosa Cifuentes-Riquelme, María Luisa Lozano, Horacio Pérez-Sánchez, and Javier Corral. "Analysis of AlphaFold and molecular dynamics structure predictions of mutations in serpins." PLOS ONE 19, no. 7 (July 5, 2024): e0304451. http://dx.doi.org/10.1371/journal.pone.0304451.

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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 unrelated patients based on functional, biochemical, and crystallographic evidence supporting a folding defect. AlphaFold gave an accurate prediction for the wild-type structure. However, it also produced native structures for all variants, regardless of complexity or conformational consequences in vivo. Similarly, molecular dynamics of up to 1000 ns at temperatures causing conformational transitions did not show significant changes in the native structure of wild-type and variants. In conclusion, AlphaFold and molecular dynamics force predictions into the native conformation at conditions with experimental evidence supporting a conformational change to other structures. It is necessary to improve predictive strategies for serpins that consider the conformational sensitivity of these molecules.

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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.

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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 natural product structural framework (reasonable chaos), can be directed to confer dynamically new protein–ligand interactions beyond the basic lock–key model (imaginative order). Here we summarise our work on exploring conformational diversity from fluorinated natural product fragments, and how this approach of conformation-coupled diversity-oriented synthesis can be used to iteratively derive ligands with enhanced specificity against highly homologous protein domains. Our results demonstrate that the conformation entropic states of highly conserved protein domains differ significantly, and this conformational diversity, beyond primary sequence analysis, can be duly captured and exploited by natural-product derived ligands with complementary conformational dynamics for enhancing recognition specificity in drug lead discovery.

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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 (June 1, 1994): 1596–604. http://dx.doi.org/10.1139/v94-199.

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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 corresponding to experimentally observed conformations. The energy minimization of a randomly and significantly altered geometry of 1,2-dilauroyl-dl-phosphatidylethanolamine resulted in a head group conformation that closely agreed with ab initio theoretical calculations. The utility of AM1 in molecular mechanics parameterization was demonstrated.

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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.

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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 (May 15, 2008): 348–62. http://dx.doi.org/10.1107/s0108768108005442.

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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 torsion angles in the molecule. Special subsets of environments are also analysed, namely polymorphs, co-crystals and solvates. In general, conformational diversity increases with an increasing number of different crystal environments and with an increasing number of flexible torsion angles. Overall, molecules with one or more acyclic flexible torsion angle are observed to exist in more than one conformation in ca 40% of cases. There is evidence that solvated molecules exhibit more conformational flexibility on average, compared with polymorphs and co-crystals.

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26

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 (June 1, 1996): 535–49. http://dx.doi.org/10.1107/s010876819501696x.

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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 molecular scene. In addition, IMEM does not require the user to have any a priori knowledge of an expected number of conformational classes within a given dataset. The IMEM approach is applied to several datasets derived from the Cambridge Structural Database and, in all cases, chemically correct and sensible conformational classifications were discovered. This is confirmed by a rigorous comparison of IMEM results with published conformational data obtained by energy-minimization and numerical clustering methods. Conformational analysis tools have an important part to play in the conversion of raw molecular databases to knowledge bases.

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Elgeti, Matthias, and Wayne L. Hubbell. "DEER Analysis of GPCR Conformational Heterogeneity." Biomolecules 11, no. 6 (May 22, 2021): 778. http://dx.doi.org/10.3390/biom11060778.

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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 and rational design of improved therapeutics. To this end, the combination of site-directed spin labeling and EPR spectroscopy, in particular double electron–electron resonance (DEER), is exceedingly valuable as it has access to sub-Angstrom spatial resolution and provides a detailed picture of the number and populations of conformations in equilibrium. This review gives an overview of existing DEER studies on GPCRs with a focus on the delineation of structure/function frameworks, highlighting recent developments in data analysis and visualization. We introduce “conformational efficacy” as a parameter to describe ligand-specific shifts in the conformational equilibrium, taking into account the loose coupling between receptor segments observed for different GPCRs using DEER.

