Relevant bibliographies by topics / Membrane proteins; Biophysics

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers

Academic literature on the topic 'Membrane proteins; Biophysics'

Author: Grafiati
Published: 4 June 2021
Last updated: 8 February 2022

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Journal articles on the topic "Membrane proteins; Biophysics"

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Chin, G. J. "BIOPHYSICS: Deconstructing Membrane Proteins." Science 307, no. 5713 (February 25, 2005): 1173a. http://dx.doi.org/10.1126/science.307.5713.1173a.

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Thompson, Lynmarie K., and Merritt Maduke. "Special Issue: Molecular Biophysics of Membranes and Membrane Proteins." Biochimica et Biophysica Acta (BBA) - Biomembranes 1862, no. 1 (January 2020): 183116. http://dx.doi.org/10.1016/j.bbamem.2019.183116.

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Sawada, Ryusuke, Runcong Ke, Toshiyuki Tsuji, Masashi Sonoyama, and Shigeki Mitaku. "Ratio of membrane proteins in total proteomes of prokaryota." BIOPHYSICS 3 (2007): 37–45. http://dx.doi.org/10.2142/biophysics.3.37.

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Thoma, Johannes, and Björn M. Burmann. "Fake It ‘Till You Make It—The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics." International Journal of Molecular Sciences 22, no. 1 (December 23, 2020): 50. http://dx.doi.org/10.3390/ijms22010050.

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Membrane proteins evolved to reside in the hydrophobic lipid bilayers of cellular membranes. Therefore, membrane proteins bridge the different aqueous compartments separated by the membrane, and furthermore, dynamically interact with their surrounding lipid environment. The latter not only stabilizes membrane proteins, but directly impacts their folding, structure and function. In order to be characterized with biophysical and structural biological methods, membrane proteins are typically extracted and subsequently purified from their native lipid environment. This approach requires that lipid membranes are replaced by suitable surrogates, which ideally closely mimic the native bilayer, in order to maintain the membrane proteins structural and functional integrity. In this review, we survey the currently available membrane mimetic environments ranging from detergent micelles to bicelles, nanodiscs, lipidic-cubic phase (LCP), liposomes, and polymersomes. We discuss their respective advantages and disadvantages as well as their suitability for downstream biophysical and structural characterization. Finally, we take a look at ongoing methodological developments, which aim for direct in-situ characterization of membrane proteins within native membranes instead of relying on membrane mimetics.
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Separovic, Frances, J. Antoinette Killian, Myriam Cotten, David D. Busath, and Timothy A. Cross. "Modeling the Membrane Environment for Membrane Proteins." Biophysical Journal 100, no. 8 (April 2011): 2073–74. http://dx.doi.org/10.1016/j.bpj.2011.02.058.

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Fischer, Wolfgang B., Gerhard Thiel, and Rainer H. A. Fink. "Viral membrane proteins." European Biophysics Journal 39, no. 7 (August 12, 2009): 1041–42. http://dx.doi.org/10.1007/s00249-009-0525-y.

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Garni, Martina, Sagana Thamboo, Cora-Ann Schoenenberger, and Cornelia G. Palivan. "Biopores/membrane proteins in synthetic polymer membranes." Biochimica et Biophysica Acta (BBA) - Biomembranes 1859, no. 4 (April 2017): 619–38. http://dx.doi.org/10.1016/j.bbamem.2016.10.015.

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Smith, Steven O., Kathryn Aschheim, and Michel Groesbeek. "Magic angle spinning NMR spectroscopy of membrane proteins." Quarterly Reviews of Biophysics 29, no. 4 (December 1996): 395–449. http://dx.doi.org/10.1017/s0033583500005898.

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The passage of molecules and information across cell membranes is mediated largely by membrane-spanning proteins acting as channels, pumps, receptors and enzymes. These proteins perform many tasks: they control electrochemical gradients across the membrane, receive signals from the environment or from other cells, convert light energy into chemical signals, transport small molecules into and out of cells, and harness proton gradients to generate the energy consumed in metabolism. Indeed, of the estimated 50000–100000 genes in the human genome, fully 20–40 % are thought to encode integral membrane proteins. If one also includes membrane-associated proteins, which are attached to the membrane surface through fatty acyl chains or electrostatic interactions, this percentage is likely to be much higher.
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Fischer, Wolfgang B. "Assembling Within The Lipid Membrane: Viral Membrane Proteins." Biophysical Journal 96, no. 3 (February 2009): 338a—339a. http://dx.doi.org/10.1016/j.bpj.2008.12.3823.

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Lavi, Yael, Michael A. Edidin, and Levi A. Gheber. "Dynamic Patches of Membrane Proteins." Biophysical Journal 93, no. 6 (September 2007): L35—L37. http://dx.doi.org/10.1529/biophysj.107.111567.

