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Ceres, Nicoletta. "Coarse-grain modeling of proteins : mechanics, dynamics and function". Thesis, Lyon 1, 2012. http://www.theses.fr/2012LYO10030.
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Les protéines sont des molécules flexibles, qui accomplissent une variété de tâches cellulaires à travers des mouvements mécaniques et des changements conformationnels encodés dans leur structure tridimensionnelle. Parmi les approches théoriques qui contribuent à une meilleure compréhension de la relation entre structure, mécanique, dynamique et fonction des protéines, les modèles gros-grains sont un outil très puissant. Ils permettent d’intégrer des informations structurales et dynamiques à un coût computationnel réduit, car le traitement explicite des degrés de liberté moins importants est supprimé. Dans le cadre de cette thèse, des études comparatives rapides de la flexibilité et de la mécanique des protéines ont été menées en se servant du simple modèle gros-grains de Réseau Élastique. La dépendance des résultats de la conformation de départ, ainsi que une liberté dynamique de la chaine principale plutôt limitée, imposée par l’approximation harmonique, nous ont motivé à développer une nouvelle approche, permettant une exploration plus extensive de l’espace conformationnel. Les efforts ont conduit à PaLaCe, modèle gros-grains qui permet des changements majeurs de la structure secondaire, tout en gardant la spécificité de la séquence des acides aminés grâce à une représentation à basse résolution. En utilisant PaLaCe nous avons simulé deux processus impliquant la plasticité protéique: le dépliement du domaine I27 de la protéine musculaire titine et la dynamique à l’équilibre autour de la structure native de deux enzymes homologues adaptées à des températures différentes. Les résultats obtenus concordent avec les données expérimentales et les résultats issus de modèles tout-atom déjà publiés. PaLaCe s’avère donc être un modèle fiable, avec des temps de calcul restreints par rapport aux modèles tout-atome, tout en conservant un bon niveau de détail. Il offre ainsi la possibilité d’effectuer une recherche systématique sur les liens entre mécanique, dynamique et fonction des protéinesProteins are flexible molecules, which accomplish a variety of cellular tasks through mechanical motions and conformational fluctuations encoded in their three-dimensional structure. Amongst the theoretical approaches contributing to a better understanding of the relationship between protein structure, mechanics, dynamics and function, coarse-grain models are a powerful tool. They can be used to integrate structural and dynamic information over broad time and size scales at a low computational cost, achieved by averaging out the less important degrees of freedom. In this work, fast comparative studies of protein flexibility and mechanics have been performed with the simple coarse-grain Elastic Network Model. However, the dependency of the results on the starting conformation, and the rather constrained backbone dynamics imposed by the harmonic approximation, motivated the development of a new approach, for a more extensive exploration of conformational space. These efforts led to the PaLaCe model, designed to allow significant changes in secondary structure, while maintaining residue specificity despite a lower-level resolution. Using PaLaCe, we were able to reproduce two processes involving protein plasticity: the mechanical unfolding of the I27 domain of the giant muscle protein titin and the near-native dynamics of two homologous enzymes adapted to work at different temperatures. Agreement with experimental data and results from published atomistic models demonstrate that PaLaCe is a reliable, sufficiently accurate, but computationally inexpensive approach. It therefore opens the doors for a systematic investigation of the link between protein dynamics/mechanics and function
2
Kragelj, Jaka. "Structure and dynamics of intrinsically disordered regions of MAPK signalling proteins". Thesis, Grenoble, 2014. http://www.theses.fr/2014GRENV060/document.
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Les voies de transduction du signal cellulaire permettent aux cellules de répondre aux signaux de l'environnement et de les traiter. Les voies de transduction de kinases MAP (MAPK) sont bien conservées dans toutes les cellules eucaryotes et sont impliquées dans la régulation de nombreux processus cellulaires importants. Les régions intrinsèquement désordonnées (RID), présentes dans de nombreuses MAPK, n'étaient pas encore structurellement caractérisées. Les RID de MAPK sont particulièrement importantes car elles contiennent des motifs de liaison qui contrôlent les interactions entre les protéines MAPK elles-mêmes et aussi entre les protéines MAPK et d'autres protéines contenant les mêmes motifs. La résonance magnétique nucléaire (RMN) en combinaison avec d'autres techniques biophysiques a été utilisée pour étudier les RID de kinase des voies de transduction du signal MAPK. La spectroscopie RMN est bien adaptée pour l'étude des protéines intrinsèquement désordonnées à l'échelle atomique. Les déplacements chimiques et couplages dipolaires résiduels peuvent être utilisés conjointement avec des méthodes de sélection d'ensemble pour étudier la structure résiduelle dans les RID. La relaxation de spin nucléaire nous renseigne sur les mouvements rapides. Des titrations par RMN et des techniques de spectroscopie d'échange peuvent être utilisées pour surveiller la cinétique d'interactions protéine-protéine. Cette étude contribuera à la compréhension du rôle des RID dans les voies de transduction du signal cellulaireProtein signal transduction pathways allow cells respond to and process signals from the environment. A group of such pathways, called mitogen-activated protein kinase (MAPK) signal transduction pathways, is well conserved in all eukaryotic cells and is involved in regulating many important cell processes. Long intrinsically disordered region (IDRs), present in many MAPKs, have remained structurally uncharacterised. The IDRs of MAPKs are especially important as they contain docking-site motifs which control the interactions between MAPK proteins themselves and also between MAPKs and other interacting proteins containing the same motifs. Nuclear magnetic resonance (NMR) spectroscopy in combination with other biophysical techniques was used to study IDRs of MAPKs. NMR spectroscopy is well suited for studying intrinsically disordered proteins (IDPs) at atomic-level resolution. NMR observables, such as for example chemical shifts and residual dipolar couplings, can be used together with ensemble selection methods to study residual structure in IDRs. Nuclear spin relaxation informs us about fast pico-nanosecond motions. NMR titrations and exchange spectroscopy techniques can be used to monitor kinetics of protein-protein interactions. The mechanistic insight into function of IDRs and motifs will contribute to understanding of how signal transduction pathways work
3
Murzycki, Jennifer E. "Probing Protein Dynamics Through Mutational and Computational Studies of HIV-1 Protease: A Dissertation". eScholarship@UMMS, 2006. https://escholarship.umassmed.edu/gsbs_diss/166.
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How proteins undergo conformational changes to bind a ligand is one of the most fundamental questions of protein biology. MD simulations provide a useful computational tool for studying the theoretical movements of protein in solution on nanosecond timescales. The results of these simulations can be used to guide experimental design. By correlating the theoretical models with the results of experimental studies, we can obtain a significant amount of information about protein dynamics. This study represents the application of both computational and traditional experimental techniques to study protein dynamics in HIV-1 protease. The results provide a novel mechanism for the conformational changes in proteins and address the role of residues outside the active site in protein dynamics. Additionally, these results are applied to the complex role of non-active site mutations in the development of drug resistance.
Chapter II examines an invariant Thr80 at the apex of the P1 loop of HIV-1, HIV-2, and simian immunodeficiency virus protease. Sequence variability associated with human immunodeficiency virus type 1 (HIV-1) is useful for inferring structural and/or functional constraints at specific residues within the viral protease. Positions that are invariant even in the presence of drug selection define critically important residues for protease function. Three protease variants (T80V, T80N, and T80S) were examined for changes in structure, dynamics, enzymatic activity, affinity for protease inhibitors, and viral infectivity. While all three variants were structurally similar to the wild type, only T80S was functionally similar. T80V significantly decreased the ability of the enzyme to cleave a peptide substrate but maintained infectivity, while T80N abolished both activity and viral infectivity. Additionally, T80N decreased the conformational flexibility of the flap region, as observed by simulations of molecular dynamics. Taken together, these data indicate that HIV-1 protease functions best when residue 80 is a small polar residue and that mutations to other amino acids significantly impair enzyme function, possibly by affecting the flexibility of the flap domain.