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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 (October 1993): 289–99. http://dx.doi.org/10.1177/095632029300400505.

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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 activity. We also found that any rationalization of the activity or inactivity of nucleosides in terms of the gauche effect of electronegative substituents on the furanose ring conformation, could not be demonstrated by using the semiempirical quantum chemical AM 1 method. Calculations of C3′-X3′ bond polarities indicate that anti-HIV activity in C3′-substituted nucleoside analogues is consistent with the presence of a positive C3′-X3′ bond polarity. Exploration of the conformational space of χ vs. γ for C3′- endo, C2′- endo and C3′- exo sugar puckering modes using the same AM1 method, reveals that although the C3′- endo [ P = 10°) region is about 2 kcal mol−1 lower than the C2′- endo region ( P = 170°), the C2′ - endo sugar puckering mode is the most accessible one due to the conformational flexibility about the minima. Our results also suggest that as P increases from 10°, through 170°, to 210°, the preferred range for -y dramatically shifts from almost exclusively around 50° (+ sc) at P = 10° to almost exclusively non + sc at P = 210°.

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29

Dubovskii, Peter V., Kira M. Dubova, Gleb Bourenkov, Vladislav G. Starkov, Anastasia G. Konshina, Roman G. Efremov, Yuri N. Utkin, and Valeriya R. Samygina. "Variability in the Spatial Structure of the Central Loop in Cobra Cytotoxins Revealed by X-ray Analysis and Molecular Modeling." Toxins 14, no. 2 (February 18, 2022): 149. http://dx.doi.org/10.3390/toxins14020149.

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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 observed by NMR for a single cytotoxin 1 from N. oxiana (CT1No) in detergent micelle. Both CT13Nn and CT1No are S-type CTs. Membrane-binding of these CTs probably involves an additional step—the conformational transformation of the loop-2. To confirm this suggestion, we conducted molecular dynamics simulations of both CT1No and CT13Nn in the Highly Mimetic Membrane Model of palmitoiloleoylphosphatidylglycerol, starting with their “water” NMR models. We found that the both toxins transform their “water” conformation of loop-2 into the “membrane” one during the insertion process. This supports the hypothesis that the S-type CTs, unlike their P-type counterparts, require conformational adaptation of loop-2 during interaction with lipid membranes.

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Bishayee, Anupam, Laura Beguinot, and Subal Bishayee. "Conformational Analysis of the Phosphorylated Epidermal Growth Factor Receptor." Bioscience Reports 19, no. 5 (October 1, 1999): 397–402. http://dx.doi.org/10.1023/a:1020260105524.

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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.

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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 (February 1, 2012): 248–55. http://dx.doi.org/10.2478/s11532-011-0136-1.

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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 in agreement with the experimental data. The conformational interconversion between the global minimum and the twist form requires 20.88 kcal mol-1 at the MP2/6-31G(d)//B3LYP/6-311++G(d,p) level of theory. Our results allow us to form a concise idea about the internal intricacies of the PEHSs of this cyclic tripeptide, describing the conformations as well as the conformational interconversion processes in this hypersurface. In addition, a comparative analysis between the conformational behaviors of cyclotrisarcosyl with that previously reported for cyclotriglycine was carried out

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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.

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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 activation barrier for the conformational interconversion of the twist-chair conformers to their corresponding boat conformers. The simplest conformational process and the one with the lowest barrier is the degenerate interconversion of the twist-chair 3 (TC3) conformation with itself via the CS symmetric chair (C2) transition state. The calculated strain energy barrier for this process is 2.41 kJ mol-1. The highest conformational interconversion barrier is between TC2 and twistboat 3 (TB3) forms, which was found to be 75.62 kJ mol-1.

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33

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 (April 1, 2006): 685–91. http://dx.doi.org/10.1139/v06-040.