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Dissertations / Theses on the topic "Membrane proteins; Biophysics"

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Zhang, Dongmei. "Rotational motion and organization studies of cell membrane proteins." Thesis, Colorado State University, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10137939.

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Cell membranes are dynamic structures with complex organization. The complexity of the cell membrane arises from intrinsic membrane structure, membrane microdomains within the plasma membrane and the membrane cytoskeleton. Plasma membrane receptors are integral membrane proteins with diverse structures and functions which bind specific ligands to trigger cellular responses. Due to compartmentalization of the plasma membrane and the formation of membrane microdomains, receptors are distributed non-homogeneously in the cell membrane bilayer. Both lateral and rotational diffusion of membrane receptors reflects different kinds of intermolecular interactions within the plasma membrane environment. Understanding protein diffusion within the membrane is very important to further understanding biomolecular interactions in vivo during complex biological processes including receptor-mediated signaling.

Rotational diffusion depends linearly on the in-membrane volume of the rotating proteins. Relative to lateral diffusion, rotational diffusion is a more sensitive probe of an individual molecule’s size and local environment. We have used asymmetric quantum dots (QD) to conduct imaging measurements of individual 2H3 cell Type I Fcϵ receptor rotation on timescales down to 10 msec per frame. We have also used time-tagged single photon counting measurements of individual QD to examine µsec timescales, although rapid timescales are limited by QD emission rates. In both approaches, decays of time-autocorrelation functions (TACF) for fluorescence polarization fluctuations extend into the millisecond timescale, as implied by time-resolved phosphorescence anisotropy results. Depending on instrumental parameters used in data analysis, polarization fluctuation TACFs can contain a contribution from the intensity fluctuation TACF arising from QD blinking. Such QD blinking feed-through is extremely sensitive to these analysis parameters which effectively change slightly from one measurement to another. We discuss approaches based on the necessary statistical independence of polarization and intensity fluctuations to guarantee removal of a blinking-based component from rotation measurements. Imaging results demonstrate a range of rotational behavior among individual molecules. Such slow motions, not observable previously, may occur with large signaling complexes, which are important targets of study in cell biology. These slow motions appear to be a property of the membrane itself, not of the receptor state. Our results may indicate that individual mesoscale membrane regions rotate or librate with respect to the overall cell surface.

The luteinizing hormone receptor (LHR) is a seven transmembrane domain receptor and a member of the GPCR family. It is located on luteal cells, granulosa and theca cells in females. Understanding how these protein receptors function on the plasma membrane will lead to better understanding of mammalian reproduction. LHR becomes aggregated upon binding hCG when receptors are expressed at physiological numbers. Binding of hormone to LHR leads to activation of adenylate cyclase (AC) and an increase in intracellular cyclic AMP (cAMP). ICUE3 is an Epac-based cAMP sensor with two fluorophores, cyan fluorescent protein (CFP) and the YFP variant, cpVenus, and a membrane-targeting motif which can be palmitoylated. Upon binding cAMP, ICUE3 undergoes a conformational change that separates CFP and YFP, significantly reducing FRET and thus increasing the ratio of CFP to YFP fluorescence upon excitation with an arc lamp or 405nm laser source. Hence we have investigated hLHR signal transduction using the cyclic AMP reporter probe, ICUE3. A dual wavelength emission ratio (CFP/YFP) imaging method was used to detect a conformational change in ICUE3 upon binding cAMP. This technique is useful in understanding the sequence of intercellular events following hormone binding to receptor and in particular, the time course involved in signal transduction in a single cell. Our data suggested that CHO cells expressing ICUE3 and directly treated with different concentrations of cAMP with saponin can provide a dose-dependent relationship for changes in intracellular cAMP levels. Forskolin (50µM) causes maximal activation of the intracellular cAMP and an increase in the CFP/YFP emission ratio. In CHO cells expressing both ICUE3 and hLHR-mCherry, the CFP/YFP ratio increased in cells treated with forskolin and in hCG- treated cells. In flow cytometry studies, similar results were obtained when CHO cells expressed < 60k LHR-mCherry per cell. Our results indicate that ICUE3 can provide real time information on intracellular cAMP levels, and the ICUE3 is a reliable cAMP reporter can be used to examine various aspects of LH receptor-mediated signaling.

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Ranatunga, Kishani M. "Computational studies of ion channel permeation and selectivity." Thesis, University of Oxford, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.325774.

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Orwick, Marcella Christine. "Biophysical and magnetic resonance studies of membrane proteins." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:e7974f5f-a5ab-4867-aa5f-feff99716c0f.

