Journal articles on the topic 'Conformation'
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1
Pavelčík, František, and Eva Luptáková. "The empirical conformational surface of the co(ethylenediamine) ring." Collection of Czechoslovak Chemical Communications 55, no. 6 (1990): 1427–34. http://dx.doi.org/10.1135/cccc19901427.
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The conformational surface of the Co(en) chelate ring was studied by the method of structural correlation. The reduction of dimensionality of the conformation problem was achieved by employing the pseudorotation concept. The empirical potential surface was obtained by statistical treatment of 743 independent conformations from the Cambridge Structural Database. The theoretical potential surface was obtained by molecular mechanics. The minimal-energy conformation is gauche with the Co atom on the two-fold axis. Conformational flexibility also includes an envelope conformation with the N atom bent out of the plane. The transition between the mirror-image symmetrical conformations can occur by a pseudorotation pathway and is accompanied by increased planarity of the ring. The transition state is an envelope conformation with an out-plane Co atom.
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Cresti, Julianna R., Abramo J. Manfredonia, Christopher E. Bragança, Joseph A. Boscia, Christina M. Hurley, Mary D. Cundiff, and Daniel A. Kraut. "Proteasomal conformation controls unfolding ability." Proceedings of the National Academy of Sciences 118, no. 25 (June 14, 2021): e2101004118. http://dx.doi.org/10.1073/pnas.2101004118.
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The 26S proteasome is the macromolecular machine responsible for the bulk of protein degradation in eukaryotic cells. As it degrades a ubiquitinated protein, the proteasome transitions from a substrate-accepting conformation (s1) to a set of substrate-processing conformations (s3 like), each stabilized by different intramolecular contacts. Tools to study these conformational changes remain limited, and although several interactions have been proposed to be important for stabilizing the proteasome’s various conformations, it has been difficult to test these directly under equilibrium conditions. Here, we describe a conformationally sensitive Förster resonance energy transfer assay, in which fluorescent proteins are fused to Sem1 and Rpn6, which are nearer each other in substrate-processing conformations than in the substrate-accepting conformation. Using this assay, we find that two sets of interactions, one involving Rpn5 and another involving Rpn2, are both important for stabilizing substrate-processing conformations. Mutations that disrupt these interactions both destabilize substrate-processing conformations relative to the substrate-accepting conformation and diminish the proteasome’s ability to successfully unfold and degrade hard-to-unfold substrates, providing a link between the proteasome’s conformational state and its unfolding ability.
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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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Wang, Zhangqian, Jieya Deng, Muhammad Umer, Naureen Anwar, Yidang Wang, XingXing Dong, Hua Xu, Yi He, and Chao Gao. "RHPS4 shifted the conformation ensemble equilibrium of Tel24 by preferentially stabilizing the (3 + 1) hybrid-2 conformation." RSC Advances 12, no. 40 (2022): 26011–15. http://dx.doi.org/10.1039/d2ra03959a.
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Tel24 G-quadruplex can form a conformational ensemble consisting of parallel and (3 + 1) hybrid-2 conformations. RHPS4 preferentially stabilized the hybrid-2 conformation and shifted the conformational ensemble equilibrium.
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Su, Yang, Wei Xia, Jing Li, Thomas Walz, Martin J. Humphries, Dietmar Vestweber, Carlos Cabañas, Chafen Lu, and Timothy A. Springer. "Relating conformation to function in integrin α5β1." Proceedings of the National Academy of Sciences 113, no. 27 (June 17, 2016): E3872—E3881. http://dx.doi.org/10.1073/pnas.1605074113.
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Whether β1 integrin ectodomains visit conformational states similarly to β2 and β3 integrins has not been characterized. Furthermore, despite a wealth of activating and inhibitory antibodies to β1 integrins, the conformational states that these antibodies stabilize, and the relation of these conformations to function, remain incompletely characterized. Using negative-stain electron microscopy, we show that the integrin α5β1 ectodomain adopts extended-closed and extended-open conformations as well as a bent conformation. Antibodies SNAKA51, 8E3, N29, and 9EG7 bind to different domains in the α5 or β1 legs, activate, and stabilize extended ectodomain conformations. Antibodies 12G10 and HUTS-4 bind to the β1 βI domain and hybrid domains, respectively, activate, and stabilize the open headpiece conformation. Antibody TS2/16 binds a similar epitope as 12G10, activates, and appears to stabilize an open βI domain conformation without requiring extension or hybrid domain swing-out. mAb13 and SG/19 bind to the βI domain and βI–hybrid domain interface, respectively, inhibit, and stabilize the closed conformation of the headpiece. The effects of the antibodies on cell adhesion to fibronectin substrates suggest that the extended-open conformation of α5β1 is adhesive and that the extended-closed and bent-closed conformations are nonadhesive. The functional effects and binding sites of antibodies and fibronectin were consistent with their ability in binding to α5β1 on cell surfaces to cross-enhance or inhibit one another by competitive or noncompetitive (allosteric) mechanisms.
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Almahmoud, Suliman, Xiaofang Wang, Jonathan L. Vennerstrom, and Haizhen A. Zhong. "Conformational Studies of Glucose Transporter 1 (GLUT1) as an Anticancer Drug Target." Molecules 24, no. 11 (June 7, 2019): 2159. http://dx.doi.org/10.3390/molecules24112159.
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Glucose transporter 1 (GLUT1) is a facilitative glucose transporter overexpressed in various types of tumors; thus, it has been considered as an important target for cancer therapy. GLUT1 works through conformational switching from an outward-open (OOP) to an inward-open (IOP) conformation passing through an occluded conformation. It is critical to determine which conformation is preferred by bound ligands because the success of structure-based drug design depends on the appropriate starting conformation of the target protein. To find out the most favorable GLUT 1 conformation for ligand binding, we ran systemic molecular docking studies for different conformations of GLUT1 using known GLUT1 inhibitors. Our data revealed that the IOP is the preferred conformation and that residues Phe291, Phe379, Glu380, Trp388, and Trp412 may play critical roles in ligand binding to GLUT1. Our data suggests that conformational differences in these five amino acids in the different conformers of GLUT1 may be used to design ligands that inhibit GLUT1.
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Guo, Qing, Yufan He, and H. Peter Lu. "Interrogating the activities of conformational deformed enzyme by single-molecule fluorescence-magnetic tweezers microscopy." Proceedings of the National Academy of Sciences 112, no. 45 (October 28, 2015): 13904–9. http://dx.doi.org/10.1073/pnas.1506405112.
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Characterizing the impact of fluctuating enzyme conformation on enzymatic activity is critical in understanding the structure–function relationship and enzymatic reaction dynamics. Different from studying enzyme conformations under a denaturing condition, it is highly informative to manipulate the conformation of an enzyme under an enzymatic reaction condition while monitoring the real-time enzymatic activity changes simultaneously. By perturbing conformation of horseradish peroxidase (HRP) molecules using our home-developed single-molecule total internal reflection magnetic tweezers, we successfully manipulated the enzymatic conformation and probed the enzymatic activity changes of HRP in a catalyzed H2O2–amplex red reaction. We also observed a significant tolerance of the enzyme activity to the enzyme conformational perturbation. Our results provide a further understanding of the relation between enzyme behavior and enzymatic conformational fluctuation, enzyme–substrate interactions, enzyme–substrate active complex formation, and protein folding–binding interactions.
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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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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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Bierzyński, A. "Methods of peptide conformation studies." Acta Biochimica Polonica 48, no. 4 (December 31, 2001): 1091–99. http://dx.doi.org/10.18388/abp.2001_3870.
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In solution most of the peptides assume multiple flexible conformations. Determination of the dominant conformers and evaluation of their populations is the aim of peptide conformation studies, in which theoretical and experimental methods play complementary roles. Molecular dynamics or Monte Carlo methods are quite effective in searching the conformational space accessible to a peptide but they are not able to estimate, precisely enough, the populations of various conformations. Therefore, they must be supplemented by experimental data. In this paper, a short review of the experimental methods, most widely used in peptide conformational studies, is presented. Among them NMR plays the leading role. Valuable information is also obtained from hydrogen exchange, fluorescence resonance energy transfer, and circular dichroism measurements. The advantages and shortcomings of these methods are discussed.