Chapter III focuses on residues within the hydrophobic core of each monomer in HIV-1 protease. Many hydrophobic residues located in the core of this dimeric enzyme frequently mutate in patients undergoing protease inhibitor therapy. The mechanism by which these mutations aid the development of drug resistance is not well understood. Using MD simulations, this study suggests that the hydrophobic residues outside the active site facilitate the conformational change that occurs in HIV-1 protease upon binding substrates and inhibitors. In these simulations, the core of each monomer significantly rearranges to assist in the expansion of the active site as hydrophobic core residues slide by each other, exchanging one hydrophobic contact for another. Such hydrophobic sliding may represent a general mechanism by which proteins undergo conformational changes. Mutation of these hydrophobic core residues would alter the packing of the hydrophobic core. Thus, these residues could facilitate drug resistance in HIV-1 protease by altering dynamic properties of HIV-1 protease preferentially affecting the relative affinity for inhibitors versus substrates.
Chapter IV concentrates on a residue in the flap region, Ile54, which is significantly correlated with the development of drug resistance. A series of patient sequences containing the mutation I54A were evaluated for the most frequently occurring co-mutations. I54A was found to occur with mutations that were previously correlated with I54V mutations, including L10I, G48V, and V82A. Based on the results of this evaluation, the binding properties of five variant proteases were investigated: MDI54V, MDRI54A, I54V, I54A, and G48V. MDRI54V and MDRI54Aeach contained the mutations L10I, G48V, and V82A, and either I54V or I54A, respectively. The other variants contained only the mutation indicated. Mutations at Ile54 were able to significantly impact the thermodynamics of binding to saquinavir, amprenavir, and the recently approved darunavir. The magnitude of this impact depended on the presence or absence of other drug resistance mutations, including another mutation in the flap region, G48V. Therefore, while residues 48 and 54 are not in contact with each other, mutations at both sites had a cooperative effect that varies between inhibitors.
The results demonstrate that residues outside the active site of HIV-1 protease are clearly important to enzyme function, possibly through their role in the dynamic properties of protease. Mutations outside the active site of protease that are known to cause drug resistance could alter the conformational flexibility of protease. While the role of protein dynamics in molecular recognition is still not fully understood, the results of this study indicate that altering the dynamic properties of a protein affects its ability to recognize ligands. Therefore, to design better inhibitors we will have to develop a more thorough understanding of protein dynamics.
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Abyzov, Anton. "Nuclear Magnetic Resonance Studies of the Dynamics and Thermodynamics of Intrinsically Disordered Proteins". Thesis, Université Grenoble Alpes (ComUE), 2016. http://www.theses.fr/2016GREAY026/document.
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Les protéines intrinsèquement désordonnées sont des hétéropolymères très flexibles, impliqués dans des activités cellulaires importantes (transduction du signal, reconnaissance moléculaire, traduction etc.), représentant des cibles potentielles de médicaments contre les maladies neurodégénératives et cancers, et dont les modes dynamiques définissent leur fonction biologique. Même si les états conformationnels qu'elles échantillonnent sont relativement bien connus, ce n'est pas le cas des échelles de temps de la dynamique associée. Dans ce travail nous étudions le comportement conformationnel du domaine C-terminal intrinsèquement désordonné de la nucléoprotéine de virus de Sendai (NTAIL), qui interagit avec le domaine PX de la phosphoprotéine. Des études précédentes montrent que le site d'interaction échantillonne un équilibre entre trois hélices discrètes dans l’état libre, et que l’interaction avec PX passe d’abord par la formation d'un pré-complexe, où l’une des conformation hélicoïdales de NTAIL est stabilisée, puis par sa diffusion sur la surface de PX, et enfin sa rétention sur le site de liaison. Cependant, aucun renseignement n'existe sur les échelles de temps de mouvements de la chaine de NTAIL, qui influencent certainement la cinétique de cette interaction, en particulier sa constante de vitesse d’association. Cette protéine de 124 acides aminés représente aussi un système modèle pertinent contenant à la fois de longs domaines dépliés et des régions de structure résiduelle. La mesure d’un vaste et cohérent ensemble de taux de relaxation à différents champs magnétiques et différentes températures nous a permis de caractériser la dynamique de NTAIL à un niveau de détail sans précèdent. A l’aide d’analyse « model-free » étendu, nous avons montré que les composants rapides de la fonction de corrélation nous informent sur les librations. Le mode dominant se situe à des échelles de temps autour d’une nanoseconde et est lié à l’échantillonnage de l’espace de Ramachandran par le squelette peptidique. Enfin, le composant lent (5-25 ns) nous informe sur les mouvements de segments de la chaine peptidique. La description des mouvements intrinsèques des protéines désordonnées et leurs échelles de temps contribuera à notre compréhension du comportement et des fonctions de ces protéinesIntrinsically disordered proteins (IDPs) are highly flexible heteropolymers, implicated in important cellular activities (signal transduction, molecular recognition, transcription, translation, etc.) and representing potential drug targets against cancer and neurodegenerative diseases, whose dynamic modes define their biological function. Although the conformational states sampled by IDPs are relatively well understood, essentially nothing is known about the associated dynamic timescales. In this study we investigate the conformational behavior of the intrinsically disordered C-terminal domain of the nucleoprotein of Sendai virus (NTAIL), which interacts with the PX domain of the phosphoprotein. The interaction site has been shown to sample an equilibrium of discrete helices in the free state, which forms an encounter complex implicating the stabilization of one of the helical conformers upon interaction with PX, prior to diffusing on the surface of PX and engaging in the actual binding site. However, very little is known about the timescales of chain motions, which surely play a role in the interaction kinetics, in particular in terms of the on-rate of the interaction. This 124 amino acid protein also provides a good model system, containing long unfolded domains with chain-like dynamics and regions with residual structure. The measurement of extensive set of coherent relaxation rates at multiple magnetic fields, multiple temperatures and in three different length constructs of the same IDP has allowed us to characterize the dynamic nature of NTAIL in unprecedented detail. By analyzing the relaxation data using extended model-free approach, we show that fast (≤ 50 ps) components of the correlation function report on librational motions. A dominant mode occurs on timescales around one nanosecond, apparently reporting on backbone sampling within Ramachandran sub-states, while a slower component (5-25 ns) reports on segmental dynamics dominated by the chain-like nature of the protein. The ability to delineate intrinsic modes and timescales will improve our understanding of the behavior and function of IDPs
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Link, Justin J. "Ultrafast Protein Conformation Dynamics". The Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=osu1230584570.
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Dorywalska, Magdalena. "Conformational dynamics of protein synthesis /". May be available electronically:, 2007. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.
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Zang, Chen. "Ultrafast Spectroscopic Study of Protein Conformation Dynamics and Hydration Dynamics". The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1299481658.
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Bossa, Cecilia. "Conformational fluctuations in proteins. A molecular dynamics based study". Doctoral thesis, La Sapienza, 2005. http://hdl.handle.net/11573/916821.
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Chen, Wei. "Molecular dynamics simulations of binding, unfolding, and global conformational changes of signaling and adhesion molecules". Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/28118.
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Thesis (M. S.)--Mechanical Engineering, Georgia Institute of Technology, 2009.Committee Chair: Zhu, Cheng; Committee Member: Harvey, Stephen; Committee Member: Hud, Nicholas; Committee Member: Zamir, Evan; Committee Member: Zhu, Ting.
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Bruce, Neil John. "Investigating protein conformational change via molecular dynamics simulation". Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/investigating-protein-conformational-change-via-molecular-dynamics-simulation(17145939-f643-4b23-bbb9-029cf5489c15).html.