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Bacteriorhodopsin (bR) is a 7TM membrane protein expressed in Halobacterium salinarum. Due to its stability and high expression levels, bR serves as a model for other 7TM membrane proteins. Neurotensin receptor 1 (NTS1) is a member of pharmacologically relevant G protein-coupled receptor superfamily, and is the high affinity receptor for neurotensin, a 13mer peptide that can be found in the brain, gut, and central nervous system. NTS1 is a target for Parkinson’s, Schizophrenia, and drug addiction. This thesis aims to develop pulsed magnetic resonance techniques and sample preparation forms for high resolution structural studies on 7TM proteins. In this thesis, pulsed dipolar distance electron paramagnetic resonance (EPR) methods for the study of proteins in their native membrane are established. bR is spin-labeled, and a wellresolved distance distribution is measured in excellent agreement with other structural data. Preliminary distance data for a photoexcited state of bR suggests quaternary rearrangements in the native membrane that are agreement with published AFM results. A fitting method is developed to enable measurements of systems with rapid signal decay, a common feature in reconstituted systems studied by pulsed EPR methods. A physical chemical characterization of nanosized-bilayer discs termed Lipodisqs®, and the successful incorporation of bR is presented. Lipodisqs® are formed from DMPC and a polymer that is able to solubilize DMPC vesicles into discrete particles. Lipodisqs® possess a broad phase transition with increased lipid ordering compared to a DMPC dispersion. The SMA polymer interacts with the lipid tails, but does not perturb the headgroup. BR is incorporated in the monomeric form, and EPR dynamic and distance measurements confirm that Lipodisqs® preserve the native structure of bR, whilst detergent solubilisation increases the overall mobility compared to bR in its native membrane, suggesting that Lipodisqs® serve as an excellent medium for EPR studies on 7TM membrane proteins. A cysteine-depleted mutant of active, ligand binding NTS1 is constructed. Cysteines are reintroduced at positions that may be able to monitor agonist and inverse-agonist induced conformational and dynamic changes. A spin-labeling protocol is developed, and preliminary EPR measurements are discussed. Dynamic nuclear polarization (DNP) results are presented with uniformly-13C-labelled bR in the PM, resulting in a DNP enhancement of 16 using the biradical nitroxide polarizing agent, TOTAPOL. DNP-enhanced solid state NMR (ssNMR) is typically carried out at cryogenic temperatures, resulting in poor spectral resolution compared to ambient temperatures. Two different forms of samples are prepared that could potentially lead to better-resolved DNP spectra. BR is reverse labelled by adding natural abundance amino acids to isotopically labelled growth medium, resulting in the partial depletion of resonance signals that may obscure and crowd the NMR spectra. A crystalline sample of bR is prepared using the LCP method for crystallization, which is to date the most successful method for the crystallization of GPCRs. In summary, the first pulsed dipolar measurements of a protein in its native membrane are shown, Lipodisqs® are characterized and found to be a suitable medium for structural and functional studies of 7 TM membrane proteins, the first preliminary EPR studies on a ligand binding GPCR are presented, and novel sample preparation techniques are developed for the nitroxide-based DNP enhancement of ssNMR data. This thesis opens up several avenues for future research into 7TM membrane proteins.
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Sergeev, Mikhail. "Measurement of oligomerization states of membrane proteins via spatial fluorescence intensity fluctuation analysis." Thesis, McGill University, 2011. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=96703.