11
Seo, Udeok, Ku-Jin Kim, and Beom Kang. "An Algorithm for Computing Side Chain Conformational Variations of a Protein Tunnel/Channel." Molecules 23, no. 10 (September 26, 2018): 2459. http://dx.doi.org/10.3390/molecules23102459.
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In this paper, a novel method to compute side chain conformational variations for a protein molecule tunnel (or channel) is proposed. From the conformational variations, we compute the flexibly deformed shapes of the initial tunnel, and present a way to compute the maximum size of the ligand that can pass through the deformed tunnel. By using the two types of graphs corresponding to amino acids and their side chain rotamers, the suggested algorithm classifies amino acids and rotamers which possibly have collisions. Based on the divide and conquer technique, local side chain conformations are computed first, and then a global conformation is generated by combining them. With the exception of certain cases, experimental results show that the algorithm finds up to 327,680 valid side chain conformations from 128~1233 conformation candidates within three seconds.
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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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Solopova, O. N., L. P. Pozdnyakova, N. E. Varlamov, M. N. Bokov, E. V. Morozkina, Т. А. Yagudin, and P. G. Sveshnikov. "Conformational Differences between Active Angiotensins and Their Inactive Precursors." Acta Naturae 4, no. 1 (March 15, 2012): 74–77. http://dx.doi.org/10.32607/20758251-2012-4-1-74-77.
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The peptide conformation in the context of a protein polypeptide chain is influenced by proximal amino acid residues. However, the mechanisms of this interference remain poorly understood. We studied the conformation of angiotensins 1, 2 and 3, which are produced naturally in a sequential fashion from a precursor protein angiotensinogen and contain an identical peptide core structure. Using the example of angiotensins 1, 2 and 3, it was shown that similar amino acid sequences may have significant conformational differences in various molecules. In order to assess the conformational changes, we developed a panel of high-affinity mouse monoclonal antibodies against angiotensins 1, 2 and 3 and studied their cross-reactivity in indirect and competitive ELISAs. It was found that the conformations of inactive angiotensin1 and the corresponding fragment of angiotensinogen are similar; the same is true for the conformations of active angiotensins 2 and 3, whereas the conformations of homologous fragments in the active and inactive angiotensins differ significantly.
14
Roh, Soung-Hun, Corey F. Hryc, Hyun-Hwan Jeong, Xue Fei, Joanita Jakana, George H. Lorimer, and Wah Chiu. "Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM." Proceedings of the National Academy of Sciences 114, no. 31 (July 14, 2017): 8259–64. http://dx.doi.org/10.1073/pnas.1704725114.
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Single-particle electron cryo-microscopy (cryo-EM) is an emerging tool for resolving structures of conformationally heterogeneous particles; however, each structure is derived from an average of many particles with presumed identical conformations. We used a 3.5-Å cryo-EM reconstruction with imposed D7 symmetry to further analyze structural heterogeneity among chemically identical subunits in each GroEL oligomer. Focused classification of the 14 subunits in each oligomer revealed three dominant classes of subunit conformations. Each class resembled a distinct GroEL crystal structure in the Protein Data Bank. The conformational differences stem from the orientations of the apical domain. We mapped each conformation class to its subunit locations within each GroEL oligomer in our dataset. The spatial distributions of each conformation class differed among oligomers, and most oligomers contained 10–12 subunits of the three dominant conformation classes. Adjacent subunits were found to more likely assume the same conformation class, suggesting correlation among subunits in the oligomer. This study demonstrates the utility of cryo-EM in revealing structure dynamics within a single protein oligomer.
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Giri Rao, V. V. Hemanth, and Shachi Gosavi. "On the folding of a structurally complex protein to its metastable active state." Proceedings of the National Academy of Sciences 115, no. 9 (January 17, 2018): 1998–2003. http://dx.doi.org/10.1073/pnas.1708173115.
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For successful protease inhibition, the reactive center loop (RCL) of the two-domain serine protease inhibitor, α1-antitrypsin (α1-AT), needs to remain exposed in a metastable active conformation. The α1-AT RCL is sequestered in a β-sheet in the stable latent conformation. Thus, to be functional, α1-AT must always fold to a metastable conformation while avoiding folding to a stable conformation. We explore the structural basis of this choice using folding simulations of coarse-grained structure-based models of the two α1-AT conformations. Our simulations capture the key features of folding experiments performed on both conformations. The simulations also show that the free energy barrier to fold to the latent conformation is much larger than the barrier to fold to the active conformation. An entropically stabilized on-pathway intermediate lowers the barrier for folding to the active conformation. In this intermediate, the RCL is in an exposed configuration, and only one of the two α1-AT domains is folded. In contrast, early conversion of the RCL into a β-strand increases the coupling between the two α1-AT domains in the transition state and creates a larger barrier for folding to the latent conformation. Thus, unlike what happens in several proteins, where separate regions promote folding and function, the structure of the RCL, formed early during folding, determines both the conformational and the functional fate of α1-AT. Further, the short 12-residue RCL modulates the free energy barrier and the folding cooperativity of the large 370-residue α1-AT. Finally, we suggest experiments to test the predicted folding mechanism for the latent state.
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Ağar, Çetin, Gwendolyn M. A. van Os, Matthias Mörgelin, Richard R. Sprenger, J. Arnoud Marquart, Rolf T. Urbanus, Ronald H. W. M. Derksen, Joost C. M. Meijers, and Philip G. de Groot. "β2-Glycoprotein I can exist in 2 conformations: implications for our understanding of the antiphospholipid syndrome." Blood 116, no. 8 (August 26, 2010): 1336–43. http://dx.doi.org/10.1182/blood-2009-12-260976.
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Abstract The antiphospholipid syndrome is defined by the presence of antiphospholipid antibodies in blood of patients with thrombosis or fetal loss. There is ample evidence that β2-glycoprotein I (β2GPI) is the major antigen for antiphospholipid antibodies. The autoantibodies recognize β2GPI when bound to anionic surfaces and not in solution. We showed that β2GPI can exist in at least 2 different conformations: a circular plasma conformation and an “activated” open conformation. We also showed that the closed, circular conformation is maintained by interaction between the first and fifth domain of β2GPI. By changing pH and salt concentration, we were able to convert the conformation of β2GPI from the closed to the open conformation and back. In the activated open conformation, a cryptic epitope in the first domain becomes exposed that enables patient antibodies to bind and form an antibody-β2GPI complex. We also demonstrate that the open conformation of β2GPI prolonged the activated partial thromboplastin time when added to normal plasma, whereas the activated partial thromboplastin time is further prolonged by addition of anti-β2GPI antibodies. The conformational change of β2GPI, and the influence of the autoantibodies may have important consequences for our understanding of the antiphospholipid syndrome.
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Huang, Shupei, Haizhong An, Xiangyun Gao, Xiaoqing Hao, and Xuan Huang. "The Multiscale Conformation Evolution of the Financial Time Series." Mathematical Problems in Engineering 2015 (2015): 1–9. http://dx.doi.org/10.1155/2015/563145.
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Fluctuations of the nonlinear time series are driven by the traverses of multiscale conformations from one state to another. Aiming to characterize the evolution of multiscale conformations with changes in time and frequency domains, we present an algorithm that combines the wavelet transform and the complex network. Based on defining the multiscale conformation using a set of fluctuation states from different frequency components at each time point rather than the single observable value, we construct the conformational evolution complex network. To illustrate, using data of Shanghai’s composition index with daily frequency from 1991 to 2014 as an example, we find that a few major conformations are the main contributors of evolution progress, the whole conformational evolution network has a clustering effect, and there is a turning point when the size of the chain of multiscale conformations is 14. This work presents a refined perspective into underlying fluctuation features of financial markets.
