Dissertations / Theses: '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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2

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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3

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

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4

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

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5

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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6

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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7

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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8

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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9

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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10

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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11

McColl, Iain H. "Raman optical activity studies of model polypeptide conformations." Thesis, University of Glasgow, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.410833.

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12

Dias, Cristiano L. "Models of the stability of proteins." Thesis, McGill University, 2007. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=103378.

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Although the native conformation of a protein is thermodynamically its most stable form, this stability is only marginal. As a consequence, globular proteins have a certain amount of flexibility in their backbones which allows for conformational changes in the course of their biological function. In the course of this thesis, we study protein models at the edge of stability in different contexts: (1) First, we use molecular dynamics to determine the force needed to rupture a chain molecule (an unfolded protein) being stretched at constant loading rate and temperature. When all energy bonds of the molecule are identical, we find that the force F depends on the pulling rate r and temperature T according to F ~ const -- T 1/3|ln(r/T)|1/3 When a single weak bond is introduced, this result is modified to F ~ const -- T2/3|ln(r/ T)|2/3 This scaling, which is model independent, can be used with force-spectroscopy experiment to quantitatively extract relevant microscopic parameters of biomolecules. (2) Second, we study the structural stability of models of proteins for which the selected folds are unusually stable to mutation, that is, designable. A two-dimensional hydrophobic-polar lattice model is used to determine designable folds and these folds were investigated under shear through Langevin dynamics. We find that the phase diagram of these proteins depends on their designability. In particular, highly designable folds are found to be weaker, i.e. easier to unfold, than low designable ones. This is argued to be related to protein flexibility. (3) Third, we study the mechanism of cold denaturation through constant-pressure simulations for a model of hydrophobic molecules in an explicit solvent. We find that the temperature dependence of the hydrophobic effect is the driving force for cold denaturation. The physical mechanism underlying this phenomenon is identified as the destabilization of hydrophobic contact in favor of solvent separated configurations, the same mechanism seen in pressure induced denaturation. A phenomenological explanation proposed for the mechanism is suggested as being responsible for cold denaturation in real proteins.

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13

Li, Shuxiang. "Computer simulations exploring conformational preferences of short peptides and developing a bacterial chromosome model." Diss., University of Iowa, 2017. https://ir.uiowa.edu/etd/5960.

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Computer simulations provide a potentially powerful complement to conventional experimental techniques in elucidating the structures, dynamics and interactions of macromolecules. In this thesis, I present three applications of computer simulations to investigate important biomolecules with sizes ranging from two-residue peptides, to proteins, and to whole chromosome structures. First, I describe the results of 441 independent explicit-solvent molecular dynamics (MD) simulations of all possible two-residue peptides that contain the 20 standard amino acids with neutral and protonated histidine. 3JHNHα coupling constants and δHα chemical shifts calculated from the MD simulations correlated quite well with recently published experimental measurements for a corresponding set of two-residue peptides. Neighboring residue effects (NREs) on the average 3JHNHα and δHα values of adjacent residues were also reasonably well reproduced. The intrinsic conformational preferences of each residue, and their NREs on the conformational preferences of adjacent residues, were analyzed. Finally, these NREs were compared with corresponding effects observed in a coil library and the average β-turn preferences of all residue types were determined. Second, I compare the abilities of three derivatives of the Amber ff99SB force field to reproduce a recent report of 3JHNHα scalar coupling constants for hundreds of two-residue peptides. All-atom MD simulations of 256 two-residue peptides were performed and the results showed that a recently-developed force field (RSFF2) produced a dramatic improvement in the agreement with experimental 3JHNHα coupling constants. I further show that RSFF2 also improved modestly agreement with experimental 3JHNHα coupling constants of five model proteins. However, an analysis of NREs on the 3JHNHα coupling constants of the two-residue peptides indicated little difference between the force fields’ abilities to reproduce experimental NREs. I speculate that this might indicate limitations in the force fields’ descriptions of nonbonded interactions between adjacent side chains or with terminal capping groups. Finally, coarse-grained (CG) models and multi-scale modeling methods are used to develop structural models of entire E. coli chromosomes confined within the experimentally-determined volume of the nucleoid. The final resolution of the chromosome structures built here was one-nucleotide-per-bead (1 NTB), which represents a significant increase in resolution relative to previously published CG chromosome models, in which one bead corresponds to hundreds or even thousands of basepairs. Based on the high-resolution final 1 NTB structures, important physical properties such as major and minor groove widths, distributions of local DNA bending angles, and topological parameters (Linking Number (Lk), Twist (Tw) and Writhe (Wr)) were accurately computed and compared with experimental measurements or predictions from a worm-like chain (WLC) model. All these analyses indicated that the chromosome models built in this study are reasonable at a microscopic level. This chromosome model provides a significant step toward the goal of building a whole-cell model of a bacterial cell.