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The objective of this thesis is the development and use of a novel fluorescence fluctuation technique for determining the oligomeric state of fluorescently labeled proteins in situ via microscopy imaging. High order moment analysis of fluorescence intensity fluctuations from individual confocal laser scanning microscopy (CLSM) images applied to study monomer-oligomer distributions of fluorescently labeled proteins was developed. Using computer simulations and experiments with fluorescent microspheres and organic fluorescent dyes, the detection limits and accuracy of this statistical approach were determined. A series of control experiments were carried out to support the membrane receptor oligomerization studies in this thesis. The methods were then applied to study oligomerization states in various biological systems. Epidermal growth factor receptors (EGFR) play a critical role in cell growth, proliferation and survival. The activation steps of signal transduction pathways are known to involve EGFR oligomerization. Pharmacodynamic studies of ligand-induced clustering of EGF receptors were carried out. Spatial intensity distribution analysis (SpIDA), which accurately measures monomer-dimer distributions, was used to measure the increase in EGFR dimeric population upon addition of EGF ligand. The distribution of aggregates forming in the course of EGFR internalization was evaluated using two-population moment analysis. The findings supported an existing model proposing two distinct receptor internalization pathways. The electrogenic sodium bicarbonate cotransporter NBCe1-A plays an important role in absorbing sodium bicarbonate across the basolateral membrane of the proximal tubule. The fluorescence moment image analysis and SpIDA were applied to study the oligomeric state of NBCe1-A in cultured mammalian cells expressing various mutants of cotransporter. Spatial fluctuation analysis revealed that NBCe1-A existed on the cell membrane predominantly as a monomer and negligibly as higher order oligomers. To measure the oligomerization state of the native cotransporter, samples of rat kidney tissues were prepared and the native NBCe1-A was immunostained using fluorescently labeled primary antibody against the wild type cotransporter. The image analysis showed that NBCe1-A was present on the proximal tubule basolateral membrane in predominantly dimeric and rarely monomeric or higher order oligomeric states. Human immunodeficiency virus (HIV) diverts the cellular ESCRT machinery to promote the release of newly formed virions from host cells. The ATPase, VPS4A, acts at a late stage of ESCRT function. It provides energy for dissociation of ESCRT complexes and membrane abscision. The fluorescence moment analysis of VPS4A-eGFP images revealed the monomeric distribution of the protein in the plasma membrane outside budding sites and formation of two to five VPS4A dodecamers at the budding sites. The combination of the results of VPS4A dynamics studies together with the VPS4A burst size analysis shed light on steps in the HIV lifecycle and release.
L'objectif de cette thèse réside dans le développement et l'utilisation d'une nouvelle technique de mesure de fluctuation de fluorescence. Cette technique d'imagerie par microscopie permet de déterminer in situ l'état d'oligomérisation de protéines couplées à un fluorophore. L'analyse par mesure de moments d'ordres supérieurs d'intensité de fluctuation de fluorescence d'images obtenues à partir d'un microscope confocal à balayage laser (CLSM) a été développée afin de mesurer la distribution en monomères/oligomères de protéines marquées par fluorescence. En utilisant des simulations par ordinateur ainsi que des expériences avec des microsphères fluorescentes, les limites de détection et l'exactitude de cette approche statistique ont pu être déterminées. Une série d'expériences contrôles a été effectuée afin de valider l'étude d'état d'oligomérisation de récepteurs membranaires présentée dans cette thèse. Cette méthode a ensuite été appliquée à l'étude de l'état d'oligomérisation dans divers systèmes biologiques. Le récepteur au facteur de croissance épidermique (EGFR) joue un rôle critique dans la croissance, la prolifération et la survie cellulaire. Les étapes d'activation des voies de transduction du signal sont connues pour impliquer l'oligomérisation de l'EGFR. Des études de pharmaco-dynamique d'agglomération provoquée par liaison d'un ligand ont été conduites. La technique d'analyse de distribution spatiale d'intensité (SpIDA), qui permet de mesurer précisément la distribution de monomères/dimères a été utilisée pour mesurer l'augmentation de la population de dimères d'EGFR après liaison du ligand (EGF). La distribution des agrégats se formant au cours de l'internalisation d'EGFR a été mesurée par analyse de moments pour deux populations. Les résultats confirment une hypothèse proposant deux voies distinctes d'internalisation du récepteur. Le co-transporteur électrogénique au bicarbonate de sodium NBCe1-A joue un rôle important dans l'absorption du bicarbonate de sodium à travers la membrane baso-latérale du tubule proximal rénal. Les analyses par moments de fluorescence et SpIDA ont été appliquées pour étudier l'état d'oligomérisation de NBCe1-A dans des cellules mammifères en cultures exprimant plusieurs mutants du co-transporteur. L'analyse de fluctuation spatiale montre que NBCe1-A est présent majoritairement sous forme de monomère sur la membrane cellulaire et de façon négligeable sous forme d'oligomères d'ordres supérieurs. Afin de mesurer l'état d'oligomérisation du co-transporteur naturel, des échantillons de reins de rats ont été préparés et NBCe1-A a été marqué par immunoréaction avec des anticorps fluorescents reconnaissant le type naturel du co-transporteur. L'analyse d'image indique que NBCe1-A est présent sous forme de dimère et rarement sous forme de monomère ou d'oligomères d'ordre supérieurs sur la membrane baso-latérale des tubules proximaux. Le virus humain d'immunodéficience (VIH) détourne la machinerie cellulaire ESCRT pour promouvoir la sortie de la cellule hôte de virions nouvellement formés. L'ATPase VPS4A est impliquée à une étape avancée de la fonction ESCRT en produisant de l'énergie pour la dissociation du complexe ESCRT et l'invagination de la membrane plasmique. L'analyse du moment de fluorescence d'images de VPS4A-eGFP montre une distribution monomérique à l'extérieur des sites de bourgeonnement ainsi que la présence de deux à quatre dodécamères sur les sites de bourgeonnement. La combinaison des résultats des études de la dynamique de VPS4A ainsi que l'analyse de la taille des pics d'intensité lumineux permet de mieux comprendre le cycle de vie du VIH ainsi que son processus de relargage.
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Kim, Irene. "Mechanisms of Membrane Disruption by Viral Entry Proteins." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10192.

