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Journal articles on the topic 'Molecular dynamics conformational analysis'

Author: Grafiati

Published: 4 June 2025

Last updated: 1 August 2025

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1

Krukenberg, Kristin A., Timothy O. Street, Laura A. Lavery, and David A. Agard. "Conformational dynamics of the molecular chaperone Hsp90." Quarterly Reviews of Biophysics 44, no. 2 (2011): 229–55. http://dx.doi.org/10.1017/s0033583510000314.

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AbstractThe ubiquitous molecular chaperone Hsp90 makes up 1–2% of cytosolic proteins and is required for viability in eukaryotes. Hsp90 affects the folding and activation of a wide variety of substrate proteins including many involved in signaling and regulatory processes. Some of these substrates are implicated in cancer and other diseases, making Hsp90 an attractive drug target. Structural analyses have shown that Hsp90 is a highly dynamic and flexible molecule that can adopt a wide variety of structurally distinct states. One driving force for these rearrangements is the intrinsic ATPase ac

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2

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

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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 showe

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3

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

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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 unrel

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4

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

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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 a

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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 (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 hylambat

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Tafi, A., Fabrizio Manetti, Federico Corelli, Stefano Alcaro, and Maurizio Botta. "Structural flexibility of hyaluronan oligomers as probed by molecular modelling." Pure and Applied Chemistry 75, no. 2-3 (2003): 359–66. http://dx.doi.org/10.1351/pac200375020359.

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In the last few years, molecular modeling studies have been published that are devoted to a better understanding of the structural flexibility of hyaluronan (HA). Further conformational investigations, however, are needed on this polysaccharide, such as the application of statistical methods to perform enhanced one-step conformational analyses of its subunits. Moreover, the adjustment of assisted model building and energy refinement (AMBER) force field could provide the appropriate computational tool to study the interactions of HA and its derivatives with proteins. The present paper reports a

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Miller, Chad, Steven Schildcrout, Howard Mettee, and Ganesaratnam Balendiran. "Molecular dynamics of fibric acids." European Journal of Chemistry 13, no. 2 (2022): 186–95. http://dx.doi.org/10.5155/eurjchem.13.2.186-195.2275.

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1H- and 13C-NMR chemical shifts were measured for four fibric acids (bezafibrate, clofibric acid, fenofibric acid, and gemfibrozil), which are lipid-lowering drugs. Correlation is found with DFT-computed chemical shifts from the conformational analysis. Equilibrium populations of optimized conformers at 298 K are very different when based on computed Gibbs energies rather than on potential energies. This is due to the significant entropic advantages of extended rather than bent conformational shapes. Abundant conformers with intramolecular hydrogen bonding via five-member rings are computed fo

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Andrałojć, Witold, Enrico Ravera, Loïc Salmon, Giacomo Parigi, Hashim M. Al-Hashimi, and Claudio Luchinat. "Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations." Physical Chemistry Chemical Physics 18, no. 8 (2016): 5743–52. http://dx.doi.org/10.1039/c5cp03993b.

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9

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

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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

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10

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 t

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11

Ohno, Shiho, Noriyoshi Manabe, Takumi Yamaguchi, Jun Uzawa, and Yoshiki Yamaguchi. "Ribitol in Solution Is an Equilibrium of Asymmetric Conformations." Molecules 26, no. 18 (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 h

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12

CHUMAN, Hiroshi. "Conformational analysis and molecular dynamics of peptides." Journal of Synthetic Organic Chemistry, Japan 45, no. 11 (1987): 1098–106. http://dx.doi.org/10.5059/yukigoseikyokaishi.45.1098.

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13

Ping, Jie, Pei Hao, Yi-Xue Li, and Jing-Fang Wang. "Molecular Dynamics Studies on the Conformational Transitions of Adenylate Kinase: A Computational Evidence for the Conformational Selection Mechanism." BioMed Research International 2013 (2013): 1–7. http://dx.doi.org/10.1155/2013/628536.

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Escherichia coliadenylate kinase (ADK) is a monomeric phosphotransferase enzyme that catalyzes reversible transfer of phosphoryl group from ATP to AMP with a large-scale domain motion. The detailed mechanism for this conformational transition remains unknown. In the current study, we performed long time-scale molecular dynamics simulations on both open and closed states of ADK. Based on the structural analyses of the simulation trajectories, we detected over 20 times conformational transitions between the open and closed states of ADK and identified two novel conformations as intermediate stat

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14

Li, Haiyan, Zanxia Cao, Guodong Hu, Liling Zhao, Chunling Wang, and Jihua Wang. "Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations." Technology and Health Care 29 (March 25, 2021): 103–14. http://dx.doi.org/10.3233/thc-218011.

