Relevant bibliographies by topics / Molecular dynamics conformational analysis

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Academic literature on the topic 'Molecular dynamics conformational analysis'

Author: Grafiati
Published: 4 June 2025
Last updated: 6 July 2025

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Journal articles on the topic "Molecular dynamics conformational analysis"

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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 activity of Hsp90, as seen with other chaperones. However, unlike other chaperones, studies have shown that the ATPase cycle of Hsp90 is not conformationally deterministic. That is, rather than dictating the conformational state, ATP binding and hydrolysis only shift the equilibria between a pre-existing set of conformational states. For bacterial, yeast and human Hsp90, there is a conserved three-state (apo–ATP–ADP) conformational cycle; however; the equilibria between states are species specific. In eukaryotes, cytosolic co-chaperones regulate the in vivo dynamic behavior of Hsp90 by shifting conformational equilibria and affecting the kinetics of structural changes and ATP hydrolysis. In this review, we discuss the structural and biochemical studies leading to our current understanding of the conformational dynamics of Hsp90, as well as the roles that nucleotide, co-chaperones, post-translational modification and substrates play. This view of Hsp90's conformational dynamics was enabled by the use of multiple complementary structural methods including, crystallography, small-angle X-ray scattering (SAXS), electron microscopy, Förster resonance energy transfer (FRET) and NMR. Finally, we discuss the effects of Hsp90 inhibitors on conformation and the potential for developing small molecules that inhibit Hsp90 by disrupting the conformational dynamics.
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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 (2024): 1072. http://dx.doi.org/10.3390/molecules29051072.

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Ribitol (C5H12O5) is an acyclic sugar alcohol that was recently identified in O-mannose glycan on mammalian α-dystroglycan. The conformation and dynamics of acyclic sugar alcohols such as ribitol are dependent on the stereochemistry of the hydroxyl groups; however, the dynamics are not fully understood. To gain insights into the conformation and dynamics of sugar alcohols, we carried out comparative analyses of ribitol, d-arabitol and xylitol by a crystal structure database search, solution NMR analysis and molecular dynamics (MD) simulations. The crystal structures of the sugar alcohols showed a limited number of conformations, suggesting that only certain stable conformations are prevalent among all possible conformations. The three-bond scholar coupling constants and exchange rates of hydroxyl protons were measured to obtain information on the backbone torsion angle and possible hydrogen bonding of each hydroxyl group. The 100 ns MD simulations indicate that the ribitol backbone has frequent conformational transitions with torsion angles between 180∘ and ±60∘, while d-arabitol and xylitol showed fewer conformational transitions. Taking our experimental and computational data together, it can be concluded that ribitol is more flexible than d-arabitol or xylitol, and the flexibility is at least in part defined by the configuration of the OH groups, which may form intramolecular hydrogen bonds.
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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 unrelated patients based on functional, biochemical, and crystallographic evidence supporting a folding defect. AlphaFold gave an accurate prediction for the wild-type structure. However, it also produced native structures for all variants, regardless of complexity or conformational consequences in vivo. Similarly, molecular dynamics of up to 1000 ns at temperatures causing conformational transitions did not show significant changes in the native structure of wild-type and variants. In conclusion, AlphaFold and molecular dynamics force predictions into the native conformation at conditions with experimental evidence supporting a conformational change to other structures. It is necessary to improve predictive strategies for serpins that consider the conformational sensitivity of these molecules.
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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 analysis, 2D nuclear Overhauser effect spectroscopy spectra analysis and molecular dynamics simulation. The conformational evolution and desolvation path was illustrated according to the 1H NMR spectra of solutions with different concentrations. Finally, based on all the above analysis, the molecular conformational evolution path during nucleation of 5-nitrofurazone was illustrated. The results presented in this work shed a new light on the molecular mechanism of conformational polymorphism nucleation in solution.
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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 hylambatin significantly increases the level of glucose and insulin in blood plasma. In this paper, the conformational flexibility of the hylambatin molecule was studied by methods of molecular mechanics and molecular dynamics. The conformational calculation of the peptide took into account non-valent and electrostatic interactions, hydrogen bonds and torsion potentials. Based on fragmentary analysis, stable spatial structures of the hylambatin dodecapeptide were determined, which can be represented as a set of conformations characterized by a relatively labile N-terminal tetrapeptide and a conformationally rigid C-terminal octapeptide. In the calculated stable conformational states, the effective interactions of the side chains of residues and hydrogen bonds were refined and energetically evaluated. It has been shown that the hylambatin molecule preferably forms practically isoenergetic conformations with various structural types at the N-end of the peptide chain, passing into the alpha helix at the C-end. By the method of molecular dynamics, the pattern of intramolecular mobility of stable conformations of the hylambatin molecule was modeled both in vacuum and surrounded by water molecules. Based on the calculated values of the dihedral angles, molecular models of energetically preferred conformational states of the hylambatin dodecapeptide were constructed.
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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 combined Monte Carlo (MC) and molecular dynamics (MD) approach applied to the conformational study of HA, using an adjusted version of AMBER force field and the generalized Born solvent-accessible surface area (GB/SA) continuum solvation model. The MC approach turned out to be extremely effective to outline a conformational survey of the disaccharides constituting HA. Complete sets of conformations of the monomers were provided for the first time, some of which had never been predicted. MD technique, integrating the MC results, correctly reproduced the unusual stiffness of HA and predicted the existence of a minor skew-boat conformation of the β-d-glucuronic moiety. The computational approach, as a whole, improved the comprehension of the dynamic behavior of HA and offered a clear causal explanation of the relative dynamics of the glycosidic linkages.
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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 for three fibric acids, but not gemfibrozil, which lacks suitable connectivity of carboxyl and phenoxy groups. Trends in computed atom-positional deviations, molecular volumes, surface areas, and dipole moments among the fibric acids and their constituent conformations indicate that bezafibrate has the greatest hydrophilicity and fenofibric acid has the greatest flexibility. Theoretical and experimental comparison of chemical shifts of standards with sufficient overlap of fragments containing common atoms, groups, and connectivity may provide a reliable minimal set to benchmark and generate leads.
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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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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 a suitable combination of energy and volume profiles.
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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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Dissertations / Theses on the topic "Molecular dynamics conformational analysis"

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Hyvönen, M. (Marja). "Molecular dynamics simulations on phospholipid membranes." Doctoral thesis, University of Oulu, 2001. http://urn.fi/urn:isbn:9514259432.