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To enter and infect cells, viruses must overcome the barrier presented by the cell membrane. Enveloped viruses, which possess their own lipid bilayer, fuse their viral membrane with the cell membrane. Non-enveloped viruses, whose outer surface is composed of proteins, penetrate through the hydrophobic interior of the cell membrane. Viruses accomplish the processes by coupling conformational changes in viral "entry proteins" to membrane disruption. This dissertation investigates the membrane disruption mechanisms of rotavirus, a non-enveloped virus, and vesicular stomatitis virus (VSV), an enveloped virus. Rotavirus uses proteins of its outer capsid to penetrate the membrane and deliver a transcriptionally-active core particle into the cell cytoplasm. \(VP5^*\), an outer capsid protein, undergoes a foldback rearrangement that translocates three clustered hydrophobic loops by \(\sim 180^{\circ}\). This rearrangement resembles the foldback rearrangements of enveloped virus fusion proteins. In the first half of my dissertation, I show that the hydrophobicity of the \(VP5^*\) apex is required for membrane disruption during rotavirus cell entry by mutating hydrophobic residues within the loop to hydrophilic residues. One particular mutation diminishes liposome interaction by the protein, blocks membrane penetration by virus particles in cells, and reduces particle infectivity by 10,000-fold. VSV uses its fusion protein, G, to fuse at low pH. Unlike other viral fusion proteins, pH-induced conformational changes in G are reversible. In the second half of my dissertation, I measure the fusion kinetics of individual VSV particles using a single-particle fusion assay previously developed for influenza virus. I find that hemifusion by VSV consists of at least two steps, an initial step that is pH-dependent and reversible, and a second step that is pH-independent. At low pHs, the second step becomes the sole rate-limiting step. I also show that at pH 6.6, the VSV particle enters a stable intermediate state that binds tightly to membranes but does not precede to fusion. This dissertation uses a variety of experimental approaches to arrive at a more detailed understanding of how viruses use their entry proteins to either penetrate or fuse with the cell membrane.
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Robson, Alex J. "Single particle tracking as a tool to investigate the dynamics of integrated membrane complexes in vivo." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:7769f80c-a56d-4513-9123-1d65ef8c9911.

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The last decade has seen substantial advances in single-molecule tracking methods with nano-metre level precision. A powerful tool in single-molecule tracking is fluorescence imaging. One particular application, total internal reflection microscopy, can capture biological processes at high contrast video rate imaging at the single-particle level. This thesis presents methodologically novel methods in analysing single particle tracking data. Presented here is an application of a Bayesian statistical approach that can discriminate between the different diffusive modes that appear with the presence of membrane architecture. This algorithm is denoted BARD; a Bayesian Analysis to Ranking Diffusion. These algorithms are applied to a total internal fluorescence microscopy based experimental data of a novel membrane probe in Escherichia coli. This probe is a plasmid expressed, non-native membrane integrating trans-membrane helix and thus acts as an ideal protein based probe under no specific native control. Two experiments were performed using a combination of varying helix probe size and growth temperature experiments effectively altering the transition temperature of the membrane. These data are suggestive of a passive partitioning of the helix protein into mobile and immobile domains that emerge from the underlying phase behaviour of the membrane.
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Oglęcka, Kamila. "Biophysical studies of membrane interacting peptides derived from viral and Prion proteins." Doctoral thesis, Stockholm University, Department of Biochemistry and Biophysics, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-7109.

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This thesis focuses on peptides derived from the Prion, Doppel and Influenza haemagglutinin proteins in the context of bilayer interactions with model membranes and live cells. The studies involve spectroscopic techniques like fluorescence, fluorescence correlation spectroscopy (FCS), circular and linear dichroism (CD and LD), confocal fluorescence microscopy and NMR.

The peptides derived from the Prion and Doppel proteins combined with their subsequent nuclear localization-like sequences, makes them resemble cell-penetrating peptides (CPPs). mPrPp(1-28), corresponding to the first 28 amino acids of the mouse PrP, was shown to translocate across cell membranes, concomitantly causing cell toxicity. Its bovine counterpart bPrPp(1-30) was demonstrated to enter live cells, with and without cargo, mainly via macropinocytosis. The mPrPp(23-50) peptide sequence overlaps with mPrPp(1-28) sharing the KKRPKP sequence believed to encompass the driving force behind translocation. mPrPp(23-50) was however found unable to cross over cell membranes and had virtually no perturbing effects on membranes.

mDplp(1-30), corresponding of the first 30 N-terminal amino acids of the Doppel protein, was demonstrated to be almost as membrane perturbing as melittin. NMR experiments in bicelles implied a transmembrane configuration of its alpha-helix, which was corroborated by LD in vesicle bilayers. The positioning of the induced alpha-helix in transportan was found to be more parallel to the bilayer surface in the same model system.

