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Relevant bibliographies by topics / Ligands (Biochemistry) Membrane proteins

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Academic literature on the topic 'Ligands (Biochemistry) Membrane proteins'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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Journal articles on the topic "Ligands (Biochemistry) Membrane proteins"

1

Senisterra, Guillermo A., Hamed Ghanei, Galina Khutoreskaya, Elena Dobrovetsky, Aled M. Edwards, Gilbert G. Privé, and Masoud Vedadi. "Assessing the Stability of Membrane Proteins to Detect Ligand Binding Using Differential Static Light Scattering." Journal of Biomolecular Screening 15, no. 3 (February 11, 2010): 314–20. http://dx.doi.org/10.1177/1087057109357117.

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Protein stabilization upon ligand binding has frequently been used to identify ligands for soluble proteins. Methods such as differential scanning fluorimetry (DSF) and differential static light scattering (DSLS) have been employed in the 384-well format and have been useful in identifying ligands that promote crystallization and 3D structure determination of proteins. However, finding a generic method that is applicable to membrane proteins has been a challenge as the high hydrophobicity of membrane proteins and the presence of detergents essential for their solubilization interfere with fluorescence-based detections. Here the authors used MsbA (an adenosine triphosphate binding cassette transporter), CorA (a Mg++ channel), and CpxA (a histidine kinase) as model proteins and show that DSLS is not sensitive to the presence of detergents or protein hydrophobicity and can be used to monitor thermodenaturation of membrane proteins, assess their stability, and detect ligand binding in a 384-well format.

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Siligardi, Giuliano, Charlotte S. Hughes, and Rohanah Hussain. "Characterisation of sensor kinase by CD spectroscopy: golden rules and tips." Biochemical Society Transactions 46, no. 6 (December 4, 2018): 1627–42. http://dx.doi.org/10.1042/bst20180222.

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This is a review that describes the golden rules and tips on how to characterise the molecular interactions of membrane sensor kinase proteins with ligands using mainly circular dichroism (CD) spectroscopy. CD spectroscopy is essential for this task as any conformational change observed in the far-UV (secondary structures (α-helix, β-strands, poly-proline of type II, β-turns, irregular and folding) and near-UV regions [local environment of the aromatic side-chains of amino acid residues (Phe, Tyr and Trp) and ligands (drugs) and prosthetic groups (porphyrins, cofactors and coenzymes (FMN, FAD, NAD))] upon ligand addition to the protein can be used to determine qualitatively and quantitatively ligand-binding interactions. Advantages of using CD versus other techniques will be discussed. The difference CD spectra of the protein–ligand mixtures calculated subtracting the spectra of the ligand at various molar ratios can be used to determine the type of conformational changes induced by the ligand in terms of the estimated content of the various elements of protein secondary structure. The highly collimated microbeam and high photon flux of Diamond Light Source B23 beamline for synchrotron radiation circular dichroism (SRCD) enable the use of minimal amount of membrane proteins (7.5 µg for a 0.5 mg/ml solution) for high-throughput screening. Several examples of CD titrations of membrane proteins with a variety of ligands are described herein including the protocol tips that would guide the choice of the appropriate parameters to conduct these titrations by CD/SRCD in the best possible way.

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Baptist, Matilda, Candace Panagabko, Shamshad Cockcroft, and Jeffrey Atkinson. "Ligand and membrane-binding behavior of the phosphatidylinositol transfer proteins PITPα and PITPβ." Biochemistry and Cell Biology 94, no. 6 (December 2016): 528–33. http://dx.doi.org/10.1139/bcb-2015-0152.

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Phosphatidylinositol transfer proteins (PITPs) are believed to be lipid transfer proteins because of their ability to transfer either phosphatidylinositol (PI) or phosphatidylcholine (PC) between membrane compartments, in vitro. However, the detailed mechanism of this transfer process is not fully established. To further understand the transfer mechanism of PITPs we examined the interaction of PITPs with membranes using dual polarization interferometry (DPI), which measures protein binding affinity on a flat immobilized lipid surface. In addition, a fluorescence resonance energy transfer (FRET)-based assay was also employed to monitor how quickly PITPs transfer their ligands to lipid vesicles. DPI analysis revealed that PITPβ had a higher affinity to membranes compared with PITPα. Furthermore, the FRET-based transfer assay revealed that PITPβ has a higher ligand transfer rate compared with PITPα. However, both PITPα and PITPβ demonstrated a preference for highly curved membrane surfaces during ligand transfer. In other words, ligand transfer rate was higher when the accepting vesicles were highly curved.