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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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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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Toepfer, Christopher N., Amanda C. Garfinkel, Gabriela Venturini, Hiroko Wakimoto, Giuliana Repetti, Lorenzo Alamo, Arun Sharma, et al. "Myosin Sequestration Regulates Sarcomere Function, Cardiomyocyte Energetics, and Metabolism, Informing the Pathogenesis of Hypertrophic Cardiomyopathy." Circulation 141, no. 10 (March 10, 2020): 828–42. http://dx.doi.org/10.1161/circulationaha.119.042339.
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Background: Hypertrophic cardiomyopathy (HCM) is caused by pathogenic variants in sarcomere protein genes that evoke hypercontractility, poor relaxation, and increased energy consumption by the heart and increased patient risks for arrhythmias and heart failure. Recent studies show that pathogenic missense variants in myosin, the molecular motor of the sarcomere, are clustered in residues that participate in dynamic conformational states of sarcomere proteins. We hypothesized that these conformations are essential to adapt contractile output for energy conservation and that pathophysiology of HCM results from destabilization of these conformations. Methods: We assayed myosin ATP binding to define the proportion of myosins in the super relaxed state (SRX) conformation or the disordered relaxed state (DRX) conformation in healthy rodent and human hearts, at baseline and in response to reduced hemodynamic demands of hibernation or pathogenic HCM variants. To determine the relationships between myosin conformations, sarcomere function, and cell biology, we assessed contractility, relaxation, and cardiomyocyte morphology and metabolism, with and without an allosteric modulator of myosin ATPase activity. We then tested whether the positions of myosin variants of unknown clinical significance that were identified in patients with HCM, predicted functional consequences and associations with heart failure and arrhythmias. Results: Myosins undergo physiological shifts between the SRX conformation that maximizes energy conservation and the DRX conformation that enables cross-bridge formation with greater ATP consumption. Systemic hemodynamic requirements, pharmacological modulators of myosin, and pathogenic myosin missense mutations influenced the proportions of these conformations. Hibernation increased the proportion of myosins in the SRX conformation, whereas pathogenic variants destabilized these and increased the proportion of myosins in the DRX conformation, which enhanced cardiomyocyte contractility, but impaired relaxation and evoked hypertrophic remodeling with increased energetic stress. Using structural locations to stratify variants of unknown clinical significance, we showed that the variants that destabilized myosin conformations were associated with higher rates of heart failure and arrhythmias in patients with HCM. Conclusions: Myosin conformations establish work-energy equipoise that is essential for life-long cellular homeostasis and heart function. Destabilization of myosin energy-conserving states promotes contractile abnormalities, morphological and metabolic remodeling, and adverse clinical outcomes in patients with HCM. Therapeutic restabilization corrects cellular contractile and metabolic phenotypes and may limit these adverse clinical outcomes in patients with HCM.
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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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van Roey, P., W. A. Pangborn, R. F. Schinazi, G. Painter, and D. C. Liotta. "Absolute Configuration of the Antiviral Agent (−)-cis-5-Fluoro-1-[2-Hydroxymethyl)-1,3-Oxathiolan-5-yl]Cytosine." Antiviral Chemistry and Chemotherapy 4, no. 6 (December 1993): 369–75. http://dx.doi.org/10.1177/095632029300400609.
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The structure and absolute configuration of (−)- cis-5-fluoro-1-[2-(hydroxymethyl)-1,3-oxathiolan-5-yl]cytosine (FTC), has been determined by X-ray crystallographic analysis. The results confirm that the L-isomer of the nucleoside analogue is the most active enantiomer and that the correct absolute configuration of (−)-FTC is 5-fluoro-(2′R,5′S)-(−)-1-[2-hydroxymethyl)oxathiolan-5-yl]-fluorocytosine. The two molecules in the asymmetric unit show conformations that combine conformational features of two other classes of potent antiviral nucleosides. Both oxathiolane rings have the 3′-sulphur atom in nearly perfect S3′- exo envelope conformations, similar to what is observed for 3′-azido-3′-deoxythymidine (AZT) and 2′,3′-dideoxycytidine. One of the two molecules has a glycosylic link conformation in which the base is eclipsed with the C5′-O1′ bond. This mimics the high- anti conformation that has been observed in the structures of several 2′,3′-didehydro-2′,3′-dideoxypyrimidine nucleosides but is inaccessible for saturated pyrimidine nucleosides. However, the observed conformations cannot be superimposed adequately with other active antiviral nucleosides to suggest a common ‘active site’ conformation.
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Williams, Howard J., A. Ian Scott, Reiner A. Dieden, Charles S. Swindell, Lisa E. Chirlian, Michelle M. Francl, Julia M. Heerding, and Nancy E. Krauss. "NMR and molecular modeling study of active and inactive taxol analogues in aqueous and nonaqueous solution." Canadian Journal of Chemistry 72, no. 1 (January 1, 1994): 252–60. http://dx.doi.org/10.1139/v94-038.
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The conformations of the biologically active taxol analogs Taxotere®, 3R, 4R, and 4S, and the biologically inactive analog 3S were evaluated in CDCl3 and DMSO–water solution using 1H NMR coupling constant and NOESY data and molecular modeling. The solution structures of Taxotere® were very similar to those detected previously for taxol. The A-ring side chain conformations of analogs 3 and 4 could not be defined with the same precision as had been possible for taxol, but the conformational possibilities could be significantly limited by the data. Analogs 3R, 4R, and 4S (but not 3S) can mimic the dominant conformation of taxol in chloroform, but no logical relationship between biological activity and aqueous solution conformation could be detected.
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Halder, Bijoy K., Angelica M. Palomino, and Jordan Hicks. "Influence of polyacrylamide conformation on fabric of “tunable” kaolin–polymer composite." Canadian Geotechnical Journal 55, no. 9 (September 2018): 1295–312. http://dx.doi.org/10.1139/cgj-2017-0200.
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“Tunable” clay–polymer composites have the potential to improve the engineering properties of clay materials. The importance of these materials derives from the ability of the responsive polymer to adopt various conformations (coiled, partially extended or extended), which in turn impacts the mesoscale properties of the material. However, the influence of polymer molecule conformation on particle arrangement and overall composite behavior is not well understood. The purpose of this study is to understand the fabric development due to the conformational behavior of the polymer, and thus the clay–polymer composite, over a wide range of solids content and stress levels. The polymer molecule conformation was controlled using selected fluid pH and ionic concentrations. Results show that the polymer conformation significantly influences clay fabric formation. When the polymer molecules are likely to have extended conformation, the dominant fabric mode is face-to-face and particle mobilization increases. Both face-to-face and edge-to-edge fabric formation dominate the behavior of the composite when coiled conformation is likely, resulting in a decrease in interparticle movement. Thus, the polymer conformation can be used to manipulate both the interparticle spacing between particles and (or) aggregates and arrangement of particles.
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Terada, Yukimasa, Tomoo Matsuura, Yukari Mori, and Shosuke Yamamura. "Theoretical studies of model compounds of lathyrane-type diterpenes." Canadian Journal of Chemistry 82, no. 1 (January 1, 2004): 11–18. http://dx.doi.org/10.1139/v03-171.
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The conformation of the 11-membered ring of the lathyrane skeleton has been investigated using NMR spectra and theoretical calculations. Some other skeletons, such as jatrophane, jatrapholane, and tigliane, seem to be derived from this framework, and the conformation is important in connection with the configuration of the resultant diterpenes. The conformation of lathyrane is principally defined by the orientation of the two methyl groups; namely, the methyl groups on C1 and C6 directed above or below the ring plane. Theoretical calculations revealed that the predominant conformation is altered depending on the oxygen functional groups on the ring. As far as the bond lengths, bond angles, and dihedral angles are concerned, all calculation methods afforded reasonable results. In contrast, as regards conformational stability, only the ab initio molecular orbital method (RHF/6-31G*) predicted the most stable conformation, consistent with NOE experiments. On the other hand, the stable conformations predicted by the ab initio method (RHF/STO-3G), the semi-empirical molecular orbital method (MOPAC(PM3)), and the molecular mechanics calculations (MM3) did not necessarily agree with the conformers suggested by the NOE experiments.Key words: ab initio MO, semi-empirical MO, molecular mechanics, 11-membered ring conformation, NOE.