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BACKGROUND: The ribose-binding protein (RBP) from Escherichia coli is one of the representative structures of periplasmic binding proteins. Binding of ribose at the cleft between two domains causes a conformational change corresponding to a closure of two domains around the ligand. The RBP has been crystallized in the open and closed conformations. OBJECTIVE: With the complex trajectory as a control, our goal was to study the conformation changes induced by the detachment of the ligand, and the results have been revealed from two computational tools, MD simulations and elastic network models.

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15

Wu, Shanshan, Tam T. T. N. Nguyen, Olga V. Moroz, et al. "Conformational heterogeneity of Savinase from NMR, HDX-MS and X-ray diffraction analysis." PeerJ 8 (June 26, 2020): e9408. http://dx.doi.org/10.7717/peerj.9408.

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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

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

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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-te

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AALTEN, Daan M. F. van, Bert L. de GROOT, Herman J. C. BERENDSEN, and John B. C. FINDLAY. "Conformational analysis of retinoids and restriction of their dynamics by retinoid-binding proteins." Biochemical Journal 319, no. 2 (1996): 543–50. http://dx.doi.org/10.1042/bj3190543.

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An exhaustive sampling of the configurational space of all-trans retinol using a 0.1 µs molecular-dynamics simulation is presented. The essential dynamics technique is used to describe the conformational changes in retinol using only three degrees of freedom. The different conformational states of retinol are analysed, and differences in free energy are calculated. The essential dynamics description allows a detailed comparison of free retinol and retinoids bound to retinoid-binding proteins and opens new possibilities in the small-molecule docking field. The dynamics of retinoids when complex

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18

Samsonov, Sergey A., Stephan Theisgen, Thomas Riemer, Daniel Huster, and M. Teresa Pisabarro. "Glycosaminoglycan Monosaccharide Blocks Analysis by Quantum Mechanics, Molecular Dynamics, and Nuclear Magnetic Resonance." BioMed Research International 2014 (2014): 1–11. http://dx.doi.org/10.1155/2014/808071.

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Glycosaminoglycans (GAGs) play an important role in many biological processes in the extracellular matrix. In a theoretical approach, structures of monosaccharide building blocks of natural GAGs and their sulfated derivatives were optimized by a B3LYP6311ppdd//B3LYP/6-31+G(d) method. The dependence of the observed conformational properties on the applied methodology is described. NMR chemical shifts and proton-proton spin-spin coupling constants were calculated using the GIAO approach and analyzed in terms of the method's accuracy and sensitivity towards the influence of sulfation, O1-methylat

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19

Balogh, Gábor, and Zsuzsanna Bereczky. "The Interaction of Factor Xa and IXa with Non-Activated Antithrombin in Michaelis Complex: Insights from Enhanced-Sampling Molecular Dynamics Simulations." Biomolecules 13, no. 5 (2023): 795. http://dx.doi.org/10.3390/biom13050795.

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The interaction between coagulation factors Xa and IXa and the activated state of their inhibitor, antithrombin (AT),have been investigated using X-ray diffraction studies. However, only mutagenesis data are available for non-activated AT. Our aim was to propose a model based on docking and advanced-sampling molecular dynamics simulations that can reveal the conformational behavior of the systems when AT is not binding a pentasaccharide. We built the initial structure for non-activated AT-FXa and AT-FIXa complexes using HADDOCK 2.4. The conformational behavior was studied using Gaussian accele

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20

IKEDA, Kazuyoshi, and Junichi HIGO. "Protein Conformational Analysis by Multicanonical Molecular Dynamics Simulation." Seibutsu Butsuri 43, no. 2 (2003): 64–69. http://dx.doi.org/10.2142/biophys.43.64.

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21

Ha, S. N., L. J. Madsen, and J. W. Brady. "Conformational analysis and molecular dynamics simulations of maltose." Biopolymers 27, no. 12 (1988): 1927–52. http://dx.doi.org/10.1002/bip.360271207.

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22

Queyroy, Séverine, Florian Müller-Plathe, and David Brown. "Molecular Dynamics Simulations of Cellulose Oligomers: Conformational Analysis." Macromolecular Theory and Simulations 13, no. 5 (2004): 427–40. http://dx.doi.org/10.1002/mats.200300054.

