Relevant bibliographies by topics / Chemistry, Physical. Biophysics, Medical. Biophysics, General

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  1. Journal articles
  2. Dissertations / Theses
  3. Books

Academic literature on the topic 'Chemistry, Physical. Biophysics, Medical. Biophysics, General'

Author: Grafiati
Published: 4 June 2021
Last updated: 15 February 2022

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Journal articles on the topic "Chemistry, Physical. Biophysics, Medical. Biophysics, General"

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Vlasov, Alexey V., Nina L. Maliar, Sergey V. Bazhenov, Evelina I. Nikelshparg, Nadezda A. Brazhe, Anastasiia D. Vlasova, Stepan D. Osipov, et al. "Raman Scattering: From Structural Biology to Medical Applications." Crystals 10, no. 1 (January 15, 2020): 38. http://dx.doi.org/10.3390/cryst10010038.

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This is a review of relevant Raman spectroscopy (RS) techniques and their use in structural biology, biophysics, cells, and tissues imaging towards development of various medical diagnostic tools, drug design, and other medical applications. Classical and contemporary structural studies of different water-soluble and membrane proteins, DNA, RNA, and their interactions and behavior in different systems were analyzed in terms of applicability of RS techniques and their complementarity to other corresponding methods. We show that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases. In particular, the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS), which would help to further the development of protein structural crystallography and would result in a number of novel high-resolution structures of membrane proteins—drug targets; and, structural studies of photoactive membrane proteins (rhodopsins, photoreceptors, etc.) for the development of new optogenetic tools. Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed. All of these techniques have been extensively developed during recent several decades. A number of interesting applications of CARS, resonant, and surface-enhanced Raman spectroscopy methods are also discussed.
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Boregowda, Satish, Rod Handy, Darrah Sleeth, and Naomi Riches. "Using Thermodynamic Degradation Approach to Quantify Human Stress Response." Journal of Thermodynamics 2017 (September 11, 2017): 1–5. http://dx.doi.org/10.1155/2017/7546823.

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The present study provides a thermodynamic degradation approach to model human stress response. Finger skin temperature was used as an indicator of stress response to a stressor (or stressful event) followed by a recovery. The entropy change (ΔS) is calculated using heat transfer (δQ) from the peripheral skin and finger skin temperature (Tf). It was hypothesized that the human stress response, as evidenced by finger skin temperature change, is a quasi-static process. The entropy approach is demonstrated using data from a medical school experimental study. The finger skin temperature was measured under three conditions (relaxation, stressor task, and recovery) during the physiological test profile. The entropy change (ΔS) is postulated as entropy damage (ΔSD), which is a metric for measuring the aging or system degradation. The aging-ratio, Aaging-ratio, that is, the ratio of entropy change due to stressor to that of recovery, is presented for both male and female subjects. The statistical t-tests demonstrate statistical significance in human stress response to stressor and recovery states within and between male and female subjects. This novel approach could be valuable to medical researchers, particularly in the field of occupational health to evaluate human exposure to stressful environments.
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Boregowda, Satish, Rod Handy, Darrah Sleeth, and Andrew Merryweather. "Measuring Entropy Change in a Human Physiological System." Journal of Thermodynamics 2016 (February 22, 2016): 1–8. http://dx.doi.org/10.1155/2016/4932710.

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The paper presents a novel approach involving the use of Maxwell relations to combine multiple physiological measures to provide a measure of entropy change. The physiological measures included blood pressure (BP), heart rate (HR), skin temperature (ST), electromyogram (EMG), and electrodermal response (EDR). The multiple time-series physiological data were collected from eight subjects in an experimental pilot study conducted at the Human Engineering Laboratory of NASA Langley Research Center. The methodology included data collection during a relaxation period of eighteen minutes followed by a sixty-minute cognitive task. Two types of entropy change were computed: (a) entropy change (ΔSBP) due to blood pressure, heart rate, and skin temperature and (b) entropy change (ΔSEMG) due to electromyogram, electrodermal response, and skin temperature. The results demonstrate that entropy change provides a valuable composite measure of individual physiological response to various stressors that could be valuable in the areas of medical research, diagnosis, and clinical practice.
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Bünzli, Jean-Claude G. "Lanthanide light for biology and medical diagnosis." Journal of Luminescence 170 (February 2016): 866–78. http://dx.doi.org/10.1016/j.jlumin.2015.07.033.