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Nakae, Setsu, Maho Kitamura, Daisuke Fujiwara, Masaaki Sawa, Tsuyoshi Shirai, Ikuo Fujii, and Toshiji Tada. "Structure of mitogen-activated protein kinase kinase 1 in the DFG-out conformation." Acta Crystallographica Section F Structural Biology Communications 77, no. 12 (November 25, 2021): 459–64. http://dx.doi.org/10.1107/s2053230x21011687.
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Eukaryotic protein kinases contain an Asp-Phe-Gly (DFG) motif, the conformation of which is involved in controlling the catalytic activity, at the N-terminus of the activation segment. The motif can be switched between active-state (DFG-in) and inactive-state (DFG-out) conformations: however, the mechanism of conformational change is poorly understood, partly because there are few reports of the DFG-out conformation. Here, a novel crystal structure of nonphosphorylated human mitogen-activated protein kinase kinase 1 (MEK1; amino acids 38–381) complexed with ATP-γS is reported in which MEK1 adopts the DFG-out conformation. The crystal structure revealed that the structural elements (the αC helix and HRD motif) surrounding the active site are involved in the formation/stabilization of the DFG-out conformation. The ATP-γS molecule was bound to the canonical ATP-binding site in a different binding mode that has never been found in previously determined crystal structures of MEK1. This novel ATP-γS binding mode provides a starting point for the design of high-affinity inhibitors of nonphosphorylated inactive MEK1 that adopts the DFG-out conformation.
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Roither, Bernhard, Chris Oostenbrink, Georg Pfeiler, Heinz Koelbl, and Wolfgang Schreiner. "Pembrolizumab Induces an Unexpected Conformational Change in the CC′-loop of PD-1." Cancers 13, no. 1 (December 22, 2020): 5. http://dx.doi.org/10.3390/cancers13010005.
Full textAbstract:
To improve cancer immunotherapy, a clearer understanding of key targets such as the immune checkpoint receptor PD-1 is essential. The PD-1 inhibitors nivolumab and pembrolizumab were recently approved by the FDA. The CC′-loop of PD-1 has been identified as a hotspot for drug targeting. Here, we investigate the influence of nivolumab and pembrolizumab on the molecular motion of the CC′-loop of PD-1. We performed molecular dynamics simulations on the complete extracellular domain of PD-1, in complex with PD-L1, and the blocking antibodies nivolumab and pembrolizumab. Conformations of the CC′-loop were analyzed unsupervised with the Daura et al. clustering algorithm and multidimensional scaling. Surprisingly, two conformations found were seen to correspond to the ‘open’ and ‘closed’ conformation of CC′-loop in apo-PD-1, already known from literature. Unsupervised clustering also surprisingly reproduced the natural ligand, PD-L1, exclusively stabilizing the ‘closed’ conformation, as also known from literature. Nivolumab, like PD-L1, was found to shift the equilibrium towards the ‘closed’ conformation, in accordance with the conformational selection model. Pembrolizumab, on the other hand, induced a third conformation of the CC′-loop which has not been described to date: Relative to the conformation ‘open’ the, CC′-loop turned 180° to form a new conformation which we called ‘overturned’. We show that the combination of clustering and multidimensional scaling is a fast, easy, and powerful method in analyzing structural changes in proteins. Possible refined antibodies or new small molecular compounds could utilize the flexibility of the CC′-loop to improve immunotherapy.
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Ohno, Shiho, Noriyoshi Manabe, Takumi Yamaguchi, Jun Uzawa, and Yoshiki Yamaguchi. "Ribitol in Solution Is an Equilibrium of Asymmetric Conformations." Molecules 26, no. 18 (September 8, 2021): 5471. http://dx.doi.org/10.3390/molecules26185471.
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Ribitol (C5H12O5), an acyclic sugar alcohol, is present on mammalian α-dystroglycan as a component of O-mannose glycan. In this study, we examine the conformation and dynamics of ribitol by database analysis, experiments, and computational methods. Database analysis reveals that the anti-conformation (180°) is populated at the C3–C4 dihedral angle, while the gauche conformation (±60°) is seen at the C2–C3 dihedral angle. Such conformational asymmetry was born out in a solid-state 13C-NMR spectrum of crystalline ribitol, where C1 and C5 signals are unequal. On the other hand, solution 13C-NMR has identical chemical shifts for C1 and C5. NMR 3J coupling constants and OH exchange rates suggest that ribitol is an equilibrium of conformations, under the influence of hydrogen bonds and/or steric hinderance. Molecular dynamics (MD) simulations allowed us to discuss such a chemically symmetric molecule, pinpointing the presence of asymmetric conformations evidenced by the presence of correlations between C2–C3 and C3–C4 dihedral angles. These findings provide a basis for understanding the dynamic structure of ribitol and the function of ribitol-binding enzymes.
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Košovan, Peter, Zuzana Limpouchová, and Karel Procházka. "Charge Distribution and Conformations of Weak Polyelectrolyte Chains in Poor Solvents." Collection of Czechoslovak Chemical Communications 73, no. 4 (2008): 439–58. http://dx.doi.org/10.1135/cccc20080439.
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In this work we study the effect of mobility of charges in annealed polyelectrolytes on their conformational behavior in poor solvents. A combination of molecular dynamics and Monte Carlo simulation techniques was used to take the dissociation into account. We investigated the relation between the conformation of the polyelectrolyte and the distribution of charges along the chain. The results suggest that in sufficiently poor solvents the local degree of charging differs significantly from the average. When a pearl-necklace conformation is formed, the degree of charging of the pearls is significantly lower than that of the strings. The redistribution of charges stabilizes the pearl-necklace conformation and enables the formation of asymmetric conformations with a single pearl at one chain end and a string at the other end.
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Toti, Kiran S., John R. Jimah, Veronica Salmaso, Jenny E. Hinshaw, and Kenneth A. Jacobson. "Synthesis and Effect of Conformationally Locked Carbocyclic Guanine Nucleotides on Dynamin." Biomolecules 12, no. 4 (April 16, 2022): 584. http://dx.doi.org/10.3390/biom12040584.
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Guanine nucleotides can flip between a North and South conformation in the ribose moiety. To test the enzymatic activity of GTPases bound to nucleotides in the two conformations, we generated methanocarba guanine nucleotides in the North or South envelope conformations, i.e., (N)-GTP and (S)-GTP, respectively. With dynamin as a model system, we examined the effects of (N)-GTP and (S)-GTP on dynamin-mediated membrane constriction, an activity essential for endocytosis. Dynamin membrane constriction and fission activity are dependent on GTP binding and hydrolysis, but the effect of the conformational state of the GTP nucleotide on dynamin activity is not known. After reconstituting dynamin-mediated lipid tubulation and membrane constriction in vitro, we observed via cryo-electron microscopy (cryo-EM) that (N)-GTP, but not (S)-GTP, enables the constriction of dynamin-decorated lipid tubules. These findings suggest that the activity of dynamin is dependent on the conformational state of the GTP nucleotide. However, a survey of nucleotide ribose conformations associated with dynamin structures in nature shows almost exclusively the (S)-conformation. The explanation for this mismatch of (N) vs. (S) required for GTP analogues in a dynamin-mediated process will be addressed in future studies.
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Sun, Shangwu, Rui Zhu, Mengyao Zhu, Qi Wang, Na Li, and Bei Yang. "Visualization of conformational transition of GRP94 in solution." Life Science Alliance 7, no. 2 (November 10, 2023): e202302051. http://dx.doi.org/10.26508/lsa.202302051.