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14

Mark, Pekka. "Molecular dynamics studies of water and biomolecules /." Stockholm, 2002. http://diss.kib.ki.se/2002/91-7349-251-5.

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15

Veissier, Valérie. "Etude de la dynamique locale dans les polymeres en masse par declin d'anisotropie de fluorescence." Paris 6, 1987. http://www.theses.fr/1987PA066063.

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La fonction d'autocorrelation orientationnelle a ete ajutee au modele de diffusion et perte generalisee (gdl). La signification physique des temps de correlation relatifs aux modeles conformationels a ete precisee et l'influence de la structure du polymere sur ces parametres a ete demontree. Etude de l'interaction entre la sonde fluorescente et le polymere et etude theorique de son influence sur la dynamique de chaine

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16

Furois-Corbin, Sylvie. "Contribution à l'étude théorique des biopolymères : acides nucléiques et protéines membranaires." Paris 6, 1987. http://www.theses.fr/1987PA066384.

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17

Prinsloo, Wilma. "Computational models for conformations of cell wall mycolates from Mycobacterium tuberculosis." Diss., Pretoria : [s.n.], 2009. http://upetd.up.ac.za/thesis/available/etd-06122009-114802/.

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18

Noble, Olivier. "Les galactomannanes en solution aqueuse : conformation, interactions et gélification." Grenoble 1, 1988. http://www.theses.fr/1988GRE10033.

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La reticulation des galactomannanes par les ions borate en milieu alcalin et par les ions hexahydroxoantimonate v en milieu neutre a ete etudiee. L'existence d'un mecanisme de gelification en milieu alcalin a ete mis en evidence. Les proprietes mecaniques de ces gels ont ete abordees par des mesures de module d'young, de relaxation et de fluage effectuees en compression uniaxiale

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19

Romano, Pablo. "Markov Models for the Conformational Kinetics in DNA Breathing Fluctuations." Thesis, University of Oregon, 2018. http://hdl.handle.net/1794/23126.

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As the genetic content is internally located within DNA duplexed form, it has long been hypothesized that DNA undergoes a series of thermally induced conformational changes that assist in protein recognition events. The biological mechanisms for protein-DNA interactions have long been sought after, as little is still known mechanistically about how these complexes form. To study the local contributions to these breathing modes several atomistic simulations of DNA oligonucleotides were generated and analyzed by statistical models to predict metastable conformational states, the system timescales, and the kinetic pathways between states. In order to sample time-series DNA constructs, microsecond molecular dynamics (MD) simulation were performed. MD simulations provide atomstic resolution of macromolecules in explicit solvent and with modern computational workflows can extend well into microsecond timescales. While MD is a powerful tool, it creates a tremendous amount of time-dependent data. In recent years, Markov State Models (MSM), which project the dynamics of MD simulations onto discrete coordinates that follow a Markov chain, have become an invaluable tool to model and describe the kinetics of these large datasets. These models can be coarse-grained for chemical insight, however there does not yet exist a method which consistently and ``crisply'' describe the metastable barriers. To address this, I developed a new method, called Gradient Adaptive Decomposition (GRAD), which optimizes the macrostate model by refining borders with respect to the gradient along the free energy surface. The proposed method requires only a small number of initial microstates because it corrects for errors produced by limited number of seeds. Whereas many methods rely on fuzzy, or overlapping, partitions for proper statstical analysis of timescales, GRAD retains accuracy and crisp decomposition. I present a workflow of GRAD refined MSM to analyze the long timescale MD simulations of DNA oligonucleotides to assess the stacking conformational dynamics of DNA. Evaluating the complex network of transitions accessible found evidence suggesting that chiral directed mechanisms are critical in how DNA bases unstack. I explore how these local effects may be significant to long timescale dynamics and the biological impact in relation to breathing fluctuations. This dissertation includes unpublished co-authored material.