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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 the carbonyl carbon atom. Of the other three low energy conformations, only one had a gauche arrangement of these atoms, and only in one of the four lower energy conformations was evidence found for a S-O()···C(+)-O electrostatic interaction. In contrast, the results were consistent with the operation of nS → [Formula: see text] stabilizing orbital interactions. Further support for this hypothesis was obtained from the increased C=O bond lengths in these four conformations relative to the other conformations, and by the torsional angle distortion away from ideal geometry, presumably to maximize the stabilizing orbital interaction. We propose that this conformational preference is a manifestation of a generalized exo-anomeric effect. The longer C2S bond in the axial isomers was also interpreted in terms of a stabilizing πC=O → [Formula: see text] interaction, analogous to an endo-anomeric interaction. Comparison of the computational results to available experimental data on the conformational equilibrium of each diastereomer in solution suggests which conformers are present in each of the equilibria. The available data for the solid state indicate that the RR and RS isomers both crystallize in high energy conformations, stabilized by intermolecular interactions.Key words: 2-phenylsulfinylcyclohexanones, configurational isomers, conformational preferences, DFT calculations, exo-anomeric effect.

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34

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 (May 1, 1998): 247–56. http://dx.doi.org/10.1139/o98-066.

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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 7.4 reveals that its conformational mobility is less than that of H5 as indicated by the observation of backbone cross peaks alphaN (i, i + 1) and NN (i, i + 1) and the slow exchanging amide protons in the C-terminus. However, H3 remains essentially unordered as suggested by the lack of longer range nuclear Overhauser effects (NOEs) in the NOESY spectrum. H3 becomes much more ordered in a mixture of 50:50 H2O - dimethyl sulfoxide as indicated by the numerous NOEs, including several side chain to side chain and side chain to backbone conectivities. Our data suggest that in these conditions H3 contains a turn in the region of K13 to K17 and possibly a 310 helix at the C-terminus. This study demonstrates that H3 and H5 are both conformationally mobile and that each adopt different types of conformations in aqueous and nonaqueous solutions.Key words: histatins, NMR, antimicrobial.

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35

Guerrini, Giuditta, Dora Mehn, Francesco Fumagalli, Sabrina Gioria, Mattia Pedotti, Luca Simonelli, Filippo Bianchini, Davide F. Robbiani, Luca Varani, and Luigi Calzolai. "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 (October 3, 2023): 14875. http://dx.doi.org/10.3390/ijms241914875.

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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, which is typically applied for molecular mass determination of biomolecules as a powerful tool for detecting functionally relevant quaternary protein conformations.

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36

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 (August 16, 2010): 4965–76. http://dx.doi.org/10.1128/mcb.00827-10.

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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 that p65 interacts with and stimulates conformational changes in regions of TER beyond stem IV. Several TER mutants exhibited telomerase activity only in the presence of p65, revealing the importance of p65 in promoting the correct RNP assembly pathway. In addition, p65 rescued TERT assembly mutants but not TERT activity mutants. Taken together, these results suggest that p65 stimulates telomerase assembly and activity in two ways. First, by sequestering stems I and IV, p65 limits the ensemble of structural conformations of TER, thereby presenting TERT with the active conformation of TER. Second, p65 acts as a molecular buttress within the assembled RNP, mutually stabilizing TER and TERT in catalytically active conformations.

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37

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 (December 2013): 485–94. http://dx.doi.org/10.1590/s1413-70542013000600001.

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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 approach and semi-empirical calculations did not achieve all possible minima for 2,4-D. In addition, the conformations and respective energies obtained by the semi-empirical AM1 method do not match the calculated trends obtained by a high level DFT method. Similar findings were obtained for the carboxylate anion, which is the bioactive form. Finally, the crystal bioactive structure of 2,4-D was not found as a minimum when using Monte-Carlo/AM1 and is similarly populated with another conformer in implicit water solution according to optimization at the B3LYP/aug-cc-pVDZ level. Therefore, quantitative structure-activity relationship (QSAR) methods based on three dimensional chemical structures are not fundamental to provide predictive models for 2,4-D congeners as TIR1 ubiquitin ligase ligands, since they do not necessarily reflect the bioactive conformation of this molecule. This probably extends to other systems.

