Relevant bibliographies by topics / Protein folding studies

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

Academic literature on the topic 'Protein folding studies'

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

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Journal articles on the topic "Protein folding studies"

1

Baker, David. "Protein folding, structure prediction and design." Biochemical Society Transactions 42, no. 2 (March 20, 2014): 225–29. http://dx.doi.org/10.1042/bst20130055.

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I describe how experimental studies of protein folding have led to advances in protein structure prediction and protein design. I describe the finding that protein sequences are not optimized for rapid folding, the contact order–protein folding rate correlation, the incorporation of experimental insights into protein folding into the Rosetta protein structure production methodology and the use of this methodology to determine structures from sparse experimental data. I then describe the inverse problem (protein design) and give an overview of recent work on designing proteins with new structures and functions. I also describe the contributions of the general public to these efforts through the Rosetta@home distributed computing project and the FoldIt interactive protein folding and design game.
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Bustamante, Carlos, Lisa Alexander, Kevin Maciuba, and Christian M. Kaiser. "Single-Molecule Studies of Protein Folding with Optical Tweezers." Annual Review of Biochemistry 89, no. 1 (June 20, 2020): 443–70. http://dx.doi.org/10.1146/annurev-biochem-013118-111442.

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Manipulation of individual molecules with optical tweezers provides a powerful means of interrogating the structure and folding of proteins. Mechanical force is not only a relevant quantity in cellular protein folding and function, but also a convenient parameter for biophysical folding studies. Optical tweezers offer precise control in the force range relevant for protein folding and unfolding, from which single-molecule kinetic and thermodynamic information about these processes can be extracted. In this review, we describe both physical principles and practical aspects of optical tweezers measurements and discuss recent advances in the use of this technique for the study of protein folding. In particular, we describe the characterization of folding energy landscapes at high resolution, studies of structurally complex multidomain proteins, folding in the presence of chaperones, and the ability to investigate real-time cotranslational folding of a polypeptide.
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Lu, Diannan, and Zheng Liu. "Studies of protein folding pathways." Annual Reports Section "C" (Physical Chemistry) 106 (2010): 259. http://dx.doi.org/10.1039/b903487k.

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Freisner, R. A., and J. R. Gunn. "Computational Studies of Protein Folding." Annual Review of Biophysics and Biomolecular Structure 25, no. 1 (June 1996): 315–42. http://dx.doi.org/10.1146/annurev.bb.25.060196.001531.

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Skolnick, J., and A. Kolinski. "Computational studies of protein folding." Computing in Science and Engineering 3, no. 5 (September 2001): 40–50. http://dx.doi.org/10.1109/mcise.2001.947107.

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Doerr, Allison. "Protein folding studies go global." Nature Methods 14, no. 9 (September 2017): 834. http://dx.doi.org/10.1038/nmeth.4418.

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Skolnick, J., and A. Kolinski. "Computational studies of protein folding." Computing in Science & Engineering 3, no. 3 (2001): 40–50. http://dx.doi.org/10.1109/5992.919264.

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Hanazono, Yuya, Kazuki Takeda, and Kunio Miki. "Crystallographic studies for the folding of an extending peptide." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1150. http://dx.doi.org/10.1107/s2053273314088494.

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Full-length proteins can fold into thermodynamically stable structures at an exceptionally fast rate as shown by in vitro experiments. In contrast, it takes much more time to finish nascent protein folding than full-length protein folding, because nascent protein folding depends on the rate of ribosome biosynthesis in the living cell. Therefore nascent polypeptide chains in vivo fold co-translationally in different manners from the full-length proteins. However, the transient structures and the co-translational folding pathway are not well understood. In order to reveal the atomic details of nascent protein folding, we studied the hPin1 WW domain, which consists of two beta-hairpins between the three-stranded beta-sheets. Here we report a series of WW domain N-terminal fragment structures with increasing amino acid length by using circular dichroism spectroscopy and X-ray crystallography. In crystallization, maltose-binding protein was fused just behind the WW domain fragments to fix the C-terminus as nascent proteins are anchored to the ribosome. Co-translational folding of beta-sheet-rich proteins is discussed based on our finding that intermediate-length fragments unexpectedly take a helical conformation, even though the full-length protein has no helical regions. Furthermore, in a region of one of the loop structures of the full-length protein, these fragments take different formations. Our results suggest that the newly synthesized polypeptides adopt the most stable conformation during the course of peptide extension and fold into the native structures, eventually.
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Dodson, C. A., N. Ferguson, T. J. Rutherford, C. M. Johnson, and A. R. Fersht. "Engineering a two-helix bundle protein for folding studies." Protein Engineering Design and Selection 23, no. 5 (February 3, 2010): 357–64. http://dx.doi.org/10.1093/protein/gzp080.