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Accumulation and aggregation of the 42-residue amyloid-[beta] (A[beta]) protein fragment, which originates from the cleavage of amyloid precursor protein by beta and gamma secretase, correlates with the pathology of Alzheimer's disease (AD). Possible therapies for AD include peptides based on the A[beta] sequence, and recently identified small molecular weight compounds designed to mimic these, that interfere with the aggregation of A[beta] and prevent its toxic effects on neuronal cells in culture. Here, we use molecular dynamics simulations to compare the mode of interaction of an active (LPFFD) and inactive (LHFFD) [beta]-sheet breaker peptide with an A[beta] fibril structure from solid state NMR studies. We found that LHFFD had a weaker interaction with the fibril than the active peptide, LPFFD, from geometric and energetic considerations, as estimated by the MM/PBSA approach. Cluster analysis and computational alanine scanning identified important ligand-fibril contacts, including a possible difference in the effect of histidine on ligand-fibril [pi]-stacking interactions, and the role of the proline residue establishing contacts that compete with those essential for maintenance of the inter-monomer [beta]-sheet structure of the fibril. Our results show that molecular dynamics simulations can be a useful way to classify the stability of docking sites. These mechanistic insights into the ability of LPFFD to reverse aggregation of toxic A[beta] will guide the redesign of lead compounds, and aid in developing realistic therapies for AD and other diseases of protein aggregation. We have also performed long explicit solvent MD simulations of unliganded amyloid fibril in three putative protonation states, in order to better understand the energetic and mechanical features of the fibril receptor. Over 100 ns MD simulations, the trajectories where fibril has Glu11 and Glu22 side-chains protonated exhibit the least deviation from the initial solid state NMR structures. Free energy calculations on these rajectories suggest that the weakest fibril interface lies in the lateral rather than transverse direction and that there is little dependence on whether the lateral interface is situated at the edge or middle of the fibril. This agrees with recent reported steered molecular dynamics calculations. Secondly, in an effort to improve the ability of atomistic simulation techniques to directly resolve protein tertiary structure from primary amino acid sequence, we explore the use of a molecular dynamics technique based on swarm intelligence, called SWARM-MD, to identify the native states of two peptides, polyalanine and AEK17, as well as Trp-cage miniprotein. We find that the presence of cooperative swarm interactions significantly enhanced the efficiency of molecular dynamics simulations in predicting native conformation. However, it also is evident that the presence of outlying simulation replicas can adversely impact correctly folded replica structures. By slowly removing the swarm potential after folding simulations, the negative effect of the swarm potential can be alleviated and better agreement with experiment obtained.
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D'Rozario, Robert S. G. "Conformational dynamics of proline-containing transmembrane helices". Thesis, University of Oxford, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.670181.
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Budi, Bunarta Hendra (Akin), i akin budi@rmit edu au. "On the effects of external stresses on protein conformation". RMIT University. School of Applied Sciences, 2006. http://adt.lib.rmit.edu.au/adt/public/adt-VIT20061116.123431.
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The use of electromagnetic devices such as microwave ovens and mobile phones has certainly brought convenience to our lives. At the same time, the proliferation of said devices has increased public awareness of the potential health hazards. It is generally assumed that there is little or no risk associated with the use of electromagnetic devices, based on the small amount of power associated with those devices. However, case studies on animals indicate that the risk cannot be entirely ruled out. It has long been known that proteins are sensitive to stress, arising from various sources such as temperature, chemical, pressure, and changes in pH condition. In all of these cases, the protein exhibits clear signs of damage and distress, which range from slight unfolding to complete loss of structure. Frequently, the damage to the protein is alleviated by refolding, either by itself or by the aid of molecular chaperones. However, if the damage to the protein is too great, the protein will generally undergo proteolysis. Opinion has been divided over the implication of prolonged use of electromagnetic devices to human health. Studies conducted on animals so far have given conflicting results. The studies on the separate components, electric and magnetic fields, also give inconclusive results. This indicates that our understanding on how electric and magnetic fields interact with biological matter is incomplete. In this project, we use molecular dynamics to explore the behaviour of two forms of insulin chain-B, isolated and monomeric (in the presence of chain-A with all disulfide bonds intact), at ambient conditions and under the influence of various stress. Specifically, we focus our attention to thermal stress and electric field stress. The electric field stress considered in this study takes several forms: static and oscillating with three different frequencies. These fields have strength ranging from 1806 V/m to 109 V/m. By performing molecular dynamics simulations totalling over 500 ns, we have gained valuable insights into the effects of elevated temperature and electric field on insulin chain-B. We observed differences in the damage mechanisms by the application of static electric field and oscillating field. The application of static fields restricts the conformational freedom of a protein, whereas the application of oscillating fields increases the mobility and flexibility of the protein, similar to the effect of thermal stress. Both of these interfere with the normal behaviour of a protein. We have also observed frequency-dependent effects, with low frequency fields having static field-like characteristics in damage mechanism.
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Reiner, Andreas. "Conformational dynamics and stability of structured peptides and small proteins /". Basel : [s.n.], 2009. http://edoc.unibas.ch/diss/DissB_8562.
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Anderson, William David. "Conformational dynamics of interleukin-1beta and protein-membrane interactions". Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2007. http://wwwlib.umi.com/cr/ucsd/fullcit?p3249669.
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Thesis (Ph. D.)--University of California, San Diego, 2007.Title from first page of PDF file (viewed April 4, 2007). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 119-127).
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Bransford, Philip W. "Insights into protein function from evolutionary and conformational dynamics". Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/76112.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2011.Cataloged from PDF version of thesis.
Includes bibliographical references (p. 125-144).
The volume of protein structure data has grown rapidly over the past 30 years, leaving a wake of facts that still require explanation. We endeavored to answer a few open questions on the structure-function relationship of intriguing mechanochemical protein systems. To this end this thesis work contains five studies that offer novel insights into molecular biomechanical systems that may guide future basic research or applications development. The first study concerns the biophysics of cadherin-mediated cell sorting observed in developing solid tissue. We investigated the evolutionary dynamics of the cadherin superfamily of cell-cell adhesion proteins to infer a structural basis for their paradoxical mixture of pairwise binding specificity and promiscuity. Our analysis predicts a small set of specificity-determining residues located within the protomer-protomer binding interface. The putative specificity-determinants form a design space with potential for engineering novel cell-cell adhesive interactions. The second study addresses the open question of how to automatically identify regions within a protein that engage in allosteric communication. To identify allostery we developed and tested two computational tools that operate on protein conformational dynamics data. These tools are useful for generating testable hypotheses about proteins with multiple functional sites for the design of non-competitive protein inhibitors. The third study asks, "What is the consequence of allosteric cooperation between the tandem binding sites in a class of proteins that bundle filamentous actin (F-actin)?" Through simulation we demonstrate that cooperative F-actin bundling tends to strengthen bundles by driving the formation of cross-links between neighboring filaments while depleting F-actin binding sites that are occupied but not cross-linked. We hence propose that allostery may be a natural feature of ABPs with tandem F-actin binding sites if nature indeed selects for sturdy F-actin bundles. The final two studies examine the impact of two structural perturbations to Factin on its mechanics. Using structure-based computer modeling we develop a simple explanation for the mechanism by which the structure of actin's polymorphic subdomain 2 mediates 4-fold changes in F-actin's flexibility. We further demonstrate that two calponin homology domains stabilize F-actin by binding in a configuration that tends to relax the stress concentration at actin-actin interfaces.
by Philip W. Bransford.
Ph.D.
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Stone, Benjamin. "Evaluating experimental and theoretical measures of protein conformational dynamics". Thesis, Aston University, 2016. http://publications.aston.ac.uk/31759/.