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Abstract Phospholipids are the main components of cell membranes, lipoproteins and other membrane structures in living organisms. Properties of lipid molecules are important to the overall behaviour and interactions of membranes. Furthermore, characteristics of the biological membranes act as important regulators of membrane functions. Molecular dynamics (MD) simulations were applied in this thesis to study properties of biological membranes. A certain degree of acyl chain polyunsaturation is essential for the proper functioning of membranes, but earlier MD simulations had not addressed the effects of polyunsaturation. Therefore a solvated all-atom bilayer model consisting of diunsaturated 1-palmitoyl-2-linoleoyl-3-phosphatidylcholine (PLPC) molecules was simulated. The analysis of the simulation data was focused on the effects of double bonds on a membrane structure. Self-organising neural networks were applied to the analysis of the conformational data from the 1-ns simulation of PLPC membrane. Mapping of 1.44 million molecular conformations to a two-dimensional array of neurons revealed, without human intervention or requirement of a priori knowledge, the main conformational features. This method provides a powerful tool for gaining insight into the main molecular conformations of any simulated molecular assembly. Furthermore, an application of MD simulations in the comparative analysis of the effects of lipid hydrolysis products on the membrane structure was introduced. The hydrolysis products of the phospholipase A2 (PLA2) enzyme are known to have a role in a variety of physiological processes and the membrane itself acts as an important regulator of this enzyme. The simulations revealed differences in the bilayer properties between the original and hydrolysed phospholipid membranes. This study provides further evidence that MD simulations on biomembranes are able to provide information on the properties of biologically and biochemically important lipid systems at the molecular level.
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Chen, Wei. "Molecular dynamics simulations of binding, unfolding, and global conformational changes of signaling and adhesion molecules." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/28118.

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Thesis (M. S.)--Mechanical Engineering, Georgia Institute of Technology, 2009.<br>Committee Chair: Zhu, Cheng; Committee Member: Harvey, Stephen; Committee Member: Hud, Nicholas; Committee Member: Zamir, Evan; Committee Member: Zhu, Ting.
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Atzori, Alessio. "Conformational analysis of peptides and proteins for drug design using molecular simulations." Thesis, University of Manchester, 2015. https://www.research.manchester.ac.uk/portal/en/theses/conformational-analysis-of-peptides-and-proteins-for-drug-design-using-molecular-simulations(050ba296-a4c4-4a5b-87bf-66d90f7ddc5a).html.

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The intrinsic plasticity of biological systems provides opportunities for rational design of selective and potent ligands. Increasingly, computational methods are being applied to predict biomolecular flexibility. However, the motions involved in these processes can be large and occur on time scales generally difficult to achieve with standard simulation methods. In order to overcome the intrinsic limitations of classical molecular dynamics, this Ph.D. project focuses on the application of advanced sampling computational techniques to capture the plasticity of diverse biological systems. The first of these applications involved the evaluation of the secondary structure of the N-terminal portion of p53 and its inverse, reverse and retro-inverso sequences by using replica exchange molecular dynamics simulations in implicit solvent. In this study, we also evaluated the effects of reversal of sequence and stereochemistry in mimicking an inhibitory pharmacophoric conformation. The results showed how the ability to mimic the parent peptide is severely compromised by backbone orientation (for D-amino acids) and side-chain orientation (for reversed sequences). Moreover, the structural information obtained from simulations showed good agreement with NMR and circular dichroism studies, confirming the validity of the combination of replica exchange molecular dynamics with the ff99SB force field and Generalized Born solvent model for computational modelling of D-peptide conformations.In a second work, we explored conformations of the DFG motif of the p38α mitogen-activated protein (MAP) kinase. To achieve this, we employed an advanced sampling simulation method that has been developed in-house, called swarm-enhanced sampling molecular dynamics (sesMD). In contrast to multiple independent MD simulations, swarm-coupled sesMD trajectories were able to sample a wide range of DFG conformations, some of which map onto existing crystal structures. Simulated structures intermediate between DFG-in and DFG-out conformations were predicted to have druggable pockets of interest for structure-based ligand design. Overall, sesMD shows promise as a useful tool for enhanced sampling of complex conformational landscapes. Finally, we used microsecond MD simulations to evaluate the molecular plasticity of R-spondins, a class of proteins involved in the activation of the Wnt pathway. The unbound R-spondin 1 is characterised by a closed conformation, while, when complexed to proteins LGR and RNF43/ZNRF3, assumes an open and more extended arrangement. This is true also for R-spondin 2, in both its unbound or bound forms. From our simulation, we find that the closed R-spondin 1 conformation is stable, whilst, R-spondin 1 and 2 from their open conformation explore several intermediate structures. In addition, we evaluated the druggability of a potential binding site located at the interface between the second and the third β-hairpin moiety of the first furin domain. The computational screening with small molecular fragments provided interesting insights about the druggability and the pharmacophoric features of the potential binding pockets identified, outlining promising future perspectives of structure-based design of Wnt pathway inhibitors.
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Zhang, Wei. "Computational simulation of biological systems studies on protein folding and protein structure prediction /." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file 2.84Mb, 184 p, 2005. http://wwwlib.umi.com/dissertations/fullcit/3181881.

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Hafner, Melanie Salome [Verfasser]. "Structural conformational analysis of molecular dynamics of a P-glycoprotein homology model and generated intermediate structures / Melanie Salome Hafner." Bonn : Universitäts- und Landesbibliothek Bonn, 2019. http://d-nb.info/119893316X/34.

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Tippel, Franziska [Verfasser], Johannes [Akademischer Betreuer] Buchner, Michael [Gutachter] Sattler, and Johannes [Gutachter] Buchner. "Mechanistic Analysis of Conformational Dynamics of the Molecular Chaperone Hsp90 / Franziska Tippel ; Gutachter: Michael Sattler, Johannes Buchner ; Betreuer: Johannes Buchner." München : Universitätsbibliothek der TU München, 2017. http://d-nb.info/1173898832/34.