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Borgia, Alessandro, Philip M. Williams, and Jane Clarke. "Single-Molecule Studies of Protein Folding." Annual Review of Biochemistry 77, no. 1 (June 2008): 101–25. http://dx.doi.org/10.1146/annurev.biochem.77.060706.093102.

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Dissertations / Theses on the topic "Protein folding studies"

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Vasilkoski, Zlatko. "Protein folding computational studies /." Thesis, Connect to Dissertations & Theses @ Tufts University, 2003.

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Thesis (Ph.D.)--Tufts University, 2003.
Adviser: David L. Weaver. Submitted to the Dept. of Physics. Includes bibliographical references. Access restricted to members of the Tufts University community. Also available via the World Wide Web;
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Badcoe, Ian Geoffrey. "Computer studies of protein folding." Thesis, University of Bristol, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.385585.

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Nymeyer, Hugh. "Computational studies of protein folding /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC IP addresses, 2001. http://wwwlib.umi.com/cr/ucsd/fullcit?p3022207.

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Geierhaas, Christian D. "Computational studies of protein folding." Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.613877.

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Perrett, Sarah Elizabeth Dorothy. "Biophysical studies on protein folding." Thesis, University of Cambridge, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627049.

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Hart, Tanya Clare. "Mutational studies of prion protein folding." Thesis, Imperial College London, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.418318.

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Wain, Rachel. "Studies of protein folding and aggregation." Thesis, University of Oxford, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.270186.

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Woolfson, Derek Neil. "Studies on protein folds and folding." Thesis, University of Cambridge, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.239742.

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Matouschek, Andreas T. E. L. "Studies on the folding of barnase." Thesis, University of Cambridge, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.240039.

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Eyles, Stephen J. "Studies of protein folding by NMR spectroscopy." Thesis, University of Oxford, 1995. http://ora.ox.ac.uk/objects/uuid:06b8fb16-790c-4b72-80d0-8317920655fe.

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This thesis describes an investigation of the folding and stability of a series of derivatives of the proteins lysozyme and α-lactalbumin which lack one or more of their four native disulphide bridges. Removal of the disulphide bridge which links the N- and C-termini from hen lysozyme results in a three-disulphide derivative (CM6,127-lysozyme). This has a profound effect on its stability against thermal denaturation, the Tm for unfolding being reduced by 25°C at pH 3.8. Calorimetric measurements performed on this three-disulphide derivative indicate that this reduction in stability may be attributed entirely to an increase in the entropy difference between the native and denatured states. Kinetic refolding studies of CM6,127-lysozyme using stopped flow optical methods and hydrogen exchange pulse labelling in conjunction with NMR and electrospray ionisation mass spectrometry (ESI-MS) suggest that this reduced stability manifests itself primarily in the α-domain of the protein. A transient intermediate populated during refolding of the unmodified protein can no longer be detected during folding of the derivative resulting in highly cooperative folding under the conditions investigated. The structure and stability of a three- and two-disulphide derivative of the homologous protein, α-lactalbumin have been investigated by NMR spectroscopy. The three-disulphide species, like its lysozyme counterpart, can adopt native structure but this is much more unstable than the intact protein. Removal of a second disulphide bridge, however, destabilises α-lactalbumin to the extent that the native state is no longer formed. Instead, in the presence of Ca2+ and high concentrations of salt, a partially structured state is induced which has some elements of tertiary structure present. Novel techniques of ESI-MS have been developed to study protein folding and stability using hydrogen exchange techniques. Applications to the investigation of cooperativity in protein folding, stability in native, partially folded and unfolded states, and the interactions of a partially folded protein with the chaperone GroEL are described.
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Books on the topic "Protein folding studies"

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Holmgren, Anders. Structural studies of PapD, a chaperone protein involved in pili assembly, from E. coli. Uppsala: Sveriges Lantbruksuniversitet, 1993.

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Valkonen, Mari. Functional studies of the secretory pathway of filamentous fungi: The effect of unfolded protein response on protein production. Espoo [Finland]: VTT Technical Research Centre of Finland, 2003.