Positioning of the native Influenza derived fusion peptide in bilayers showed no pH dependence. The glutamic acid enriched variant however, changed its insertion angle from 70 deg to a magic angle alignment relative the membrane normal upon a pH drop from 7.4 to 5.0. Concomitantly, the alpha-helical content dramatically rose from 18% to 52% in partly anionic membranes, while the native peptide’s helicity increased only from 39% to 44% in the same conditions.

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Raychaudhuri, Pinky. "Bilayer formation with fluorinated amphiphiles and applications in membrane protein studies." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:f8d7ec23-7b2f-4610-b7c8-395b2660464a.

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Every cell is enclosed by a membrane which gives structure to the cell and allows for the passage of nutrients and wastes into and out of the cell. Membranes are made up of amphiphilic lipid molecules, with one water-soluble end, and one hydrophobic end. Naturally occurring and synthetic membranes are made up of double-chained amphiphiles derived from hydrocarbons. Recently, a novel class of amphiphilic molecules derived from fluorocarbons have been reported. The properties of fluorinated amphiphiles are very different to that of hydrocarbon based amphiphiles. Fluorinated amphiphiles have been previously reported to be useful in the studies of membrane proteins. In this thesis, we explore some novel uses of fluorinated amphiphiles. Chapter one: Provides a comprehensive review of the properties of fluorocarbon-based amphiphiles and discusses the existing uses of fluorinated amphiphiles in biochemical and biomedical research. Chapter two: Describes some of the important materials and methods used in this thesis including a detailed description of the proteins used and the working principles behind the techniques used in the study. Chapter three: Looks at the stability of pre-formed planar lipid bilayers in the presence of fluorinated amphiphiles (F-amphiphiles), and characterizes the behaviour of alpha-haemolysin and other proteins in liposomes and planar lipid bilayers in the presence of F-amphiphiles. We found that F-amphiphiles have an inhibitory effect on the insertion of protein into lipid bilayers, and this property has been exploited to control the number of proteins in the bilayer. Chapter four: Using droplet interface bilayers, we investigate the electrical properties and behaviour of protein(s) in bilayers formed by F-amphiphiles. The results obtained with fluorinated bilayers are compared with results obtained in conventional DPhPC lipid bilayers. This is the first ever report to carry out such an investigation and it provides insights into the formation, stability and utility of fluorinated bilayers. Chapter five: In Chapter five, we explore another aspect of droplet interface bilayers: the feasibility of using droplet interface bilayers to screen for membrane protein libraries. I have chosen to focus on certain fundamental aspects of the screening process that are sufficient to establish the feasibility of the method and to act as the proof of concept. Chapter six: Summarizes all the important results in the thesis and discusses some possible future directions of this project.
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Bottorf, Lauren Marie. "Developing Electron Paramagnetic Resonance Spectroscopy Methods for Secondary Structural Characterization of Membrane Proteins." Miami University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=miami1510164534760125.

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Cheng, Zhiliang. "Posttargeting Events in Cotranslational Translocation Through the Sec61 Complex: a Thesis." eScholarship@UMMS, 2006. https://escholarship.umassmed.edu/gsbs_diss/1.

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The cytoplasmic surface of Sec61p is the binding site for the ribosome and has been proposed to interact with the signal recognition particle receptor during targeting of the ribosome nascent chain complex to the translocation channel. Point mutations in cytoplasmic loops six (L6) and eight (L8) of yeast Sec61p cause reductions in growth rates and defects in translocation of nascent polypeptides that utilize the cotranslational translocation pathway. Sec61 heterotrimers isolated from the L8 sec61 mutants have a greatly reduced affinity for 80S ribosomes. Cytoplasmic accumulation of protein precursors demonstrates that the initial contact between the large ribosomal subunit and the Sec61 complex is important for efficient insertion of a nascent polypeptide into the translocation pore. In contrast, point mutations in L6 of Sec61p inhibit cotranslational translocation without significantly reducing the ribosome binding activity, indicating that the L6 and L8 sec61 mutants impact different steps in the cotranslational translocation pathway. Integral membrane proteins are cotranslationally inserted into the endoplasmic reticulum via the protein translocation channel, which mediates the translocation of lumenal domains, retention of cytosolic domains and integration of transmembrane spans into the phospholipid bilayer. We analyzed the in vivo kinetics of integration of model membrane proteins in Saccharomyces cerevisiae using ubiquitin translocation assay reporters. A signal anchor sequence from a type II membrane protein gates the translocon pore less rapidly than a cleavable signal sequence from a secretory protein. Transmembrane spans and lumenal domains are exposed to the cytosol during integration of a poly topic membrane protein. The conformational changes in the translocon that permit opening of the lumenal and lateral channel gates occur less rapidly than elongation of the nascent polypeptide. Cytosolic exposure of transmembrane spans and lumenal domains poses a challenge to the fidelity of membrane protein integration.
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Books on the topic "Membrane proteins; Biophysics"

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Postis, Vincent L. G., and Adrian Goldman, eds. Biophysics of Membrane Proteins. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0724-4.