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Linton, Kenneth J. "Structure and Function of ABC Transporters." Physiology 22, no. 2 (April 2007): 122–30. http://dx.doi.org/10.1152/physiol.00046.2006.

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ATP binding cassette transporters are ubiquitous integral membrane proteins that actively transport ligands across biological membranes, a process critical for most aspects of cell physiology. These proteins are important clinically and economically. Their dysfunction underlies a number of human genetic diseases, and the ability of some to pump cytotoxic molecules from cells confers resistance to antibiotics, herbicides, and chemotherapeutic drugs. Recent structure analyses interpreted in light of a large body of biochemistry has resulted in the ATP-switch model for function in which the paired nucleotide binding domains switch between an ATP-dependent closed conformation and a nucleotide-free, open conformation to drive the translocation of ligand.

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Bergsdorf, Christian, Cédric Fiez-Vandal, David A. Sykes, Pascal Bernet, Sonia Aussenac, Steven J. Charlton, Ulrich Schopfer, Johannes Ottl, and Myriam Duckely. "An Alternative Thiol-Reactive Dye to Analyze Ligand Interactions with the Chemokine Receptor CXCR2 Using a New Thermal Shift Assay Format." Journal of Biomolecular Screening 21, no. 3 (December 7, 2015): 243–51. http://dx.doi.org/10.1177/1087057115619597.

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Integral membrane proteins (IMPs) play an important role in many cellular events and are involved in numerous pathological processes. Therefore, understanding the structure and function of IMPs is a crucial prerequisite to enable successful targeting of these proteins with low molecular weight (LMW) ligands early on in the discovery process. To optimize IMP purification/crystallization and to identify/characterize LMW ligand-target interactions, robust, reliable, high-throughput, and sensitive biophysical methods are needed. Here, we describe a differential scanning fluorimetry (DSF) screening method using the thiol-reactive BODIPY FL-cystine dye to monitor thermal unfolding of the G-protein-coupled receptor (GPCR), CXCR2. To validate this method, the seven-transmembrane protein CXCR2 was analyzed with a set of well-characterized antagonists. This study showed that the new DSF assay assessed reliably the stability of CXCR2 in a 384-well format. The analysis of 14 ligands with a potency range over 4 log units demonstrated the detection/characterization of LMW ligands binding to the membrane protein target. Furthermore, DSF results cross-validated with the label-free differential static light scattering (DSLS) thermal denaturation method. These results underline the potential of the BODIPY assay format as a general tool to investigate membrane proteins and their interaction partners.

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Sankararamakrishnan, Ramasubbu. "Recognition of GPCRs by Peptide Ligands and Membrane Compartments theory: Structural Studies of Endogenous Peptide Hormones in Membrane Environment." Bioscience Reports 26, no. 2 (June 22, 2006): 131–58. http://dx.doi.org/10.1007/s10540-006-9014-z.

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One of the largest family of cell surface proteins, G-protein coupled receptors (GPCRs) regulate virtually all known physiological processes in mammals. With seven transmembrane segments, they respond to diverse range of extracellular stimuli and represent a major class of drug targets. Peptidergic GPCRs use endogenous peptides as ligands. To understand the mechanism of GPCR activation and rational drug design, knowledge of three-dimensional structure of receptor–ligand complex is important. The endogenous peptide hormones are often short, flexible and completely disordered in aqueous solution. According to “Membrane Compartments Theory”, the flexible peptide binds to the membrane in the first step before it recognizes its receptor and the membrane-induced conformation is postulated to bind to the receptor in the second step. Structures of several peptide hormones have been determined in membrane-mimetic medium. In these studies, micelles, reverse micelles and bicelles have been used to mimic the cell membrane environment. Recently, conformations of two peptide hormones have also been studied in receptor-bound form. Membrane environment induces stable secondary structures in flexible peptide ligands and membrane-induced peptide structures have been correlated with their bioactivity. Results of site-directed mutagenesis, spectroscopy and other experimental studies along with the conformations determined in membrane medium have been used to interpret the role of individual residues in the peptide ligand. Structural differences of membrane-bound peptides that belong to the same family but differ in selectivity are likely to explain the mechanism of receptor selectivity and specificity of the ligands. Knowledge of peptide 3D structures in membrane environment has potential applications in rational drug design.

