Dissertations / Theses on the topic 'Proteins Molecular Dynamics Computational Biophysics'
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Rigoli, Marta. "The structure-dynamics-function relation in proteins: bridging all-atom molecular dynamics, experiments, and simplified models." Doctoral thesis, Università degli studi di Trento, 2022. https://hdl.handle.net/11572/330870.
Full textParton, Daniel L. "Pushing the boundaries : molecular dynamics simulations of complex biological membranes." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:7ab91b51-a5ae-46b4-b6dc-3f0dd3f0b477.
Full textHirst-Dunton, Thomas Alexander. "Using molecular simulations to parameterize discrete models of protein movement in the membrane." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:893568e9-696f-47e7-8495-59ecfb810459.
Full textDutta, Priyanka. "Computational Modeling of Allosteric Stimulation of Nipah Virus Host Binding Protein." Scholar Commons, 2016. http://scholarcommons.usf.edu/etd/6227.
Full textParra, Katherine Cristina. "Combination of the Computational Methods: Molecular dynamics, Homology Modeling and Docking to Design Novel Inhibitors and study Structural Changes in Target Proteins for Current Diseases." Scholar Commons, 2014. https://scholarcommons.usf.edu/etd/5093.
Full textGuinto, Ferdiemar Cardenas Jr. "Investigating Secondary Structure Features of YAP1 Protein Fragments Using Molecular Dynamics (MD) and Steered Molecular Dynamics (SMD) Simulations." Scholarly Commons, 2017. https://scholarlycommons.pacific.edu/uop_etds/2973.
Full textLumb, Craig Nicholas. "Computational studies of signalling at the cell membrane." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:d5b2db00-1050-4191-8eff-3521a4885a0c.
Full textPavlovicz, Ryan Elliott. "Investigation of Protein/Ligand Interactions Relating Structural Dynamics to Function: Combined Computational and Experimental Approaches." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1397220613.
Full textCardoch, Sebastian. "Computational study of single protein sensing using nanopores." Thesis, Uppsala universitet, Materialteori, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-423441.
Full textZhou, 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.
Full textPh.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
Buch, Mundó Ignasi 1984. "Investigation of protein-ligand interactions using high-throughput all-atom molecular dynamics simulations." Doctoral thesis, Universitat Pompeu Fabra, 2012. http://hdl.handle.net/10803/101407.
Full textRajapaksha, Suneth P. "Single Molecule Spectroscopy Studies of Membrane Protein Dynamics and Energetics by Combined Experimental and Computational Analyses." Bowling Green State University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1337141955.
Full textDahl, Anna Caroline E. "Membrane protein mechanotransduction : computational studies and analytics development." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:67798647-8ed5-46e0-bde9-c71235fe70ba.
Full textSchmidt, Matthias Rene. "K+ channels : gating mechanisms and lipid interactions." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:51dc4149-d943-4dcd-bf5b-f04130456d84.
Full textPham, Khoa Ngoc. "Conformational Dynamics and Stability Associated with Magnesium or Calcium Binding to DREAM in the Regulation of Interactions between DREAM and DNA or Presenilins." FIU Digital Commons, 2016. http://digitalcommons.fiu.edu/etd/2589.
Full textChakraborty, Srirupa. "Computational modeling of structural dynamics and energetics of two allosteric proteins| Kinesins and Acetylcholine Receptors." Thesis, State University of New York at Buffalo, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10242471.
Full textTo quote famous physicist and Nobel laureate, Dr. Richard Feynman, “…everything that living things do can be understood in terms of the jigglings and wigglings of atoms.” It is these jigglings and wigglings of atoms that form the focus of my dissertation, which studies the structural dynamics of two different allosteric proteins through computational simulations. Protein allostery is a field that has been investigated widely. But the structural details of how signals initiating at one site transmit through the network of residues in different proteins and result in the alteration of their functional states, still remains largely unresolved. Here, we independently study the kinesin motor protein and the neuromuscular acetylcholine receptor (nAChR) – both of which play crucial roles in cellular signaling. Kinesins are intracellular porters, carrying organelles, molecules and other cargo within the cell, while nAChRs are transmembrane receptors that aid in intercellular communication at nerve-to-muscle synapses. These two protein families are structurally and functionally very different, but both are allosteric in nature, with interesting protein dynamics that efficiently convert chemical energy to mechanical motions in order to perform their cellular functions.
The total timescale of an entire allosteric transition is currently too long for complete all-atom molecular dynamics simulations. Thus, in this dissertation, for both the projects, we begin at different equilibrium states of the proteins and carry out comparative analyses of conformation and dynamics at those states, which aids in elucidating the structural and functional correlates for these systems.