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20

Zhou, Guangfeng. "STATISTICAL MODELS AND THEIR APPLICATIONS IN STUDYING BIOMOLECULAR CONFORMATIONAL DYNAMICS." Diss., Temple University Libraries, 2017. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/478773.

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Chemistry
Ph.D.
It remains a major challenge in biophysics to understand the conformational dynamics of biomolecules. As powerful tools, molecular dynamics (MD) simulations have become increasingly important in studying the full atomic details of conformational dynamics of biomolecules. In addition, many statistical models have been developed to give insight into the big datasets from MD simulations. In this work, I first describe three statistical models used to analyze MD simulation data: Lifson-Roig Helix-Coil theory, Bayesian inference models, and Markov state models. Then I present the applications of each model in analyzing MD simulations and revealing insight into the conformational dynamics of biomolecules. These statistical models allow us to bridge microscopic and macroscopic mechanisms of biological processes and connect simulations with experiments.
Temple University--Theses

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21

Petrov, Eugene P., and Petra Schwille. "Diffusion and conformational dynamics in locally perturbed model membrane systems." Diffusion fundamentals 23 (2015) 4, S. 1-17, 2015. https://ul.qucosa.de/id/qucosa%3A14583.

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In this article, we review our results on diffusion and phase separation in lipid membranes, as well as on interaction of membranes with colloidal particles, biomacromolecules, and supramolecular assemblies, which were obtained within the framework of the Saxon Research Unit FOR 877 “From Local Constraints to Macroscopic Transport”.

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22

Petrov, Eugene P., and Petra Schwille. "Diffusion and conformational dynamics in locally perturbed model membrane systems." Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-198919.

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In this article, we review our results on diffusion and phase separation in lipid membranes, as well as on interaction of membranes with colloidal particles, biomacromolecules, and supramolecular assemblies, which were obtained within the framework of the Saxon Research Unit FOR 877 “From Local Constraints to Macroscopic Transport”.

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23

DIDIER, BRUNO. "Analyse conformationnelle infographique et construction de pharmacophore : critique des methodes, description de systemes modeles et exemples d'application." Strasbourg 1, 1998. http://www.theses.fr/1998STR15065.

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24

Chen, Chong. "Nonnative Contact Properties in a 3D Protein Model and the Influence of Interactions on Conformation Space." University of Akron / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=akron1289419338.

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25

Tello, Cajiao John James 1990. "The influence of the DNA conformation on the radiation-induced DNA damage probabilities = A influência da conformação do DNA nas probabilidades de dano induzido por radiações." [s.n.], 2016. http://repositorio.unicamp.br/jspui/handle/REPOSIP/305738.