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Molecular biologists have traditionally interpreted the B-factor data of a protein crystal structure as a reflection of the protein's conformational flexibility. Crystallographers, in contrast, are wary of assigning too much significance to B-factors since they can also be attributed to processes unrelated to conformational dynamics such as experimental imprecision; crystal imperfections; or rigid body motion. In this study, the usefulness of both isotropic and anisotropic B-factors as measures of conformational dynamics were evaluated using high resolution structures. Alpha-carbon B-factor values were analysed in relation to structural properties generally accepted to be correlates of conformational variability. The influence of secondary structure, amino acid type, surface exposure, distance to the centre of mass and packing density were investigated. The results support the argument that B-factors measure conformational variability by demonstrating that atoms with the highest B-factors are typically located in regions expected to have a high degree of conformational freedom. Nevertheless, the results also highlight some of the limitations of crystallographic data. Despite using high quality crystal structures, only very general qualitative trends between B-factors values and the properties investigated could be established. Thus, B-factors appear to be influenced, to a significant degree, by the numerous sources of error in a crystallographic experiment. By considering proteins with multiple published crystal structures, the existence of consensus B-factor profiles were identified. These consensus profiles were hypothesised to represent the dynamics within the crystal with a high degree of accuracy since much of the variation between individual experiments would be eliminated. However, when compared against measurements derived from molecular dynamic simulations, these consensus profiles only weakly correlated with the predictions of the computer models. Therefore, although there is some evidence to suggest that B-factors reflect conformational variability, B-factors cannot be assumed to be reliable descriptors of the internal dynamics of a protein within a crystal.
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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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ChemistryPh.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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Atzori, Alessio. "Conformational analysis of peptides and proteins for drug design using molecular simulations". Thesis, University of Manchester, 2015. https://www.research.manchester.ac.uk/portal/en/theses/conformational-analysis-of-peptides-and-proteins-for-drug-design-using-molecular-simulations(050ba296-a4c4-4a5b-87bf-66d90f7ddc5a).html.
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The intrinsic plasticity of biological systems provides opportunities for rational design of selective and potent ligands. Increasingly, computational methods are being applied to predict biomolecular flexibility. However, the motions involved in these processes can be large and occur on time scales generally difficult to achieve with standard simulation methods. In order to overcome the intrinsic limitations of classical molecular dynamics, this Ph.D. project focuses on the application of advanced sampling computational techniques to capture the plasticity of diverse biological systems. The first of these applications involved the evaluation of the secondary structure of the N-terminal portion of p53 and its inverse, reverse and retro-inverso sequences by using replica exchange molecular dynamics simulations in implicit solvent. In this study, we also evaluated the effects of reversal of sequence and stereochemistry in mimicking an inhibitory pharmacophoric conformation. The results showed how the ability to mimic the parent peptide is severely compromised by backbone orientation (for D-amino acids) and side-chain orientation (for reversed sequences). Moreover, the structural information obtained from simulations showed good agreement with NMR and circular dichroism studies, confirming the validity of the combination of replica exchange molecular dynamics with the ff99SB force field and Generalized Born solvent model for computational modelling of D-peptide conformations.In a second work, we explored conformations of the DFG motif of the p38α mitogen-activated protein (MAP) kinase. To achieve this, we employed an advanced sampling simulation method that has been developed in-house, called swarm-enhanced sampling molecular dynamics (sesMD). In contrast to multiple independent MD simulations, swarm-coupled sesMD trajectories were able to sample a wide range of DFG conformations, some of which map onto existing crystal structures. Simulated structures intermediate between DFG-in and DFG-out conformations were predicted to have druggable pockets of interest for structure-based ligand design. Overall, sesMD shows promise as a useful tool for enhanced sampling of complex conformational landscapes. Finally, we used microsecond MD simulations to evaluate the molecular plasticity of R-spondins, a class of proteins involved in the activation of the Wnt pathway. The unbound R-spondin 1 is characterised by a closed conformation, while, when complexed to proteins LGR and RNF43/ZNRF3, assumes an open and more extended arrangement. This is true also for R-spondin 2, in both its unbound or bound forms. From our simulation, we find that the closed R-spondin 1 conformation is stable, whilst, R-spondin 1 and 2 from their open conformation explore several intermediate structures. In addition, we evaluated the druggability of a potential binding site located at the interface between the second and the third β-hairpin moiety of the first furin domain. The computational screening with small molecular fragments provided interesting insights about the druggability and the pharmacophoric features of the potential binding pockets identified, outlining promising future perspectives of structure-based design of Wnt pathway inhibitors.
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Cao, Jin. "Single Molecular Spectroscopy and Atomic Force Manipulation of Protein Conformation and Dynamics". Bowling Green State University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1416588612.
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López, Asamar Abraham. "Study of the conformational dynamics of prolyl oligopeptidase". Doctoral thesis, Universitat de Barcelona, 2015. http://hdl.handle.net/10803/301430.
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Prolyl oligopeptidase (POP) is an 81-KDa bidomain enzyme which hydrolyses short proline-containing peptides. This enzyme is involved in mnemonic and cognitive processes, and the dysregulation of POP activity is related to mental diseases. Probably, POP modulates the phosphoinositide signalling pathway through protein-protein interactions (PPI). Hence, the development of POP inhibitors is an area of great interest for the treatment of cognitive deficits associated with mental and neurodegenerative diseases. Recently, it has been found that the administration of POP inhibitors increases the clearance of a-synuclein aggregates in vivo, indicating that POP can be related to some extend with the pathogenic conditions of Parkinson’s disease (PD). Probably, this increase in the a-synuclein catabolism might be a consequence of a direct interaction between the two proteins. For this reason, POP inhibitors might be drug candidates for the preventive treatment of PD.
Although the X-ray structure of POP is well studied, it is not clear which are the conformational fluctuations responsible for the circulation of substrates and products during the catalytic cycle. Several studies suggest that loops surrounding the active site are involved in a gating mechanism, while others postulate that interdomain separation might expose the active site. Moreover, such conformational transitions might be essential for the recognition events of POP. The elucidation of the conformational landscape of POP is a challenging task due to the high molecular weight of the enzyme.
In this PhD thesis we have used a combination of robust biophysical tools (in particular, NMR and SAXS) together with molecular dynamics simulations (MD) in order to decipher the conformational dynamics of POP in solution. In addition, POP was also analysed by ion mobility mass spectrometry, an emerging biophysical tool in structural biology. Finally, we performed preliminary studies of the interaction between POP and a-synuclein by NMR.
The results obtained in this PhD thesis demonstrated that POP exists in solution in a slow conformational exchange between open and closed conformations. The conformational transitions involved the periodic separation of the two domains in a hinge-type motion. Relaxation dispersion experiments showed that this long range conformational transition was better described by several independent motions of different amplitudes, stressing the highly dynamic behaviour of POP. Moreover, the analysis of SAXS data complemented by MD simulations found that the interdomain separation caused the inactive arrangement of the active site. This suggests that the separation between domains might be critical for substrate recruitment and product release. Of interest, inhibitors caused the total displacement of this equilibrium towards the stabilized closed conformation, therefore quenching dynamics and the catalytic activity.
The study of the interaction between POP and a-synuclein by NMR disclosed that both proteins might be involved in a weak and transient interaction. Of interest, this interaction showed more affinity in the case of POP bound to inhibitors. In this case, interaction specially affected a broad segment of the C-terminal region of a-synuclein. This result suggested that the recognition between the two proteins depends on the conformational state of POP. Therefore, modulating the conformational landscape of POP by inhibitors might control this interaction.