For the kinesin-microtubule (KIN-MT) system, we have built atomistic structure models for the key nucleotide-binding states of the kinesin-MT complex from lower resolution cryo-EM maps, by suitably modifying the MD potential with the EM map force. We have also studied ligand-protein (ADP/ATP-kinesin) interactions and predicted the sequence of structural changes in kinesin-MT complex during its conformational transitions between important biochemical states and pinpointed key contributing residues.
Simultaneously, we have also characterized the transmitter binding sites of neuromuscular acetylcholine receptors and analyzed the energy asymmetries between the fetal and adult endplate receptors. Through large-scale simulations of the fetal and adult binding sites, we have come across compelling evidence of the structural causes that explain these asymmetries and were successful in identifying the minimum construct that is both necessary and sufficient to exchange the function between adult and fetal binding sites in AChRs. Our in silico models and predictions act as important tools to further guide mutational and functional experiments.
Abd, Halim Khairul Bariyyah. "Molecular dynamics simulation studies of transmembrane signalling proteins." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:bc9e1e0e-433c-4adb-8374-1065eac0f37e.
Full textMohammadiarani, Hossein. "Simulation Studies of Signaling and Regulatory Proteins." Thesis, University of New Hampshire, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10685640.
Full textI used molecular dynamics (MD) simulations as a primary tool to study folding and dynamics of signaling and regulatory proteins. Specifically, I have studied two classes of proteins: the first part of my thesis reports studies on peptides and receptors of the insulin family, and the second part reports on studies of regulatory proteins from the G-protein coupled receptor family. The first problem that I investigated was understanding the folding mechanism of the insulin B-chain and its mimetic peptide (S371) which were studied using enhanced sampling simulation methods. I validated our simulation approaches by predicting the known solution structure of the insulin B-chain helix and then applied them to study the folding of the mimetic peptide S371. Potentials of mean force (PMFs) along the reaction coordinate for each peptide are further resolved using the metadynamics method. I further proposed receptor-bound models of S371 that provide mechanistic explanations for competing binding properties of S371 and a tandem hormone-binding element of the receptor known as the C-terminal (CT) peptide. Next, I studied the all-atom structural models of peptides containing 51 residues from the transmembrane regions of IR and the type-1 insulin-like growth factor receptor (IGF1R) in a lipid membrane. In these models, the transmembrane regions of both receptors adopt helical conformations with kinks at Pro961 (IR) and Pro941 (IGF1R), but the C-terminal residues corresponding to the juxta-membrane region of each receptor adopt unfolded and flexible conformations in IR as opposed to a helix in IGF1R. I also observe that the N-terminal residues in IR form a kinked-helix sitting at the membrane-solvent interface, while homologous residues in IGF1R are unfolded and flexible. These conformational differences result in a larger tilt-angle of the membrane-embedded helix in IGF1R in comparison to IR to compensate for interactions with water molecules at the membrane-solvent interfaces. The metastable/stable states for the transmembrane domain of IR, observed in a lipid bilayer, are consistent with a known NMR structure of this domain determined in detergent micelles, and similar states in IGF1R are consistent with a previously reported model of the dimerized transmembrane domains of IGF1R. I further studied dimerization propensities of IR transmembrane domains using three different constructs in a lipid bilayer (isolated helices, ectodomain-anchored helices, and kinase-anchored helices). These studies revealed that the transmembrane domains can dimerize in isolation and in kinase-anchored forms, but not significantly in the ectodomain construct. The final studies in my thesis are focused on interplay of protein dynamics and small-molecule inhibition in a set of regulatory proteins known as the Regulators of G-protein Signaling (RGS) proteins. Thiadiazolidinone (TDZD) compounds have been shown to inhibit the protein-protein interaction between RGS and the alpha subunit of G-proteins by covalent modification of cysteine residues in RGS proteins. However, some of these cysteines in RGS proteins are not surface-exposed. I hypothesized that transient binding pockets expose cysteine residues differentially between different RGS isoforms. To explore this hypothesis, long time-scale classical MD simulations were used to probe the dynamics of three RGS proteins (RGS4, RGS8, and RGS19), and characterize flexibility in various helical motifs. The results from simulation studies were validated by hydrogen-deuterium exchange (HDX) studies, and revealed motions indicating solvent exposure of buried cysteine residues, thereby providing insights into inhibitor binding mechanisms. In addition, I used different published HDX models which have resulted in a comprehensive comparison of existing models. Furthermore, I developed the new HDX models with optimized parameters which had comparable accuracy and more computational efficiency compared to other models. Overall, my thesis has resulted in the development and applications of several state-of-the-art computational methods that have provided a detailed mechanistic understanding of peptide and small-molecule based inhibitors and their interactions with large proteins that are potentially useful in designing novel approaches to target protein-protein interactions.