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Bhadane, Mahesh S., Shahzad Akhtar, S. S. Dahiwale, K. Hareesh, K. Asokan, D. Kanjilal, V. N. Bhoraskar, and S. D. Dhole. "Evaluation of thermoluminescence of 200 keV carbon ion irradiated CaSO4:Dy nanophosphors for medical dosimetry." Journal of Luminescence 192 (December 2017): 695–700. http://dx.doi.org/10.1016/j.jlumin.2017.07.042.

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Glaser, R. "An Introduction of Biophysics with Medical Orientation." Bioelectrochemistry and Bioenergetics 28, no. 3 (October 1992): 499. http://dx.doi.org/10.1016/0302-4598(92)80043-g.

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Rontó, G. "BR 60 — An Introduction to Biophysics with Medical Orientation." Bioelectrochemistry and Bioenergetics 17, no. 3 (November 1987): 584–85. http://dx.doi.org/10.1016/0302-4598(87)80072-7.

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Bezzi, Georgina, Ernesto J. Piga, Andrés Binolfi, and Pablo Armas. "CNBP Binds and Unfolds In Vitro G-Quadruplexes Formed in the SARS-CoV-2 Positive and Negative Genome Strands." International Journal of Molecular Sciences 22, no. 5 (March 5, 2021): 2614. http://dx.doi.org/10.3390/ijms22052614.

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The Coronavirus Disease 2019 (COVID-19) pandemic has become a global health emergency with no effective medical treatment and with incipient vaccines. It is caused by a new positive-sense RNA virus called severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). G-quadruplexes (G4s) are nucleic acid secondary structures involved in the control of a variety of biological processes including viral replication. Using several G4 prediction tools, we identified highly putative G4 sequences (PQSs) within the positive-sense (+gRNA) and negative-sense (−gRNA) RNA strands of SARS-CoV-2 conserved in related betacoronaviruses. By using multiple biophysical techniques, we confirmed the formation of two G4s in the +gRNA and provide the first evidence of G4 formation by two PQSs in the −gRNA of SARS-CoV-2. Finally, biophysical and molecular approaches were used to demonstrate for the first time that CNBP, the main human cellular protein bound to SARS-CoV-2 RNA genome, binds and promotes the unfolding of G4s formed by both strands of SARS-CoV-2 RNA genome. Our results suggest that G4s found in SARS-CoV-2 RNA genome and its negative-sense replicative intermediates, as well as the cellular proteins that interact with them, are relevant factors for viral genes expression and replication cycle, and may constitute interesting targets for antiviral drugs development.
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Reinsalu, Olavi, Anneli Samel, Elen Niemeister, and Reet Kurg. "MAGEA4 Coated Extracellular Vesicles Are Stable and Can Be Assembled In Vitro." International Journal of Molecular Sciences 22, no. 10 (May 14, 2021): 5208. http://dx.doi.org/10.3390/ijms22105208.

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Extracellular vesicles (EVs) are valued candidates for the development of new tools for medical applications. Vesicles carrying melanoma-associated antigen A (MAGEA) proteins, a subfamily of cancer-testis antigens, are particularly promising tools in the fight against cancer. Here, we have studied the biophysical and chemical properties of MAGEA4-EVs and show that they are stable under common storage conditions such as keeping at +4 °C and −80 °C for at least 3 weeks after purification. The MAGEA4-EVs can be freeze-thawed two times without losing MAGEA4 in detectable quantities. The attachment of MAGEA4 to the surface of EVs cannot be disrupted by high salt concentrations or chelators, but the vesicles are sensitive to high pH. The MAGEA4 protein can bind to the surface of EVs in vitro, using robust passive incubation. In addition, EVs can be loaded with recombinant proteins fused to the MAGEA4 open reading frame within the cells and also in vitro. The high stability of MAGEA4-EVs ensures their potential for the development of EV-based anti-cancer applications.
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Gardner, Kevin H. "Molecular biophysics at UT Southwestern Medical Center: Strength through breadth." Biopolymers 89, no. 4 (2008): 244–47. http://dx.doi.org/10.1002/bip.20927.

