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Relevant bibliographies by topics / Modele conformation

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Academic literature on the topic 'Modele conformation'

Author: Grafiati

Published: 4 June 2021

Last updated: 17 February 2022

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Journal articles on the topic "Modele conformation"

1

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

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

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Shang, Jinsai, Richard Brust, Patrick R. Griffin, Theodore M. Kamenecka, and Douglas J. Kojetin. "Quantitative structural assessment of graded receptor agonism." Proceedings of the National Academy of Sciences 116, no. 44 (October 14, 2019): 22179–88. http://dx.doi.org/10.1073/pnas.1909016116.

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Ligand–receptor interactions, which are ubiquitous in physiology, are described by theoretical models of receptor pharmacology. Structural evidence for graded efficacy receptor conformations predicted by receptor theory has been limited but is critical to fully validate theoretical models. We applied quantitative structure–function approaches to characterize the effects of structurally similar and structurally diverse agonists on the conformational ensemble of nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ). For all ligands, agonist functional efficacy is correlated to a shift in the conformational ensemble equilibrium from a ground state toward an active state, which is detected by NMR spectroscopy but not observed in crystal structures. For the structurally similar ligands, ligand potency and affinity are also correlated to efficacy and conformation, indicating ligand residence times among related analogs may influence receptor conformation and function. Our results derived from quantitative graded activity–conformation correlations provide experimental evidence and a platform with which to extend and test theoretical models of receptor pharmacology to more accurately describe and predict ligand-dependent receptor activity.

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3

LEE, HO-JIN, HYUN-MEE PARK, and KANG-BONG LEE. "CONFORMATIONAL PREFERENCES OF N-ACETYL–GLYCINE–GLYCINE–N′-METHYLAMIDE: A THEORETICAL STUDY." Journal of Theoretical and Computational Chemistry 08, no. 05 (October 2009): 799–811. http://dx.doi.org/10.1142/s0219633609005118.

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The conformational preferences of peptide models have been investigated to understand the protein folding mechanism and to develop the force field. Here, we report the minimum energy conformations for a model peptide, N-acetyl–glycine–glycine–N′-methylamide ( Ac–1Gly–2Gly–NHMe(I) ) at the HF/3-21G, HF/6-31G*, and the B3LYP/6-31G* level of theory. At the B3LYP/6-31G* level, the 31 minima were identified and the 10 β-turn structures among the minima were observed in gas-phase. The conformational preferences of Gly residue in the model peptide, I depend on its relative position and conformation of neighboring Gly residue. The Gly residue in this model dipeptide has an asymmetric energy profile as one of Gly residue adopts a specific conformation. This study sheds some lights on understanding the unique conformational preferences of Gly residue in protein including two consecutive Gly residues.

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Whitmore, Elizabeth K., Devon Martin, and Olgun Guvench. "Constructing 3-Dimensional Atomic-Resolution Models of Nonsulfated Glycosaminoglycans with Arbitrary Lengths Using Conformations from Molecular Dynamics." International Journal of Molecular Sciences 21, no. 20 (October 18, 2020): 7699. http://dx.doi.org/10.3390/ijms21207699.

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Glycosaminoglycans (GAGs) are the linear carbohydrate components of proteoglycans (PGs) and are key mediators in the bioactivity of PGs in animal tissue. GAGs are heterogeneous, conformationally complex, and polydisperse, containing up to 200 monosaccharide units. These complexities make studying GAG conformation a challenge for existing experimental and computational methods. We previously described an algorithm we developed that applies conformational parameters (i.e., all bond lengths, bond angles, and dihedral angles) from molecular dynamics (MD) simulations of nonsulfated chondroitin GAG 20-mers to construct 3-D atomic-resolution models of nonsulfated chondroitin GAGs of arbitrary length. In the current study, we applied our algorithm to other GAGs, including hyaluronan and nonsulfated forms of dermatan, keratan, and heparan and expanded our database of MD-generated GAG conformations. Here, we show that individual glycosidic linkages and monosaccharide rings in 10- and 20-mers of hyaluronan and nonsulfated dermatan, keratan, and heparan behave randomly and independently in MD simulation and, therefore, using a database of MD-generated 20-mer conformations, that our algorithm can construct conformational ensembles of 10- and 20-mers of various GAG types that accurately represent the backbone flexibility seen in MD simulations. Furthermore, our algorithm efficiently constructs conformational ensembles of GAG 200-mers that we would reasonably expect from MD simulations.

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5

Giri Rao, V. V. Hemanth, and Shachi Gosavi. "On the folding of a structurally complex protein to its metastable active state." Proceedings of the National Academy of Sciences 115, no. 9 (January 17, 2018): 1998–2003. http://dx.doi.org/10.1073/pnas.1708173115.