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SZYMKIEWICZ, Iwona, Oleg SHUPLIAKOV, and Ivan DIKIC. "Cargo- and compartment-selective endocytic scaffold proteins." Biochemical Journal 383, no. 1 (September 24, 2004): 1–11. http://dx.doi.org/10.1042/bj20040913.

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The endocytosis of membrane receptors is a complex and tightly controlled process that is essential for maintaining cellular homoeostasis. The removal of receptors from the cell surface can be constitutive or ligand-induced, and occurs in a clathrin-dependent or -independent manner. The recruitment of receptors into specialized membrane domains, the formation of vesicles and the trafficking of receptors together with their ligands within endocytic compartments are regulated by reversible protein modifications, and multiple protein–protein and protein–lipid interactions. Recent reports describe a variety of multidomain molecules that facilitate receptor endocytosis and function as platforms for the assembly of protein complexes. These scaffold proteins typically act in a cargo-specific manner, recognizing one or more receptor types, or function at the level of endocytic cellular microcompartments by controlling the movement of cargo molecules and linking endocytic machineries to signalling pathways. In the present review we summarize present knowledge on endocytic scaffold molecules and discuss their functions.

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Zhang, Dachuan, Anatoly Kiyatkin, Jeffrey T. Bolin, and Philip S. Low. "Crystallographic structure and functional interpretation of the cytoplasmic domain of erythrocyte membrane band 3." Blood 96, no. 9 (November 1, 2000): 2925–33. http://dx.doi.org/10.1182/blood.v96.9.2925.

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Abstract The red blood cell membrane (RBCM) is a primary model for animal cell plasma membranes. One of its major organizing centers is the cytoplasmic domain of band 3 (cdb3), which links multiple proteins to the membrane. Included among its peripheral protein ligands are ankyrin (the major bridge to the spectrin-actin skeleton), protein 4.1, protein 4.2, aldolase, glyceraldehyde-3-phosphate dehydrogenase, phosphofructokinase, deoxyhemoglobin, p72syk protein tyrosine kinase, and hemichromes. The crystal structure of cdb3 is reported at 0.26 nm (2.6 Å) resolution. A tight symmetric dimer is formed by cdb3; it is stabilized by interlocked dimerization arms contributed by both monomers. Each subunit also includes a larger peripheral protein binding domain with an α+ β-fold. The binding sites of several peripheral proteins are localized in the structure, and the nature of the major conformational change that regulates membrane-skeletal interactions is evaluated. An improved structural definition of the protein network at the inner surface of the RBCM is now possible.

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Zhang, Dachuan, Anatoly Kiyatkin, Jeffrey T. Bolin, and Philip S. Low. "Crystallographic structure and functional interpretation of the cytoplasmic domain of erythrocyte membrane band 3." Blood 96, no. 9 (November 1, 2000): 2925–33. http://dx.doi.org/10.1182/blood.v96.9.2925.h8002925_2925_2933.

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The red blood cell membrane (RBCM) is a primary model for animal cell plasma membranes. One of its major organizing centers is the cytoplasmic domain of band 3 (cdb3), which links multiple proteins to the membrane. Included among its peripheral protein ligands are ankyrin (the major bridge to the spectrin-actin skeleton), protein 4.1, protein 4.2, aldolase, glyceraldehyde-3-phosphate dehydrogenase, phosphofructokinase, deoxyhemoglobin, p72syk protein tyrosine kinase, and hemichromes. The crystal structure of cdb3 is reported at 0.26 nm (2.6 Å) resolution. A tight symmetric dimer is formed by cdb3; it is stabilized by interlocked dimerization arms contributed by both monomers. Each subunit also includes a larger peripheral protein binding domain with an α+ β-fold. The binding sites of several peripheral proteins are localized in the structure, and the nature of the major conformational change that regulates membrane-skeletal interactions is evaluated. An improved structural definition of the protein network at the inner surface of the RBCM is now possible.