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GRP94, an ER paralog of the heat-shock protein 90 family, binds and hydrolyses ATP to chaperone the folding and maturation of its selected clients. Compared with other hsp90 proteins, the in-solution conformational dynamics of GRP94 along the ATP hydrolysis cycle are less understood, hindering our understanding of its chaperoning mechanism. Leveraging small-angle X-ray scattering, negative-staining EM, and hydrogen–deuterium exchange coupled mass-spec, here we show that in its apo form, ∼60% of mouse GRP94 (mGRP94) populates an “extended” conformation, whereas the rest exist in either “close V” or “twist V” like “compact” conformations. Different from other hsp90 proteins, the presence of AMPPNP only impacts the relative abundance of the two compact conformations, rather than shifting the equilibrium between the “extended” and “compact” conformations of mGRP94. HDX-MS study of apo, AMPPNP-bound, and ADP-bound mGRP94 suggests a conformational transition from “twist V” to “close V” upon ATP binding and a back transition from “close V” to “twist V” upon ATP hydrolysis. These results illustrate the dissimilarities of GRP94 in conformation transition during ATP hydrolysis from other hsp90 paralogs.
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Grininger, Christoph, Mario Leypold, Philipp Aschauer, Tea Pavkov-Keller, Lina Riegler-Berket, Rolf Breinbauer, and Monika Oberer. "Structural Changes in the Cap of Rv0183/mtbMGL Modulate the Shape of the Binding Pocket." Biomolecules 11, no. 9 (September 1, 2021): 1299. http://dx.doi.org/10.3390/biom11091299.
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Tuberculosis continues to be a major threat to the human population. Global efforts to eradicate the disease are ongoing but are hampered by the increasing occurrence of multidrug-resistant strains of Mycobacterium tuberculosis. Therefore, the development of new treatment, and the exploration of new druggable targets and treatment strategies, are of high importance. Rv0183/mtbMGL, is a monoacylglycerol lipase of M. tuberculosis and it is involved in providing fatty acids and glycerol as building blocks and as an energy source. Since the lipase is expressed during the dormant and active phase of an infection, Rv0183/mtbMGL is an interesting target for inhibition. In this work, we determined the crystal structures of a surface-entropy reduced variant K74A Rv0183/mtbMGL in its free form and in complex with a substrate mimicking inhibitor. The two structures reveal conformational changes in the cap region that forms a major part of the substrate/inhibitor binding region. We present a completely closed conformation in the free form and semi-closed conformation in the ligand-bound form. These conformations differ from the previously published, completely open conformation of Rv0183/mtbMGL. Thus, this work demonstrates the high conformational plasticity of the cap from open to closed conformations and provides useful insights into changes in the substrate-binding pocket, the target of potential small-molecule inhibitors.
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Xu, Xiaojun, Tao Yu, and Shi-Jie Chen. "Understanding the kinetic mechanism of RNA single base pair formation." Proceedings of the National Academy of Sciences 113, no. 1 (December 22, 2015): 116–21. http://dx.doi.org/10.1073/pnas.1517511113.
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RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA folding is the closing and opening of a base pair. Understanding this elementary rate process is the basis for RNA folding kinetics studies. Previous studies mostly focused on the unfolding of base pairs. Here, based on a hybrid approach, we investigate the folding process at level of single base pairing/stacking. The study, which integrates molecular dynamics simulation, kinetic Monte Carlo simulation, and master equation methods, uncovers two alternative dominant pathways: Starting from the unfolded state, the nucleotide backbone first folds to the native conformation, followed by subsequent adjustment of the base conformation. During the base conformational rearrangement, the backbone either retains the native conformation or switches to nonnative conformations in order to lower the kinetic barrier for base rearrangement. The method enables quantification of kinetic partitioning among the different pathways. Moreover, the simulation reveals several intriguing ion binding/dissociation signatures for the conformational changes. Our approach may be useful for developing a base pair opening/closing rate model.
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Shang, Jinsai, Richard Brust, Patrick R. Griffin, Theodore M. Kamenecka, and Douglas J. Kojetin. "Quantitative structural assessment of graded receptor agonism." Proceedings of the National Academy of Sciences 116, no. 44 (October 14, 2019): 22179–88. http://dx.doi.org/10.1073/pnas.1909016116.
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Ligand–receptor interactions, which are ubiquitous in physiology, are described by theoretical models of receptor pharmacology. Structural evidence for graded efficacy receptor conformations predicted by receptor theory has been limited but is critical to fully validate theoretical models. We applied quantitative structure–function approaches to characterize the effects of structurally similar and structurally diverse agonists on the conformational ensemble of nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ). For all ligands, agonist functional efficacy is correlated to a shift in the conformational ensemble equilibrium from a ground state toward an active state, which is detected by NMR spectroscopy but not observed in crystal structures. For the structurally similar ligands, ligand potency and affinity are also correlated to efficacy and conformation, indicating ligand residence times among related analogs may influence receptor conformation and function. Our results derived from quantitative graded activity–conformation correlations provide experimental evidence and a platform with which to extend and test theoretical models of receptor pharmacology to more accurately describe and predict ligand-dependent receptor activity.
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McGinnis, Jennifer L., Qi Liu, Christopher A. Lavender, Aishwarya Devaraj, Sean P. McClory, Kurt Fredrick, and Kevin M. Weeks. "In-cell SHAPE reveals that free 30S ribosome subunits are in the inactive state." Proceedings of the National Academy of Sciences 112, no. 8 (February 9, 2015): 2425–30. http://dx.doi.org/10.1073/pnas.1411514112.
Full textAbstract:
It was shown decades ago that purified 30S ribosome subunits readily interconvert between “active” and “inactive” conformations in a switch that involves changes in the functionally important neck and decoding regions. However, the physiological significance of this conformational change had remained unknown. In exponentially growing Escherichia coli cells, RNA SHAPE probing revealed that 16S rRNA largely adopts the inactive conformation in stably assembled, mature 30S subunits and the active conformation in translating (70S) ribosomes. Inactive 30S subunits bind mRNA as efficiently as active subunits but initiate translation more slowly. Mutations that inhibited interconversion between states compromised translation in vivo. Binding by the small antibiotic paromomycin induced the inactive-to-active conversion, consistent with a low-energy barrier between the two states. Despite the small energetic barrier between states, but consistent with slow translation initiation and a functional role in vivo, interconversion involved large-scale changes in structure in the neck region that likely propagate across the 30S body via helix 44. These findings suggest the inactive state is a biologically relevant alternate conformation that regulates ribosome function as a conformational switch.
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MIKHAILOV, Dmitri, J. Robert LINHARDT, and H. Kevin MAYO. "NMR solution conformation of heparin-derived hexasaccharide." Biochemical Journal 328, no. 1 (November 15, 1997): 51–61. http://dx.doi.org/10.1042/bj3280051.
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The solution conformation of homogeneous, heparin-derived hexasaccharide (residues A, B, C, D, E, F) has been investigated by using 1H-NMR spectroscopy. Intra-ring conformations have been defined by J-coupling constants and inter-proton nuclear Overhauser effects (NOEs), and the orientation of one ring with respect to the other has been defined by inter-ring NOEs. NOE-based conformational modelling has been done by using the iterative relaxation matrix approach (IRMA), restrained energy minimization to refine structures and to distinguish between minor structural differences and equilibria between various intra-ring forms. All glucosamine residues B, D and F are in the 4C1 chair conformation. The uronate (A) residue is mostly represented by the 1H2 form, whereas internal iduronates (C and E) exist in equilibrium between the chair and skewed boat forms. Deviations in some NOEs indicate a minor contribution of the 2H1 form to the A ring. Glycosidic dihedral angles, which define the overall oligosaccharide conformation, were further refined by combining in vacuo energy map calculations and restrained energy minimization in explicit solvent water. Conformational stability was further assessed by subjecting NOE and IRMA-derived structures to 600 ps of unrestrained molecular dynamics in explicit solvent.