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Ron, Elber, ed. Recent developments in theoretical studies of proteins. Singapore: World Scientific, 1996.

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Gnaneshan, Saravanamuttu. Topological analysis of membrane proteins in bacteria and studies of factors involved in protein folding. 2000.

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Zhou, Huan-Xiang, and Jian-Min Yuan. Biophysics and Biochemistry of Protein Folding and Aggregation: Experimental and Theoretical Studies on Folding, Misfolding, and Self-Assembly of Amyloidogenic Peptides. World Scientific Publishing Co Pte Ltd, 2017.

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Clarke, Andrew. Water. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780199551668.003.0005.

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Liquid water is essential for life, and a metabolically active cell is ~70% water. The physical properties of liquid water, and their temperature dependence, are dictated to a significant extent by the properties of hydrogen bonds. From an ecological perspective, the important properties of liquid water include its high latent heats of fusion and vapourisation, its high specific heat, the ionisation, low dynamic viscosity and high surface tension. The solubility in water of oxygen, carbon dioxide and the calcium carbonate used to build skeletons in many invertebrates groups all increase with decreasing temperature. The hydrophobic interaction is important in the formation of cellular membranes and the folding of proteins; its strength increases with temperature, which may be a factor in the cold-denaturation of cellular macromolecules. The cell is extremely crowded with macromolecules. Coupled with the highly structured water close to membranes or protein surfaces and the hydration shells around ions, this means that the behaviour of water in cells is different from that of bulk water. The thermal behaviour of isolated cellular components studied in dilute aqueous buffers many not reflect accurately their behaviour in the intact cell or tissue.
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Book chapters on the topic "Protein folding studies"

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Scheraga, Harold A., Ming-Hong Hao, and Jaroslaw Kostrowicki. "Theoretical Studies of Protein Folding." In Methods in Protein Structure Analysis, 457–64. Boston, MA: Springer US, 1995. http://dx.doi.org/10.1007/978-1-4899-1031-8_41.

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Moayed, Fatemeh, Roeland J. van Wijk, David P. Minde, and Sander J. Tans. "Protein Tethering for Folding Studies." In Single Molecule Analysis, 43–51. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7271-5_3.

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Wang, Chunyu. "Solution NMR Studies of Aβ Monomers and Oligomers." In Protein and Peptide Folding, Misfolding, and Non-Folding, 389–411. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2012. http://dx.doi.org/10.1002/9781118183373.ch13.

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Elam, W. Austin, Travis P. Schrank, and Vincent J. Hilser. "Experimental and Computational Studies of Polyproline II Propensity." In Protein and Peptide Folding, Misfolding, and Non-Folding, 159–85. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2012. http://dx.doi.org/10.1002/9781118183373.ch6.

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Rao, J. Srinivasa, Brigita Urbanc, and Luis Cruz. "Computational Studies of Folding and Assembly of Amyloidogenic Proteins." In Protein and Peptide Folding, Misfolding, and Non-Folding, 479–527. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2012. http://dx.doi.org/10.1002/9781118183373.ch16.

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Dobson, Christopher M. "NMR Studies of Protein Dynamics and Folding." In Protein Structure and Engineering, 193–207. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4684-5745-2_12.

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Baldwin, Robert L. "Experimental Studies of Pathways of Protein Folding." In Ciba Foundation Symposium 161 - Protein Conformation, 190–205. Chichester, UK: John Wiley & Sons, Ltd., 2007. http://dx.doi.org/10.1002/9780470514146.ch12.

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Nienhaus, G. Ulrich. "Single-Molecule Fluorescence Studies of Protein Folding." In Methods in Molecular Biology, 311–37. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-367-7_13.

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Caflisch, Amedeo, and Martin Karplus. "Molecular Dynamics Studies of Protein and Peptide Folding and Unfolding." In The Protein Folding Problem and Tertiary Structure Prediction, 193–230. Boston, MA: Birkhäuser Boston, 1994. http://dx.doi.org/10.1007/978-1-4684-6831-1_7.

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Clarke, David T. "Circular Dichroism and Its Use in Protein-Folding Studies." In Methods in Molecular Biology, 59–72. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-60327-223-0_5.

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Conference papers on the topic "Protein folding studies"

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Truskett, Thomas M. "How Concentration and Crowding Impact Protein Stability: Insights From a Coarse-Grained Model." In ASME 2008 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2008. http://dx.doi.org/10.1115/sbc2008-192239.