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De Gerónimo, Eduardo, Lisandro J. Falomir-Lockhart, María Ximena Guerbi, David C. Wilton, and Betina Córsico. "Protein-membrane interaction and ligand transfer to membranes from intestinal fatty acid binding proteins (FABPs) employing natural ligands." Chemistry and Physics of Lipids 149 (September 2007): S50. http://dx.doi.org/10.1016/j.chemphyslip.2007.06.112.

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Dissertations / Theses on the topic "Ligands (Biochemistry) Membrane proteins"

1

Leng, Ying. "Neuron-ligand pathfinding on surfaces modified by laminin and laminin-derived peptides." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 78 p, 2006. http://proquest.umi.com/pqdweb?did=1203562381&sid=8&Fmt=2&clientId=8331&RQT=309&VName=PQD.

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Millman, Jonathan Scott Andrews David. "Characterization of membrane-binding by FtsY, the prokaryote SRP receptor /." *McMaster only, 2002.

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Ma, Jerome H. Y. "Atomistic studies of the dynamics of P-glycoprotein and its ligands." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:e2e2bbe0-d4ae-4351-b339-c8e02ef3d3d9.

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A signifficant obstacle facing the healthcare industry is the phenomenon of multidrug resistance (MDR) in which a cell acquires simultaneous resistance to many unrelated drugs that it has never been exposed to. At the molecular level, MDR can be characterised by a reduction of intracellular drug levels due to their active efflux by multidrug transporters such as P-glycoprotein (Pgp). Pgp is able to efflux a phenomenally wide variety of chemically unrelated drugs and causal relationships have been established between its expression and the acquisition of MDR to numerous anticancer and central nervous system (CNS) drugs. There has thus been much effort to understand the molecular biology of Pgp and how it functions. However, many aspects of its functioning remain unclear. From a drug discovery viewpoint, we have yet to fully understand what features make some drugs susceptible to Pgp-mediated efflux (substrates) and what makes others able to inhibit Pgp function (inhibitors). From a mechanistic viewpoint, it is still uncertain what the exact nature of Pgp's binding site is, the role of ATP binding and hydrolysis in transport and how both of these interplay with ligand binding. The work presented in this thesis attempts to answer these questions from two perspectives. Firstly the mouse Pgp crystal structure [PDB 3G60] was used as a unique starting point for molecular dynamics (MD) simulations to characterise the dynamics and conformational exibility of Pgp, properties believed to be integral to its function. The simulations revealed Pgp to be a highly dynamic molecule at both its transmembrane (TM) and nucleotide binding domains (NBDs). The latter exhibited a conformational asymmetry that supports the Constant Contact model of ATPase activity. In the presence of the Pgp substrate, daunorubicin, the NBDs exhibited tighter asymmetric dimerisation leading to increased affinity for ATP. In contrast, the presence of the Pgp inhibitor, QZ59-RRR led to NBD conformational changes that reduced their affinity for ATP. Thus providing an appealing mechanism for how QZ59-RRR inhibits Pgp ATPase activity. MD simulation was also used to provide atomic-detail interpretations of multiple binding stoichiometries of drug and lipid molecules observed by collaborator-led mass spectrometry experiments. This also provided opportunity to validate the Pgp simulations against novel experimental data. The second strand of the thesis explored the membrane permeation dynamics of CNS therapeutics in order to identify differences in protonation states, conformations, orientations and membrane localisation that might distinguish those that are Pgp substrates and from those that are not. These properties were studied using complementary MD simulation and nuclear magnetic resonance (NMR) techniques. The simulations revealed a novel set of criteria that in uence the likelihoodof a drug to 'flip-flop' across a membrane, a behaviour that may make drugs more susceptible to Pgp efflux. These observations were broadly consistent with the NMR experiments. However, the NMR data also highlighted limitations in the simulation approaches used in this thesis and emphasised the need to also consider the kinetics of permeation in addition to its thermodynamics.

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Christie, Shaun Michael. "Elucidation of Membrane Protein Interactions Under Native and Ligand Stimulated Conditions Using Fluorescence Correlation Spectroscopy." University of Akron / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=akron1594383686413803.

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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.