Ainsley, Jon. "Computational simulations of enzyme dynamics and the modelling of their reaction mechanisms." Thesis, Northumbria University, 2017. http://nrl.northumbria.ac.uk/36286/.
Full textShorthouse, David Robert. "Computational methods for the study of immunoglobulin aggregation." Thesis, University of Oxford, 2015. http://ora.ox.ac.uk/objects/uuid:43c0950e-7f58-48b9-899d-74dcfee35887.
Full textKrammer, André Thomas. "Computational studies of protein-membrane interactions and forced unfolding of proteins /." Thesis, Connect to this title online; UW restricted, 2000. http://hdl.handle.net/1773/9697.
Full textKarolak, Aleksandra. "Application and Development of Computational Methods in Conformational Studies of Bio-molecules." Scholar Commons, 2015. https://scholarcommons.usf.edu/etd/5520.
Full textTangar, Antonija. "Structure-Function Relationships in Hexacoordinate Heme Proteins: Mechanism of Cytoglobin Interactions with Exogenous Ligands." FIU Digital Commons, 2018. https://digitalcommons.fiu.edu/etd/3729.
Full textWesterlund, 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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Kotecha, Abhay. "Structure and dynamics of picornavirus capsids to inform vaccine design." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:df739a5f-fdb2-4930-909f-d94ce274ce33.
Full textKognole, Abhishek A. "UNDERSTANDING CARBOHYDRATE RECOGNITION MECHANISMS IN NON-CATALYTIC PROTEINS THROUGH MOLECULAR SIMULATIONS." UKnowledge, 2018. https://uknowledge.uky.edu/cme_etds/80.
Full textChetwynd, Alan. "Computational studies of transmembrane helix insertion and association." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:440da098-5bd6-4fcb-8396-645517ac2122.
Full textNadas, Janos Istvan. "Computational Structure Activity Relationship Studies on the CD1d/Glycolipid/TCR Complex using AMBER and AUTODOCK." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1251145085.
Full textChotikasemsri, Pongsathorn. "Computational Prediction of the Agregated Structure of Denatured Lysozyme." TopSCHOLAR®, 2009. http://digitalcommons.wku.edu/theses/120.
Full textWalker, Alice Rachel. "Computational Simulations of Cancer and Disease-Related Enzymatic Systems Using Molecular Dynamics and Combined Quantum Methods." Thesis, University of North Texas, 2018. https://digital.library.unt.edu/ark:/67531/metadc1157647/.
Full textMarklund, Erik. "Gas-Phase Protein Structure Under the Computational Microscope : Hydration, Titration, and Temperature." Doctoral thesis, Uppsala universitet, Beräknings- och systembiologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-151006.
Full textSchwing, Gregory John. "Implementation of Replica Exchange with Dynamic Scaling in GROMACS 2018." ScholarWorks@UNO, 2018. https://scholarworks.uno.edu/honors_theses/117.
Full textDabdoub, Shareef Majed. "Applied Visual Analytics in Molecular, Cellular, and Microbiology." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1322602183.
Full textDinescu, Adriana. "Modeling wild type and mutant glutathione synthetase." Thesis, University of North Texas, 2004. https://digital.library.unt.edu/ark:/67531/metadc5556/.
Full textStelzl, Lukas Sebastian. "Studying marcomolecular transitions by NMR and computer simulations." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:6e4bbe06-fc58-471b-a932-d940fe78b9a5.
Full textHarrison, Ryan M. "Molecular biophysics of strong DNA bending and the RecQ DNA helicase." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:f02fc167-b705-4275-a413-21d13b5d94c3.
Full textNobrega, Robert P. "Early Folding Biases in the Folding Free-Energy Surface of βα-Repeat Proteins: A Dissertation." eScholarship@UMMS, 2014. https://escholarship.umassmed.edu/gsbs_diss/723.
Full textNobrega, Robert P. "Early Folding Biases in the Folding Free-Energy Surface of βα-Repeat Proteins: A Dissertation." eScholarship@UMMS, 2007. http://escholarship.umassmed.edu/gsbs_diss/723.
Full textViveca, Lindahl. "Optimizing sampling of important events in complex biomolecular systems." Doctoral thesis, KTH, Fysik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-217837.
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Trovato, Fabio. "Molecular Dynamics Simulations of biopolymers within the cell environment: Minimalist models for the Nucleic Acids and Green Fluorescent Proteins in the cytoplasm." Doctoral thesis, Scuola Normale Superiore, 2013. http://hdl.handle.net/11384/85896.
Full textSánchez, Martínez Melchor. "Protein Flexibility: From local to global motions. A computational study." Doctoral thesis, Universitat de Barcelona, 2014. http://hdl.handle.net/10803/288044.