In summary, the results obtained in this PhD thesis demonstrated that POP undergo slow exchange between open and closed conformations in solution, and found that inhibitors have deep effects in the native conformational landscape of POP. Of interest, these conformational transitions might be essential for regulating the PPI necessary for the biological function of POP. Hence, the in vivo effects of POP inhibitors might result as a consequence of the alterations in the recognition events of POP.La prolil oligopeptidasa (POP) es un enzim de 81 KDa que hidrolitza pèptids curts amb contingut en prolina. La POP actua en el sistema nerviós central mitjançant interaccions proteïna-proteïna (IPP), i la seva funció biològica està relacionada amb la memòria i els processos cognitius. Per aquesta raó, els inhibidors de la POP són compostos d’interès terapèutic per al tractament dels dèficits cognitius. Recentment, s’ha descobert que els inhibidors de la POP poden prevenir la patogènesis de la malaltia de Pàrkinson, probablement a través d’una interacció directa entre la POP i l’a-sinucleïna (la principal proteïna causant dels processos neurodegeneratius de la malaltia de Parkinson). Tot i que l’estructura cristal·logràfica de la POP està ben definida, no es sap quines són les transicions conformacionals que permeten completar el cicle catalític de la POP. Probablement, aquesta riquesa conformacional també té un paper rellevant en el control de les IPP. Malauradament, l’estudi conformacional complet de la POP és tot un repte degut al seu elevat pes molecular. En aquesta tesis doctoral s’ha emprat una combinació de tècniques biofísiques avançades (en concret, la resonància magnètica nuclear, la dispersió de raigs X de baix angle, i l’espectrometria de masses de mobilitat iònica) conjuntament amb simulacions de dinàmica molecular, per tal d’analitzar la dinàmica conformacional de la POP en solució. A més, s’ha estudiat la possible interacció entre la POP i l’a-sinucleïna mitjançant experiments de RMN. Els resultats obtinguts en aquesta tesi doctoral han demostrat que la POP es troba en solució en un equilibri conformacional lent entre conformacions obertes i tancades, originades a partir de la separació entre dos dominis. Els inhibidors de la POP causen una gran estabilització de la conformació tancada, amb la qual cosa l’equilibri dinàmic es desplaça totalment cap a aquesta conformació. A més, es va poder detectar una interacció dèbil i transitòria entre la POP i l’a-sinucleïna, que esdevenia especialment afavorida en la presència d’inhibidors. Així, els nostres resultats suggereixen que la diversitat conformacional de la POP es necessària per a la seva funció, i que els inhibidors poden desencadenar la seva funció biològica desplaçant l’equilibri conformacional.
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Jones, Kevin C. (Kevin Chapman). "Temperature-jump 2D IR spectroscopy to study protein conformational dynamics". Thesis, Massachusetts Institute of Technology, 2012. http://hdl.handle.net/1721.1/73358.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2012."June 2012." Cataloged from PDF version of thesis.
Includes bibliographical references.
Temperature-jump (T-jump) two-dimensional infrared spectroscopy (2D IR) is developed, characterized, and applied to the study of protein folding and association. In solution, protein conformational changes span a wide range of timescale from nanoseconds to minutes. Ultrafast 2D IR spectroscopy measures time-dependent structural changes within the protein ensemble by probing the frequency changes associated with amide I backbone vibrations. Combining 2D IR with a perturbing laser-induced T-jump enables the study of conformational dynamics from 5 ns to 50 ms. To access a finer time-sampling of the conformational evolution, a one-dimensional variant of 2D IR, heterodyne-detected dispersed vibrational echo spectroscopy (HDVE), is implemented. The framework for interpreting transient HDVE and 2D IR spectra is developed, and we propose a method to remove the linear absorption distortions along both frequency axes. We first present the T-jump 2D IR spectra of a dipeptide to reveal the general amide I baseline response expected in the absence of conformational change. To facilitate the analysis of T-jump data, singular value decomposition (SVD) is employed for reducing noise, identifying the number of distinguishable states, and separating spectral changes based on shared timescales. Finally, T-jump 2D IR spectroscopy is applied to study the unfolding of ubiquitin, disordering of the 12-residue p-hairpin peptide trpzip2 (TZ2), and the dissociation of insulin dimers to monomers. Experimental results for ubiquitin highlight the importance of linear absorption corrections for interpretation of the data. In response to the T-jump, 2D IR results indicate p-sheet structure melts in ubiquitin with a small amplitude (~10 gs) and large amplitude (17 ms) response. Isotope-labeling T-jump experiments on TZ2 allow for the proposal of a free energy surface in which transitions from a native and misfolded state proceed through a disordered hub-like state with a 1-2 gs timescale. Multiple timescales are observed in the T-jump induced dissociation of insulin. Based on their spectral features and concentration dependence, the insulin timescales can be assigned to dissociation, disordering, and oligomerization processes. With these applications, we demonstrate the capability of T-jump 2D IR spectroscopy to reveal detailed molecular dynamics.
by Kevin C. Jones.
Ph.D.
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Chatterjee, P. "Protein thermal stability, conformational dynamics and solvent properties: insights with atomistic molecular dynamics simulations". Thesis(Ph.D.), CSIR-National Chemical Laboratory, Pune, 2015. http://dspace.ncl.res.in:8080/xmlui/handle/20.500.12252/2242.
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Gillespie, D. Blake. "Conformational dynamics and intermediates in the folding pathway of T4 lysozyme /". view abstract or download file of text, 1999. http://wwwlib.umi.com/cr/uoregon/fullcit?p9957566.
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Thesis (Ph. D.)--University of Oregon, 1999.Typescript. Includes vita and abstract. Includes bibliographical references (leaves 101-110). Also available for download via the World Wide Web; free to University of Oregon users. Address: http://wwwlib.umi.com/cr/uoregon/fullcit?p9957566.
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Majumdar, Devdoot. "Probing the conformational dynamics of membrane-associated proteins using single molecule fluorescence". Diss., Restricted to subscribing institutions, 2009. http://proquest.umi.com/pqdweb?did=1973051401&sid=3&Fmt=2&clientId=1564&RQT=309&VName=PQD.
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Lukman, Suryani. "The functional significance of the conformational dynamics of monomeric and multimeric proteins". Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609894.
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Menon, S. "Triggers for protein conformational changes and self-assembly probed with fully atomistic computer simulations". Thesis(Ph.D.), CSIR-National Chemical Laboratory, Pune, 2019. http://dspace.ncl.res.in:8080/xmlui/handle/20.500.12252/5845.
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Karolak, Aleksandra. "Application and Development of Computational Methods in Conformational Studies of Bio-molecules". Scholar Commons, 2015. https://scholarcommons.usf.edu/etd/5520.
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The work presented in my dissertation focuses on the conformational studies of bio-molecules including proteins and DNA using computational approaches. Conformational changes are important in numerous molecular bioprocesses such as recognition, transcription, replication and repair, etc. Proteins recognize specific DNA sequences and upon binding undergo partial or complete folding or partial unfolding in order to find the optimal conformational fit between molecules involved in the complex. In addition to sequence specific recognition, proteins are able to distinguish between subtle differences in local geometry and flexibility associated with DNA that may further affect their binding affinities. Experimental techniques provide high-resolution details to the static structures but the structural dynamics are often not accessible with these methods; but can be probed using computational tools. Various well-established molecular dynamics methods are used in this work to study differences in geometry and mechanical properties of specific systems under unmodified and modified conditions. Briefly, the studies of several protein and DNA systems investigated the importance of local interactions and modifications for the stability, geometry and mechanical properties using standard and enhanced molecular dynamics simulations. In addition to the conformational studies, the development of a new method for enhanced sampling of DNA step parameters and its application to DNA systems is discussed.
Chapter 1 reviews the importance of the conformational changes in bioprocesses and the theory behind the computational methods used in this work. In the project presented in chapter 2 unbiased molecular dynamics and replica exchange molecular dynamics are employed to identify the specific local contacts within the inhibitory module of ETS-1. ETS-1 is a human transcription factor important for normal but also malignant cell growth. An increased concentration of this protein is related to a negative prognosis in many cancers. A part of the inhibitory module, inhibitory helix 1 (HI-1) is located on the site of the protein opposite to the DNA binding site and although loosely packed, stays folded in the apo state and unfolds upon ETS-1 binding to DNA. Our study investigated the character and importance of contacts between HI-1 and neighboring helices of the inhibitory module: HI-2 and H4. We also identified a mutant of HI-1, which possessed the higher helical propensity than the original construct. This study supported the experimental findings and enhanced the field by the identification of new potential target for experimental tests of the system, which plausibly inhibits binding to DNA.