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For successful protease inhibition, the reactive center loop (RCL) of the two-domain serine protease inhibitor, α1-antitrypsin (α1-AT), needs to remain exposed in a metastable active conformation. The α1-AT RCL is sequestered in a β-sheet in the stable latent conformation. Thus, to be functional, α1-AT must always fold to a metastable conformation while avoiding folding to a stable conformation. We explore the structural basis of this choice using folding simulations of coarse-grained structure-based models of the two α1-AT conformations. Our simulations capture the key features of folding experiments performed on both conformations. The simulations also show that the free energy barrier to fold to the latent conformation is much larger than the barrier to fold to the active conformation. An entropically stabilized on-pathway intermediate lowers the barrier for folding to the active conformation. In this intermediate, the RCL is in an exposed configuration, and only one of the two α1-AT domains is folded. In contrast, early conversion of the RCL into a β-strand increases the coupling between the two α1-AT domains in the transition state and creates a larger barrier for folding to the latent conformation. Thus, unlike what happens in several proteins, where separate regions promote folding and function, the structure of the RCL, formed early during folding, determines both the conformational and the functional fate of α1-AT. Further, the short 12-residue RCL modulates the free energy barrier and the folding cooperativity of the large 370-residue α1-AT. Finally, we suggest experiments to test the predicted folding mechanism for the latent state.

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6

Ludwiczak, Jan, Ewa Szczęsna, Antônio Marinho da Silva Neto, Piotr Cieplak, Andrzej A. Kasprzak, and Adam Jarmuła. "Interactions between motor domains in kinesin-14 Ncd — a molecular dynamics study." Biochemical Journal 476, no. 17 (September 10, 2019): 2449–62. http://dx.doi.org/10.1042/bcj20190484.

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Abstract Minus-end directed, non-processive kinesin-14 Ncd is a dimeric protein with C-terminally located motor domains (heads). Generation of the power-stroke by Ncd consists of a lever-like rotation of a long superhelical ‘stalk’ segment while one of the kinesin's heads is bound to the microtubule. The last ∼30 amino acids of Ncd head play a crucial but still poorly understood role in this process. Here, we used accelerated molecular dynamics simulations to explore the conformational dynamics of several systems built upon two crystal structures of Ncd, the asymmetrical T436S mutant in pre-stroke/post-stroke conformations of two partner subunits and the symmetrical wild-type protein in pre-stroke conformation of both subunits. The results revealed a new conformational state forming following the inward motion of the subunits and stabilized with several hydrogen bonds to residues located on the border or within the C-terminal linker, i.e. a modeled extension of the C-terminus by residues 675–683. Forming of this new, compact Ncd conformation critically depends on the length of the C-terminus extending to at least residue 681. Moreover, the associative motion leading to the compact conformation is accompanied by a partial lateral rotation of the stalk. We propose that the stable compact conformation of Ncd may represent an initial state of the working stroke.

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7

Lane, A. N., T. C. Jenkins, D. J. Brown, and T. Brown. "N.m.r. determination of the solution conformation and dynamics of the A.G mismatch in the d(CGCAAATTGGCG)2 dodecamer." Biochemical Journal 279, no. 1 (October 1, 1991): 269–81. http://dx.doi.org/10.1042/bj2790269.

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A.G base-paired mismatches that occur during replication are among the most difficult to detect by repair enzymes. Such purine.purine mispairs can exist in two conformations, one of which is stabilized by protons [Gao & Patel (1988) J. Am. Chem. Soc. 110, 5178-5182]. We have undertaken a 1H-n.m.r. and 31P-n.m.r. study of the mismatched dodecamer d(CGCAAATTGGCG)2 as a function of both temperature and pH to determine the conformational features of the A.G mismatch. At pH greater than 7 the mispaired bases are each in the anti conformation and are stacked in the B-like helix. As the pH is decreased, a second conformation becomes populated (apparent pKa approx. 5.9) with concomitant changes in the chemical shifts of protons of the mispaired bases and their nearest neighbours. Data from two-dimensional nuclear-Overhauser-enhancement spectroscopy show unequivocally that, at low pH, the dominant conformation is one in which the mismatched G residues are in the syn conformation and are hydrogen-bonded to the A residues that remain in the anti conformation. Residues not adjacent to the A.G sites are almost unaffected by the transition or the mispairing, suggesting considerable local flexibility of the unconstrained duplexes. Despite the bulging of the mispaired bases, the conformation of the A(anti).G(anti) duplex is very similar to the native dodecamer, whereas the AH+(anti).G(syn) duplex shows a greater variation in the backbone conformation at the mismatched site. According to the chemical shifts, the duplex retains twofold symmetry in solution. The equilibrium between the syn and anti conformations of G9/G21 is strongly dependent on pH, but only weakly dependent on temperature (delta H approx. 16 kJ.mol-1). The first-order rate constant for the transition is approx. 9 s-1 at 283 K and approx. 60 s-1 at 298 K, with an activation enthalpy of approx. 100 kJ.mol-1. The stabilization of the A(anti).G(syn) conformation by protons is consistent with models invoking N1 protonation of adenine. Using the derived glycosidic torsion angles we have used restrained molecular dynamics to build models of the neutral and protonated d(CGCAAATTGGCG)2 oligomers. The results confirm that the A(anti).G(anti) and AH+(anti).G(syn) conformations are favoured at high pH and low pH respectively, in accord with n.m.r. and single-crystal X-ray data.