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Dissertations / Theses on the topic "Chemistry, Physical. Biophysics, Medical. Biophysics, General"

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Wang, Yin 1951. "Influences of membrane biophysical properties on the Metarhodopsin I to Metarhodopsin II transition in visual excitation." Diss., The University of Arizona, 1997. http://hdl.handle.net/10150/282520.

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Current biophysical studies of membrane proteins are centered on the relation of their structures to key biological functions of membranes in terms of lipid-protein interactions. The conformational transition of rhodopsin from Metarhodopsin I to Metarhodopsin II (Meta I-Meta II) is the triggering event for the visual process. Meta II is the activated form of the visual receptor and binds a signal transducing G protein (transducin), followed by two amplification stages which lead to generation of a visual nerve impulse. Herein, flash photolysis and surface plasmon resonance (SPR) spectroscopy techniques have been used to monitor the Meta I-Meta II transition of rhodopsin in various membrane recombinants. The flash photolysis experiments clearly show a substantial shift to the left of the Meta I-Meta II equilibrium for rhodopsin in egg phosphatidylcholine recombinant membranes. Investigation of the influences on rhodopsin function by non-lamellar forming lipids reveals a characteristic relationship between the Gibbs free energy change for the Meta I-Meta II equilibrium of rhodopsin and the intrinsic curvature of the lipid bilayer. Complementary SPR studies suggest a protrusion of the protein at the activated Meta II state which may be associated with exposure of recognition sites for the signal transducing G protein on the cytoplasmic surface of rhodopsin. All the experimental results obtained here are consistent with the hypothesis of a new flexible surface biomembrane model. The Meta II state is favored by a negative spontaneous curvature of the bilayer, corresponding to an imbalance of the lateral forces within the polar head groups and acyl chains. The mean curvature of membrane bilayer in the Meta II state reflects the small spontaneous curvature of the lipid bilayer in the vicinity of protein. Relief of the lipid curvature frustration in the Meta II state energetically couples the lipids to the photoexcitation of rhodopsin. Consideration of the various energetic contributions suggests the bilayer curvature free energy provides a reservoir of work in the modulation of rhodopsin function in the visual process. These studies that biophysical properties of the liquid-crystalline lipid bilayer are important in relation to protein function and may be relevant to the biomedical investigations of visual dysfunction.
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McCarthy, William James 1964. "An ab initio study of low-frequency, large-amplitude molecular vibrations." Diss., The University of Arizona, 1996. http://hdl.handle.net/10150/290692.

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The ab initio treatments of molecular vibrational motion often invoke only the harmonic oscillator approximation. For vibrational modes whose amplitudes access anharmonic regions of the potential energy surface, the harmonic oscillator approximation fails. Low-frequency large-amplitude vibrations, in particular, can access anharmonic regions in addition to other minima of the potential energy surface. Ab initio harmonic frequencies are often scaled to lower values by empirical factors which presumably account for anharmonicity effects as well as an incomplete basis set and account of electron correlation. However, the scaling of those ab initio harmonic frequencies corresponding to low-frequency large-amplitude vibrations results in theoretical values that are still typically several times larger than the experimental values. It is demonstrated in this dissertation that transforming the nuclear motion Hamiltonian to internal coordinates facilitates construction of ab initio potential energy curves, or surfaces, pertaining to low-frequency large-amplitude molecular vibrational modes. The use of internal coordinates complicates the expression of the kinetic energy in the Hamiltonian, and makes it difficult to obtain. Six different methods for determining the kinetic energy expression in internal coordinates are presented and reviewed. The computational implementation of these six methods was performed to allow their critique. Several example calculations of the presented methodology are given. The solution for the vibrational expectation values of the modes expressed by the developed Hamiltonian was also computationally implemented. The resultant theoretical transition frequencies of the molecular systems of 2-sulpholene and 2-aminopyrimidine are combined with experimental studies, and demonstrate the practical usefulness of the presented methodology.
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Choi, Jeong-Mo. "Multi-Scale Theoretical Investigations of Protein Interactions and Evolution." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493545.