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Tippel, Franziska Verfasser], Johannes [Akademischer Betreuer] [Buchner, Michael [Gutachter] Sattler, and Johannes [Gutachter] Buchner. "Mechanistic Analysis of Conformational Dynamics of the Molecular Chaperone Hsp90 / Franziska Tippel ; Gutachter: Michael Sattler, Johannes Buchner ; Betreuer: Johannes Buchner." München : Universitätsbibliothek der TU München, 2017. http://nbn-resolving.de/urn:nbn:de:bvb:91-diss-20170217-1341437-1-7.

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Alonso, Gil Santiago. "Conformational and mechanistic analyses of α- and β-glycosidase substrates by ab initio QM/MM methods". Doctoral thesis, Universitat de Barcelona, 2017. http://hdl.handle.net/10803/462805.

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Carbohydrates are one of the most important biochemical molecules due to their role as energetic resource for non-photosynthetic organisms, cell-cell recognition and adhesion, protection of cell membranes of bacteria and plants and ensure the proper functionality of several enzymes. Glycoproteins are important components of cell surfaces and the extracellular medium where molecular-cell interactions take place. Defects in the activity of glycoproteins are the cause of several human diseases, such as diabetes and lysosomal storage diseases. Glycoside hydrolases (GHs) are one of the most relevant glycoproteins. They catalyse the cleavage of glycosidic bonds of oligosaccharides to generate smaller oligosaccharides or monosaccharides with relevant biological roles. To know the proper way to modulate the activity of these enzymes, it is crucial to understand their molecular mechanisms of action. Sugars are very flexible molecules, most of them formed by 6- membered rings whose conformation changes during the reaction catalysed by GHs. Capturing these conformations, in particular the one at the reaction transition state, is important in inhibitor design. Experiments aimed at characterizing (indirectly) the transition state conformation of GHs include crystallizing the Michaelis complex (MC), which usually is done using thioglycoside derivatives of the natural substrate (i.e. the glycosidic oxygen is substituted by sulfur) or enzyme mutants (e.g. the catalytic acid/base residue mutated to glutamine or asparagine). However, in some cases, the degree of resemblance of the sugar conformation in thioglycosides or enzyme mutants with respect to the natural/wild type counterparts unclear. In last years, our group has demonstrated that the conformational free energy landscape (FEL) of natural sugars (e.g. β-glucose, α,β-mannose and β-xylose) can be used to predict catalytic pathways of GHs. The conformational FEL is explored using Cremer & Pople puckering coordinates as collective variables in the metadynamics method. A natural extension of these studies is to explore the conformational FEL of 7-membered sugar rings (septanosides), which are currently the focus of great interest as potential GH substrates. In this Thesis, we applied Car-Parrinello molecular dynamics methods, within the QM/MM approach, to elucidate the catalytic mechanism of a family 13 retaining GH, (amylosucrase) and a family 125 inverting GH (exo-1,6-α-mannosidase). In both cases, prior structural information was available from enzyme mutants and/or thioderivative substrates. In addition, we have extended previous ring conformational analyses of pyranoses to septanosides in order to assess their potential as new substrates of selected GHs. The Thesis is organised as follows: Chapters I and II focuses on the conformational flexibility of carbohydrates, GH mechanisms and experimental techniques aimed to trap the MC, as well as the methodology used in this Thesis. In Chapter III, we investigate the conformational landscape of α-glucose and the conformational itinerary that an α-glucoside (fructose) follows during catalysis by GH13 amylosucrase (both hydrolysis and polymerization have been investigated). In Chapter IV, we present the results of conformational study of a thioglycoside vs the natural substrate in a GH125 α-mannosidase, including a mechanistic analysis that uncovered the conformational catalytic itinerary for family 125 GHs. In Chapter V, we investigate four MC structures of a promiscuous GH3 β- glucohydrolase, able to cleave several types of glycosidic linkages, for which only structures with thioglycosides are available. The reconstruction of the structure with the natural substrate allowed us to predict the mechanism of action of these enzymes. In Chapter VI, we apply the Cremer & Pople puckering coordinates for 7-membered rings as collective variable for metadynamics on several septanoside molecules (both isolated and “on-enzyme”) and assess their potential as substrate/inhibitors of GHs. Finally, Chapter VII contains the main conclusions of this work.<br>Los carbohidratos son una de las biomoléculas más importantes debido a su papel como fuente de energía para organismos no-fotosintéticos, reconocimiento célula-célula, protección de la membrana celular de bacterias y plantas y por asegurar la buena funcionalidad de algunas enzimas. Las glicoproteínas son componentes esenciales en la superficie de las células y en el medio extracelular. Defectos en la actividad de estas proteínas son la causa de varias enfermedades humanas, como la diabetes o problemas en el lisosoma. Las glicosil hidrolasas (GHs) son una de las glicoproteínas más relevantes. Catalizan la rotura de enlaces glicosídicos de oligosacáridos para generar monosacáridos o cadenas más pequeñas de azúcares con relevancia biológica. Para encontrar una manera adecuada de modular la actividad de estas enzimas, es crucial entender sus mecanismos moleculares. Los azúcares son moléculas muy flexibles, la mayoría formados por anillos de 6 átomos cuya conformación cambia durante la reacción en GHs. Capturar estas conformaciones, en particular la del estado de transición, es clave para diseñar inhibidores. La manera de caracterizar indirectamente la conformación de ese estado de transición es cristalizando el complejo de Michaelis de la GH con un tioderivado del sustrato natural (el oxígeno glicosídico es substituido por azufre) o usando mutantes de la enzima. No obstante, en algunos casos, la semejanza a nivel conformacional del mímico y el sustrato natural no queda suficientemente clara. En los últimos años, nuestro grupo ha demostrado el uso para predecir itinerarios catalíticos de GHs a partir de las superficies de energía libre conformacional de los azúcares naturales (glucosa, manosa y xilosa). Estas superficies se exploran utilizando las coordenadas de empaquetamiento de Cremer y Pople como variables colectivas en el método de metadinámica. Una extensión de estos estudios es el análisis conformacional de azúcares formados por anillos de 7 átomos (septanósidos), que están actualmente en el foco de interés como sustratos de GHs. En la presente Tesis, aplicamos métodos basados en dinámica molecular Car- Parrinello, dentro de la aproximación QM/MM, para estudiar el mecanismo catalítico de las GHs de la familia 13 (amilosucrasa), la familia 125 (exo-1,6-α-manosidasa) y la familia 3 (enzima HvExoI). Además, hemos extendido el estudio conformacional de anillos a los septanósidos para poder predecir su potencial como nuevos sustratos de GHs concretas.
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Posgai, Monica Therese. "Energetic and dynamic characterization of the IgA1:FcαRI interaction reveals long-range conformational changes in IgA1 upon receptor binding". University of Cincinnati / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1354043317.