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Kumar, Sivakumar Prasanth, and Prakash Chandra Jha. "Multi-Pharmacophore Modeling of Caspase-3 Inhibitors using Crystal, Dock and Flexible Conformation Schemes." Combinatorial Chemistry & High Throughput Screening 21, no. 1 (March 20, 2018): 26–40. http://dx.doi.org/10.2174/1386207321666180102114917.

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Aim and Objective: Numerous caspase-3 drug discovery projects were found to have relied on single receptor as the template to recognize most promising small molecule candidates using docking approach. Alternatively, some researchers were contingent upon ligand-based alignment to build up an empirical relationship between ligand functional groups and caspase-3 inhibitory activity quantitatively. To connect both caspase-3 receptor details and its inhibitors chemical functionalities, this study was undertaken to develop receptor- and ligand-pharmacophore models based on different conformational schemes. Material and Methods: A multi-pharmacophore modeling strategy is carried out based on three conformational schemes of pharmacophore hypothesis generation to screen caspase-3 inhibitors from database. The schemes include (i) flexible (conformations unrestricted or flexible during pharmacophore mapping), (ii) dock (conformations obtained using FlexX docking method) and (iii) crystal (extracted from multiple caspase-3-ligand complexes from PDB repository) conformations of query ligands. The pharmacophore models developed using these conformational schemes were then used to identify probable caspase-3 inhibitors from ZINC database. Results: We noticed better sensitivity with good specificity measures returned by candidate pharmacophore hypotheses across each conformation type and recognized crucial pharmacophore features that enable caspase-3 binding. Pharmacophore modeling based on flexible conformational scheme indicated that the crystal structure 3KJF (AAAADH) is the best receptor structure to perform receptor-based pharmacophore screening of caspase-3 inhibitors. When multiple crystal structures were included, the hypothesis (HAAA) is more generalized. Superimposition of multiple co-crystal ligands from various caspase-3 PDB entries in crystallographic binding mode revealed similar hypothesis (HAAA). Further, FlexX-guided dock conformations of validation dataset showed that the crystal structure 1RE1 is the best-suited for dock-based pharmacophore models. Database screening using these pharmacophore hypotheses identified N'-[6-(benzimidazol-1-yl)-5-nitro-pyrimidin-4-yl]-4 methylbenzenesulfonohydrazide and 2-nitro-N'-[5-nitro-6-[N'-(p-tolylsulfonyl)hydrazino]pyrimidin-4- yl]benzohydrazide as the probable caspase-3 inhibitors. Conclusion: N'-[6-(benzimidazol-1-yl)-5-nitro-pyrimidin-4-yl]-4 methylbenzenesulfonohydrazide and 2-nitro-N'-[5-nitro-6-[N'-(p-tolylsulfonyl)hydrazino]pyrimidin-4-yl]benzohydrazide may be tested for caspase-3 inhibition. We believe that potential caspase-3 inhibitors can be recognized efficiently by adapting multi-pharmacophore models in database screening.

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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. METHODS: Molecular dynamics (MD) simulations were performed to study the conformation changes of RBP starting from the open-apo, closed-holo and closed-apo conformations. RESULTS: The evolution of the domain opening angle θ clearly indicates large structural changes. The simulations indicate that the closed states in the absence of ribose are inclined to transition to the open states and that ribose-free RBP exists in a wide range of conformations. The first three dominant principal motions derived from the closed-apo trajectories, consisting of rotating, bending and twisting motions, account for the major rearrangement of the domains from the closed to the open conformation. CONCLUSIONS: The motions showed a strong one-to-one correspondence with the slowest modes from our previous study of RBP with the anisotropic network model (ANM). The results obtained for RBP contribute to the generalization of robustness for protein domain motion studies using either the ANM or PCA for trajectories obtained from MD.