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Orientador: Mario Antonio Bernal Rodriguez
Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Física Gleb Wataghin
Made available in DSpace on 2018-08-30T22:42:12Z (GMT). No. of bitstreams: 1 TelloCajiao_JohnJames_M.pdf: 2614936 bytes, checksum: e5bdfc91b42434b003cad0b5fa850afb (MD5) Previous issue date: 2016
Resumo: O objetivo deste trabalho é estudar a influência da conformação do DNA na probabilidade de dano direto produzido por partículas ionizantes. Além disso, os fundamentos mecanicísticos do modelo Linear-Quadrático são investigadas através de um modelo biofísico desenvolvido neste trabalho, baseado na TADR (Teoria da Ação Dual da Radiação). Para este fim, três modelos geométricos do material genético foram construídos. Os modelos têm resolução atomística e levam em conta ? 10^9 pares de base (bps) nas configurações A,B e Z do DNA. A partir de um único bp, os diferentes níveis organizacionais no interior do núcleo da célula foram criados por meio de transformações lineares. Em seguida, o código Monte Carlo (MC) GEANT4-DNA foi usado para simular o transporte de prótons de 0.5, 1, 5, 7 e 10 MeV assim como de partículas alfa de 2, 5, 7 e 10M eV . O número de partículas em cada caso é de tal modo que as doses absorvidas estão entre 0.5 ? 16Gy. Os três modelos foram consistentes com as dimensões das estruturas reais. Em particular, os modelos foram compatíveis com a exigência de que o diâmetro da cromatina seja de 30 nm, bem como com os volumes bp reportados em outros trabalhos. Os rendimentos tanto das quebras totais quanto das quebras duplas (TSBY e DSBY) foram obtidos para cada qualidade de radiação. Além disso, a probabilidade de impacto (SHP) definida como a razão entre o volume do DNA e o volume núcleo, foi calculada teoricamente e a partir das simulações. O modelo biofísico em conjunto com as simulações MC forneceu o número de lesões letais (N_LL) em função da dose, para prótons de 0,5 e 10 MeV, e para partículas alfa de 2 e 10 MeV . Os N_LL puderam ser divididos em aqueles criados por uma única trajetória e aqueles originados pela interacção de duas trajetórias. Concluiu-se que o TSBY é praticamente determinada pela SHP e depende fracamente da qualidade de radiação incidente. No entanto, o DSBY mostrou forte dependência tanto da conformação do DNA quanto da qualidade de radiação. Isto é devido à relação entre a capacidade de agrupamento das deposições de energia para uma radiação dada e o empacotamento do DNA. Por outro lado, a análise dos mecanismos de produção de dano, baseada na TADR e testada com o modelo biofísico desenvolvido, mostraram que os efeitos de uma única trajetória (de primeira ordem) dependem linearmente com a dose. Além disso, os efeitos inter-trajetórias seguem um comportamento quadrático com a dose, com um termo linear que influencia o mecanismo de primeira ordem. Isto significa que o comportamento linear-quadrático do N_LL com a dose, tem fundamentos mecanicistas, pelo menos, na primeira fase do dano
Abstract: The aim of this work is to study the influence of the DNA conformation on the probability of direct damage induction by ionizing particles. Also, the mechanistic grounds of the Linear-Quadratic radiobiological model are investigated through the eyes of a home-made biophysical model based on the DRAT (Dual Radiation Action Theory). To this end, three geometrical models of the genetic material were constructed. The models have atomistic resolution and account for ? 10^9 base pairs (bps) in the A-, B- and Z-DNA configurations. Starting from a single bp, the different organizational levels inside the cell nucleus were created by means of linear transformations. Next, the Monte Carlo (MC) code GEANT4-DNA was used to simulate the transport of protons of 0.5, 1, 5, 7 and 10 MeV , and alpha particles of 2, 5, 7 and 10 MeV. The number of particles in each case is such that the absorbed doses range between 0.5 Gy and 16 Gy. The three models proved to be consistent with the dimensions of the real structures. In particular, the models were compatible with the 30 nm chromatin fiber diameter requirement as well as with the bp volumes reported in other works. The Total and Double Strand Break Yields (TSBY and DSBY) were obtained for every radiation quality. Also, the Site-Hit Probability (SHP) defined as the total target to the nucleus volume ratio, was computed theoretically and from the simulations. The biophysical model in conjunction with the MC simulations furnished the number of lethal lesions (N_LL) as a function of dose, for protons of 0.5 and 10 MeV , and for alpha particles of 2 and 10 MeV . The N_LL could be split into those created by a single track and those originated by interaction of two tracks. It is concluded that the TSBY is practically determined by the SHP and depends weakly on the incident radiation quality. Nevertheless, the DSBY showed strong dependence on both the DNA conformation and the radiation quality. This is due to the interplay between the energy deposition clustering capacity of a given radiation and the DNA spatial packing. On the other hand, the analysis of the mechanisms of damage production based on the DRAT and tested with the biophysical model developed, showed that single-track (first order) effects depend linearly on the dose. Moreover, inter-track effects follows a quadratic behavior with the dose, having a linear term that influences the first order mechanism. This means that the Linear-Quadratic behavior of the N_LL with the dose, has mechanistic groundings at least at the first stage of the damage
Mestrado
Física
Mestre em Física
1370449/2014
CAPES

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26

Westerlund, Annie M. "Computational Study of Calmodulin’s Ca2+-dependent Conformational Ensembles." Licentiate thesis, KTH, Biofysik, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-234888.