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WANG, DI-FEI, and YUN-DONG WU. "A THEORETICAL COMPARISON OF CONFORMATIONAL FEATURES OF CALIX[4]AROMATICS." Journal of Theoretical and Computational Chemistry 03, no. 01 (March 2004): 51–68. http://dx.doi.org/10.1142/s0219633604000908.
Full textAbstract:
Although there are tremendous studies about the conformational feature of calix[4]arenes and its analogies, no theoretical study has been done systematically about why some structural modifications could completely lead to a change of conformational preference. For example, calix[4]arene 1 adopts a cone conformation while its analogue calix[4]pyrrole 7 only adopts a 1,3-alternate conformation. So if this is only because of the effect of OH—OH hydrogen bonds, then why does O-methyl substituted calix[4]arene 2 still has cone conformation? In this paper, the conformational features of a series of seven calix[4]aromatics, calix[4]arene and calix[4]pyrrole related structures, have been investigated at BLYP/6–31G* level both in the gas phase and in CH 2 Cl 2 solution. The calculations demonstrated that three main factors influence the conformational preference of these calix[4]aromatics, i.e. the intramolecular hydrogen bond, the adjacent ring-ring electrostatic interaction and the intrinsic flexibility of the [14] metacyclophane framework. Calix[4]benzene 3 and calix[4]pyridine 4 have little conformational preferences due to their flexible [14] metacyclophane framework, the lack of hydrogen-bonding interactions and weak ring-ring electrostatic interactions. In contrast, calix[4]aromatics 1 and 5–7 have either intramolecular hydrogen bonds (1) or ring-ring electrostatic interactions (5–7). Consequently, calix[4]arene 1 has the cone preference and calix[4]pyrrole, calix[4]furan, and calixthiophene (5–7) have the 1,3-alternate preference. Methoxy calix[4]arene prefers a cone or partial cone conformation, because the 1,3-alternate and 1,2-alternate conformations are destabilized by electrostatic repulsions involving the methoxy group and the adjacent phenyl ring.
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Mizutani, Tadashi, and Shigeyuki Yagi. "Linear tetrapyrroles as functional pigments in chemistry and biology." Journal of Porphyrins and Phthalocyanines 08, no. 03 (March 2004): 226–37. http://dx.doi.org/10.1142/s1088424604000210.
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1,19,21,24-tetrahydro-1,19-bilindione is the framework of pigments frequently found in nature, which includes biliverdin IX α, phytochromobilin and phycocyanobilin. 1,19-bilindiones have unique features such as (1) photochemical and thermal cis-trans isomerization, (2) excited energy transfer, (3) chiroptical properties due to the cyclic helical conformation, (4) redox activity, (5) coordination to various metals, and (6) reconstitution to proteins. 1,19-bilindione can adopt a number of conformations since it has exocyclic three double bonds and three single bonds that are rotatable thermally and photochemically. In solution, biliverdin and phycocyanobilin adopt a cyclic helical ZZZ, syn, syn, syn conformation, but other conformations are stabilized depending on the experimental conditions and substituents on the bilin framework. The conformational changes in 1,19-bilindiones are related to the biological functions of a photoreceptor protein, phytochrome. Structural and conformational studies of bilindiones are summarized both in solution and in protein. The conformational changes of bilins can be used for other functions such as a chirality sensor. The bilindiones and the zinc complexes of bilindiones can be employed as a chirality sensor due to the helically chiral structure and the dynamics of racemization of enantiomers. In this paper, we discuss the conformational equilibria and dynamics of bilindiones and its implications in photobiology and materials science.
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LEE, HO-JIN, HYUN-MEE PARK, and KANG-BONG LEE. "CONFORMATIONAL PREFERENCES OF N-ACETYL–GLYCINE–GLYCINE–N′-METHYLAMIDE: A THEORETICAL STUDY." Journal of Theoretical and Computational Chemistry 08, no. 05 (October 2009): 799–811. http://dx.doi.org/10.1142/s0219633609005118.
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The conformational preferences of peptide models have been investigated to understand the protein folding mechanism and to develop the force field. Here, we report the minimum energy conformations for a model peptide, N-acetyl–glycine–glycine–N′-methylamide ( Ac–1Gly–2Gly–NHMe(I) ) at the HF/3-21G, HF/6-31G*, and the B3LYP/6-31G* level of theory. At the B3LYP/6-31G* level, the 31 minima were identified and the 10 β-turn structures among the minima were observed in gas-phase. The conformational preferences of Gly residue in the model peptide, I depend on its relative position and conformation of neighboring Gly residue. The Gly residue in this model dipeptide has an asymmetric energy profile as one of Gly residue adopts a specific conformation. This study sheds some lights on understanding the unique conformational preferences of Gly residue in protein including two consecutive Gly residues.
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Nguyen, Binh, Yerdos Ordabayev, Joshua E. Sokoloski, Elizabeth Weiland, and Timothy M. Lohman. "Large domain movements upon UvrD dimerization and helicase activation." Proceedings of the National Academy of Sciences 114, no. 46 (October 30, 2017): 12178–83. http://dx.doi.org/10.1073/pnas.1712882114.
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Escherichia coli UvrD DNA helicase functions in several DNA repair processes. As a monomer, UvrD can translocate rapidly and processively along ssDNA; however, the monomer is a poor helicase. To unwind duplex DNA in vitro, UvrD needs to be activated either by self-assembly to form a dimer or by interaction with an accessory protein. However, the mechanism of activation is not understood. UvrD can exist in multiple conformations associated with the rotational conformational state of its 2B subdomain, and its helicase activity has been correlated with a closed 2B conformation. Using single-molecule total internal reflection fluorescence microscopy, we examined the rotational conformational states of the 2B subdomain of fluorescently labeled UvrD and their rates of interconversion. We find that the 2B subdomain of the UvrD monomer can rotate between an open and closed conformation as well as two highly populated intermediate states. The binding of a DNA substrate shifts the 2B conformation of a labeled UvrD monomer to a more open state that shows no helicase activity. The binding of a second unlabeled UvrD shifts the 2B conformation of the labeled UvrD to a more closed state resulting in activation of helicase activity. Binding of a monomer of the structurally similar Escherichia coli Rep helicase does not elicit this effect. This indicates that the helicase activity of a UvrD dimer is promoted via direct interactions between UvrD subunits that affect the rotational conformational state of its 2B subdomain.
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Mlejnek, M., and S. Kuchinsky. "Volumetric Changes Between Different Conformations of Two SiOH Groups in SiO2 Glass." Advanced Materials Research 39-40 (April 2008): 89–92. http://dx.doi.org/10.4028/www.scientific.net/amr.39-40.89.
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We present numerical studies of possible modifications of SiOH groups in “wet” SiO2 glass with 193 nm laser irradiation. We focus on structural changes associated with two conformations: (i) two nearby hydrogen bonded SiOH groups, and (ii) oxygen triclusters, i.e. bridging oxygen forming a third covalent bond with a hydrogen atom. The energies of these two systems and the activation barrier of thermal relaxation between them identify the latter conformation as a candidate for a product formed under 193 nm laser exposure, when we consider the former conformation as an initial state. We investigate the effects of local volume changes associated with the changes in conformation and find it has non-negligible effect on the index of refraction. These conformational changes thus appear able to contribute to the permanent changes in index of refraction and absorption of the glass after UV irradiation.
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Puchkov, S. V., and Yu V. Nepomnyashchikh. "“Chair”–“Boat” Conformational Transition of Cyclohexanone during the Oxidation of Cyclohexane." Журнал физической химии 97, no. 8 (August 1, 2023): 1155–60. http://dx.doi.org/10.31857/s0044453723080198.