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10

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

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A common practice to compute ligand conformations of compounds with various degrees of freedom to be used in molecular modeling (QSAR and docking studies) is to perform a conformational distribution based on repeated random sampling, such as Monte-Carlo methods. Further calculations are often required. This short review describes some methods used for conformational analysis and the implications of using selected conformations in QSAR. A case study is developed for 2,4-dichlorophenoxyacetic acid (2,4-D), a widely used herbicide which binds to TIR1 ubiquitin ligase enzyme. The use of such an approach and semi-empirical calculations did not achieve all possible minima for 2,4-D. In addition, the conformations and respective energies obtained by the semi-empirical AM1 method do not match the calculated trends obtained by a high level DFT method. Similar findings were obtained for the carboxylate anion, which is the bioactive form. Finally, the crystal bioactive structure of 2,4-D was not found as a minimum when using Monte-Carlo/AM1 and is similarly populated with another conformer in implicit water solution according to optimization at the B3LYP/aug-cc-pVDZ level. Therefore, quantitative structure-activity relationship (QSAR) methods based on three dimensional chemical structures are not fundamental to provide predictive models for 2,4-D congeners as TIR1 ubiquitin ligase ligands, since they do not necessarily reflect the bioactive conformation of this molecule. This probably extends to other systems.

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Dissertations / Theses on the topic "Modele conformation"

1

Colloc'h, Nathalie. "Analyse qualitative des surfaces moleculaires a l'aide de fonctions de lissage b-spline et etudes topologiques quantitatives : application aux proteines." Paris 6, 1988. http://www.theses.fr/1988PA066162.

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Haxaire, Katia. "Conformation du hyaluronane et interactions en solution et à l'état solide." Université Joseph Fourier (Grenoble ; 1971-2015), 2000. http://www.theses.fr/2000GRE10156.

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Cette etude fournit des informations conformationnelles permettant une meilleure comprehension de la conformation du hyaluronane (ha) en solution et a l'etat solide. Dans un premier temps, nous avons determine les conformations de basse energie des sous-unites disaccharidiques par modelisation moleculaire. A partir de ces resultats nous avons pu predire de nombreuses conformations helicoidales. La structure en double helice anti-parallele a egalement ete exploree. Nous avons egalement genere des chaines statistiques a partir des cartes d'energie des tetrasaccharides et determine des grandeurs physico-chimiques telles que la longueur de persistance. Toutes ces donnees ont ete comparees a celles donnees dans la litterature et un bon accord a ete observe. Afin de valider les donnees obtenues par le calcul, nous nous sommes interesses a la conformation en solution du ha et a l'influence de parametres tels que la temperature, la concentration en polymere et le ph sur la rigidite de la chaine. Pour cela nous avons utilise la rmn 1h, le dichroisme circulaire et la diffusion de la lumiere. Cette derniere technique nous a egalement permis de mettre en evidence l'apparition d'un mode lent pour des concentrations superieures a la concentration critique de recouvrement c*. Il est attribue a la formation d'associations physiques du polymere qui diffuseraient dans la solution semi-diluee. Le mode rapide est caracteristique d'un mecanisme de diffusion cooperatif des blobs en regime semi-dilue. Enfin, nous presentons une etude originale de l'hydratation du ha par spectroscopie infrarouge.

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Etchebest, Catherine. "Etudes theoriques d'un canal ionique transmembranaire : la gramicidine a." Paris 6, 1987. http://www.theses.fr/1987PA066049.

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Ghanem, Antoine. "Analyse conformationnelle de polyesters thermotropes." Grenoble 2 : ANRT, 1987. http://catalogue.bnf.fr/ark:/12148/cb376053879.

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Pavard-Ohanessian, Jacqueline. "Contribution à l'étude de la stéréochimie des chaines glycaniques de glycoprotéines et à l'étude de leurs interactions avec la lectine d'arachide spécifique des substrats d-galactosyles terminaux." Paris 13, 1986. http://www.theses.fr/1986PA132005.

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Pattou, Denis. "Modelisation moleculaire assistee par ordinateur : etude et realisation du logiciel mol3d." Université Louis Pasteur (Strasbourg) (1971-2008), 1986. http://www.theses.fr/1986STR13020.

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Amerein, Béatrice. "Modelisation et representation dynamique de macromolecules biologiques." Université Louis Pasteur (Strasbourg) (1971-2008), 1988. http://www.theses.fr/1988STR13040.

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Sahnoun, Leila. "Etude de la structure et de la flexibilité d'oligonucléotides contenant un site abasique par modélisation moléculaire." Université Joseph Fourier (Grenoble), 1999. http://www.theses.fr/1999GRE10076.