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Bougueroua, Sana. "Caractérisation de structures explorées dans les simulations de dynamique moléculaire." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLV099/document.

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L’objectif de cette thèse est d’analyser et prédire les conformations d’un système moléculaire en combinant la théorie des graphes et la chimie computationnelle.Dans le cadre des simulations de dynamique moléculaire, une molécule peut avoir une ou plusieurs conformations au cours du temps. Dans les trajectoires de simulation de dynamique moléculaire, on peut avoir des trajectoires n’explorant qu’une seule conformation ou des trajectoires explorant plusieurs conformations, donc plusieurs transitions entre conformations sont observées. L’exploration de ces conformations dépend du temps de la simulation et de l'énergie (température) fixée dans le système. Pour avoir une bonne exploration des conformations d’un système moléculaire, il faut générer et analyser plusieurs trajectoires à différentes énergies. Notre objectif est de proposer un algorithme universel qui permet d’analyser la dynamique conformationnelle de ces trajectoires d’une façon rapide et automatique. Les trajectoires fournissent les positions cartésiennes des atomes du système moléculaire à des intervalles de temps réguliers. Chaque intervalle contenant un ensemble de positions est appelé image. L’algorithme utilise des règles de géométrie (distances, angles, etc.) sur les positions pour trouver les liaisons (liaisons covalentes, liaisons hydrogène et interactions électrostatiques) créées entre les atomes, permettant par la suite d’obtenir le graphe mixte qui modélise une conformation. Nous ne considérons un changement conformationnel que s’il y a un changement dans les liaisons calculées à partir des positions données. L’algorithme permet de donner l’ensemble des conformations explorées sur une ou plusieurs trajectoires, la durée d’exploration de chaque conformation, ainsi que le graphe de transitions qui contient tous les changements conformationnels observés.Les conformations se caractérisent par une énergie appelée énergie potentielle. Cette énergie est représentée par une courbe appelée surface d’énergie potentielle. En chimie théorique et computationnelle, certains s’intéressent à trouver des points particuliers sur cette surface. Il s'agit des minima qui représentent les conformations les plus stables et des maxima ou états de transition qui représentent les points de passage d'une conformation à une autre. En effet, d'une part, la conformation la plus stable est celle de plus basse énergie. D'autres part, pour aller d’une conformation à une autre il faut une énergie supplémentaire, le point maximum représente l'état de transition. Les méthodes développées pour calculer ces points nécessitent une connaissance de l’énergie potentielle ce qui est coûteux en temps et en calculs. Notre objectif est de proposer une méthode alternative en utilisant des mesures ah doc basées sur des propriétés des graphes qu’on a utilisées dans le premier algorithme et sans faire appel à la géométrie ni aux calculs moléculaires. Ces mesures permettent de générer des conformations avec un classement énergétique ainsi de définir le coût énergétique de chaque transition permise. Les conformations possibles avec les transitions représentent respectivement les sommets et les arcs de ce qu’on appelle le “graphe des possibles”. Les hypothèses utilisées dans le modèle proposé est que seules les liaisons hydrogène peuvent changer entre les conformations et que le nombre de liaisons hydrogène présentes dans le système permet de déterminer son coût énergétique.L’algorithme d'analyser des trajectoires a été testé sur trois types de systèmes moléculaires en phase gazeuse de taille et de complexité croissantes. Bien que la complexité théorique de l’algorithme est exponentielle (tests d’isomorphisme) les résultats ont montré que l’algorithme est rapide (quelques secondes). De plus, cet algorithme peut être facilement adapté et appliqué à d’autres systèmes. Pour la prédiction conformationnelle, le modèle proposé a été testé sur des peptides isolés<br>This PhD is part of transdisciplinary works, combining graph theory and computational chemistry.In molecular dynamics simulations, a molecular system can adopt different conformations over time. Along a trajectory, one conformation or more can thus be explored. This depends on the simulation time and energy within the system. To get a good exploration of the molecular conformations, one must generate and analyse several trajectories (this can amount to thousands of trajectories). Our objective is to propose an automatic method that provides rapid and efficient analysis of the conformational dynamics explored over these trajectories. The trajectories of interest here are in cartesian coordinates of the atoms that constitute the molecular system, recorded at regular time intervals (time-steps). Each interval containing a set of positions is called a snapshot. At each snapshot, our developed algorithm uses geometric rules (distances, angles, etc.) to compute bonds (covalent bonds, hydrogen bonds and any other kind of intermolecular criterium) formed between atoms in order to get the mixed graph modelling one given conformation. Within our current definitions, a conformational change is characterized by either a change in the hydrogen bonds or in the covalent bonds. One choice or the other depends on the underlying physics and chemistry of interest. The proposed algorithm provides all conformations explored along one or several trajectories, the period of time for the existence of each one of these conformations, and also provides the graph of transitions that shows all conformational changes that have been observed during the trajectories. A user-friendly interface has been developed, that can de distributed freely.Our proposed algorithm for analysing the trajectories of molecular dynamics simulations has been tested on three kinds of gas phase molecular systems (peptides, ionic clusters). This model can be easily adapted and applied to any other molecular systems as well as to condensed matter systems, with little effort. Although the theoretical complexity of the algorithm is exponential (isomorphism tests), results have shown that the algorithm is rapid.We have also worked on computationally low cost graph methods that can be applied in order to pre-characterize specific conformations/points on a potential energy surface (it describes the energy of a system in terms of positions of the atoms). These points are the minima on the surface, representing the most stable conformations of a molecular system, and the maxima on that surface, representing transition states between two conformers. Our developed methods and algorithms aim at getting these specific points, without the prerequisite knowledge/calculation of the potential energy surface by quantum chemistry methods (or even by classical representations). By avoiding an explicit calculation of the potential energy surface by quantum chemistry methods, one saves computational time and effort. We have proposed an alternative method using ad doc measures based on properties of the graphs (already used in the first part of the PhD), without any knowledge of energy and/or molecular calculations. These measures allow getting the possible conformations with a realistic energy classification, as well as transition states, at very low computational cost. The algorithm has been tested on gas phase peptides
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Books on the topic "Molecular dynamics conformational analysis"