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23

Weber, Piotr, Piotr Bełdowski, Krzysztof Domino, Damian Ledziński, and Adam Gadomski. "Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations." Entropy 22, no. 4 (2020): 405. http://dx.doi.org/10.3390/e22040405.

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This work presents the analysis of the conformation of albumin in the temperature range of 300 K – 312 K , i.e., in the physiological range. Using molecular dynamics simulations, we calculate values of the backbone and dihedral angles for this molecule. We analyze the global dynamic properties of albumin treated as a chain. In this range of temperature, we study parameters of the molecule and the conformational entropy derived from two angles that reflect global dynamics in the conformational space. A thorough rationalization, based on the scaling theory, for the subdiffusion Flory–De Gennes t

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Musavizadeh, Zahra, Alessandro Grottesi, Giulia Guarguaglini, and Alessandro Paiardini. "Phosphorylation, Mg-ADP, and Inhibitors Differentially Shape the Conformational Dynamics of the A-Loop of Aurora-A." Biomolecules 11, no. 4 (2021): 567. http://dx.doi.org/10.3390/biom11040567.

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The conformational state of the activation loop (A-loop) is pivotal for the activity of most protein kinases. Hence, the characterization of the conformational dynamics of the A-loop is important to increase our understanding of the molecular processes related to diseases and to support the discovery of small molecule kinase inhibitors. Here, we carry out a combination of molecular dynamics (MD) and essential dynamics (ED) analyses to fully map the effects of phosphorylation, ADP, and conformation disrupting (CD) inhibitors (i.e., CD532 and MLN8054) on the dynamics of the A-loop of Aurora-A. M

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Ramirez-Mondragon, Carlos A., Megin E. Nguyen, Jozafina Milicaj, et al. "Conserved Conformational Hierarchy across Functionally Divergent Glycosyltransferases of the GT-B Structural Superfamily as Determined from Microsecond Molecular Dynamics." International Journal of Molecular Sciences 22, no. 9 (2021): 4619. http://dx.doi.org/10.3390/ijms22094619.

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It has long been understood that some proteins undergo conformational transitions en route to the Michaelis Complex to allow chemistry. Examination of crystal structures of glycosyltransferase enzymes in the GT-B structural class reveals that the presence of ligand in the active site triggers an open-to-closed conformation transition, necessary for their catalytic functions. Herein, we describe microsecond molecular dynamics simulations of two distantly related glycosyltransferases that are part of the GT-B structural superfamily, HepI and GtfA. Simulations were performed using the open and cl

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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 (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 ro

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Barth, Anders, Oleg Opanasyuk, Thomas-Otavio Peulen, et al. "Unraveling multi-state molecular dynamics in single-molecule FRET experiments. I. Theory of FRET-lines." Journal of Chemical Physics 156, no. 14 (2022): 141501. http://dx.doi.org/10.1063/5.0089134.

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Conformational dynamics of biomolecules are of fundamental importance for their function. Single-molecule studies of Förster Resonance Energy Transfer (smFRET) between a tethered donor and acceptor dye pair are a powerful tool to investigate the structure and dynamics of labeled molecules. However, capturing and quantifying conformational dynamics in intensity-based smFRET experiments remains challenging when the dynamics occur on the sub-millisecond timescale. The method of multiparameter fluorescence detection addresses this challenge by simultaneously registering fluorescence intensities an

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

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

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

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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 obs

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Khan, Muhammad Naseem, Umar Farooq, Aneela Khushal, Tanveer A. Wani, Seema Zargar, and Sara Khan. "Unraveling potential EGFR kinase inhibitors: Computational screening, molecular dynamics insights, and MMPBSA analysis for targeted cancer therapy development." PLOS One 20, no. 5 (2025): e0321500. https://doi.org/10.1371/journal.pone.0321500.

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EGFR is critical for tumor angiogenesis and cancer progression, but existing treatments like erlotinib face limitations such as acquired resistance and side effects. To address these issues, this study employs structure-based drug design techniques including virtual screening, molecular docking, and molecular dynamics simulations to identify new small molecule inhibitors targeting the EGFR kinase domain. From an initial selection of 633,000 compounds from diverse databases, top candidates were identified based on their binding affinity and stability. The virtual screening and docking analyses

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Sović, Karlo, Tea Ostojić, Ines Primožič, et al. "Conformational Analysis of Cinhonine and Cinhonidine by Tensor Decomposition of Molecular Dynamics Trajectories." Croatica chemica acta 92, no. 2 (2019): 259–67. http://dx.doi.org/10.5562/cca3557.