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Notre travail s'inscrit dans le cadre de l'etude par modelisation moleculaire d'une lesion majeure de l'adn, le site abasique qui induit des modifications structurales notables encore mal decrites. Nous avons d'abord confirme que la presence d'un site abasique dans une sequence particuliere induit un coude au niveau de la region abasique en comparant les structures d'un oligomere naturel et d'un homologue abasique, obtenues par ailleurs par rmn et modelisation moleculaire. Nous avons montre que la proce dure jumna est capable de reproduire les caracteristiques structurales des conformations abasiques sans l'utilisation de contraintes experimentales. Nous avons etudie les effets de la sequence sur les conformations d'adn contenant des sites abasiques. Nous avons considere les lesions correspondant a toutes les bases non appariees possibles (x), adenine, guanine, cytosine ou thymine situees dans des sequences differentes, cxc et gxg. Les calculs sont faits sur des 11-meres, en utilisant differentes techniques de recherches conformationnelles et la contribution de la solvatation est introduite par un terme electrostatique calcule en utilisant l'equation de poisson-boltzmann. Les resultats sont en tres bon accord avec les donnees experimentales disponibles et montrent des effets de sequences sur la position de la base non appariee (intra- ou extrahelicoidale) et sur la courbure globale induite par la lesion abasique. Pour cxc, les purines non appariees sont a l'interieur de l'helice, les pyrimidines non appariees sont a l'exterieur ou en equilibre entre des formes intra- et extrahelicoidales. Pour gxg, toutes les bases non appariees sont a l'interieur de l'helice, mais avec des differences marquees sur les courbures globales induites. Finalement, nous avons utilise des deformations de flexion et de torsion pour etudier l'effet de la presence du site abasique sur la flexibilite de l'adn. Nous avons montre que la presence de ces lesions augmente generalement la flexibilite sauf pour les structures extrahelicoidales. Les effets structuraux et dynamiques de ce type de lesion de l'adn peuvent avoir des roles notoires dans les mecanismes de reparation.

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Bolin, Kimberly Anne. "Conformational studies of protein fragments." Thesis, University of Oxford, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.239325.

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Winsborrow, BeAtrice G. "Glycolipid conformation and dynamics in model and biological membranes." Thesis, University of Ottawa (Canada), 1993. http://hdl.handle.net/10393/6811.

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The focus of this dissertation has been the biophysical analysis of two related research subjects: a model membrane glycolipid system and glycolipid-rich biomembranes. The objective of the model system study was to provide a biological understanding of the molecular conformation and dynamics at the membrane surface. The biomembrane project is in the first stages of development where the immediate goal is to observe the structure and phase behaviour of cyanobacterial thylakoid membranes. It has been possible to apply a motional model deduced for the glycerol C3$\sp\prime$ position of 1,2-di-O-tetradecyl-3-O-$(\beta$-D-glucopyranosyl)-sn-glycerol $(\beta$-DTGL) in the gel state not only to the more fluid liquid crystalline state, but also to the analysis of the glucose head group ($\{$1-$\rm \sp2H\sb1\})$ motions. The above model, however, did not completely simulate the relaxation data of the $\beta$-DTGL glucose head group. Therefore, conformational energy calculations have been used to assess the flexibility of the head group about its glycosidic bond, in a liquid-crystalline membrane matrix. Algal thylakoid membranes are known for their ability to undergo conformational changes during periods of photosynthetic activity. The ultimate goal of the biomembrane project was to use $\sp2$H NMR to study such conformational changes in thylakoid membranes. However, this project is in the first stages of development; the more modest but attainable short term goal was to observe directly the structure and phase behaviour of two strains of cyanobacterial thylakoid membranes, Anacystis nidulans and A. nidulans R2. In both the previous studies and this study, it was found that the heterogeneous systems undergo broad phase transitions and that acyl chain unsaturation lowers the phase transition temperature of the membranes. Although pure digalactosyldiacyglycerol is known to stabilize lamellar membrane phases, it appears as though phosphatidylglycerol (PG) is more influential in stabilizing the lamellar membrane structure of the cyanobacterial thylakoid membranes. This effect was more noticeable for the spectra of extracted lipids; in the absence of protein and with low PG levels, the lipids formed non-lamellar phases at lower temperatures. (Abstract shortened by UMI.)

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Books on the topic "Modele conformation"

1

Protein structure prediction. 3rd ed. New York: Humana Press, 2014.

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Wendt, Hans. Leucine zipper peptides as models for protein folding. Konstanz: Hartung-Gorre, 1995.

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Leopoldina, Symposium on the Structure Self-organization and Stability of Proteins (2000 Wittenberg Germany). Structure, Self-organization and Stability of Proteins: Experiments and models : Faltertage 2000 : Leopoldina Symposium : Leucorea in Wittenberg, Germany, September 21, 2000 to September 23, 2000. Halle: Deutsche Akademie der Naturforscher Leopoldina, 2001.

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Mattice, Wayne L. Conformational theory of large molecules: The rotationalisomeric state model in macromolecular systems. New York: Wiley, 1994.

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1935-, Suter U., ed. Conformational theory of large molecules: The rotational isomeric state model in macromolecular systems. New York: Wiley, 1994.

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Harmke, Kamminga, and Whipple Museum of the History of Science., eds. Representations of the double helix. Cambridge: Whipple Museum of the History of Science, 2002.