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Careful treatment of water molecules in ligand-protein interactions is required in many cases if the correct binding pose is to be identified for molecular docking. Water can form complex bridging networks and can play a critical role in dictating the binding mode of ligands. A particularly striking example of this can be found in the ionotropic glutamate receptors (iGluRs), a family of ligand gated ion channels that are responsible for a majority of the fast synaptic neurotransmission in the central nervous system that are thought to be essential in memory and learning. Thus, pharmacological intervention at these neuronal receptors is a valuable therapeutic strategy. This thesis relies on various computational studies and X-ray crystallography to investigate the role of ligand-water mediated interactions in iGluRs bound to glutamate and α-amino-3-hydroxy-5-methyl-4- isoxazole-propionic acid (AMPA). Comparative molecular dynamics (MD) simulations of each subtype of iGluRs bound to glutamate revealed that crystal water positions were reproduced and that all but one water molecule, W5, in the binding site can be rearranged or replaced with water molecules from the bulk. Further density functional theory calculations (DFT) have been used to confirm the MD results and characterize the energetics of W5 and another water molecule implicated in influencing the dynamics of a proposed switch in these receptors. Additional comparative studies on the AMPA subtypes of iGluRs show that each step of the calculation must be considered carefully if the results are to be meaningful. Crystal structures of two ligands, glutamate and AMPA revealed two distinct modes of binding when bound to an AMPA subtype of iGluRs, GluA2. The difference is related to the position of water molecules within the binding pocket. DFT calculations investigated the interaction energies and polarisation effects resulting in a prediction of the correct binding mode for glutamate. For AMPA alternative modes of binding have similar interaction energies as a result of a higher internal energy than glutamate. A combined MD and X-ray crystallographic study investigated the binding of the ligand AMPA in the AMPA receptor subtypes. Analysis of the binding pocket show that AMPA is not preserved in the crystal bound mode and can instead adopt an alternative mode of binding. This involves a displacement of a key water molecule followed by AMPA adopting the pose seen by glutamate. Thus, this thesis makes use of various studies to assess the energetics and dynamics of water molecules in iGluRs. The resulting data provides additional information on the importance of water molecules in mediating ligand interactions as well as identifying key water molecules that can be useful in the de novo design of new selective drugs against iGluRs.

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Rapp, Mikaela. "The Ins and Outs of Membrane Proteins : Topology Studies of Bacterial Membrane Proteins." Doctoral thesis, Stockholm : Department of Biochemistry and Biophysics, Stockholm University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-1330.

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Davies, R. J. "Monolayer studies on intrinsic erythrocyte membrane proteins." Thesis, University of Manchester, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.356110.

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Boekel, Carolina. "Integration and topology of membrane proteins." Doctoral thesis, Stockholm : Department of Biochemistry and Biophysics, Stockholm University, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-8575.

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Yue, Kevin Kin Man. "Assembly of outer membrane proteins in Escherichia coli." Thesis, University of Liverpool, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.257436.

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Fairbairn, L. J. "Investigations on erythrocyte membrane proteins using molecular cloning techniques." Thesis, University of Bristol, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.379600.

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Books on the topic "Ligands (Biochemistry) Membrane proteins"

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Azzi, A. Membrane Proteins: Isolation and Characterization. Berlin, Heidelberg: Springer Berlin Heidelberg, 1986.

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Latruffe, Norbert. Dynamics of Membrane Proteins and Cellular Energetics. Berlin, Heidelberg: Springer Berlin Heidelberg, 1988.

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3

Siegfried, Schwarz. Molecules of life & mutations: Understanding diseases by understanding proteins. Basel: Karger, 2002.

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Schwarz, Siegfried. Molecules of life & mutations: Understanding diseases by understanding proteins. Basel: Karger, 2002.

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Schwarz, Siegfried. Molecules of life & mutations: Understanding diseases by understanding proteins. Basel: Karger, 2002.

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Working Party on Platelet Membrane: Biochemistry and Physicology (1987 Villard de Lans, France). Biochemistry and physiopathology of platelet membrane: Proceedings of the Working Party on Platelet Membrane, Biochemistry, and Physiopathology, held in Villard-de-Lans (France) 29-31 January 1987 = Biochimie et physiopathologie de la membrane plaquettaire. Paris: Editions INSERM, 1988.

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Jerusalem Symposium on Quantum Chemistry and Biochemistry (25th 1992). Membrane proteins: Structures, interactions and models : proceedings of the twenty-fifth Jerusalem Symposium on Quantum Chemistry and Biochemistry held in Jerusalem, Israel, May 18-21, 1992. Dordrecht: Kluwer Academic Publishers, 1992.