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Mitsuru, Nagasawa, Kurata Michio 1925-, and Toyota Conference, (1st : 1987 : Inuyama City,Japan), eds. Molecular conformation and dynamics of macromolecules in condensed systems. Elsevier, 1988.

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Keresü, G. M. Molecular mechanics and conformational analysis in drug design. Blackwell Science, 1999.

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Toyota Conference (1st 1987 Inuyama-shi, Japan). Molecular conformation and dynamics of macromolecules in condensed systems: A collection of contributions based on lectures presented at the 1st Toyota Conference, Inuyama City, Japan, 28 September-1 October 1987. Elsevier, 1988.

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Yu, Haibo. Biomolecular simulation: Inclusion of polarizability, prediction of conformational stability, and analysis of peptide folding and association. Shaker Verlag, 2004.

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Livesay, Dennis R. Protein dynamics: Methods and protocols. Humana Press, 2013.

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Dodziuk, Helena. Modern conformational analysis: Elucidating novel exciting molecular structures. VCH, 1995.

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Crippen, G. M. Distance geometry and molecular conformation. Research Studies Press, 1988.

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D, Fasman Gerald, ed. Circular dichroism and the conformational analysis of biomolecules. Plenum Press, 1996.

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D, Brasseur Robert Ph, ed. Molecular description of biological membranes by computer aided conformational analysis. CRC Press, 1990.

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Eusebio, Juaristi, ed. Conformational behavior of six-membered rings: Analysis, dynamics, and stereochemical effects. VCH, 1995.

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Book chapters on the topic "Molecular dynamics conformational analysis"

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Caves, Leo S. D., Dzung T. Nguyen, and Roderick E. Hubbard. "Conformational Variability of Insulin: a Molecular Dynamics Analysis." In Molecular Dynamics. Macmillan Education UK, 1991. http://dx.doi.org/10.1007/978-1-349-11044-5_2.

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Barnickel, G., and E. Merck. "Conformational Analysis of Peptides Using Molecular Dynamics." In Supercomputer and Chemistry. Springer Berlin Heidelberg, 1990. http://dx.doi.org/10.1007/978-3-642-75917-8_8.

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Elber, R., and M. Karplus. "Multiple Conformational States of Myoglobin: A Molecular Dynamics Analysis." In Structure, Dynamics and Function of Biomolecules. Springer Berlin Heidelberg, 1987. http://dx.doi.org/10.1007/978-3-642-71705-5_4.

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Frank, Martin. "Conformational Analysis of Oligosaccharides and Polysaccharides Using Molecular Dynamics Simulations." In Methods in Molecular Biology. Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2343-4_22.

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Jørgensen, Flemming Steen, Inge Thøger Christensen, and Anja Rabijns. "From Cyclohexane to FK506 — Conformational Analysis by Molecular Dynamics." In Structure-Based Drug Design. Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-015-9028-0_9.

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Hruby, Victor J., Wieslaw Kazmierski, B. Montgomery Pettitt, and Fahad Al-Obeidi. "Conformational Constraints in the Design of Receptor Selective Peptides: Conformational Analysis and Molecular Dynamics." In Molecular Biology of Brain and Endocrine Peptidergic Systems. Springer US, 1988. http://dx.doi.org/10.1007/978-1-4684-8801-2_2.

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Deuflhard, Peter. "From Molecular Dynamics to Conformation Dynamics in Drug Design." In Trends in Nonlinear Analysis. Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05281-5_6.

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Toro-Labbe, A., and J. Maruani. "Symmetry Analysis and Conformational Dependence of The Properties of Rigid Molecules Embedded in Crystal Sites." In Structure and Dynamics of Molecular Systems. Springer Netherlands, 1986. http://dx.doi.org/10.1007/978-94-009-4662-0_2.

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Scheraga, Harold A. "Conformational Analysis of Polypeptides and Proteins for the Study of Protein Folding, Molecular Recognition, and Molecular Design." In Structure and Dynamics of Nucleic Acids, Proteins, and Membranes. Springer US, 1986. http://dx.doi.org/10.1007/978-1-4684-5308-9_1.

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Hamrick, Grayson S., Casey H. Londergan, and Louise K. Charkoudian. "Heterologous Expression, Purification, and Characterization of Type II Polyketide Synthase Acyl Carrier Proteins." In Methods in Molecular Biology. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2273-5_13.

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AbstractThe enzymes that comprise type II polyketide synthases (PKSs) are powerful biocatalysts that, once well-understood and strategically applied, could enable cost-effective and sustainable access to a range of pharmaceutically relevant molecules. Progress toward this goal hinges on gaining ample access to materials for in vitro characterizations and structural analysis of the components of these synthases. A central component of PKSs is the acyl carrier protein (ACP), which serves as a hub during the biosynthesis of type II polyketides. Herein, we share methods for accessing type II PKS ACPs via heterologous expression in E. coli. We also share how the installation of reactive and site-specific spectroscopic probes can be leveraged to study the conformational dynamics and interactions of type II PKS ACPs.
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Conference papers on the topic "Molecular dynamics conformational analysis"

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Sauer, M., K. H. Drexhage, K. T. Han, S. Nord, and C. Zander. "Following the Dynamics of Single Oligonucleotide Molecules in Water." In Laser Applications to Chemical and Environmental Analysis. Optica Publishing Group, 1998. http://dx.doi.org/10.1364/lacea.1998.lmc.14.