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Rupp, Bernhard. Biomolecular crystallography: Principles, practice, and application to structural biology. New York: Garland Science, 2010.

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Rigden, Daniel John. From protein structure to function with bioinformatics. [Dordrecht]: Springer, 2009.

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Rupp, Bernhard. Biomolecular crystallography. New York, NY: Garland Science, 2010.

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Rupp, Bernhard. Biomolecular crystallography. New York, NY: Garland Science, 2010.

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Book chapters on the topic "Modele conformation"

1

Brackley, C. A., M. C. Pereira, J. Johnson, D. Michieletto, and D. Marenduzzo. "Predictive Models for 3D Chromosome Organization: The Transcription Factor and Diffusive Loop Extrusion Models." In Modeling the 3D Conformation of Genomes, 97–114. Boca Raton : Taylor & Francis, 2018. | Series: Series in computational biophysics ; 4: CRC Press, 2019. http://dx.doi.org/10.1201/9781315144009-5.

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Benedetti, Fabrizio, Dusan Racko, Julien Dorier, and Andrzej Stasiak. "Introducing Supercoiling into Models of Chromosome Structure." In Modeling the 3D Conformation of Genomes, 115–38. Boca Raton : Taylor & Francis, 2018. | Series: Series in computational biophysics ; 4: CRC Press, 2019. http://dx.doi.org/10.1201/9781315144009-6.

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Moro, Giorgio J., Alberta Ferrarini, Antonino Polimeno, and Pier Luigi Nordio. "Models of Conformational Dynamics." In Reactive and Flexible Molecules in Liquids, 107–39. Dordrecht: Springer Netherlands, 1989. http://dx.doi.org/10.1007/978-94-009-1043-0_7.

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Scherer, Philipp O. J., and Sighart F. Fischer. "Random Walk Models for the Conformation." In Biological and Medical Physics, Biomedical Engineering, 3–20. Berlin, Heidelberg: Springer Berlin Heidelberg, 2017. http://dx.doi.org/10.1007/978-3-662-55671-9_1.

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Scherer, Philipp, and Sighart F. Fischer. "Random Walk Models for the Conformation." In Biological and Medical Physics, Biomedical Engineering, 3–18. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-540-85610-8_1.

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Bianco, Simona, Andrea M. Chiariello, Carlo Annunziatella, Andrea Esposito, Luca Fiorillo, and Mario Nicodemi. "The Strings and Binders Switch Model of Chromatin." In Modeling the 3D Conformation of Genomes, 57–68. Boca Raton : Taylor & Francis, 2018. | Series: Series in computational biophysics ; 4: CRC Press, 2019. http://dx.doi.org/10.1201/9781315144009-3.

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Carreau, P. J., A. Ait Kadi, and M. Grmela. "A conformation model for polymer solutions." In Progress and Trends in Rheology II, 91–93. Heidelberg: Steinkopff, 1988. http://dx.doi.org/10.1007/978-3-642-49337-9_21.

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Langmead, Christopher James. "Generative Models of Conformational Dynamics." In Advances in Experimental Medicine and Biology, 87–105. Cham: Springer International Publishing, 2013. http://dx.doi.org/10.1007/978-3-319-02970-2_4.

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Grajcar, L., N. Leygue, M. H. Baron, S. Becouarn, S. Czernecki, and J. M. Valery. "Marker of Local Conformation of Oligonucleotides." In Spectroscopy of Biological Molecules: Modern Trends, 235–36. Dordrecht: Springer Netherlands, 1997. http://dx.doi.org/10.1007/978-94-011-5622-6_104.

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Dea, Phoebe K., and Hendrik Keyzer. "Conformation and Electronic Aspects of Chlor promazine in Solution." In Modern Bioelectrochemistry, 481–501. Boston, MA: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4613-2105-7_18.

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Conference papers on the topic "Modele conformation"

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Hagani, Fouad, M'hamed Boutaous, Ronnie Knikker, Shihe Xin, and Dennis Siginer. "Numerical Modeling of Non-Affine Viscoelastic Fluid Flow Including Viscous Dissipation Through a Square Cross-Section Duct: Heat Transfer Enhancement due to the Inertia and the Elastic Effects." In ASME 2020 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2020. http://dx.doi.org/10.1115/imece2020-23558.