In the studies discussed in chapters 3-5 the conformational dynamics of DNA under normal conditions and upon specific epigenetic modifications are presented. Since DNA conformation can be accurately described by six base pair step parameters: twist, tilt, roll, shift, slide and rise, these were extensively analyzed and the results elucidated insights into the properties of the systems. In order to enhance unbiased simulations and allow for easier crossing of the energy barriers, we developed and implemented a novel method to control DNA base pair step parameters. With this approach we obtained the free energy estimates of e.g. DNA rearrangements in a more efficient manner. This advanced computational method, supported by standard and additional enhanced techniques, was then applied in the studies of DNA methylation on cytosine or adenine bases and oxidative damage of cytosine.
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Hibbs, Ryan E. "Conformational dynamics of the acetylcholine binding protein, a Nicotinic receptor surrogate". Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2006. http://wwwlib.umi.com/cr/ucsd/fullcit?p3237010.
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Thesis (Ph. D.)--University of California, San Diego, 2006.Title from first page of PDF file (viewed December 8, 2006). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.
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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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ChemistryPh.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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Guan, Xiao, i 关晓. "NMR approaches to protein conformation and backbone dynamics: studies on hyperthermophilicacylphosphatase and neuropeptide secretoneurin". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2010. http://hub.hku.hk/bib/B44079230.
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Guo, Qing. "Single Molecule Optical Magnetic Tweezers Microscopy Studies of Protein Dynamics". Bowling Green State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1435334948.
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Zhang, Wei. "Computational simulation of biological systems studies on protein folding and protein structure prediction /". Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file 2.84Mb, 184 p, 2005. http://wwwlib.umi.com/dissertations/fullcit/3181881.
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Guan, Xiao. "NMR approaches to protein conformation and backbone dynamics studies on hyperthermophilic acylphosphatase and neuropeptide secretoneurin /". Click to view the E-thesis via HKUTO, 2010. http://sunzi.lib.hku.hk/hkuto/record/B44079230.
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Tamura, Kouichi. "Atomistically Deciphering Functional Large Conformational Changes of Proteins with Molecular Simulations". 京都大学 (Kyoto University), 2016. http://hdl.handle.net/2433/215334.
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Astudillo, Luisana. "Conformational Dynamics Associated with Ligand Binding to Vertebrate Hexa-coordinate Hemoglobins". FIU Digital Commons, 2014. http://digitalcommons.fiu.edu/etd/1177.
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Neuroglobin (Ngb) and cytoglobin (Cygb) are two new additions to the globin family, exhibiting heme iron hexa-coordination, a disulfide bond and large internal cavities. These proteins are implicated in cytoprotection under hypoxic-ischemic conditions, but the molecular basis of their cytoprotective function is unclear.
Herein, a photothermal and spectroscopic study of the interactions of diatomic ligands with Ngb, Cygb, myoglobin and hemoglobin is presented. The impact of the disulfide bond in Ngb and Cygb and role of conserved residues in Ngb His64, Val68, Cys55, Cys120 and Tyr44 on conformational dynamics associated with ligand binding/dissociation were investigated. Transient absorption and photoacoustic calorimetry studies indicate that CO photo-dissociation from Ngb leads to a volume expansion (13.4±0.9 mL mol-1), whereas a smaller volume change was determined for Ngb with reduced Cys (ΔV=4.6±0.3 mL mol-1). Furthermore, Val68 side chain regulates ligand migration between the distal pocket and internal hydrophobic cavities since Val68Phe geminate quantum yield is ~2.7 times larger than that of WT Ngb. His64Gln and Tyr44Phe mutations alter the thermodynamic parameters associated with CO photo-release indicating that electrostatic/hydrogen binding network that includes heme propionate groups, Lys 67, His64, and Tyr 44 in Ngb modulates the energetics of CO photo-dissociation. In Cygb, CO escape from the protein matrix is fast (< 40 ns) with a ΔH of 18±2 kcal mol-1 in Cygbred, whereas disulfide bridge formation promotes a biphasic ligand escape associated with an overall enthalpy change of 9±4 kcal mol-1. Therefore, the disulfide bond modulates conformational dynamics in Ngb and Cygb. I propose that in Cygb with reduced Cys the photo-dissociated ligand escapes through the hydrophobic tunnel as occurs in Ngb, whereas the CO preferentially migrates through the His64 gate in Cygbox.
To characterize Cygb surface 1,8-ANS interactions with Cygb were investigated employing fluorescence spectroscopy, ITC and docking simulations. Two 1,8-ANS binding sites were identified. One binding site is located close to the extended N-terminus of Cygb and was also identified as a binding site for oleate. Furthermore, guanidinium hydrochloride-induced unfolding studies of Cygb reveal that the disulfide bond does not impact Cygb stability, whereas binding of cyanide slightly increases the protein stability.
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Ahlstrom, Logan Sommers. "Molecular Dynamics Simulation of the Effect of the Crystal Environment on Protein Conformational Dynamics and Functional Motions". Diss., The University of Arizona, 2012. http://hdl.handle.net/10150/255200.
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Proteins are dynamic and interconvert between different conformations to perform their biological functions. Simulation methodology drawing upon principles from classical mechanics - molecular dynamics (MD) simulation - can be used to simulate protein dynamics and reconstruct the conformational ensemble at a level of atomic detail that is inaccessible to experiment. We use the dynamic insight achieved through simulation to enhance our understanding of protein structures solved by X-ray crystallography. Protein X-ray structures provide the most important information for structural biology, yet they depict just a single snapshot of the solution ensemble, which is under the influence of the confined crystal medium. Thus, we ask a fundamental question - how well do static X-ray structures represent the dynamic solution state of a protein? To understand how the crystal environment affects both global and local protein conformational dynamics, we consider two model systems. We first examine the variation in global conformation observed in several solved X-ray structures of the λ Cro dimer by reconstructing the solution ensemble using the replica exchange enhanced sampling method, and show that one X-ray conformation is unstable in solution. Subsequent simulation of Cro in the crystal environment quantitatively assesses the strength of packing interfaces and reveals that mutation in the lattice affects the stability of crystal forms. We also evaluate the Cro models solved by nuclear magnetic resonance spectroscopy and demonstrate that they represent unstable solution states. In addition to our studies of the Cro dimer, we investigate the effect of crystal packing on side-chain conformational dynamics through solution and crystal MD simulation of the HIV microbicide Cyanovirin-N. We find that long, polar surface side-chains can undergo a strong reduction in conformational entropy upon incorporation into crystal contacts, which supports the application of surface engineering to facilitate protein crystallization. Finally, we outline a general framework for using network visualization to aid in the functional interpretation of conformational ensembles generated from MD simulation. Our results will enhance the understanding of X-ray data in establishing protein structure-function-dynamics relationships.
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Craigo, Kevin Alan. "Ultrafast Spectroscopic Study of Hydration and Conformational Dynamics in Calmodulin". The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1311089745.
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Miyashita, Osamu. "ROLE OF CONFORMATIONAL DYNAMICS ON ELECTRON AND ENERGY TRANSFER IN A PROTEIN MOLECULE". 京都大学 (Kyoto University), 2000. http://hdl.handle.net/2433/151675.
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Kim, So Yeon. "Observing protein dynamics and conformational changes by ensemble and single-molecule fluorescence spectroscopy /". May be available electronically:, 2008. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.
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Pao, Ya-Lan. "Conformational and dynamic studies of the influence of glycosylation on peptides and proteins". Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285416.
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Chan, Yao Chong Maud. "Structure et dynamique de protéines intrinsèquement désordonnées : Caractérisation par une approche combinant dynamique moléculaire avancée et SAXS". Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS257.