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Full conformational space of cinchonine and cinchonidine has been investigated by means of statistical analysis of quantum chemical molecular dynamics simulations. Recently developed procedure comprising principal component analysis of molecular dynamics trajectories was applied on cinchonine and cinchonidine as well as on their protonated and methylated quaternary derivatives. The method for full conformational analysis includes Cartesian coordinates sampling through quantum chemical molecular dynamics simulations, reduction of dimensionality by principal component analysis, determination of

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Bigman, Lavi S., and Yaakov Levy. "Conformational Analysis of Charged Homo-Polypeptides." Biomolecules 13, no. 2 (2023): 363. http://dx.doi.org/10.3390/biom13020363.

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Many proteins have intrinsically disordered regions (IDRs), which are often characterized by a high fraction of charged residues with polyampholytic (i.e., mixed charge) or polyelectrolytic (i.e., uniform charge) characteristics. Polyelectrolytic IDRs include consecutive positively charged Lys or Arg residues (K/R repeats) or consecutive negatively charged Asp or Glu residues (D/E repeats). In previous research, D/E repeats were found to be about five times longer than K/R repeats and to be much more common in eukaryotes. Within these repeats, a preference is often observed for E over D and fo

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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

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Agaeva, G. A., and G. Z. Najafova. "Conformational particularities of beta-amyloid peptide 25-35." Биофизика 68, no. 5 (2023): 871–77. http://dx.doi.org/10.31857/s0006302923050058.

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In Alzheimer's disease, beta-amyloid peptide (Ав) plays an important role in the mechanism of neurodegeneration. A small fragment of Лв(25-35) (with the sequence GSNKGAIIGLLM) is regarded to be the functional domain of Лв, responsible for its neurotoxic properties and represents the biological active region of Лв. Conformational analysis of each C-terminal segment of the peptide by the method of molecular mechanics revealed a limited number of most probable conformations and quite clearly helped to clarify what forces stabilize the structures. The obtained results showed that Лв(25-35) energet

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McIntyre, Deane D., Markus W. Germann, and Hans J. Vogel. "Conformational analysis and complete assignment of the proton and carbon NMR spectra of ouabain and ouabagenin." Canadian Journal of Chemistry 68, no. 8 (1990): 1263–70. http://dx.doi.org/10.1139/v90-195.

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The 1H and 13C NMR spectra of the cardenolide ouabain and its aglycon ouabagenin have been completely assigned by two-dimensional NMR techniques, including phase-sensitive COSY and carbon–proton correlation (HETCOR, HMQC, and COLOC) spectra. The major conformer of these two compounds in solution is all-chair as determined from proton–proton coupling constants and is similar to that in the crystal lattice as previously determined by X-ray diffraction. The conformations of the A and D rings of ouabain in water are somewhat different than in DMSO/CDCl3 (2:1). At lower temperatures (−20 °C) signal

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Pandey, Bharati, Chetna Tyagi, Gopal Kumar Prajapati, et al. "Analysis of mutations of defensin protein using accelerated molecular dynamics simulations." PLOS ONE 15, no. 11 (2020): e0241679. http://dx.doi.org/10.1371/journal.pone.0241679.

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Plant defensins possess diverse biological functions that include antifungal and antibacterial activities and α-amylase and trypsin inhibitory properties. Two mutations, G9R and V39R, were confirmed to increase the antifungal activity of Raphanus sativus antifungal protein 2 (RsAFP2). Accelerated Molecular Dynamics (aMD) were carried out to examine the conformational changes present in these RsAFP2 mutants, and its two closest homologs compared to the wild-type protein. Specifically, the root mean square fluctuation values for the eight cysteine amino acids involved in the four disulfide bonds

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Leitgeb, B., A. Szekeres, and G. Tóth. "Conformational analysis of endomorphin-1 by molecular dynamics methods." Journal of Peptide Research 62, no. 4 (2003): 145–57. http://dx.doi.org/10.1034/j.1399-3011.2003.00084.x.

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Leitgeb, Balázs, Ferenc Ötvös, and Géza Tóth. "Conformational analysis of endomorphin-2 by molecular dynamics methods." Biopolymers 68, no. 4 (2003): 497–511. http://dx.doi.org/10.1002/bip.10333.