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Abstract Non-isothermal laminar flow of a viscoelastic fluid including viscous dissipation through a square cross–section duct is analyzed. Viscoelastic stresses are described by Giesekus modele orthe Phan-Thien–Tanner model and the solvent shear stress is given by the linear Newtonian constitutive relationship. The flow through the tube is governed by the conservation equations of energy, mass, momentum associated with to one non–affine rheological model mentioned above. The mixed type of the governing system of equations (elliptic–parabolic–hyperbolic) requires coupling between discretisation methods designed for elliptic–type equations and techniques adapted to transport equations. To allow appropriate spatial discretisation of the convection terms, the system is rewritten in a quasi-linear first-order and homogeneous form without the continuity and energy equations. With the rheological models of the Giesekus type, the conformation tensor is by definition symmetrical and positive-definite, with the PTT model the hyperbolicity condition is subject to restrictions related to the rheological parameters. Based on this hyperbolicity condition, the contribution of the hyperbolic part is approximated by applying the characteristic method to extract pure advection terms which are then discretized by high ordre schemes WENO and HOUC. The algorithm thus developed makes it possible, to avoid the problems of instabilities related to the high Weissenberg number without the use of any stabilization method. Finally, a Nusselt number analysis is given as a function of inertia, elasticity, viscous dissipation, for constant solvent viscosity ratio and constant material and rheological parameters.

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Maghsoodi, Ameneh, Anupam Chatterjee, Ioan Andricioaei, and Noel Perkins. "An Approximate Model of the Dynamics of the Bacteriophage T4 Injection Machinery." In ASME 2016 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/detc2016-60281.

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Bacteriophage T4 is one of the most common and complex of the tailed viruses that infect host bacteria using an intriguing contractile tail assembly. Despite extensive progress in resolving the structure of T4, the dynamics of the injection machinery remains largely unknown. This paper contributes a first model of the injection machinery that is driven by elastic energy stored in a structure known as the sheath. The sheath is composed of helical strands of protein that suddenly collapse from an energetic, extended conformation prior to infection to a relaxed, contracted conformation during infection. We employ Kirchhoff rod theory to simulate the nonlinear dynamics of a single protein strand coupled to a model for the remainder of the virus, including the coupled translation and rotation of the head (capsid), neck and tail tube. Doing so provides an important building block towards the future goal of modeling the entire sheath structure which is composed of six interacting helical protein strands. The resulting numerical model exposes fundamental features of the injection machinery including the time scale and energetics of the infection process, the nonlinear conformational change experienced by the sheath, and the contribution of hydrodynamic drag on the head (capsid).

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Subramanian, Raghavendran, and Kazem Kazerounian. "Residue Level Inverse Kinematics of Peptide Chains in the Presence of Observation Inaccuracies and Bond Length Changes." In ASME 2005 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2005. http://dx.doi.org/10.1115/detc2005-84352.

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Dihedral angles as generalized coordinates define the geometric conformation of a peptide chain. Given the exact coordinates of the atoms, it is possible to rigorously calculate the dihedral angles. We will refer to this calculation process as the residue level inverse kinematics of peptide chains. However uncertainties and experimental observation inaccuracies in the atoms’ coordinates handicap this otherwise simple and straightforward process. In this paper, we present three new efficient methodologies to find all the dihedral angles of a peptide chain for a given conformation. Comparison of these results with the dihedral angle values reported in the PDB (Protein Data Bank) indicates significant improvements. While these improvements benefit most modeling methods in protein analysis, it is in particular, very significant in homology modeling where the dihedral angles are the structural variables. The first method presented here fits a best plane through five atoms of each peptide unit. The angle between the successive planes is defined as the dihedral angle. The second method is based on the Zero-Position analysis method. Successive links in this method rotate by the dihedral angles so as to minimize the structural error between respective atoms in the model conformation with given atoms’ coordinates. Dihedral angle final values correspond to the minimum structural error configuration. In this method, singular value decomposition (SVD) technique is used to best fit the atoms in the two conformations. The third method is a variant of the second method. In this instead of rotating all the links successively only three links are matched each time to extract the dihedral angle of the middle link. By doing so, the error accumulation on the successive links is reduced. This paper focuses on the Euclidean norm as the measure of merit (structural error) to compare different methods with the Protein Data Bank (PDB). This Euclidean norm is further, minimized by optimizing the geometrical features of the peptide plane.

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Li, Zhida, Ji Ma, and Hsi-Yung Feng. "Facial Conformation Modeling via Hierarchical Model Parameterization." In CAD'16. CAD Solutions LLC, 2016. http://dx.doi.org/10.14733/cadconfp.2016.221-225.

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Shahbazi, Zahra, Horea T. Ilies¸, and Kazem Kazerounian. "Protein Molecules as Natural Nano Bio Devices: Mobility Analysis." In ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology. ASMEDC, 2010. http://dx.doi.org/10.1115/nemb2010-13021.

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Proteins are nature’s nano-robots in the form of functional molecular components of living cells. The function of these natural nano-robots often requires conformational transitions between two or more native conformations that are made possible by the intrinsic mobility of the proteins. Understanding these transitions is essential to the understanding of how proteins function, as well as to the ability to design and manipulate protein-based nano-mechanical systems [1]. Modeling protein molecules as kinematic chains provides the foundation for developing powerful approaches to the design, manipulation and fabrication of peptide based molecules and devices. Nevertheless, these models possess a high number of degrees of freedom (DOF) with considerable computational implications. On the other hand, real protein molecules appear to exhibits a much lower mobility during the folding process than what is suggested by existing kinematic models. The key contributor to the lower mobility of real proteins is the formation of Hydrogen bonds during the folding process.