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Le travail de thèse consistera à explorer et caractériser l'ensemble conformationnel de protéines intrinsèquement désordonnées (IDPs) en utilisant plusieurs techniques complémentaires, notamment des simulations avancées de dynamique moléculaire et la diffusion des rayons X aux petits angles (SAXS). Les IDPs sont des protéines possédant une ou plusieurs régions n'ayant pas de structures secondaires stables lorsqu'elles sont isolées, mais pouvant en adopter lors de leur association avec de multiples autres protéines. La question, à laquelle ce travail souhaite répondre dans le cas de trois IDPs, est de savoir si ces éléments de structures secondaires, formés à l'interfaces des complexes protéine-protéine, pré-existent de façon transitoire, ou non, à l'état non-lié des IDPs en solution. S'il est possible d'identifier et de caractériser ces éléments de reconnaissance moléculaire dans les IDPs isolées, alors les résultats de ce travail permettront de guider par la suite la détermination des structures de complexes protéiques impliquant des IDPsThe PhD work will consist in exploring and characterizing the conformational ensemble of intrinsically disordered proteins (IDPs), by using several complementary methods, including enhanced molecular dynamics simulations and small angle X-ray scattering (SAXS). IDPs are proteins having one or several regions that lack stable secondary structures in the unbound state, but which can adopt various structured conformations to bind other proteins. In the case of three IDPs, the project aims to answer the question of whether these secondary structures formed at the protein-protein interfaces transiently pre-exist or not in the unbound state of solvated IDPs. If it is possible to identify and characterize these molecular recognition features (MoRFs) in the IDP unbound state, then the results of this work will subsequently help to determine the structures of protein complexes involving IDPs
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Unnikrishnan, Aparna. "INVESTIGATION OF PROTEIN STRUCTURE AND DYNAMICS BY NMR SPECTROSCOPY". The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1595418229203869.
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Heil, Christina Sabine [Verfasser], Martin [Gutachter] Grininger i Michael [Gutachter] Göbel. "Towards the conformational dynamics of multidomain proteins / Christina Sabine Heil ; Gutachter: Martin Grininger, Michael Göbel". Frankfurt am Main : Universitätsbibliothek Johann Christian Senckenberg, 2019. http://d-nb.info/1198932856/34.
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Wang, Zijian. "Single-Molecule Spectroscopy And Imaging Studies Of Protein Folding-Unfolding Conformational Dynamics: The Multiple-State And Multiple-Channel Energy Landscape". Bowling Green State University / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1459942296.
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Murciano, Brice. "Dynamique conformationnelle chez les protéines d'adhésion de Babesia : mythe ou réalité ?" Thesis, Montpellier 1, 2013. http://www.theses.fr/2013MON13510/document.
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L'une des infections parasitaires les plus courantes chez les animaux à travers le monde est la babésiose ou piroplasmose. Causée par le développement intraérythrocytaire d'un parasite du genre Babesia, elle présente de nombreux signes cliniques semblables à ceux du paludisme. Ce parasite, du phylum des Apicomplexes, est transmis via le vecteur tique et effectue son cycle de reproduction dans les cellules rouges du sang de l'hôte vertébré. En Europe B. divergens et B. canis sont les espèces majoritairement responsables respectivement de la babésiose bovine et la babésiose canine. Dans une stratégie de recherche vaccinale, l'étude de protéines parasitaires en contact avec la circulation sanguine est primordiale pour comprendre les interactions hôte-parasite et identifier des candidats vaccins à haut potentiel. Les protéines à ancrage GPI (glycosylphosphatidylinositol) font partie de ces protéines. La première protéine à ancrage GPI décrite chez B. divergens est Bd37.1. Elle induit une protection totale contre une infection à B. divergens à la condition qu'une séquence hydrophobe soit ajoutée en C-terminale. La résolution de la structure RMN de cette protéine a permis de mettre en évidence un probable mécanisme de changement conformationnel en fonction du pH. La structure composée de 3 sous domaines montre que celle-ci n'est maintenue que par des ponts salins qui peuvent se rompre en milieu acide. Or l'environnement membranaire dans lequel évolue Bd37.1 ancrée à la surface du parasite et/ou à l'approche du globule rouge lors de l'invasion est acide. Cette dynamique conformationnelle de la protéine Δ-Bd37, liée à l'environnement membranaire, pourrait être à l'origine du mécanisme qui confère une immunité en fonction de la présence ou non de la séquence hydrophobe en C-terminale de Bd37.1. Nous avons cherché à estimer les implications d'une telle dynamique dans les interactions hôtes-parasites à travers l'étude structurale de 2 protéines parasitaires (Bd37.1 et Bc28.1). Dans le premier cas nous étudions la dynamique conformationnelle de la protéine d'adhésion Bd37.1. Nous avons exploré les différentes conformations que pourrait adopter la protéine Bd37.1 par une approche de biophysique et nous avons stabilisé ces différentes conformations en solution par le biais de mutations pour les étudier. Parmi ces mutants, le mutant EDK-Δ-Bd37 dont les ponts salins ont été rompus montre des caractéristiques différentes de Δ-Bd37. Les données enregistrées sur ce mutant nous ont amené à résoudre sa structure et à tester son pouvoir vaccinant. Dans une seconde partie, nous caractérisons biochimiquement et fonctionnellement une autre protéine Bc28.1, l'orthologue de Bd37.1. chez B. canis, accompagnée de la résolution de sa structure. Nous montrons que Bc28.1 est une protéine d'adhésion localisée à la surface du parasite et nous comparons les structures de Bd37.1 et Bc28.1. Ces deux structures sont finalement très différentes tandis que localisation et fonction sont similairesOne of the most common parasitic infections in animals worldwide is babesiosis or piroplasmosis. Caused by the intraerythrocytic development of Babesia parasite, it has many clinical signs similar to those of malaria. This parasite of the phylum Apicomplexa, is transmitted via the tick vector and performs its reproductive cycle in red blood cells of the vertebrate host. B. In Europe divergens and B. canis species are mainly responsible respectively for bovine babesiosis and canine babesiosis. A strategy of vaccine research, the study of parasite proteins in contact with the bloodstream is essential for understanding host-parasite interactions and identify vaccine candidates with high potential. Anchored protein GPI (glycosylphosphatidylinositol) are part of these proteins. The first protein GPI anchors described in B. divergens is Bd37.1. It induces complete protection against infection with B. divergens provided a hydrophobic sequence is added at the C-terminus. Resolution NMR structure of this protein has highlighted a probable mechanism of conformational change as a function of pH. The structure consists of three sub areas shows that it is only maintained by salt bridges which can break in acidic medium. However, the environment within which Bd37.1 membrane anchored to the surface of the parasite and / or approach the red blood cell during the invasion is acidic. This conformational dynamics of the protein-Δ Bd37 linked to the membrane environment, could be at the origin of the mechanism that confers immunity depending on the presence or absence of the hydrophobic sequence at the C-terminus of Bd37.1. We sought to assess the implications of such dynamics in host-parasite interactions through structural study of two parasite proteins (Bd37.1 and Bc28.1). In the first case we study the conformational dynamics of the adhesion protein Bd37.1. We explored the different conformations that may be adopted by a protein Bd37.1 biophysical approach and we have stabilized in different conformations in solution through mutations to study. Among these mutants, the mutant Δ-Bd37-EDK including salt bridges were broken shows different characteristics Δ-Bd37. The data on this mutant led us to solve the structure and to test its power vaccinating. In a second part, we characterize biochemically and functionally Bc28.1 another protein, the ortholog Bd37.1. in B. canis, accompanied with the resolution of its structure. We show that Bc28.1 is an adhesion protein localized to the parasite surface and compare the structures and Bd37.1 Bc28.1. These two structures are ultimately very different while location and function are similar
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Foo, Alexander. "New Insights into the Role of Membrane Interactions and Conformational Dynamics in Intramembrane Proteolysis by GlpG Rhomboid". Thesis, Université d'Ottawa / University of Ottawa, 2017. http://hdl.handle.net/10393/36941.