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The dynamic fluorescence characteristics of individual dye molecules in specific local environment are of particular interest for many biological applications.1,2 Furthermore, dye molecules that are influenced by the environment can act as molecular probes, i. e. they exhibit information about neighbouring groups and changes in the microenvironment. They also allow the direct observation of individual dynamic events such as conformational changes of a biological macromolecule if they are monitored on the single-molecule level. In addition, measurements on individual molecules are well suited for the study of complex systems in which it is not known whether all molecules exhibit the same characteristics or each molecule contributes with its individual characteristics to the observed behaviour.
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Fantucci, P., T. Marino, N. Russo, and A. M. Villa. "Conformational analysis of dolastatin 10 and dolastatin 15 by molecular mechanics and molecular dynamics." In The first European conference on computational chemistry (E.C.C.C.1). AIP, 1995. http://dx.doi.org/10.1063/1.47720.

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Meddeb, S., J. Ph Demaret, J. P. Ballini, et al. "Conformational analysis of a family of potent antithrombotic peptides using high temperature molecular dynamics." In The first European conference on computational chemistry (E.C.C.C.1). AIP, 1995. http://dx.doi.org/10.1063/1.47797.

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Mukherjee, Rudranarayan M., Paul Crozier, and Kurt S. Anderson. "Multibody Molecular Dynamics II: Applications and Results." In ASME 2007 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2007. http://dx.doi.org/10.1115/detc2007-35561.

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This is the second paper in a series of two papers on using multibody dynamics algorithms and methods for coarse grained molecular dynamics simulations. In the previous paper, the theoretical discussions on this topic have been presented. This paper presents results obtained from simulating several biomolecular and bulk materials using multibody dynamics algorithms. The systems studied include water boxes, alkane chains, alanine dipeptide and carboxyl terminal fragments of Calmodulin, Ribosomal, and Rhodopsin proteins. The atomistic representations of these systems include several thousand degrees of freedom and results of several nano-second simulations of these systems are presented. The stability and validity of the simulations are studied through conservation of energy, thermodynamics properties and conformational analysis. In these simulations, a speed up of an order of magnitude is realized for conservative error bounds. A discussion is presented on the open-source software developed to facilitate future research using multibody dynamics with molecular dynamics.
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Makarov, Gennady, Olga Borodina, Artem Masunov, et al. "Combined approach to conformational analysis of 4-hydroxyproline containing podands using NMR and molecular dynamics simulation." In ACTUAL PROBLEMS OF ORGANIC CHEMISTRY AND BIOTECHNOLOGY (OCBT2020): Proceedings of the International Scientific Conference. AIP Publishing, 2022. http://dx.doi.org/10.1063/5.0069420.

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Duan, Shanzhong, and Andrew Ries. "An Efficient O(N) Algorithm for Computer Simulation of Rigid Body Molecular Dynamics." In ASME 2007 International Mechanical Engineering Congress and Exposition. ASMEDC, 2007. http://dx.doi.org/10.1115/imece2007-42032.

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Molecular dynamics is effective for a nano-scale phenomenon analysis. There are two major computational costs associated with computer simulation of atomistic molecular dynamics. They are calculation of the interaction forces and formation/solution of equations of motion. In this paper, an O(N) (order N) procedure is presented for calculation of the interaction forces and formation/solution of equations of motion. For computational costs associated with potentials or interaction forces, an internal coordinate method is used. Use of the internal coordinate method makes application of multi-rigid body molecular dynamics to an atomistic molecular system become possible. The algorithm based on the method makes the calculation considerably more practical for large-scale problems encountered in molecular dynamics such as conformation dynamics of polymers. For computational costs associated with formation/solution of equations of motion, Kane method and the internal coordinate method are used for recursive formation and solution of equations of motion of an atomistic molecular system. However, in computer simulation of atomistic molecular dynamics, the inclusion of lightly excited all degrees of freedom of an atom, such as inter-atomic oscillations and rotation about double bonds with high frequencies, introduces limitations to the simulation. The high frequencies of these degrees of freedom force the use of very small integration step sizes, which severely limit the time scales for the atomic molecular simulation over long periods of time. To improve this, holonomic constraints such as strictly constant bond lengths and bond angles are introduced to freeze these high frequency degrees of freedom since they have insignificant effect on long time scale processes in conformational dynamics. In this way, the procedure developed in multibody dynamics can be utilized to achieve higher computing efficiency and an O(N) computational performance can be realized for formation/solution of equations of motion.
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Maftouni, N., M. Amininasab, and F. Kowsari. "Pressure Field in Liquid Phase Nanomembrane System." In ASME 2010 10th Biennial Conference on Engineering Systems Design and Analysis. ASMEDC, 2010. http://dx.doi.org/10.1115/esda2010-25234.

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Nanomembrane is a very important part of living systems. Alive cells have lipid bilayer nanomembrane in liquid phase. The lateral pressure profile, or stress profile, across a cell nanomembrane is the result of the inhomogeneous nature of the interactions within a nanomembrane. It has been shown that the work exerted by the pressure profile when a protein conformational change takes place is significant, of the order of 10kBT, and that the lateral pressure profile averaged over the whole nanomembrane is modified by the inclusion of a protein. Indeed, understanding the full coupling for stress arising from protein-lipid interactions is of profound importance and calls for elucidation. Here proper ensembles for molecular dynamics simulation of inhomogeneous nanoscale system of nanomembrane-cytotoxin protein are introduced. The Virial pressure theorem together with using molecular dynamics simulation data are proposed to use to calculate pressure filed. The predicted pressure tensor of system without cytotoxin is compared with that of system including this protein. Finally deformation of nanomembrane is related to the variation of pressure tensor.
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Harada, Ryuhei, Yasutaka Nishihara, Nobuhiko Wakai, and Akio Kitao. "Conformational transition pathway and free energy analyses of proteins by parallel cascade selection molecular dynamics (PaCS-MD)." In INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2014 (ICCMSE 2014). AIP Publishing LLC, 2014. http://dx.doi.org/10.1063/1.4897682.