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Domene, Carmen, ed. Computational Biophysics of Membrane Proteins. Cambridge: Royal Society of Chemistry, 2016. http://dx.doi.org/10.1039/9781782626695.

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Dr, Janáček Karel, and Koryta Jiři, eds. Biophysical chemistry of membrane functions. Chichester: Wiley, 1988.

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Sansom, M. S. P., and Philip Charles Biggin. Molecular simulations and biomembranes: From biophysics to function. Cambridge: Royal Society of Chemistry, 2010.

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L, Longo Marjorie, Risbud Subhash H, Jue Thomas, and SpringerLink (Online service), eds. Biomembrane Frontiers: Nanostructures, Models, and the Design of Life. Totowa, NJ: Humana Press, 2009.

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Membrane structural biology: With biochemical and biophysical foundations. Cambridge: Cambridge University Press, 2008.

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service), SpringerLink (Online, ed. Biophysical Chemistry of Proteins: An Introduction to Laboratory Methods. Boston, MA: Springer Science+Business Media, LLC, 2011.

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Chattopadhyay, Amitabha, Simone Furini, Ben Corry, Carmen Domene, and Carmen Domene. Computational Biophysics of Membrane Proteins. Royal Society of Chemistry, The, 2016.

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(Editor), C. Reyes Mateo, Javier Gómez (Editor), José Villalaín (Editor), and José M. González Ros (Editor), eds. Protein-Lipid Interactions: New Approaches and Emerging Concepts (Springer Series in Biophysics). Springer, 2005.

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Berliner, Lawrence J., and Marcus A. Hemminga. ESR Spectroscopy in Membrane Biophysics (Biological Magnetic Resonance). Springer, 2007.

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Book chapters on the topic "Membrane proteins; Biophysics"

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Zhan, Ling-Peng, Chao-Zi Liu, and Zong-Xiu Nie. "Mass Spectrometry of Membrane Proteins." In Membrane Biophysics, 285–317. Singapore: Springer Singapore, 2017. http://dx.doi.org/10.1007/978-981-10-6823-2_10.

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Wang, Shenlin, Xiaojun Xu, and Yufei Yang. "Solid-State Nuclear Magnetic Resonance Spectroscopy of Membrane Proteins." In Membrane Biophysics, 251–83. Singapore: Springer Singapore, 2017. http://dx.doi.org/10.1007/978-981-10-6823-2_9.

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Lall, Sahil, and M. K. Mathew. "Dynamics of Membrane Proteins." In Springer Series in Biophysics, 219–41. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-66601-3_10.

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Goddard, Alan D., John A. Linney, Annaïg J. Rozo, Joanne Oates, and Anthony Watts. "Membrane Proteins: Structure and Organization." In Encyclopedia of Biophysics, 1–4. Berlin, Heidelberg: Springer Berlin Heidelberg, 2020. http://dx.doi.org/10.1007/978-3-642-35943-9_748-1.

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Findlay, Heather E., and Paula J. Booth. "Membrane Proteins: Folding and Stability." In Encyclopedia of Biophysics, 1471–78. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_611.

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Goddard, Alan, Joanne Oates, and Anthony Watts. "Membrane Proteins: Structure and Organization." In Encyclopedia of Biophysics, 1478–81. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_748.

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Findlay, Heather E., Nicola J. Harris, and Paula J. Booth. "Membrane Proteins: Folding and Stability." In Encyclopedia of Biophysics, 1–9. Berlin, Heidelberg: Springer Berlin Heidelberg, 2021. http://dx.doi.org/10.1007/978-3-642-35943-9_611-1.

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Jorgensen, Christian, Victoria Oakes, and Carmen Domene. "Computer Simulations of Membrane Proteins." In Springer Series in Biophysics, 351–74. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-66601-3_15.

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Chen, Tsung-Yu, Yu-Fung Lin, and Jie Zheng. "Electrophysiological Measurements of Membrane Proteins." In Fundamental Concepts in Biophysics, 1–35. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-59745-397-4_5.