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The B3LYP/6-311g++(d,p), G3, and CBS-QB3 methods (DFT) have been used to calculate the free energy and equilibrium constants of the “chair”–“boat” conformational transition of cyclohexanone in the temperature range 298.15–428.15 K. The equilibrium composition of the chair and boat conformers of cyclohexanone has been calculated. It has been shown that with an increase in the proportion of the boat conformation, the selectivity of the process of cyclohexane oxidation to cyclohexanone decreases. The transition states of addition reactions of cyclohexyl hydroperoxide at the carbonyl group of cyclohexanone for chair and boat conformations have been found by the QST2 method. The energy profiles of these reactions have been calculated. It has been established that the addition of hydroperoxide to the carbonyl group of the boat conformation of the ketone is accompanied by a transition to the chair conformation.
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Biks, Mequanint, Asaminew Tassew, and Fisseha Moges. "Conformation traits of crossbred dairy cows in the South Gondar Zone, Amhara Region, Ethiopia." Journal of Agriculture and Environmental Sciences 8, no. 1 (May 24, 2023): 40–56. http://dx.doi.org/10.4314/jaes.v8i1.3.
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Conformational variations between and within crossbred dairy cattle populations have significant economic and socio- cultural implications for producers. Therefore, this study was conducted to characterize conformation traits of crossbred dairy cows in the South Gondar zone, Amhara Region, Ethiopia. A total of 204 lactating crossbred dairy cows were selected for measurement purposes. The independent variables considered were location, stage of lactation, genotype level, and parity while linear body conformations (Stature (STA), Chest Width (CW), Body Depth (BW), Body Length (BL), Rump Length (RL), Heart Girth (HG), Neck Length (NL), and Neck Circumferences (NC)), linear udder conformation traits (Rump Width (RW), Udder Depth (UD), Udder Width (UW), Udder Circumferences (UC), Rear Udder Height (RUH), Teat Length (TL)), non-linear body conformations (Angularity (ANG), Rear Legs Rear View (RLRV), Rear Legs Side View (RLSV), Body Condition Score (BSC)) and non-linear udder conformation traits (Fore Udder Attachment (FUA), Rear Teat Placement (RTP), Front Teat Placement (FTP)), Teat Thickness (TT)) were the dependent variables. Data was analyzed using the General Linear Models procedure (GLM) of the Statistical Analysis System (SAS, 2004). The overall STA, CW, BD, BL, RL, HG, NL, NC, RW, RUH, UD, UW, UC and TL were 127.81±5.4 cm, 23.1±3.1cm, 99.2±4cm, 120.45±4.6cm, 32.2±3.9cm, 168.32±5.1cm, 56.7±3.2 cm, 92.88±3.6cm, 17.39±2.65cm, 14.27±1.8cm, 18.02±2.7cm, 16.85±2.5cm, 59.16±4.3cm and 4.65±0.88cm, respectively. Parity had a significant effect on linear conformational trait characteristics of crossbred dairy cows at (p<0.01) and (p<0.001) significant levels except for CW, BD, RL, and RUH. Similarly, genotype level had a significant effect on linear conformational trait characteristics of crossbred dairy cows at (p<0.05), (p<0.01), and (p<0.001) significant levels except for CW, RL, NL, and RUH but the stage of lactation had no significant effect (p>0.05) on linear body conformation except STA and had a significant effect (p<0.01) on linear udder traits except UD and TL of crossbred dairy cows. Therefore, selecting dairy type traits could be an ideal option to improve cow productivity and enterprise profitability. However, future studies with large populations and various genotype levels are required to associate conformation with reproductive and productive traits.
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Żyłka, Romuald, Justyna Kupiec, and Stanislaw Przestalski. "Peptides conformational changes of the erythrocyte membrane induced by organometallic tin compounds." Current Topics in Biophysics 34, no. 1 (January 1, 2011): 31–35. http://dx.doi.org/10.2478/v10214-011-0005-2.
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Peptides conformational changes of the erythrocyte membrane induced by organometallic tin compoundsThe paper presents the results of a study on the effect of selected organic chlorides of tin on peptide conformations of erythrocyte ghosts from pig blood. The following compounds were used: dibutyltin dichloride (DBT), tributyltin chloride (TBT), diphenyltin dichloride (DPhT) and triphenyltin chloride (TPhT). Peptide conformation changes were determined on the basis of measurements done with the ATR FTIR technique. This method made it possible to measure the percent share of a peptide with specified conformation in the whole amount of the peptides in the membranes studied. The investigation showed that all the tin organic compounds studied cause a several-percent decrease in the quantities of both the peptides with the α-helix and turn conformation, and about a 20% increase in ghost peptides with β-sheet conformation. It seems that the changes observed can cause disturbances in the function of proteins and, consequently, the activity of the membrane; and this may be one of the aspects of the toxic properties of organotins.
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Brenlla, Alfonso, Radoslaw P. Markiewicz, David Rueda, and Louis J. Romano. "Nucleotide selection by the Y-family DNA polymerase Dpo4 involves template translocation and misalignment." Nucleic Acids Research 42, no. 4 (November 21, 2013): 2555–63. http://dx.doi.org/10.1093/nar/gkt1149.
Full textAbstract:
Abstract Y-family DNA polymerases play a crucial role in translesion DNA synthesis. Here, we have characterized the binding kinetics and conformational dynamics of the Y-family polymerase Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) using single-molecule fluorescence. We find that in the absence of dNTPs, the binary complex shuttles between two different conformations within ∼1 s. These data are consistent with prior crystal structures in which the nucleotide binding site is either occupied by the terminal base pair (preinsertion conformation) or empty following Dpo4 translocation by 1 base pair (insertion conformation). Most interestingly, on dNTP binding, only the insertion conformation is observed and the correct dNTP stabilizes this complex compared with the binary complex, whereas incorrect dNTPs destabilize it. However, if the n+1 template base is complementary to the incoming dNTP, a structure consistent with a misaligned template conformation is observed, in which the template base at the n position loops out. This structure provides evidence for a Dpo4 mutagenesis pathway involving a transient misalignment mechanism.
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Ludwiczak, Jan, Ewa Szczęsna, Antônio Marinho da Silva Neto, Piotr Cieplak, Andrzej A. Kasprzak, and Adam Jarmuła. "Interactions between motor domains in kinesin-14 Ncd — a molecular dynamics study." Biochemical Journal 476, no. 17 (September 10, 2019): 2449–62. http://dx.doi.org/10.1042/bcj20190484.
Full textAbstract:
Abstract Minus-end directed, non-processive kinesin-14 Ncd is a dimeric protein with C-terminally located motor domains (heads). Generation of the power-stroke by Ncd consists of a lever-like rotation of a long superhelical ‘stalk’ segment while one of the kinesin's heads is bound to the microtubule. The last ∼30 amino acids of Ncd head play a crucial but still poorly understood role in this process. Here, we used accelerated molecular dynamics simulations to explore the conformational dynamics of several systems built upon two crystal structures of Ncd, the asymmetrical T436S mutant in pre-stroke/post-stroke conformations of two partner subunits and the symmetrical wild-type protein in pre-stroke conformation of both subunits. The results revealed a new conformational state forming following the inward motion of the subunits and stabilized with several hydrogen bonds to residues located on the border or within the C-terminal linker, i.e. a modeled extension of the C-terminus by residues 675–683. Forming of this new, compact Ncd conformation critically depends on the length of the C-terminus extending to at least residue 681. Moreover, the associative motion leading to the compact conformation is accompanied by a partial lateral rotation of the stalk. We propose that the stable compact conformation of Ncd may represent an initial state of the working stroke.
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Qu, Kun, Qiuluan Chen, Katarzyna A. Ciazynska, Banghui Liu, Xixi Zhang, Jingjing Wang, Yujie He, et al. "Engineered disulfide reveals structural dynamics of locked SARS-CoV-2 spike." PLOS Pathogens 18, no. 7 (July 29, 2022): e1010583. http://dx.doi.org/10.1371/journal.ppat.1010583.