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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 (April 1, 1990): 597–603. http://dx.doi.org/10.1139/v90-092.

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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.

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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 (October 1, 2022): 6498. http://dx.doi.org/10.3390/molecules27196498.

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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 spectroscopy and quantum-chemical calculations within simplified time-dependent DFT in Tamm–Dancoff approximation provided the spectroscopic signatures of staggered and gauche conformations of trisphthalocyaninates. Altogether, it allowed us to demonstrate that the butoxy-substituted complex behaves as a molecular switcher with controllable conformational state, while the crown-substituted triple-decker complex maintains a staggered conformation regardless of external factors. The analysis of noncovalent interactions within the reduced density gradient approach allowed to shed light on the nature of factors stabilizing certain conformers.

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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 (December 18, 2021): 13600. http://dx.doi.org/10.3390/ijms222413600.

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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 γ-secretase and analyze potential effects of FAD mutations in APP and PS1. We noticed that all FAD mutations in the APP transmembrane domain are predicted to cause an increase in the local disorder of its secondary structure. Based on structural analysis of known γ-secretase structures, we propose that APP can form a complex with γ-secretase in 2 potential conformations—M1 and M2. In conformation, the M1 transmembrane domain of APP forms a contact with the perimembrane domain that follows transmembrane domain 6 (TM6) in the PS1 structure. In conformation, the M2 transmembrane domain of APP forms a contact with transmembrane domain 7 (TM7) in the PS1 structure. By analyzing the effects of PS1-FAD mutations on the local protein disorder index, we discovered that these mutations increase the conformational flexibility of M2 and reduce the conformational flexibility of M1. Based on these results, we propose that M2 conformation, but not M1 conformation, of the γ secretase complex with APP leads to the amyloidogenic (Aβ42-generating) processing of APP. Our model predicts that APP processing in M1 conformation is favored by curved membranes, such as the membranes of early endosomes. In contrast, APP processing in M2 conformation is likely to be favored by relatively flat membranes, such as membranes of late endosomes and plasma membranes. These predictions are consistent with published biochemical analyses of APP processing at different subcellular locations. Our results also suggest that specific inhibitors of Aβ42 production could be potentially developed by selectively targeting the M2 conformation of the γ secretase complex with APP.

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41

Durham, Natasha D., Angela R. Howard, Ramesh Govindan, Fernando Senjobe, J. Maximilian Fels, William E. Diehl, Jeremy Luban, Kartik Chandran, and James B. Munro. "Real-Time Analysis of Individual Ebola Virus Glycoproteins Reveals Pre-Fusion, Entry-Relevant Conformational Dynamics." Viruses 12, no. 1 (January 15, 2020): 103. http://dx.doi.org/10.3390/v12010103.

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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 protein on the surface of pseudovirions. We show that in both contexts, pre-fusion GP is dynamic and samples multiple conformations. Removal of the glycan cap and NPC1 binding shift the conformational equilibrium, suggesting stabilization of conformations relevant to viral fusion. Furthermore, several neutralizing antibodies enrich alternative conformational states. This suggests that these antibodies neutralize EBOV by restricting access to GP conformations relevant to fusion. This work demonstrates previously unobserved dynamics of pre-fusion EBOV GP and presents a platform with heightened sensitivity to conformational changes for the study of GP function and antibody-mediated neutralization.

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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 (September 23, 2005): 585–94. http://dx.doi.org/10.1107/s0108768105023931.