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Tarrazó-Serrano, Daniel, Sergio Pérez-López, Sergio Castiñeira-Ibáñez, Pilar Candelas, and Constanza Rubio. "USING NUMERICAL MODELS TO UNDERSTAND ACOUSTIC BEAM CONFORMATION." In 12th International Technology, Education and Development Conference. IATED, 2018. http://dx.doi.org/10.21125/inted.2018.1333.

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Sapin, Emmanuel, Kenneth De Jong, and Amarda Shehu. "Evolving Conformation Paths to Model Protein Structural Transitions." In BCB '17: 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. New York, NY, USA: ACM, 2017. http://dx.doi.org/10.1145/3107411.3107498.

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Apap-Bologna, Angela, Ailsa Webster, Fiona Raitt, and Graham Kemp. "THE DYNAMIC STRUCTURE OF FIBRINOGEN PROBED BY SURFACE LABELLING AND CHEMICAL CROSS-LINKING." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642886.

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There is much controversy regarding the conformation of fibrinogen. Several models have been proposed ranging from an almost linear trinodular arrangement to a globular conformation. Consequently, it has been suggested that fibrinogen has a flexible structure where the actual conformation is influenced by its environment - one major factor being calcium concentration. Although the importance of tightly bound calcium ions (Kd ∼ luM) to fibrinogen structure is well established, the role of the larger number of low affinity sites (Kd∼lmM) is still a matter of debate.We have utilised the techniques of radio-active photoaffinity surface labelling and chemical cross-linking to probe the molecule's conformation under different conditions. Studies were carried out in an attempt to provide information on: (1) The relative locations of the major domains within the fibrinogen molecule (2) The regions of the chains which are exposed on the surface (3) The dependence of the conformation on the solvent composition with particular reference to the effect of calcium concentration. Our results indicate that the central, or E domain of the molecule is partially buried and that the conformation of fibrinogen is certainly influenced by changes in solvent composition. Increasing calcium concentration in the millimolar range results in an increase in the proportion of intermolecular cross-linking, mainly through the [A]α chains. There have been several reports that the C-terminal regions of the [A]α chains are in close association, forming a fourth domain within the molecule. Our results suggest that calcium ions promote the dissociation of this domain.

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Gord, Joseph, Timothy Zwier, Matthew Kubasik, and Daniel Hewett. "ASSESSING THE IMPACT OF BACKBONE LENGTH AND CAPPING AGENT ON THE CONFORMATIONAL PREFERENCES OF A MODEL PEPTIDE: CONFORMATION SPECIFIC IR AND UV SPECTROSCOPY OF 2-AMINOISOBUTYRIC ACID." In 70th International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2015. http://dx.doi.org/10.15278/isms.2015.mg13.

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Joachim, C., G. Treboux, and H. Tang. "A model conformational flip-flop molecular switch." In Molecular electronics—Science and Technology. AIP, 1992. http://dx.doi.org/10.1063/1.42677.

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Reports on the topic "Modele conformation"

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Kim, Sangtae. Microstructural Models of Interactions That Govern Protein Conformations: Algorithms for High Performance Computer Architectures. Fort Belvoir, VA: Defense Technical Information Center, January 1998. http://dx.doi.org/10.21236/ada360981.

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Schutt, Timothy C., and Manoj K. Shukla. Computational Investigation on Interactions Between Some Munitions Compounds and Humic Substances. Engineer Research and Development Center (U.S.), February 2021. http://dx.doi.org/10.21079/11681/39703.

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Humic acid substances (HAs) in natural soil and sediment environments effect the retention and degradation of insensitive munitions compounds and legacy high explosives (MCs): DNAN, DNi- NH4+, nMNA, NQ, NTO (neutral and anionic forms), TNT, and RDX.A humic acid model compound has been considered using molecular dynamics, thermodynamic integration, and density functional theory to characterize the munition binding ability, ionization potential, and electron affinity compared to that in the water solution. Humic acids bind most compounds and act as both a sink and source for electrons. Ionization potentials suggest HAs are more susceptible to oxidation than the MCs studied. The electron affinity of HAs are very conformation-dependent and spans the same range as the munition compounds. When HAs and MCs are complexed the HAs tend to radicalize first thus buffering MCs against reductive as well as oxidative attacks.

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Sadigh, B. LDRD Final Report (08-ERD-037): Important Modes to Drive Protein MD Simulations to the Next Conformational Level. Office of Scientific and Technical Information (OSTI), April 2011. http://dx.doi.org/10.2172/1022884.

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