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Ca2+ and calmodulin play important roles in many physiologically crucial pathways. The conformational landscape of calmodulin is intriguing. Conformational changes allow for binding target-proteins, while binding Ca2+ yields population shifts within the landscape. Thus, target-proteins become Ca2+-sensitive upon calmodulin binding. Calmodulin regulates more than 300 target-proteins, and mutations are linked to lethal disorders. The mechanisms underlying Ca2+ and target-protein binding are complex and pose interesting questions. Such questions are typically addressed with experiments which fail to provide simultaneous molecular and dynamics insights. In this thesis, questions on binding mechanisms are probed with molecular dynamics simulations together with tailored unsupervised learning and data analysis. In Paper 1, a free energy landscape estimator based on Gaussian mixture models with cross-validation was developed and used to evaluate the efficiency of regular molecular dynamics compared to temperature-enhanced molecular dynamics. This comparison revealed interesting properties of the free energy landscapes, highlighting different behaviors of the Ca2+-bound and unbound calmodulin conformational ensembles. In Paper 2, spectral clustering was used to shed light on Ca2+ and target protein binding. With these tools, it was possible to characterize differences in target-protein binding depending on Ca2+-state as well as N-terminal or C-terminal lobe binding. This work invites data-driven analysis into the field of biomolecule molecular dynamics, provides further insight into calmodulin’s Ca2+ and targetprotein binding, and serves as a stepping-stone towards a complete understanding of calmodulin’s Ca2+-dependent conformational ensembles.

QC 20180912

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27

Marcaud, Hélène. "Etude sur les transitions coopératives et les cinétiques de transconformation associées dans les acides nucléiques." Paris 6, 1986. http://www.theses.fr/1986PA066514.

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28

Koumanov, Assen. "Theoretical prediction of ionisation properties of proteins /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-535-2.

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Bredenberg, Johan. "Modelling biomolecular interactions /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-571-9.

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30

Imamura, Hideo. "Minimal model for the secondary structures and conformational conversions in proteins." Thesis, University of Waterloo, 2005. http://hdl.handle.net/10012/1233.

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Better understanding of protein folding process can provide physical insights on the function of proteins and makes it possible to benefit from genetic information accumulated so far. Protein folding process normally takes place in less than seconds but even seconds are beyond reach of current computational power for simulations on a system of all-atom detail. Hence, to model and explore protein folding process it is crucial to construct a proper model that can adequately describe the physical process and mechanism for the relevant time scale. We discuss the reduced off-lattice model that can express α-helix and β-hairpin conformations defined solely by a given sequence in order to investigate a protein folding mechanism of conformations such as a β-hairpin and also to investigate conformational conversions in proteins. The first two chapters introduce and review essential concepts in protein folding modelling physical interaction in proteins, various simple models, and also review computational methods, in particular, the Metropolis Monte Carlo method, its dynamic interpretation and thermodynamic Monte Carlo algorithms. Chapter 3 describes the minimalist model that represents both α-helix and β-sheet conformations using simple potentials. The native conformation can be specified by the sequence without particular conformational biases to a reference state. In Chapter 4, the model is used to investigate the folding mechanism of β-hairpins exhaustively using the dynamic Monte Carlo and a thermodynamic Monte Carlo method an effcient combination of the multicanonical Monte Carlo and the weighted histogram analysis method. We show that the major folding pathways and folding rate depend on the location of a hydrophobic. The conformational conversions between α-helix and β-sheet conformations are examined in Chapter 5 and 6. First, the conformational conversion due to mutation in a non-hydrophobic system and then the conformational conversion due to mutation with a hydrophobic pair at a different position at various temperatures are examined.