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Dobrovolska, Olena, Øyvind Strømland, Ørjan Sele Handegård, et al. "Investigating the Disordered and Membrane-Active Peptide A-Cage-C Using Conformational Ensembles." Molecules 26, no. 12 (2021): 3607. http://dx.doi.org/10.3390/molecules26123607.

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The driving forces and conformational pathways leading to amphitropic protein-membrane binding and in some cases also to protein misfolding and aggregation is the subject of intensive research. In this study, a chimeric polypeptide, A-Cage-C, derived from α-Lactalbumin is investigated with the aim of elucidating conformational changes promoting interaction with bilayers. From previous studies, it is known that A-Cage-C causes membrane leakages associated with the sporadic formation of amorphous aggregates on solid-supported bilayers. Here we express and purify double-labelled A-Cage-C and prep

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Belaidi, Salah, and Dalal Harkati. "Conformational Analysis in 18-Membered Macrolactones Based on Molecular Modeling." ISRN Organic Chemistry 2011 (April 19, 2011): 1–5. http://dx.doi.org/10.5402/2011/594242.

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Conformational analysis of 18-ring membered macrolactones has been carried out using molecular mechanics calculations and molecular dynamics. A high conformational flexibility of macrolactones was obtained, and an important stereoselectivity was observed for the complexed macrolides. For 18d macrolactone, which was presented by a most favored conformer with 20.1% without complex, it was populated with 50.1% in presence of Fe(CO)3.

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Ghoula, Mariem, Nathalie Janel, Anne-Claude Camproux, and Gautier Moroy. "Exploring the Structural Rearrangements of the Human Insulin-Degrading Enzyme through Molecular Dynamics Simulations." International Journal of Molecular Sciences 23, no. 3 (2022): 1746. http://dx.doi.org/10.3390/ijms23031746.

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Insulin-degrading enzyme (IDE) is a ubiquitously expressed metallopeptidase that degrades insulin and a large panel of amyloidogenic peptides. IDE is thought to be a potential therapeutic target for type-2 diabetes and neurodegenerative diseases, such as Alzheimer’s disease. IDE catalytic chamber, known as a crypt, is formed, so that peptides can be enclosed and degraded. However, the molecular mechanism of the IDE function and peptide recognition, as well as its conformation changes, remains elusive. Our study elucidates IDE structural changes and explains how IDE conformational dynamics is i

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Verma, Rajni, Jonathan M. Ellis, and Katie R. Mitchell-Koch. "Dynamic Preference for NADP/H Cofactor Binding/Release in E. coli YqhD Oxidoreductase." Molecules 26, no. 2 (2021): 270. http://dx.doi.org/10.3390/molecules26020270.

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YqhD, an E. coli alcohol/aldehyde oxidoreductase, is an enzyme able to produce valuable bio-renewable fuels and fine chemicals from a broad range of starting materials. Herein, we report the first computational solution-phase structure-dynamics analysis of YqhD, shedding light on the effect of oxidized and reduced NADP/H cofactor binding on the conformational dynamics of the biocatalyst using molecular dynamics (MD) simulations. The cofactor oxidation states mainly influence the interdomain cleft region conformations of the YqhD monomers, involved in intricate cofactor binding and release. The

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Verma, Rajni, Jonathan M. Ellis, and Katie R. Mitchell-Koch. "Dynamic Preference for NADP/H Cofactor Binding/Release in E. coli YqhD Oxidoreductase." Molecules 26, no. 2 (2021): 270. http://dx.doi.org/10.3390/molecules26020270.

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YqhD, an E. coli alcohol/aldehyde oxidoreductase, is an enzyme able to produce valuable bio-renewable fuels and fine chemicals from a broad range of starting materials. Herein, we report the first computational solution-phase structure-dynamics analysis of YqhD, shedding light on the effect of oxidized and reduced NADP/H cofactor binding on the conformational dynamics of the biocatalyst using molecular dynamics (MD) simulations. The cofactor oxidation states mainly influence the interdomain cleft region conformations of the YqhD monomers, involved in intricate cofactor binding and release. The

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Qu, Kun, Qiuluan Chen, Katarzyna A. Ciazynska, et al. "Engineered disulfide reveals structural dynamics of locked SARS-CoV-2 spike." PLOS Pathogens 18, no. 7 (2022): e1010583. http://dx.doi.org/10.1371/journal.ppat.1010583.

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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

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Sun, Jixue, Zibin Li, and Na Yang. "Mechanism of the Conformational Change of the Protein Methyltransferase SMYD3: A Molecular Dynamics Simulation Study." International Journal of Molecular Sciences 22, no. 13 (2021): 7185. http://dx.doi.org/10.3390/ijms22137185.