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Conn, Charlotte E. "Lipid Mesophases for Crystallizing Membrane Proteins." In Encyclopedia of Biophysics, 1269–73. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_568.

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Conference papers on the topic "Membrane proteins; Biophysics"

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Maftouni, Negin, Mehriar Amininasab, MohammadReza Ejtehadi, and Farshad Kowsari. "Multiscale Molecular Dynamics Simulation of Nanobio Membrane in Interaction With Protein." In ASME 2013 2nd Global Congress on NanoEngineering for Medicine and Biology. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/nemb2013-93054.

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One of the most important biological components is lipid nanobio membrane. The lipid membranes of alive cells and their mechanical properties play an important role in biophysical investigations. Some proteins affect the shape and properties of the nanobio membrane while interacting with it. In this study a multiscale approach is experienced: first a 100ns all atom (fine-grained) molecular dynamics simulation is done to investigate the binding of CTX A3, a protein from snake venom, to a phosphatidylcholine lipid bilayer, second, a 5 micro seconds coarse-grained molecular dynamics simulation is carried out to compute the pressure tensor, lateral pressure, surface tension, and first moment of lateral pressure. Our simulations reveal that the insertion of CTX A3 into one monolayer results in an asymmetrical change in the lateral pressure and distribution of surface tension of the individual bilayer leaflets. The relative variation in the surface tension of the two monolayers as a result of a change in the contribution of the various intermolecular forces may be expressed morphologically and lead to deformation of the lipid membrane.
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Vernerey, Franck J. "Biophysical Model of the Coupled Mechanisms of Cell Adhesion, Contraction and Spreading." In ASME 2012 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/sbc2012-80309.

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Recent research has shown that cell spreading is highly dependent on the contractility of its cytoskeleton and the mechanical properties of its surrounding environment. This extended abstract introduces a mathematical formulation of cell spreading and contraction that couples the processes of stress fiber formation, protrusion growth through actin polymerization at the cell edge and dynamics of cross-membrane protein (integrins) enabling cell-substrate attachment. The evolving cell’s cytoskeleton is modeled as a mixture of fluid, proteins and filaments that can exchange mass and generate contraction. In particular, besides self-assembling into stress fibers, actin monomers are able to polymerize into an actin meshwork at the cell’s boundary in order to push the membrane forward and generate protrusion. These processes are possible via the development of cell-substrate attachment complexes that arise from the mechano-sensitive equilibrium of membrane proteins, known as integrins. Numerical simulations show that the proposed model is able to capture the dependency of cell spreading and contraction on substrate stiffness and chemistry. The very good agreement between model predictions and experimental observations suggests that mechanics plays a strong role into the coupled mechanisms of contraction, adhesion and spreading of adherent cells.
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Monroe, D. M., D. W. Deerfield, D. L. Olson, T. N. Stewart, H. R. Roberts, R. G. Hiskey, and L. G. Pedersen. "BINDING OF CALCIUM TO HUMAN AND BOVINE FACTOR X." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643835.

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Human and bovine factor X contain 11 and 12 glutamyl residues respectively within the first forty amino terminal residues that are posttranslationally modified to y-carboxyglutamyl (Gla) residues. Calcium binding to these Gla residues and at other sites is critical for activity in factor X. We have measured calcium binding to human factor X by equilibrium dialysis for the first time. We have also re-examined calcium binding to bovine factor X in order to compare the two species. Factor X (10 μM) was incubated with 45Ca in 20 mM Tris (pH 7.5), 100 mM NaCl in a half cell separated by a 12-14000 molecular weight fast-equilib-rium disk membrane at 25°C for 24 hours. Four aliquots (100 μL each) were removed from each side of the cell and counted. Data were analyzed with a variety of models that allow for more than one class of binding site and for cooperativity among binding sites. Calcium binding to bovine factor X was best simulated by a model that assumes 1 very tight site, 3 cooperative tight sites, and 18 equivalent, non-interacting sites. Based on data from des(Gla)factor X, the first site is probably a high affinity non-Gla binding site. Our results differ from two previously published reports that indicated either 1 tight and 39 loose noncooperative sites (R.H. Yue & M.M. Gertler (1978) Thrombos. Haemostas. (Stuttg.) 40, 350) or 20 calcium binding sites with the first 4 being cooperative (M.J. Lindhout & H.C. Hemker (1978) Biochimica Biophysica Acta 533, 318). Our data on human factor X fit the same model as used for bovine factor X; however, coop-erativity is less in the 3 cooperative sites. Shown below are the first six thermodynamic equilibrium constants derived from a Scatchard analysis of binding data (values are M−1).Both proteins demonstrate the same total number of binding sites and essentially the same value for the first, tight binding site. Bovine factor X exhibits cooperativity, whereas human factor X has reduced cooperativity.
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