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31

Ranka, Mikhil Ajay. "Conformational investigations of a model polyzwitterion and its applications in oil recovery." Thesis, Massachusetts Institute of Technology, 2017. http://hdl.handle.net/1721.1/115467.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, June 2017.
Cataloged from PDF version of thesis. "June 2017"--Handwritten on title page.
Includes bibliographical references.
In recent years, nanoparticles have demonstrated immense promise for the development of next generation technologies for subsurface reservoir characterization and oil recovery. Until now however, the scope of such nanoparticles has been limited due to the significant challenge of colloidal stabilization under the extreme salinity and high temperature conditions typical of a reservoir. Previous efforts to address this problem have focused on conventional polyelectrolyte based stabilizers, which unfortunately fail at high ionic strengths due to excessive charge screening. In this thesis, we demonstrate a new approach to stabilization that overcomes this key deficiency, by specifically taking advantage of the excessive charge screening afforded by high ionic strengths. The approach is based on the anti-polyelectrolyte phenomenon, in which screening of intra-chain electrostatic interactions causes a polyzwitterion to undergo a structural transition from a collapsed globule to a more open coil-like regime. We first fundamentally investigate the anti-polyelectrolyte phenomenon in a high density comb type polyzwitterion, poly(sulfobetaine methacrylamide) (polySBMA), via small angle neutron scattering. The phenomenon is probed at a range of molecular weights by utilizing low dispersity homopolymers synthesized via controlled radical polymerization methods. Unique non gaussian behavior with significant molecular weight dependencies of size and shape is observed. An electrostatic dependence for Kuhn length is also established. Subsequently, we extend our understanding of anti-polyelectrolyte systems by characterizing the conformational dependence of polySBMA under conditions such that its responsive swelling is confined due to the segments being bound in three, six and twelve armed star architectures. Chain stretching due to solid angle exclusion, as well as, strong dependencies of size and fractal dimension on electrolyte concentration, number of arms and degree of polymerization (per arm) are noted. After gaining a detailed insight of the anti-polyelectrolyte phenomenon, its unique osmotic response is engineered into electrolyte and temperature responsive polyzwitterionic stabilizers. Robust colloidal stability of silica and polystyrene nanoparticles under reservoir relevant conditions is demonstrated, and the design principles of developing colloidally stable nanoparticles are elucidated. Finally, the polyzwitterion functionalized nanoparticles are leveraged in the form of schizophrenic diblock copolymer functionalized nanoparticles, to develop temperature tunable pickering emulsifiers. In contrast to conventional temperature responsive pickering emulsifiers, which induce phase separation upon heating, the schizophrenic diblock copolymer functionalized nanoparticles are demonstrated to function in the reverse direction, by inducing demulsification upon cooling. The unique temperature response is noted to be cyclable, and is likely to render the particles of important utility in enhanced oil recovery demulsification.
by Mikhil Ajay Ranka.
Ph. D.

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32

Zhang, Zhenyu. "Mechanical properties and pH-dependent conformation of a model polymer and biomolecule at the silica-water interface." Thesis, University of Sheffield, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.489101.

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This thesis is concerned with the mechanical properties and pH-dependent conformation of macromolecules at the silica-water interface. It is believed that the adhesion of bacteria to solids is governed by long-range interactions and by immediate interactions between bacterial surface polymers and solid surfaces. For a flexible macromolecule, the interaction of its segments with a solid surface and the conformation it takes at the interface are prominent factors in determining the net interaction to solids.

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33

Wan, Hongbin. "Efficient sampling of protein conformational dynamics and prediction of mutation effects." Diss., Temple University Libraries, 2019. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/575951.

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Chemistry
Ph.D.
Molecular dynamics (MD) simulation is a powerful tool enabling researchers to gain insight into biological processes at the atomic level. There have been many advancements in both hardware and software in the last decade to both accelerate MD simulations and increase their predictive accuracy; however, MD simulations are typically limited to the microsecond timescale, whereas biological motions can take seconds or longer. Because of this, it remains extremely challenging to restrain simulations using ensemble-averaged experimental observables. Among various approaches to elucidate the kinetics of molecular simulations, Markov State Models (MSMs) have proven their ability to extract both kinetic and thermodynamic properties of long-timescale motions using ensembles of shorter MD simulation trajectories. In this dissertation, we have implemented an MSM path-entropy method, based on the idea of maximum-caliber, to efficiently predict the changes in protein folding behavior upon mutation. Next, we explore the accuracy of different MSM estimators applied to trajectory data obtained by adaptive seeding, in which new rounds of short MD simulations are collected from states of interest, and propose a simple method to build accurate models by population re-weighting of the transition count matrix. Finally, we explore ways to reconcile simulated ensembles with Hydrogen/Deuterium exchange (HDX) protection measurements, by constructing multi-ensemble Markov State Models (MEMMs) from biased MD simulations, and reconciling these predictions against the experimental data using the BICePs (Bayesian Inference of Conformational Populations) algorithm. We apply this approach to model the native-state conformational ensemble of apomyoglobin at neutral pH.
Temple University--Theses

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34

Chen, Chong. "Investigating Nonnative Contacts in Protein Folding." University of Akron / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=akron1238087880.