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International Symposium on Structure and Dynamics of Nucleic Acids, Proteins, and Membranes (1986 Riva, Italy). Structure and dynamics of nucleic acids, proteins, and membranes. New York: Plenum Press, 1986.

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Serysheva, Irina I. Structure and function of calcium release channels. London: Academic Press, 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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Book chapters on the topic "Ligands (Biochemistry) Membrane proteins"

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Schneider, Pascal, Clément Bordier, and Robert Etges. "Membrane Proteins and Enzymes of Leishmania." In Subcellular Biochemistry, 39–72. Boston, MA: Springer US, 1992. http://dx.doi.org/10.1007/978-1-4899-1651-8_2.

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Jaenicke, R. "Structural analysis of membrane proteins." In Biochemistry of Cell Membranes, 291–96. Basel: Birkhäuser Basel, 1995. http://dx.doi.org/10.1007/978-3-0348-9057-1_20.

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Tartakoff, Alan M. "Biological Functions and Biosynthesis of Glycolipid-Anchored Membrane Proteins." In Subcellular Biochemistry, 81–93. Boston, MA: Springer US, 1993. http://dx.doi.org/10.1007/978-1-4615-2912-5_4.

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Glaeser, R. M. "Electron Crystallography of Membrane Proteins." In The Jerusalem Symposia on Quantum Chemistry and Biochemistry, 1–9. Dordrecht: Springer Netherlands, 1992. http://dx.doi.org/10.1007/978-94-011-2718-9_1.

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Crain, Richard C. "Phospholipid Transfer Proteins as Probes of Membrane Structure and Function." In Subcellular Biochemistry, 45–67. Boston, MA: Springer US, 1990. http://dx.doi.org/10.1007/978-1-4899-1621-1_3.

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Morris, Michael B., and Gregory B. Ralston. "Biophysical Characterization of Membrane and Cytoskeletal Proteins by Sedimentation Analysis." In Subcellular Biochemistry, 25–82. Boston, MA: Springer US, 1994. http://dx.doi.org/10.1007/978-1-4615-1863-1_2.

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Karpatkin, Simon. "Crossed Immunoelectrophoresis for the Study of Platelet Membrane Proteins." In Blood Cell Biochemistry, 59–75. Boston, MA: Springer US, 1991. http://dx.doi.org/10.1007/978-1-4757-9531-8_3.

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Kühlbrandt, W. "High-Resolution Electron Microscopy of Membrane Proteins." In The Jerusalem Symposia on Quantum Chemistry and Biochemistry, 11–15. Dordrecht: Springer Netherlands, 1992. http://dx.doi.org/10.1007/978-94-011-2718-9_2.

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Lakatos, Andrea, Karsten Mörs, and Clemens Glaubitz. "How to Investigate Interactions Between Membrane Proteins and Ligands by Solid-State NMR." In Membrane Protein Structure and Dynamics, 65–86. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-023-6_5.

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Durand, Grégory, Maher Abla, Christine Ebel, and Cécile Breyton. "New Amphiphiles to Handle Membrane Proteins: “Ménage à Trois” Between Chemistry, Physical Chemistry, and Biochemistry." In Membrane Proteins Production for Structural Analysis, 205–51. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-0662-8_8.

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Conference papers on the topic "Ligands (Biochemistry) Membrane proteins"

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Cuppoletti, John. "Composite Synthetic Membranes Containing Native and Engineered Transport Proteins." In ASME 2008 Conference on Smart Materials, Adaptive Structures and Intelligent Systems. ASMEDC, 2008. http://dx.doi.org/10.1115/smasis2008-449.