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The rhomboid family of intramembrane serine proteases can catalyze proteolysis of substrates that are normally embedded in the cell membrane, making them key players in a diverse range of biological processes. While X-ray crystal structures provide detailed insights into the mechanism of intramembrane hydrolysis, questions remain concerning how transmembrane (TM) substrates are able to gain access to the rhomboid active site, and whether interactions with the membrane environment can influence its structure and function. In this thesis, these questions were investigated using the E. coli rhomboid ecGlpG. In Chapter 3, the effect of hydrophobic mismatch between lipid and protein was investigated using families of amphiphiles with saturated alkyl chains. While ecGlpG displayed maximal activity against a water-soluble model substrate when solubilized in detergents containing 10-12 carbon atoms, shorter and longer chain detergents led to loss of activity. An even larger effect was observed when ecGlpG was reconstituted into phospholipid bicelles, with no proteolytic activity being detected in 14-carbon lipids. These results suggest that mismatch between the hydrophobic regions of the catalytic TM domain (TMD) and the local membrane environment is detrimental to proteolysis. To obtain further insight into the structure and dynamics of ecGlpG, sample conditions were identified in Chapter 4 that enabled, for the first time, the acquisition of NMR spectra showing signals from the ecGlpG TMD. While significant peak broadening prevented chemical shift assignment, the sensitivity and resolution of peaks corresponding to the tryptophan indole NH group allowed their use as structural probes. These were employed in Chapter 5 to characterize the open conformation of ecGlpG that is postulated to facilitate substrate entry. These spectra showed evidence of an open conformation in which the intact α5 is laterally displaced. Interactions with a substrate-derived peptide also appeared to stimulate gate opening; however, activity assays suggested that formation of the open state could compromise catalytic activity against water-soluble substrates, and that interactions with TM substrates could counter this effect. Taken together, these results provide new insight into the role of both the local membrane environment and α5-conformational dynamics on intramembrane proteolysis, and suggest a mechanism to prevent cleavage of off-target rhomboid substrates in vivo.
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Hassan, Anwar I. "Development of ¹⁹F NMR Methods for the Study of GlpG Rhomboid Protease in Detergents and Lipid Nanoparticle Systems". Thesis, Université d'Ottawa / University of Ottawa, 2021. http://hdl.handle.net/10393/42521.
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Rhomboids are a family of intramembrane serine proteases that cleave transmembrane protein substrates within the lipid membrane. They are involved in a wide range of biological processes, including signal transduction, parasite invasion, bacterial quorum sensing and apoptosis. While previous X-ray crystal structures and functional studies have provided some detailed insights into the mechanism of intramembrane hydrolysis, it is still not clear how the transmembrane substrate can gain access into the active site from the lipid environment. While several modes of action have been suggested, one hypothesis proposes a lateral movement of the fifth transmembrane helix, causing a displacement that would allow transmembrane substrates to enter the rhomboid active site. A powerful method that has the potential to yield insights into rhomboid dynamics is solution NMR; however, the large size of rhomboid protease samples has complicated conventional methods typically used to assess protein structure and dynamics. ¹⁹F NMR could allow the study of rhomboid conformational dynamics by providing a simplified spectrum with high sensitivity to changes in local chemical environments. In this thesis various methods of ¹⁹F incorporation were evaluated for utility in studying rhomboid conformational dynamics, focusing on the GlpG rhomboid from E. coli. First, GlpG samples were prepared with ¹⁹F incorporated into tryptophan sidechains, and 1D ¹⁹F NMR spectra were acquired. While spectra with decent spectral dispersion were obtained, the assignment process was complicated by low signal-to-noise, and multiple changes in the spectrum introduced by the mutation. Chemoselective labelling of cysteine residues with probes containing a trifluoromethyl group was also investigated and found to give rise to well resolved ¹⁹F NMR spectra with promising characteristics. In addition, protocols for incorporation of trifluoromethyl-phenylalanine using unnatural amino acid incorporation at introduced amber codon sites were also explored, since one of the long-term goals of this work is to study ¹⁹F-labelled GlpG in its native lipid environment. For this purpose, some protocol development was also performed to introduce GlpG into lipid nanoparticles using styrene maleic acid co-block polymers. However, low expression yields of trifluoromethyl-phenylalanine-labelled GlpG and the large size of the lipid nanoparticles are not yet compatible with solution NMR. Nonetheless, this thesis lays the groundwork for further development of these samples to allow the future study of conformational exchange of GlpG in native lipid membranes.
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Haselbach, David [Verfasser], Holger [Akademischer Betreuer] Stark i Kai [Akademischer Betreuer] Tittmann. "Conformational Dynamics of large protein Complexes / David Haselbach. Gutachter: Holger Stark ; Kai Tittmann. Betreuer: Holger Stark". Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2015. http://d-nb.info/1067626468/34.
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Subramaniam, Srisunder. "Studies of conformational changes and dynamics accompanying substrate recognition, allostery and catalysis in bacteriophage lambda integrase". The Ohio State University, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=osu1111655332.
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Burnley, B. Tom. "New tools to study the conformational dynamics of large proteins: A study of FBP-aldolase and other enzymes". Thesis, University of Leeds, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.485182.
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Proteins are inherently flexible molecules, both in structure and in function. Although multiple conformational changes appear vital for enzyme catalysis, these essential . motions are poorly understood for the majority of systems at present. Escherichia coli Class II fructose 1,6-bisphosphate aldolase (FBP-aldolase) provides an excellent model system for the study of enzyme dynamics as it has been extensively characterised and adopts the (a1~)8 barrel fold. This ubiquitous and versatile architecture represents -10% of all known enzyme structures. Multiple structures of FBP-aldolase have been solved previously, and reveal significant conformational changes. In addition;· sitedirected mutagenesis studies restricting loop flexibility have been shown to reduce catalytic rate, further highlighting the potential importance of conformational dynamics. The work presented here expands these studies by using a novel suite of NMR relaxation experiments to present the first quantified description of the su19-nanosecond dynamics of a protein that exhibits the (a/~)8 barrel.morphology. Experimental studies of this important fold have been restricted due to the size and high helical content that cause highly overlapped 20 spectra. This critically hinders NMR relaxation techniques, preventing the observation of molecular motion at atomic resolution. 20 HSQC based NMR ,sp~troscopy experiments only produce unambiguous rate measurement of less than 40% of residues in FBP-aldolase. Here, a novel sUit~ of Hadamard CO' encoded T1, T2 and NOE pulse sequences is presented· which dramatically reduce spectral crowding to allow the measurement of over 80% of the cross-peaks in FBP-aldolase spectra. The general applicability of these new methods will allow NMR relaxation studies to be conducted on significantly larger protein systems. To apply these Hadamard encoded pulse sequences, and also to assign the backbone amide chemical shifts, 2H, 13C and 15N isotopically enriched FBP-aldolase samples were prepared. Expression and purification protocols were optimised to provide suffiCient material to maximise resonance signal. These samples, in conjunction with multidimensional TROSY experiments, yielded chemical shift assignment for 55% of backbone resonances. This assignment process was aided by the production of seven samples of FBP-aldolase selectiVity labelled for specific amino' acid types. The T10 Tz and NOE relaxation rates were measured for FBP~aldolase at two high-field strengths, 750MHz and 900MHz. The data were quantified using an adapted version ·of the model-free protocol, and revealed important dynamic contributions from the major catalytic loop and the catalytic divalent cation. These experiments were repeated in the presence of the first binding substrate DHAp, which illustrated that the major loop remains flexible to accommodate the binding of the second substrate, G3P. In addition, a new protocol for the comparison of crystal structure pairs based on the distance difference matrix (DDM) is presented. An extensive database of enzyme structure pairs was generated, and the DDM-based methods were used to seek and describe structural deviation. This provided a comprehensive description of the prevalence, magnitude and manner of substrate-induced conformational changes. This study also demonstrates the conformational fluctuations present in enzyme pairs when both structures are solved either in the presence or absence of substrate. The methods developed in this work provide a detailed description of sub-nanosecond dynamics in FBP-aldolase and the conformational changes obseNed for enzymes in general. It is hoped that these novel tools will advance future investigations to further delineate the role of dynamics in enzyme catalysis.