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35

Hughes, Gareth. "Multivariate and time series models for circular data with applications to protein conformational angles." Thesis, University of Leeds, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.435790.

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36

Braunger, Julia. "Ezrin activation in vitro: Investigation of ezrin's conformation and the interaction between ezrin and F-actin." Doctoral thesis, Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2013. http://hdl.handle.net/11858/00-1735-0000-0022-609D-5.

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37

Berger, Nadja [Verfasser], Wolfram [Akademischer Betreuer] Sander, and Nils [Akademischer Betreuer] Metzler-Nolte. "Conformations and dynamics of small model cyclic tetrapeptides / Nadja Berger. Gutachter: Wolfram Sander ; Nils Metzler-Nolte." Bochum : Ruhr-Universität Bochum, 2016. http://d-nb.info/1095884794/34.

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38

Higuchi, Yuji. "Conformational transition of single semiflexible polymer chain as a coarse-grained model of DNA." 京都大学 (Kyoto University), 2011. http://hdl.handle.net/2433/142357.

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39

Hägglöf, Peter. "Plasminogen activator inhibitor type-1 : structure-function studies and its use as a reference for intramolecular distance measurements /." Umeå : Umeå University, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-177.

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40

Käll, Lukas. "Predicting transmembrane topology and signal peptides with hidden Markov models /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-719-7/.

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41

Bezkorovaynaya, Olga [Verfasser]. "Coarse-grained peptide models: conformational sampling, peptide association and dynamical properties for peptides / Olga Bezkorovaynaya." Mainz : Universitätsbibliothek Mainz, 2011. http://d-nb.info/1026802253/34.

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42

Bernard, Ayanna Malene. "Molecular modeling of poly(2-ethyl-2-oxazoline)." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/24793.

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Thesis (Ph.D.)--Chemical Engineering, Georgia Institute of Technology, 2009.
Committee Chair: Peter Ludovice; Committee Member: Amyn Teja; Committee Member: Arthur Ragauskas; Committee Member: William Koros; Committee Member: Yulin Deng.

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43

Simons, Kim T. "Deciphering the protein folding code : ab initio prediction of protein structure /." Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/9234.

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44

Gibrat, Jean-François. "Modélisation sur calculateur électronique de la structure tridimensionnelle des protéines." Paris 6, 1986. http://www.theses.fr/1986PA066471.

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45

Van, Calsteren Marie-Rose. "Phosphorus-31 and deuterium solid-state nuclear magnetic resonance studies of the headgroup conformation of phosphonolipids in biological and model membranes." Thesis, University of Ottawa (Canada), 1991. http://hdl.handle.net/10393/7929.

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Solid-state nuclear magnetic resonance (NMR) techniques were applied to the study of the phase behavior and to the determination of the headgroup conformation of phosphonolipids, both natural and synthetic. The results are compared with those for analogous phospholipids in biological and model membranes. $\sp{31}$P NMR was used to characterize the phase behavior of phospho- and phosphonolipids present in polar and total lipid extracts of the protozoa Tetrahymena thermophila. The $\sp{31}$P NMR spectra of aqueous dispersions of polar and total lipids consist in the partial superposition of two powder patterns, one for each phosphorus-containing lipid class. At low temperature, both lipid extracts give rise to lineshapes characteristic of the lamellar structure. Spectra of the polar lipids show that between 15 and 40$\sp\circ$C, a broad, reversible transition from bilayer to hexagonal phase takes place. On the other hand, the phase behavior for total lipids is different: no hexagonal phase is formed, the lipids remain in the bilayer phase at a higher temperature, and a transition to an isotropic phase occurs between 35 and 40$\sp\circ$C, which is not easily reversible. A large proportion of ethanolamine-containing lipids, both phosphate and phosphonate analogs, is responsible for the hexagonal phase formation observed with the polar lipids. When neutral lipids are present with the polar lipids, the bilayer is stabilized up to a higher temperature. One of the neutral lipid components, tetrahymanol, a pentacyclic triterpenoid, is believed to be responsible for this stabilization. The results show that the conformation of the headgroup up to the phosphorus atom is very similar in phospho- and phosphonolipids, i.e. the C2-C3-O-P torsion angle is nearly trans and the C3-O-P-C1 angle variable over the range of values investigated, with a bend at the phosphorus atom. Contrary to the phosphodiester moiety in analogous phospholipids which adopts a gauche-gauche conformation, two solutions for the next torsion angle O-P-C1-C2 were found around 100 and 130$\sp\circ$. The last segment P-C1-C2-N is nearly trans, whereas the corresponding O-C1-C2-N segment in phospholipids is gauche. Despite the differences in the torsion angle values, the overall appearance of the headgroup is similar for both phospho- and phosphonolipids. The headgroup first extends out of the bilayer plane, bending at the phosphorus atom and the terminal portion lies nearly parallel to the membrane surface. (Abstract shortened by UMI.)