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SMYD3 is a SET-domain-containing methyltransferase that catalyzes the transfer of methyl groups onto lysine residues of substrate proteins. Methylation of MAP3K2 by SMYD3 has been implicated in Ras-driven tumorigenesis, which makes SMYD3 a potential target for cancer therapy. Of all SMYD family proteins, SMYD3 adopt a closed conformation in a crystal structure. Several studies have suggested that the conformational changes between the open and closed forms may regulate the catalytic activity of SMYD3. In this work, we carried out extensive molecular dynamics simulations on a series of complexe

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Lin, Shawn H., Dacheng Zhao, Vivian Deng, et al. "Integration Host Factor Binds DNA Holliday Junctions." International Journal of Molecular Sciences 24, no. 1 (2022): 580. http://dx.doi.org/10.3390/ijms24010580.

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Integration host factor (IHF) is a nucleoid-associated protein involved in DNA packaging, integration of viral DNA and recombination. IHF binds with nanomolar affinity to duplex DNA containing a 13 bp consensus sequence, inducing a bend of ~160° upon binding. We determined that IHF binds to DNA Four-way or Holliday junctions (HJ) with high affinity regardless of the presence of the consensus sequence, signifying a structure-based mechanism of recognition. Junctions, important intermediates in DNA repair and homologous recombination, are dynamic and can adopt either an open or stacked conformat

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Wang, Xuebin, Ning Liu, Nuan Li, Shaoyong Lu, and Zongtao Chai. "Mechanistic Insights into the Mechanism of Allosteric Inhibition of Ubiquitin-Specific Protease 7 (USP7)." Biomolecules 15, no. 6 (2025): 749. https://doi.org/10.3390/biom15060749.

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Ubiquitin-specific protease 7 (USP7), a deubiquitinase enzyme responsible for removing ubiquitin (Ub) from target proteins, plays a crucial role in oncogenic pathways and has been implicated in various human diseases. X-ray crystallography has revealed distinct conformations of USP7, including apo (ligand-free), allosteric inhibitor-, and Ub-bound states. However, the dynamic mechanisms underlying the allosteric inhibition of USP7 remain unclear. This study investigates the effect of allosteric inhibitor binding on the dynamics of USP7 through multiple replica molecular dynamics simulations. O

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Salvino, Joseph M., Peter R. Seoane, and Roland E. Dolle. "Conformational analysis of bradykinin by annealed molecular dynamics and comparison to NMR-derived conformations." Journal of Computational Chemistry 14, no. 4 (1993): 438–44. http://dx.doi.org/10.1002/jcc.540140407.

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Olivos-Ramirez, Gustavo E., Luis F. Cofas-Vargas, Tobias Madl, and Adolfo B. Poma. "Conformational and Stability Analysis of SARS-CoV-2 Spike Protein Variants by Molecular Simulation." Pathogens 14, no. 3 (2025): 274. https://doi.org/10.3390/pathogens14030274.

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We performed a comprehensive structural analysis of the conformational space of several spike (S) protein variants using molecular dynamics (MD) simulations. Specifically, we examined four well-known variants (Delta, BA.1, XBB.1.5, and JN.1) alongside the wild-type (WT) form of SARS-CoV-2. The conformational states of each variant were characterized by analyzing their distributions within a selected space of collective variables (CVs), such as inter-domain distances between the receptor-binding domain (RBD) and the N-terminal domain (NTD). Our primary focus was to identify conformational state

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Stepanenko, Darya, Yuzhang Wang, and Carlos Simmerling. "Assessing pH-Dependent Conformational Changes in the Fusion Peptide Proximal Region of the SARS-CoV-2 Spike Glycoprotein." Viruses 16, no. 7 (2024): 1066. http://dx.doi.org/10.3390/v16071066.

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One of the entry mechanisms of the SARS-CoV-2 coronavirus into host cells involves endosomal acidification. It has been proposed that under acidic conditions, the fusion peptide proximal region (FPPR) of the SARS-CoV-2 spike glycoprotein acts as a pH-dependent switch, modulating immune response accessibility by influencing the positioning of the receptor binding domain (RBD). This would provide indirect coupling of RBD opening to the environmental pH. Here, we explored this possible pH-dependent conformational equilibrium of the FPPR within the SARS-CoV-2 spike glycoprotein. We analyzed hundre

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