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Much of the current understanding of the protein folding problem derives from studies of proteins in dilute solutions. However, in many systems of scientific and engineering interest, proteins must fold in concentrated, heterogeneous environments. Cells are crowded with many molecular species, and chaperones often sequester proteins and promote rapid folding. Proteins are also present in high concentrations in the manufacture, storage, and delivery of biotherapeutics. How does crowding generally affect the stability of the native state? Are all crowding agents created equal? If not, can generic structural or chemical features forecast their effects on protein stability?
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Beechem, Joseph M., Elizabeth A. James, and Ludwig Brand. "Time-resolved fluorescence studies of the protein folding process: new instrumentation, analysis, and experimental approaches." In OE/LASE '90, 14-19 Jan., Los Angeles, CA, edited by Joseph R. Lakowicz. SPIE, 1990. http://dx.doi.org/10.1117/12.17715.

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Gershenson, Anne, Christopher J. Fischer, Joseph A. Schauerte, Duncan G. Steel, and Ari Gafni. "Rapid events in protein folding studied by laser-induced pH and temperature jumps." In BiOS '98 International Biomedical Optics Symposium, edited by Joseph R. Lakowicz and J. B. Alexander Ross. SPIE, 1998. http://dx.doi.org/10.1117/12.307067.

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Piccoli, Vinicius, and Leandro Martínez. "Solvation of different folding states of ubiquitin by EMIMDCA: a study using minimum distance distribution functions." In VIII Simpósio de Estrutura Eletrônica e Dinâmica Molecular. Universidade de Brasília, 2020. http://dx.doi.org/10.21826/viiiseedmol202043.

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Ionic liquids are versatile solvents that have been used in various applications: as green solvents, catalysts, and in biotechnological systems. The optimization of ionic liquids use can be achieved by an understanding of its behavior in chemical systems. Here, the interaction between EMIMDCA and four different folding states of the ubiquitin is studied by the computation of minimum-distance distribution functions from molecular dynamics. In all systems presented here, EMIMDCA solvates the protein preferentially for all types of structures simulated, indicating a denaturation behavior in the presence of ubiquitin. The affinity of EMIMDCA to the protein conformations, with more residues exposed to the solvent, is related to the interactions of the ions with, manly, the apolar residues. Hence, we will show that as the protein structure becomes more open, the interactions between the ions and the protein start to have more influence from the dispersive interaction than the hydrogen bonds.
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Discher, Dennis E., and Colin Johnson. "Alternative Splicing for Mechanical Resilience: The Softening Effect of Filamin’s Hinge." In ASME 2007 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2007. http://dx.doi.org/10.1115/sbc2007-176751.

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Alternative splicing within proteins is common but not well understood in its influence on protein structure and stability. Filamins are ubiquitous actin-crosslinking proteins with two dozen Immunolgobulin (Ig) repeats and one alternatively-spliced ‘hinge’ that has been hypothesized to add flexibility. The hinge is also predicted to perturb folding. The molecular mechanics of filamins are probed here by AFM-forced extension, with a particular focus on the ∼30 aa hinge between repeats R15 and R16. After re-examining full-length filamin to clarify the single molecule limit for AFM experiments on long chains, short concatemers of (R15-R16)m and (R15-hinge-R16)m were studied by both AFM and solution structural methods. AFM shows that the hinged isoform extends and unfolds at smaller forces (60 pN) than the hinge-less form (80 pN), implying that the alternative splicing introduces a random coil that softens both adjacent domains. Circular Dichroism confirms that the hinge is a random coil, and thermal unfolding in solution suggests a weak destabilization by the hinge. Together with the rate-dependence of forced extension in AFM, the results reveal added resilience as the unfolding transition shifts to longer lengths upon insertion of the alternatively spliced hinge.
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Kaufman, Randal J., David G. Bole, and Andrew J. Dorner. "THE INFLUENCE OF N-LINKED GLYCOSYLATION AND BINDING PROTEIN (BiP) ASSOCIATION IN THE SECRETION EFFICIENCY OF COMPLEX GLYCOPROTEINS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644016.