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46

Robertson, Timothy Allen. "Development and validation of statistical potential functions for the prediction of protein/nucleic-acid interactions from structure /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/9268.

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47

Nguyen, Chuong Thach [Verfasser], Michael [Akademischer Betreuer] Habeck, Michael [Gutachter] Habeck, and Stephan [Gutachter] Waack. "Probabilistic models for protein conformational changes / Chuong Thach Nguyen ; Gutachter: Michael Habeck, Stephan Waack ; Betreuer: Michael Habeck." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2020. http://d-nb.info/1211816915/34.

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48

Arendall, William Bryan. "X-ray structures of novel intermediates in the thymidylate synthase models for chemical mechanism and conformational change." Diss., The University of Arizona, 2001. http://hdl.handle.net/10150/279920.

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The catalytic mechanism of thymidylate synthase (TS) was investigated using X-ray crystallography: four structures that yield new information about the early stages of TS action are reported. TS catalyzes the production of thymidylate (TMP), one of the four nucleotide bases of DNA, from the substrate, deoxyuridylate and cofactor, methylenetetrahydrofolate (MTF). Knowledge about the TS mechanism is important for both the medical and basic sciences. TS is the sole de novo source of TMP and it is thus a target for anti-proliferative drugs aimed at addressing cancer and other diseases marked by rapidly dividing cells. To aid this effort, past research on TS has developed two models to explain how TS works. A detailed, sequential chemical mechanism explains the methylene and hydride transfers from one cofactor to the substrate. And, a two state, dynamical model explains the conformational change that TS undergoes during its catalytic cycle. Combining these two models will lead to a fuller understanding of protein structure, function, and dynamics interrelationships. Two of the new structures contain cofactor in a heretofore unseen state, bound in the active site with its imidazolidine ring intact. Finding that this is an allowed enzyme-cofactor state indicates that ring opening and formation of the highly reactive iminium cation may occur relatively late in the methylene transfer, after preparation of the substrate; and, the reaction may perhaps be concerted. Further, details of these two structures show that protonation of the correct imidazolidine ring nitrogen (N10) may be selected by the geometry and environment imposed on the bent cofactor by TS. N5, the "wrong" ring nitrogen, is blocked and in a hydrophobic environment, while N10 is rehybridized to sp3 and its lone pair (nascent hydrogen) is pointed into an aqueous cavity trapped within the enzyme. A proposal coming from this dissertation is for a combination of the two models describing TS catalysis. The chemical mechanism model and the conformational change model both describe the same phenomena and these models should be connected and combined into one larger model to further increase our knowledge of the connections between structure, dynamics and function. The four structures reported here begin that connection process.

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49

Deléage, Gilbert. "Méthodes de prédiction de la structure secondaire des protéines : application à un modèle l'ATPase F1 mitochondriale : études des propriétés électriques et optiques de l'ATPase F1." Lyon 1, 1988. http://www.theses.fr/1988LYO10080.

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Une nouvelle methode de prediction a ete developpee qui donne 61% des acides amines bien predit. Cette methode a ete combinee avec celle de levin et al. Decrite en 1986 et 70% des acides amines copredits sont bien predits. Ces methodes sont incorporees dans un logiciel integre destine a la prediction des sites antigeniques potentiels d'une proteine: l'application de ces methodes a ete effectuee sur les sous-unites de l'atpase f1

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50

Cheng, Haitao. "Protein structure prediction and conformational transitions I. Improvement of protein secondary structure prediction : II. Pathways of conformational transition originating in phosphorylation : a study of CDK2 using targeted molecular dynamics and coarse grained models /." [Ames, Iowa : Iowa State University], 2009. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3360333.

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Dissertations / Theses on the topic 'Modele conformation'

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