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Our membrane transport protein laboratory has worked with material scientists, computational chemists and electrical and mechanical engineers to design bioactuators and sensing devices. The group has demonstrated that it is possible to produce materials composed native and engineered biological transport proteins in a variety of synthetic porous and solid materials. Biological transport proteins found in nature include pumps, which use energy to produce gradients of solutes, ion channels, which dissipate ion gradients, and a variety of carriers which can either transport substances down gradients or couple the uphill movement of substances to the dissipation of gradients. More than one type of protein can be reconstituted into the membranes to allow coupling of processes such as forming concentration gradients with ion pumps and dissipating them with an ion channel. Similarly, ion pumps can provide ion gradients to allow the co-transport of another substance. These systems are relevant to bioactuation. An example of a bioactuator that has recently been developed in the laboratory was based on a sucrose-proton exchanger coupled to a proton pump driven by ATP. When coupled together, the net reaction across the synthetic membrane was ATP driven sucrose transport across a flexible membrane across a closed space. As sucrose was transported, net flow of water occurred, causing pressure and deformation of the membrane. Transporters are regulated in nature. These proteins are sensitive to voltage, pH, sensitivity to a large variety of ligands and they can be modified to gain or lose these responses. Examples of sensors include ligand gated ion channels reconstituted on solid and permeable supports. Such sensors have value as high throughput screening devices for drug screening. Other sensors that have been developed in the laboratory include sensors for membrane active bacterial products such as the anthrax pore protein. These materials can be self assembled or manufactured by simple techniques, allowing the components to be stored in a stable form for years before (self) assembly on demand. The components can be modified at the atomic level, and are composed of nanostructures. Ranges of sizes of structures using these components range from the microscopic to macroscopic scale. The transport proteins can be obtained from natural sources or can be produced by recombinant methods from the genomes of all kingdoms including archea, bacteria and eukaryotes. For example, the laboratory is currently studying an ion channel from a thermophile from deep sea vents which has a growth optimum of 90 degrees centigrade, and has membrane transport proteins with very high temperature stability. The transport proteins can also be genetically modified to produce new properties such as activation by different ligands or transport of new substances such as therapeutic agents. The structures of many of these proteins are known, allowing computational chemists to help understand and predict the transport processes and to guide the engineering of new properties for the transport proteins and the composite membranes. Supported by DARPA and USARMY MURI Award and AFOSR.

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Schleuning, W. D. "THE BIOCHEMISTRY AND CELL BIOLOGY OF SINGLE CHAIN UROKINASE TYPE PLASMINOGEN ACTIVATOR." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642956.

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Urokinase was discovered in the late nineteenth century, as an enzymatic principle in urine, that initiates the dissolution of blood clots. The basis of this phenomenon was recognized more than fifty years ago as the activation of plasminogen, the precursor of a tryptic protease, then known as profibrinolysin. Despite this long history, detailed data on the biochemistry of plasminogen activation have only become available recently. Urokinase (now designated urokinase-type plasminogen activator : u-PA) is synthesized and secreted as a single chain polypeptide (Mr-: 53,000) by many cell types. Single chain u-PA (scu-PA) is with equal justification called prourokinase (pro-u-PA), notwithstanding its low catalytic activity for synthetic peptide substrates and plasminogen, as most proenzymes of proteases display a certain degree of activity. The structure of pro-u-PA has been elucidated by protein and cDNA sequencing. It consists of three domains, exhibiting characteristic homology to other proteins: a serine protease domain, homologous to trypsin, chymotrypsin and elastase; a kringle domain, likewise found in prothrombin, plasminogen, tissue-type plasminogen activator (t-PA) and Factor XII; and an epidermal growth factor (EGF)-like domain, found in many other proteins, including certain clotting factors. Pro-u-PA is activated by the cleavage of its LYS158-Ile159 h1 bY either plasmin or kallikrein. This cleavage leads to a high increase of Kcat values with respect to both plasminogen and synthetic peptide substrates, but apparently to a reduction of its affinity to plasminogen. Thrartoin inactivates pro-u-PA irreversibly by the cleavage of the Arg156-Phe157 bond. U-PA but not pro-u-PA rapidly forms ccnplexes with plasminogen activator inhibitors (PAI)-l and PAI-2: second order rate constants Kass are respectively > 107 and 0.9xl06 (M-11sec-1). Unknown enzymes process pro-u-PA and u-PA to low molecular weight (LMW) pro-u-PA and LMW u-PA (Mr: 33,000) by cutting off a fragment consisting of the kr ingle and the EGF—like region. Pro—u—PA mediated plasminogen activation is fibrin dependent in vivo, and to a certain degree in vitro. Hie biochemical basis of this fibrin specificity is at present uncertain, although there are reports indicating that it may require polyvalent cations. Through its EGF-like region HMW pro-u-PA and HMW u-PA are capable of binding to specific membrane protein receptors which are found on many cells. Thus, u-PA activity may be restricted to the cell surface. According to a recent report, binding of u—PA to the receptor may also mediate signal transduction in auto- or paracrine growth control. In cells permissive for the respective pathways, pro-u-PA gene transcription is stimulated by mechanisms of signal transduction, that include the cAMP, the tyrosine specific kinase and the protein kinase C dependent pathways. Glucocorticoid hormones downregulate pro-u-PA gene transcription in cells where the gene is canstitutively expressed. Although different cells vary greatly in their response to agents that stimulate urokinase biosynthesis, growth factors and other mitogens are in many cases effective inducers. Significantly elevated levels of u-PA are also found in many malignant tissues. These findings and many others suggest that plasminogen activation by u-PA provides localized extracellular matrix degradation which is required for invasive growth, cell migration and other forms of tissue remodelling. Fibrin represents in this view only a variant of an extracellular matrix, which is provided through the clotting system in the case of an emergency.