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Evolution of biological systems requires players of multiple layers, from atoms and molecules to organisms and populations. Expression of a gene is operated by molecular machineries for transcription, translation, regulation, and maintenance, which work in concert to produce certain macroscopic and observable phenotypes. And when these phenotypes are exposed to selective pressures, more fit phenotypes (with their genes, molecular machineries, and interaction networks) survive in the population. While the relationship of a gene to its cellular consequences is not fully elucidated, it is known that molecular interactions are one of the key factors that determine the relationship. In this dissertation, we introduce several theoretical tools to study protein interactions and evolution, and show their applications at various scales. The first tool is a coarse-grained scoring function that predicts binding free energy of a protein complex. The scoring function is a simple linear combination of exposed interface areas of different amino acids. In spite of the simplicity, it shows a reasonable predictive power, and predicts correct biochemistry qualitatively. The second is an analytical theory of a spin model on a simple graph, developed by using conventional statistical mechanics. We separated structural and energetic contributions to the free energy of the system, and also obtained a closed form of linear graph contributions. The closed form is applied to predict sequence space free energy of lattice proteins. Lastly, we introduce statistical methods to analyze cellular proteomes and transcriptomes. They can extract global responses of proteomes and transcriptomes to a perturbation, and also responses of specific gene groups. We applied the methods to E. coli and yeast systems to address questions on the genotype-phenotype relationship and evolution.
Chemistry and Chemical Biology
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Chavan, Archana G. "Exploring the molecular architecture of proteins| Method developments in structure prediction and design." Thesis, University of the Pacific, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=3609082.

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Proteins are molecular machines of life in the truest sense. Being the expressors of genotype, proteins have been a focus in structural biology. Since the first characterization and structure determination of protein molecule more than half a century ago1, our understanding of protein structure is improving only incrementally. While computational analysis and experimental techniques have helped scientist view the structural features of proteins, our concepts about protein folding remain at the level of simple hydrophobic interactions packing side-chain at the core of the protein. Furthermore, because the rate of genome sequencing is far more rapid than protein structure characterization, much more needs to be achieved in the field of structural biology. As a step in this direction, my dissertation research uses computational analysis and experimental techniques to elucidate the fine structural features of the tertiary packing in proteins. With these set of studies, the knowledge of the field of structural biology extends to the fine details of higher order protein structure.

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Wu, Yali 1974. "Numerical simulations of the effect of peripheral proteins on lipid bilayers." Thesis, McGill University, 1998. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=20980.

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We present numerical simulations of the effect of the peripheral proteins on physical properties of lipid bilayers. The ten-state Pink model, which is originally proposed to describe the main transition of pure saturated lipid bilayers, is extended in order to examine both one-component lipid bilayers and binary lipid bilayers containing peripheral proteins. The peripheral protein is introduced as a positively charged cylinder which covers seven lipid chains and the protein-lipid interaction is assumed to be mainly electrostatic.
Metropolis Monte Carlo simulations are performed to describe the thermodynamic properties of the model including lipid-protein interaction in terms of order parameters and microconfigurations. The calculations are carried out for two minimal models where the protein concentration in the bilayer surface is either fixed or varies as the external conditions are changed. The basic phase behavior of lipid-protein systems are presented for each model. In both models, the lipid-protein interaction manifests itself by changes in the physical and thermodynamic properties of lipid bilayers and protein aggregation in the main transition region due to the forming of the gel-fluid phase coexistence.
Finally, a non-equilibrium model due to Sabra and Mouristen is modified to describe the non-equilibrium phenomena of lipid bilayers with peripheral proteins which has two internal states. The steady-state of the system and its comparison to the case of integral proteins are described. The thesis is concluded in the final chapter which contains a discussion of future work.
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Nevzorov, Alexander 1969. "Dynamical and equilibrium properties of membrane constituents and nucleic acids from deuterium NMR spectroscopy." Diss., The University of Arizona, 1998. http://hdl.handle.net/10150/282662.