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Hwang, Wonmuk, and Matthew J. Lang. "Mechanism of Force Generation in Kinesin Motility." In ASME 2007 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2007. http://dx.doi.org/10.1115/sbc2007-175543.

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Conventional kinesin is a dimeric motor protein that uses adenosine triphosphate (ATP) to walk processively along the microtubule. Although its nucleotide dependent conformational switching and binding of the neck linker (NL) on the motor head are known to be key events in kinesin motility, the basic mechanism by which it amplifies a small conformational change upon ATP binding to generate the force of the walking stroke has not been known. We combined structural analysis with a set of molecular dynamics simulations to identify the 9-residue long N-terminal region, which we named the ‘cover strand’ (CS), as an additional element essential for kinesin’s power stroke. It operates by differentially forming a β-sheet with NL when ATP binds, whereby the ‘cover-neck bundle’ (CNB) has an inherent conformational bias that drives NL into its binding pocket on the motor head. After the initial stroke, the later half of NL, starting with the ‘asparagine latch’ in the middle, forms specific bonds with the motor head to ensure tight binding. We constructed the force map generated by CNB, which showed a forward bias in agreement with single molecule motility measurements. Our result is consistent with other experimental observations, including the estimated stall force and the transverse anisotropy. The novel mechanism of force generation by the dynamic folding of CNB appears to hold in various kinesin families, and elucidates the economy in the design principle of the smallest known processive motor.
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Moorthy, Narayana Subbiah Hari Narayana, Chandrabose Karthikeyan, and Elangovan Manivannan. "Molecular Dynamic Simulations-Based Conformational Analysis and Binding Study of CP-225917 on Farnesyl Transferase Enzyme." In ECMC 2022. MDPI, 2022. http://dx.doi.org/10.3390/ecmc2022-13427.

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Reports on the topic "Molecular dynamics conformational analysis"

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Rinderspacher, Berend C., Jaydeep P. Bardhan, and Ahmed E. Ismail. Wavelet Analysis for Molecular Dynamics. Defense Technical Information Center, 2015. http://dx.doi.org/10.21236/ada619816.

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Picard, Richard Roy, and Kabekode Ghanasham Bhat. Sensitivity Analysis and Uncertainty Quantification for the LAMMPS Molecular Dynamics Simulation Code. Office of Scientific and Technical Information (OSTI), 2017. http://dx.doi.org/10.2172/1372820.

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Liu, Xiang-Yang, and Anders David Andersson. Monte Carlo analysis: error of extrapolated thermal conductivity from molecular dynamics simulations. Office of Scientific and Technical Information (OSTI), 2016. http://dx.doi.org/10.2172/1331293.

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Bhatia, Harsh, Attila Gyulassy, Mitchell Ong, et al. Understanding Lithium Solvation and Diffusion through Topological Analysis of First-Principles Molecular Dynamics. Office of Scientific and Technical Information (OSTI), 2016. http://dx.doi.org/10.2172/1331475.

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Slapikas, Robert, Anindya Ghoshal, Luis Bravo, Muthuvel Murugan, and Douglas Wolfe. Molecular Dynamics Analysis and Optimization of Ultra-High-Temperature Ceramic (UHTC)Compositions for Propulsion. DEVCOM Army Research Laboratory, 2022. http://dx.doi.org/10.21236/ad1171344.

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Ruangpornvisuti, Vithaya. A Study of conformational equilibrium of semicarbazone derivatives and their complexes with cations : research report. Chulalongkorn University, 2006. https://doi.org/10.58837/chula.res.2006.36.

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The structure optimizations of picolinaldehyde N-oxide thiosemicarbazone (Hpiotsc), 2-benzoylpyridine semicarbazone (H2BzPS), their imino tautomers and their complexes with Ni(II), Cu(II) and Zn(II) were carried out using DFT calculations at the B3LYP/LANL2DZ level of theory. Thermodynamic properties of tautomerizations of Hpiotsc and H2BzPS and complexations of their complexes derived from the frequency calculations at the same level were obtained. The B3LYP/LANL2DZ-optimized geometry parameters for the complexes of [[Ni(Hpiotsc)[subscript 2]][superscript 2+]], [Cu(Hpiotsc).Cl[subscript 2]] and [Zn(Hpiotsc).Cl[subscript 2]] show good agreement with their corresponding X-ray crystallographic data. Aryl semicarbazone derivatives have been studied for the development of new antituberculous agents. The quantitative structure activity relationship (QSAR) analysis for the antituberculous activity of the aryl semicarbazones were carried out in terms of the molecular hydrophobicity and indicator variables using the multiple linear regression method. The new definition for indicator variables based on the substituents of the aryl semicarbazones was proposed and employed in the QSAR analysis.
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Pianwanit, Somsak, and Sirirat Kokpol. Theoretical analysis of photoinduced electron transfer in FMN binding protein : Effect of changes in one charge on electron transfer rate. Chulalongkorn University, 2013. https://doi.org/10.58837/chula.res.2013.32.

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Photoinduced electron transfer (PET) is an important process due to its several applications, e.g. solar energy conversion. Flavoproteins are generally selected as a model for the study of PET. In this research, effect of charge at residue 13 on the PET from Trp32, Tyr35 and Try106 to an excited isoalloxazine (Iso*) in FMN binding protein (FBP) from Desulfovibrio vulgaris (Miyazaki F) was studied. A wild type (E13 with negative charge) and four mutations of FBP at residue 13, E13K and E13R (politive charge), E13T and E13Q (neutral charge), were subjected to molecular dynamics (MD) simulations, Snap shots obtained from the MD simulations were used to evaluate the PET rate using the Kakitani and Mataga theory. The PET rates were found to largely depend on the electrostatic energies between photo-products and other ionic groups but not on other physical quantities related to the PET rate such as solvent reorganization energies. A plot of the PET rates vs. total free energy gaps displayed a parabolic function. Similarly, the plot of the PET rates vs. the net electrostatic energies between photo-products and other ionic groups also displayed a parabolic function. This reveals that the net electrostatic energies are most influential upon the ET rate, in addition to the donor-acceptor distance.
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Casey, Therese, Sameer J. Mabjeesh, Avi Shamay, and Karen Plaut. Photoperiod effects on milk production in goats: Are they mediated by the molecular clock in the mammary gland? United States Department of Agriculture, 2014. http://dx.doi.org/10.32747/2014.7598164.bard.