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Larsen, Melinda, Riffard Jean-Gilles, David Soscia, Sharon Sequeira, Michael Melfi, Anand Gadre, and James Castracane. "Development of Nanofiber Scaffolds for Engineering an Artificial Salivary Gland." In ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology. ASMEDC, 2010. http://dx.doi.org/10.1115/nemb2010-13372.

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There is currently a significant clinical need for artificial salivary glands as a therapeutic option for patients suffering from xerostomia. To achieve unidirectional fluid secretion, the epithelial acinar cells must establish and maintain polarity by partitioning the plasma membrane into distinct apical and basolateral membrane surfaces to achieve unidirectional fluid secretion. Establishment and maintenance of epithelial acinar cell polarity has been difficult to achieve in vitro, and yet is critical saliva secretion in an engineered salivary gland. Physical properties of the scaffold provided to epithelial cells will likely influence their ability to differentiate and achieve apical-basal polarity. We have engineered nanofiber matrices using the biocompatible polymer, PLGA (poly-L-lactic-co-glycolic acid) having differing topology and organization and documented the structure of these scaffolds using SEM. We evaluated the effects of several factors on epithelial cell attachment, self-organization, and apico-basal polarity on the scaffolds using confocal microscopy to examine expression and organization of apical tight junction proteins, ZO-1 and claudins, and basal markers, such as integrin α6 and the ECM protein fibronectin. The surface of the nanofiber matrix was functionalized with chemically-linked ligands to further optimize apical-basal polarity. These studies will identify an optimal scaffold for future use in an engineered functional salivary gland construct.

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Sarvestani, Alireza. "A Theoretical Analysis for the Effect of Substrate Elasticity on Cellular Adhesion." In ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology. ASMEDC, 2010. http://dx.doi.org/10.1115/nemb2010-13311.

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Cell behavior is mediated by variety of physiochemical properties of extracellular matrix (ECM). Material composition, surface chemistry, roughness, and distribution pattern of cell adhesive proteins are among the ECM properties which are known to modulate various cellular physiological functions. Mechanical stiffness of ECM in particular is found to be a major regulator for multiple aspects of cellular function. Experiments show that cells in general, exhibit an apparent adhesion preference for stiffer substrates with a larger projected spread area with increasing the substrate stiffness. In addition, it seems that the effect of substrates elasticity is strongly coupled with adhesivity of the substrate; on relatively stiff substrates the spread area of the cells exhibits strong biphasic dependence to the changes in ligand density, whereas on soft substrates their limited spreading is much less sensitive to the density of surface ligands. This study aims to propose a theoretical basis for the interplay between substrate elasticity and cellular adhesion, using an equilibrium thermodynamic model. Within this framework, the equilibrium contact area is assumed to ensure minimization of the free energy contributed by interfacial adhesive and repulsive interactions between the membrane and substrate as well as the deformation of cell and substrate. Hence, this thermodynamic model overlooks the contribution of intracellular signaling or actively regulated cytoskeleton and assumes that cell adhesion is solely a result of the balance between the membrane-substrate repulsive potentials, stored elastic energy, binding enthalpy, and mixing entropy of mobile receptors. The predictions of this purely mechanistic model for cell adhesion qualitatively follow the experimental results featuring the variation of cell spread area on compliant bio-adhesive substrates. This suggests that the mechanistic pathways inherent to membrane-substrate interactions may be equally important as intracellular signaling pathways to mediate the cellular adhesion.

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