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The chemically non-perturbing deuterium (²H) spin probe provides a unique tool for investigating equilibrium and dynamical properties of lipids, integral membrane proteins, and nucleic acids in relation to their biological activity. Analysis of ²H nuclear magnetic resonance (NMR) relaxation rates gives information about reorientation rates and mean-squared amplitudes; whereas simulation of the spectral lineshapes obtained within the biological temperature range yields bond angles and degree of ordering. In the first part of the dissertation, the frequency dependent ²H NMR spin-lattice relaxation rates (R₁(Z)) for 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) vesicles has been analyzed in combination with the corresponding ¹³C R₁(Z) relaxation rates, which enabled one for the first time to unify the ²H and ¹³C relaxation data for lipids in terms of dynamical models for slow order fluctuations. However, none of the existing models is able to account simultaneously for the ²H R₁(Z) frequency dispersion and the orientation dependent ²H R₁(Z) and quadrupolar order (R1Q relaxation rates of DMPC. A new composite membrane deformation model is proposed which simultaneously describes both the frequency and orientation dependent data. Influence of cholesterol on lipid dynamics is also investigated by analyzing the orientational anisotropy of the ²H R₁(Z) and R₁(Q) relaxation rates for DMPC-d54:cholesterol (1/1). The composite membrane deformation model including variable residual coupling tensor predicts a significant variation in the degree of chain entanglement along the acyl chains as a result of lipid-cholesterol interaction, and a smaller contribution from collective motions indicating an increase in the bilayer rigidity versus pure lipid systems. The second part of the dissertation describes a general method for calculating ²H NMR lineshapes of uniaxially-oriented samples. Several intermediate transformations of the coupling tensor are introduced, describing the position of the bond with respect to the symmetry axis, the distribution of the symmetry axes, and the orientation of the specimen as a whole. Lineshapes are calculated using a Monte Carlo method which allows one to effectively treat complicated geometries. The closed-form expression is also derived. The method has been successfully applied to the ²H NMR spectra of bacteriorhodopsin, and helped to resolve previous controversies between the different interpretations of X-ray diffraction studies versus ²H NMR regarding the conformations of Na-DNA at low humidity.
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Lemon, Christopher Michael. "Donor-Acceptor Constructs for Optical Oxygen Sensing and Corroles: Photophysics, Electronic Structure, and Photochemistry." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493300.

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Metabolic tumor profiling illustrates the spatiotemporal distribution of key analytes to assess and quantify tumor growth, metabolism, and response to therapy. Since the tumor microenvironment is characterized by hypoxia, the ability to track and quantify changes in oxygen concentration as a function of disease progression or therapy is crucial to the advancement of targeted therapeutics. The ability to monitor these changes necessitates the development of non-invasive sensors that are small enough to penetrate into tumor tissue and monitor dynamic changes with high resolution in real time. To address this challenge, this thesis details the design, synthesis, and characterization of optical oxygen sensors that combine a fluorescent semiconductor quantum dot (QD) with a Pd(II) porphyrin or Au(III) corrole as the oxygen-responsive phosphor. In these constructs, the QD donor serves as a photon antenna and transfers the absorbed energy to the appended porphyrin or corrole acceptor by Förster resonance energy transfer (FRET). The triplet state of the phosphor is quenched by molecular oxygen and is responsive over the biologically relevant 0–160 Torr O2 range. These donor–acceptor conjugates are prepared by self-assembly in organic solvents or micelle encapsulation in aqueous media. The Pd(II) porphyrin micelles were then used for in vivo imaging and oxygen sensing in murine models. In the search for alternative phosphors for optical oxygen sensing, a variety of metallocorrole complexes were prepared. Although these derivatives were not phosphorescent, they have provided insight into the photophysics, electronic structure, and photochemistry of corroles, as described in the second half of this thesis. The photophysical properties of free-base, Au(III), Sb(III), and Sb(V) corroles were interrogated. The role of corrole as a non-innocent ligand was then explored for copper and silver complexes. Analysis of these compounds reveals that copper complexes are Cu(II) corrole radical cations, while the silver analogs are authentic Ag(III) complexes. Finally, the photochemistry of Sb(V) corroles was studied for both C–H activation of organic substrates and halogen evolution as a potential solar fuel. Together, these studies examine fundamental photophysics and electronic structure, as well as provide examples where these complexes may be used to mediate photochemical transformations.
Chemistry and Chemical Biology
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Miao, Yinglong. "All-atom multiscale computational modeling of viral dynamics." [Bloomington, Ind.] : Indiana University, 2009. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3380113.