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US scientists, Dr. Theresa Casey and Dr. Karen Plaut, collaborated with Israeli scientists, Dr. SameerMabjeesh and Dr. AviShamay to conduct studies proposed in the BARD Project No. US-4715-14 Photoperiod effects on milk production in goats: Are they mediated by the molecular clock in the mammary gland over the last 3 years. CLOCK and BMAL1 are core components of the circadian clock and as heterodimers function as a transcription factor to drive circadian-rhythms of gene expression. Studies of CLOCK-mutant mice found impaired mammary development in late pregnancy was related to poor lactation performance post-partum. To gain a better understanding of role of clock in regulation of mammary development studies were conducted with the mammary epithelial cell line HC11. Decreasing CLOCK protein levels using shRNA resulted in increased mammary epithelial cell growth rate and impaired differentiation, with lower expression of differentiation markers including ad herens junction protein and fatty acid synthesis genes. When BMAL1 was knocked out using CRISPR-CAS mammary epithelial cells had greater growth rate, but reached stationary phase at a lower density, with FACS indicating cells were growing and dying at a faster rate. Beta-casein milk protein levels were significantly decreased in BMAL1 knockout cells. ChIP-seq analysis was conducted to identify BMAL1 target genes in mammary epithelial cells. Studies conducted in goats found that photoperiod duration and physiological state affected the dynamics of the mammary clock. Effects were likely independent of the photoperiod effects on prolactin levels. Interestingly, circadian rhythms of core body temperature, which functions as a key synchronizing cue sent out by the central clock in the hypothalamus, were profoundly affected by photoperiod and physiological state. Data support that the clock in the mammary gland regulates genes important to development of the gland and milk synthesis. We also found the clock in the mammary is responsive to changes in physiological state and photoperiod, and thus may serve as a mechanism to establish milk production levels in response to environmental cues.
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Sessa, Guido, and Gregory Martin. role of FLS3 and BSK830 in pattern-triggered immunity in tomato. United States Department of Agriculture, 2016. http://dx.doi.org/10.32747/2016.7604270.bard.

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Pattern-recognition receptors (PRRs) located on the plant cell surface initiate immune responses by perceiving conserved pathogen molecules known as pathogen-associated molecular patterns (PAMPs). PRRs typically function in multiprotein complexes that include transmembrane and cytoplasmickinases and contribute to the initiation and signaling of pattern-triggered immunity (PTI). An important challenge is to identify molecular components of PRR complexes and downstream signaling pathways, and to understand the molecular mechanisms that mediate their function. In research activities supported by BARD-4931, we studied the role of the FLAGELLIN SENSING 3 (FLS3) PRR in the response of tomato leaves to flagellin-derivedPAMPs and PTI. In addition, we investigated molecular properties of the tomato brassinosteroid signaling kinase 830 (BSK830) that physically interacts with FLS3 and is a candidate for acting in the FLS3 signaling pathway. Our investigation refers to the proposal original objectives that were to: 1) Investigate the role of FLS3 and its interacting proteins in PTI; 2) Investigate the role of BSK830 in PTI; 3) Examine molecular and phosphorylation dynamics of the FLS3-BSK830 interaction; 4) Examine the possible interaction of FLS3 and BSK830 with Pstand Xcveffectors. We used CRISPR/Cas9 techniques to develop plants carrying single or combined mutations in the FLS3 gene and in the paralogsFLS2.1 and FLS2.2 genes, which encode the receptor FLAGELLIN SENSING2 (FLS2), and analyzed their function in PTI. Domain swapping analysis of the FLS2 and FLS3 receptors revealed domains of the proteins responsible for PAMP detection and for the different ROS response initiated by flgII-28/FLS3 as compared to flg22/FLS2. In addition, in vitro kinase assays and point mutations analysis identified FLS2 and FLS3 domains required for kinase activity and ATP binding. In research activities on tomato BSK830, we found that it interacts with PRRs and with the co-receptor SERK3A and PAMP treatment affects part of these interactions. CRISPR/Cas9 bsk830 mutant plants displayed enhanced pathogen susceptibility and reduced ROS production upon PAMP treatment. In addition, BSK830 interacted with 8 Xanthomonastype III secreted effectors. Follow up analysis revealed that among these effectors XopAE is part of an operon, is translocated into plant cells, and displays E3 ubiquitinligase activity. Our investigation was also extended to other Arabidopsis and tomato BSK family members. Arabidopsis BSK5 localized to the plant cell periphery, interacted with receptor-like kinases, and it was phosphorylatedin vitro by the PEPR1 and EFRPRRs. bsk5 mutant plants displayed enhanced susceptibility to pathogens and were impaired in several, but not all, PAMP-induced responses. Conversely, BSK5 overexpression conferred enhanced disease resistance and caused stronger PTI responses. Genetic complementation suggested that proper localization, kinase activity, and phosphorylation by PRRs are critical for BSK5 function. BSK7 and BSK8 specifically interacted with the FLS2 PRR, their respective mutant plants were more susceptible to B. cinereaand displayed reduced flg22-induced responses. The tomato BSK Mai1 was found to interact with the M3KMAPKKK, which is involved in activation of cell death associated with effector-triggered immunity. Silencing of Mai1 in N. benthamianaplants compromised cell death induced by a specific class of immune receptors. In addition, co-expression of Mai1 and M3Kin leaves enhanced MAPKphosphorylation and cell death, suggesting that Mai1 acts as a molecular link between pathogen recognition and MAPK signaling. Finally, We identified the PP2C phosphatase Pic1 that acts as a negative regulator of PTI by interacting with and dephosphorylating the receptor-like cytoplasmickinase Pti1, which is a positive regulator of plant immunity. The results of this investigation shed new light on the molecular characteristics and interactions of components of the immune system of crop plants providing new knowledge and tools for development of novel strategies for disease control.
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