Full textAbstract:
The spike (S) protein of SARS-CoV-2 has been observed in three distinct pre-fusion conformations: locked, closed and open. Of these, the function of the locked conformation remains poorly understood. Here we engineered a SARS-CoV-2 S protein construct “S-R/x3” to arrest SARS-CoV-2 spikes in the locked conformation by a disulfide bond. Using this construct we determined high-resolution structures confirming that the x3 disulfide bond has the ability to stabilize the otherwise transient locked conformations. Structural analyses reveal that wild-type SARS-CoV-2 spike can adopt two distinct locked-1 and locked-2 conformations. For the D614G spike, based on which all variants of concern were evolved, only the locked-2 conformation was observed. Analysis of the structures suggests that rigidified domain D in the locked conformations interacts with the hinge to domain C and thereby restrains RBD movement. Structural change in domain D correlates with spike conformational change. We propose that the locked-1 and locked-2 conformations of S are present in the acidic high-lipid cellular compartments during virus assembly and egress. In this model, release of the virion into the neutral pH extracellular space would favour transition to the closed or open conformations. The dynamics of this transition can be altered by mutations that modulate domain D structure, as is the case for the D614G mutation, leading to changes in viral fitness. The S-R/x3 construct provides a tool for the further structural and functional characterization of the locked conformations of S, as well as how sequence changes might alter S assembly and regulation of receptor binding domain dynamics.
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Bharathikumar, V. M., Kris Barreto, Marciano D. Reis, John F. Decoteau, and C. Ronald Geyer. "Genetic Screen to Isolate “Lariat” Peptides for Characterizing ABL Kinase Activity and Conformation." Blood 116, no. 21 (November 19, 2010): 438. http://dx.doi.org/10.1182/blood.v116.21.438.438.
Full textAbstract:
Abstract Abstract 438 Type II Abl kinase inhibitors such as imatinib achieve high selectivity by specifically targeting the inactive Abl/c-Kit conformation. However, these inhibitors are prone to inactivation by resistance mutations that cause conformational changes. A better understanding of mutant Abl conformations would provide information to design inhibitors that recognize multiple states of Abl with lower rates of resistance. To more easily examine Abl kinase conformations, conformer specific reagents are needed that are (i) easily generated against a given Abl conformation, (ii) compatible with genetic selections, in vivo and in vitro assays, and structural studies, and (iii) amenable to chemical synthesis. Recently, we developed a novel genetic screen for isolating “lariat” peptide inhibitors of protein function. Lariats are lactone-cyclized peptides that possess the above-mentioned characteristics and can be used to evaluate the function and therapeutic potential of proteins. Previously, we isolated specific lariat inhibitors against the inactive conformation of the bacterial repressor LexA. To obtain conformer specific lariats against Abl, we screened a combinatorial seven amino acid lariat library for interactions with the Abl SH1 domain using the yeast two-hybrid (Y2H) assay. We obtained two lariat peptides named A1 (SGWQRLPFEY) and A2 (SGWHRLSEEY) that interacted with the Abl SH1 domain. In vitro studies with purified Abl kinase demonstrated that the A1 lariat competitively inhibited ATP binding with an inhibitory constant of 5.95 μM. By performing site-saturation mutagenesis, we defined acceptable and tolerable substitutions at each position of the A1 lariat. To obtain tighter binding variants of the A1 lariat, we rationally designed mutations and constructed a second-generation lariat (GWQTLDWNY) with | 10 times higher affinity for Abl. We compared the affinity of the lariats for imatinib resistant Abl kinase mutants using the lariat Y2H binding assay. Mutations that (i) promote conformational dynamics of the kinase T315I), (ii) destabilize the Abl/c-Kit like inactive state (H396R), (iii) disrupt the flexibility or hydrophobicity of the lariat-binding pocket (E355G), and (iv) distort the ATP phosphate binding loop (Y253F), have a marked decrease in lariat affinity. Together, these results show that the lariat preferentially bound to the Abl/c-Kit like inactive conformation and act similarly to type II kinase inhibitors. A specificity screen against a panel of related and distant kinases also demonstrated the conformer specific nature of the lariats. We used lariats that recognized the Abl/c-Kit like inactive state to probe various conformations of Abl His396 mutants. His396 is located in the activation loop and does not alter the Abl/c-Kit like inactive form. His396Pro and His396Arg substitutions are clinically relevant imatinib resistant mutations that alter the conformation of Abl. Previous structural studies showed that the His396Pro mutation causes Abl to adopt the active conformation. It is hypothesized that the His396Arg mutation favors the inactive Src/Cdk like state. Using inactive conformation specific Abl lariats as probes, we showed that these lariats interact weakly with the His396Arg relative to His396, suggesting that this mutation destabilized the Abl/c-Kit like inactive state. We also showed that the lariats interacted stronger with a previously unreported His396Ile mutation than His396, indicating that His396Ile shifts Abl to a highly inactive conformation. Preliminary studies suggest that this residue plays a key role in determining the flexibility of the activation loop and hence the conformational state of Abl. These results provide information on the structure and sequence requirements for maintaining an auto-inhibited activation loop conformation. In summary, we isolated lariat peptide inhibitors against the Abl SH1 domain, characterized their mechanism of action, and improved their affinity for wild type and mutant Abl SH1domains. Additionally, we demonstrated that lariat peptides can be used as affinity reagents to probe conformational states of Abl. Disclosures: No relevant conflicts of interest to declare.
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Lane, A. N., T. C. Jenkins, D. J. Brown, and T. Brown. "N.m.r. determination of the solution conformation and dynamics of the A.G mismatch in the d(CGCAAATTGGCG)2 dodecamer." Biochemical Journal 279, no. 1 (October 1, 1991): 269–81. http://dx.doi.org/10.1042/bj2790269.
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A.G base-paired mismatches that occur during replication are among the most difficult to detect by repair enzymes. Such purine.purine mispairs can exist in two conformations, one of which is stabilized by protons [Gao & Patel (1988) J. Am. Chem. Soc. 110, 5178-5182]. We have undertaken a 1H-n.m.r. and 31P-n.m.r. study of the mismatched dodecamer d(CGCAAATTGGCG)2 as a function of both temperature and pH to determine the conformational features of the A.G mismatch. At pH greater than 7 the mispaired bases are each in the anti conformation and are stacked in the B-like helix. As the pH is decreased, a second conformation becomes populated (apparent pKa approx. 5.9) with concomitant changes in the chemical shifts of protons of the mispaired bases and their nearest neighbours. Data from two-dimensional nuclear-Overhauser-enhancement spectroscopy show unequivocally that, at low pH, the dominant conformation is one in which the mismatched G residues are in the syn conformation and are hydrogen-bonded to the A residues that remain in the anti conformation. Residues not adjacent to the A.G sites are almost unaffected by the transition or the mispairing, suggesting considerable local flexibility of the unconstrained duplexes. Despite the bulging of the mispaired bases, the conformation of the A(anti).G(anti) duplex is very similar to the native dodecamer, whereas the AH+(anti).G(syn) duplex shows a greater variation in the backbone conformation at the mismatched site. According to the chemical shifts, the duplex retains twofold symmetry in solution. The equilibrium between the syn and anti conformations of G9/G21 is strongly dependent on pH, but only weakly dependent on temperature (delta H approx. 16 kJ.mol-1). The first-order rate constant for the transition is approx. 9 s-1 at 283 K and approx. 60 s-1 at 298 K, with an activation enthalpy of approx. 100 kJ.mol-1. The stabilization of the A(anti).G(syn) conformation by protons is consistent with models invoking N1 protonation of adenine. Using the derived glycosidic torsion angles we have used restrained molecular dynamics to build models of the neutral and protonated d(CGCAAATTGGCG)2 oligomers. The results confirm that the A(anti).G(anti) and AH+(anti).G(syn) conformations are favoured at high pH and low pH respectively, in accord with n.m.r. and single-crystal X-ray data.
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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.
Full textAbstract:
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.