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Thesis (Ph.D.)--Indiana University, Dept. of Chemistry, 2009.
Title from PDF t.p. (viewed on Jul 19, 2010). Source: Dissertation Abstracts International, Volume: 70-12, Section: B, page: 7590. Adviser: Peter J. Ortoleva.
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Fawzi, Nicolas Lux. "Contrasting disease and non-disease protein aggregation by molecular simulations." Diss., Search in ProQuest Dissertations & Theses. UC Only, 2007. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3289317.

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Thesis (Ph. D.)--University of California, San Francisco with the University of California, Berkeley, 2007.
Source: Dissertation Abstracts International, Volume: 68-11, Section: B, page: 7470. Adviser: Teresa Head-Gordon.
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Zou, Sirui. "The Mechanistic Basis of Dynein Microtubule Binding and Its Regulation." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:14226071.

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Eukaryotic cells use a diverse toolbox of cytoskeletal motors to transport and position cellular materials in space and time. Two microtubule-based motors—kinesin and dynein—transport organelles, RNA and protein cargos over long-distances. While multiple kinesin motors are used for long-distance plus- end-directed transport, a single type of dynein—cytoplasmic dynein 1— performs nearly all minus-end-directed tasks. Despite cytoplasmic dynein’s role in such diverse activities, many aspects of its molecular mechanism remain poorly understood. My thesis work uses a combination of cryo-electron microscope (EM) structural biology and single-molecule approaches to provide novel insights into the mechanistic basis of how dynein interacts with its microtubule track and how microtubule binding is regulated by the ubiquitous co-factor, Lis1. First, we solved a 9.7A structure of dynein’s microtubule binding domain bound to microtubules. This structure allowed us to identify large conformational changes that occur in dynein’s microtubule-binding domain upon track binding. We hypothesize that these conformational changes allosterically regulate the ATP hydrolysis cycle in dynein’s motor domain, which is located over 25 nm from the site of microtubule binding. Molecular dynamics simulations, followed by single-molecule assays, allowed us to identify dynamic salt bridge switches in dynein, which can tune its affinity for the microtubule. The native dynein, which has been selected for submaximal processivity, might allow a broader dynamic range for regulation. Second, we identified how dynein is regulated by its ubiquitous co-factor, Lis1. Our three-dimensional cryo-EM structures of the dynein-Lis1 complex showed dynein’s mechanical element, the linker, is in an altered position in the presence of Lis1. Fluorescence resonance energy transfer (FRET) and single- molecule studies indicated that Lis1 binding to dynein sterically blocks the dynein linker from reaching its normal docking site, which may interrupt dynein’s mechanochemical cycle and prevent its release from microtubules.
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Books on the topic "Chemistry, Physical. Biophysics, Medical. Biophysics, General"

1

Nicolini, Claudio A. Molecular Manufacturing. Boston, MA: Springer US, 1996.

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Nicolini, Claudio A. From Neural Networks and Biomolecular Engineering to Bioelectronics. Boston, MA: Springer US, 1995.

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Fluctuation Theory of Solutions: Applications in Chemistry, Chemical Engineering and Biophysics. Taylor & Francis Group, 2013.

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The Expected Knowledge: What can we know about anything and everything? Tiruchirappalli: Sivashanmugam Palaniappan, 2012.

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