Full textLa presente tesis se centra en el estudio computacional de la dinámica de las proteínas. Las proteínas son entidades flexibles y como tales se mueven. Este movimiento es indispensable y esta directamente relacionado con su función. La dinámica de las proteínas se puede dividir en dos grandes bloques conceptuales según el número de átomos involucrados, la escala de tiempo en que tiene lugar y la amplitud y dirección de la misma. Debido a la importancia de estos fenómenos, emerge la necesidad de tener un conocimiento profundo sobre los mismos. Debido a ello, en esta tesis doctoral se ha tratado de dar respuesta a varios fenómenos observados en relación directa con la dinámica de las proteínas. Concretamente, hemos realizado estudios a nivel local, de 'centro activo', relacionados con la catálisis enzimática y el daño proteico, así como a nivel global, con la determinación y el análisis de conjuntos conformacionales de proteínas. Estos estudios, se han desarrollado usando métodos propios de la química, la bioquímica y la biofísica computacionales, los cuales se han mostrado como herramientas muy útiles a la hora de estudiar la dinámica. De todos ellos, de forma general, podemos concluir que los métodos computacionales son una herramienta eficaz y util para caracterizar la dinámica de las proteínas. Sin embargo, los métodos computacionales actuales presentan limitaciones y para resolverlos la incorporación de datos experimentales as como su correcta interpretación es crucial. Pero aunque los metodos computacionales necesitan de los experimentales, esta necesidad también se da de manera opuesta. La convergencia de los métodos experimentales y computacionales es clave para poder profundizar en el conocimiento de la dinámica de las proteínas.
Sahai, Michelle Asha. "Computational studies of ligand-water mediated interactions in ionotropic glutamate receptors." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:b86d2f5a-3554-44c0-b985-5693241369ec.
Full textIhms, Elihu Carl. "Integrative Investigation and Modeling of Macromolecular Complexes." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1429547886.
Full textRzepala, Wojciech. "Interactions of carbon nanotubes and lipid bilayers." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:58cd5321-c61c-4594-b74d-8ca6f507c48f.
Full textTengel, Tobias. "Studies of protein structure, dynamics and protein-ligand interactions using NMR spectroscopy." Doctoral thesis, Umeå : Univ, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1472.
Full textGonzalez, Walter G. "Protein-Ligand Interactions and Allosteric Regulation of Activity in DREAM Protein." FIU Digital Commons, 2016. http://digitalcommons.fiu.edu/etd/2503.
Full textMahajan, Rahul. "Gβγ acts at an inter-subunit cleft to activate GIRK1 channels." VCU Scholars Compass, 2012. http://scholarscompass.vcu.edu/etd/3307.
Full textMigliore, Mattia. "Recherche par modélisaion moléculaire de signatures RMN et DC caractéristiques pour les coudes β et y dans les peptides bioactifs. Characterization of β-turns by electronic circular dichroism spectroscopy : a coupled molecular dynamics and time-dependent density functional theory computational study." Thesis, Normandie, 2020. http://www.theses.fr/2020NORMR001.
Full textThe aim of this work is to identify NMR and CD characteristic patterns for β- and γ-turns in bioactive peptides by molecular modelling. With helices, β- and γ-turns constitute favoured recognition motifs in bioactive peptides by their targets. Even though several classes of turns with different geometries exist in polypeptide structures (2 γ-turn types and 12 β-turn types), few experimental tools are available for their characterization. Thus, only 4 types of β-turns (I, I’, II et II’) have been, at present, described by NMR and there are no reliable reference CD spectra for turns. In order to extend the NMR data for all β- and γ-turn types, we analyzed NMR structural parameters (inter-hydrogen distances and ᶾJʜɴ-ʜꭤ coupling constants) in a representative peptide model dataset extracted from the PDB. The inter-hydrogen distance analysis allowed to identify specific NMR patterns for the two γ-turn types and for four β-turn types (IV₁, IV₂,, VIb and VIII). ᶾJʜɴ-ʜꭤ coupling constant may be used to confirm the identification and to remove ambiguities. Then, we simulated the reference CD spectra of model peptides adopting type I, I’, II and II’ β-turn conformations by combining molecular dynamic simulations and TDDFT computations. These computations allowed to determine two families of specific CD spectra : types I/II’, on one side and types I’/II, on the other. All these results indicate that the turns do not present the same patterns in both techniques. The combination of NMR and CD could therefore allow a better identification of the nature and the different types of turns
Fu, Josephine K. Y. "Functional characterization of the teleost multiple tissue (tmt) opsin family and their role in light detection." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:39bc18bb-16cb-4549-94cd-5f872daafe7e.
Full textRagland, Debra A. "The Structural Basis for the Interdependence of Drug Resistance in the HIV-1 Protease." eScholarship@UMMS, 2012. http://escholarship.umassmed.edu/gsbs_diss/879.
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