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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 detected. Both methods have been tested using the conformational classification of Csp 3 eight-membered rings described in the literature. The methods have also been employed to classify the solid-state conformation in Csp 3 eight-membered rings using data retrieved from an updated version of the Cambridge Structural Database (CSD).

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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 (February 2018): 178–89. http://dx.doi.org/10.1139/cjc-2017-0411.

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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 a suitable combination of energy and volume profiles.

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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 (October 1, 1987): 2405–10. http://dx.doi.org/10.1139/v87-401.

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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.

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45

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 (January 5, 2022): 1518–26. http://dx.doi.org/10.1055/s-0040-1719862.

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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

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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 (July 26, 2019): 1223–29. http://dx.doi.org/10.1515/pac-2018-1212.

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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 which were studied by means of NMR spectroscopy as well as molecular modelling. It was found that pentoses, being more flexible, undergo complete conformational chair inversion. Meanwhile, for hexoses the situation strongly depends on the monosaccharide configuration. Conformational changes are most pronounced in gluco-compounds though quantum chemical calculations helped to establish that no complete chair inversion occurred. In furanosides distortions of two types were observed: either the ring conformation or the conformation of the side chain changed. The presented data may be used for the analysis of chemical, physical and biological properties of sulfated carbohydrates.

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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 (November 15, 2022): 194–98. http://dx.doi.org/10.29039/rusjbpc.2022.0502.

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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 hylambatin significantly increases the level of glucose and insulin in blood plasma. In this paper, the conformational flexibility of the hylambatin molecule was studied by methods of molecular mechanics and molecular dynamics. The conformational calculation of the peptide took into account non-valent and electrostatic interactions, hydrogen bonds and torsion potentials. Based on fragmentary analysis, stable spatial structures of the hylambatin dodecapeptide were determined, which can be represented as a set of conformations characterized by a relatively labile N-terminal tetrapeptide and a conformationally rigid C-terminal octapeptide. In the calculated stable conformational states, the effective interactions of the side chains of residues and hydrogen bonds were refined and energetically evaluated. It has been shown that the hylambatin molecule preferably forms practically isoenergetic conformations with various structural types at the N-end of the peptide chain, passing into the alpha helix at the C-end. By the method of molecular dynamics, the pattern of intramolecular mobility of stable conformations of the hylambatin molecule was modeled both in vacuum and surrounded by water molecules. Based on the calculated values of the dihedral angles, molecular models of energetically preferred conformational states of the hylambatin dodecapeptide were constructed.

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48

Peng, Zhenghong. "NMR conformational analysis on cyclic decapeptide template molecule." Canadian Journal of Chemistry 77, no. 8 (August 1, 1999): 1394–404. http://dx.doi.org/10.1139/v99-128.

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We report the synthesis and conformational analysis of a series of cyclic and bicyclic decapeptide templates for combinatorial chemistry. The peptides were synthesized via solid phase synthesis and followed by solution cyclization. The conformation of the peptides was studied by proton NMR spectroscopy in DMSO and in TFE-water. The structure of the peptide template was calculated with the program DIANA and followed by SA from the NMR experimental constraints. The peptide adopts a fold comprising two β-strands and two type II β-turns. The design of such a restained cyclic decapeptide template will be discussed along with Template Assembled Synthetic Proteins (TASP).Key words: solid phase peptide synthesis, cyclic decapeptide, NMR, conformational analysis, β-sheet.

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49

Hu, Ching Han, Mingzuo Shen, and Henry F. Schaefer. "Glycine conformational analysis." Journal of the American Chemical Society 115, no. 7 (April 1993): 2923–29. http://dx.doi.org/10.1021/ja00060a046.

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50

Houseknecht, Justin B., and Todd L. Lowary. "Oligofuranosides Containing Conformationally Restricted Residues: Synthesis and Conformational Analysis." Journal of Organic Chemistry 67, no. 12 (June 2002): 4150–64. http://dx.doi.org/10.1021/jo011127p.

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Journal articles on the topic 'Conformational analysis'

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