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We have studied the role of Binding Protein (BiP) or glucose regulated protein, GRP 78) in the processing and secretion of factor VIII (fVIII), von Willebrand factor (vWF), and tissue plasminogen activator(tPA) expressed in Chinese hamster ovary cell lines.fVIII is a 300 kDa protein which has a heavily glycosylated internal domain containing 20 clustered potential N-linked glycosylation sites.A significant proportion of the expressed fVIII is bound to BiP in the endoplasmic reticulum (ER) in a stable complex andnever secreted. Deletion of the heavily glycosylatedregion results in a lesser degree of association with BiP and increased secretion. Tunicamycin treatmentof cells producing the deleted form of fVIII resultsin stable association of the unglycosylated fVIII with BiP and inhibition of efficient secretion. vWF contains 17 potential N-linked glycosylation sites which are scattered throughout the molecule. vWF is transiently associated with BiP in the ER, demonstrating that CHO cells are competent to saecrete a complex glycoprotein. tPA, which contains 3 utilized N-linked glycosylation sites, exhibits low level association with BiP and is efficiently secreted. Disruptionof normal N-linked glycosylation of tPA, by site directed mutagenesis of the 3 Asn residues to Gin residues or by tunicamycin treatment of the tPA expressing CHO cells, results in reduced levels of secretion and increased association with BiP. This effect is enhanced by high levels of expression. The findings suggest that occupancy of glycosylation sites may effect protein folding and alter secretion efficiency by influencing the extent and stability of association with BiP.
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Zuo, Lei, Xiaoming Chen, and Ming Lu. "Design and Fabrication of Differential Scanning Nanocalorimeter for Biological Applications." In ASME 2011 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2011. http://dx.doi.org/10.1115/detc2011-48704.

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This paper describes the design, fabrication, and characterization of a differential scanning nanocalorimeter that has potential to significantly reduce the sample volume to microliter and improve the temperature sensitivity to 10 μK. The nanocalorimeter consists of a polymeric freestanding membrane, four high-sensitive low-noise thermistors based on the silicon carbide (SiC), and a platinum heater and temperature sensor. With the integrated heater and sensors, temperature scanning and power compensation can be achieved for calorimetric measurement. Temperature sensing SiC film was prepared by using sintered SiC target and DC magnetron sputtering under different gas pressure and sputtering power. The SiC sensing material is characterized through the measurement of current-voltage curves and noise levels. Thermal performance of a fabricated nanocalorimeter is studied in simulation and experiment. The results indicate the device has a nano watt thermal power sensitivity, 10 μK temperature sensitivity, and long time constant to hold thermal energy, which leads to low-volume ultra sensitive nanocalorimetry for biological process, such as protein folding and ligand binding.
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Mian, Ahsan, Golam Newaz, Lakshmi Vendra, Xin Wu, and Sheng Liu. "Role of Defects on Mechanical Response of Nafion® Membranes for Fuel Cell Applications." In ASME 2004 2nd International Conference on Fuel Cell Science, Engineering and Technology. ASMEDC, 2004. http://dx.doi.org/10.1115/fuelcell2004-2528.

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Nafion® manufactured by Dupont is a widely used membrane material for polymer electrolyte membrane (PEM) fuel cell. Such membranes are made thin and also have to be hydrated during operation to increase proton conductivity of the cell. Since the membranes are made thin, and do not posses high mechanical properties, they are prone to any handling induced damage. In this paper, we have made an initial attempt to demonstrate the capability of thermal wave imaging nondestructive evaluation (NDE) technique in detecting various types of damage entities such as scratches, folding, and pin pricks in the membrane material. In addition, the effect of hydration and handling induced damage on the tensile behavior of Nafion® membrane is studied. It is observed that the damaged and as-received hydrated samples exhibit lower modulus and yield strength than the corresponding dry counterparts.
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Kumar, G. Naga Siva, Sushanta K. Mitra, and Subir Bhattacharjee. "Dielectrophoretic Mixing With Novel Electrode Geometry." In ASME 2009 Fluids Engineering Division Summer Meeting. ASMEDC, 2009. http://dx.doi.org/10.1115/fedsm2009-78260.

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Electrokinetic mixing of analytes at micro-scale is important in several biochemical applications like cell activation, DNA hybridization, protein folding, immunoassays and enzyme reactions. This paper deals with the modeling and numerical simulation of micromixing of two different types of colloidal suspensions based on principle of dielectrophoresis (DEP). A mathematical model is developed based on Laplace, Navier-Stokes, and convection-diffusion-migration equations to calculate electric field, velocity, and concentration distributions, respectively. Mixing of two colloidal suspensions is simulated in a three-dimensional computational domain using finite element analysis considering dielectrophoretic, gravitational and convective (advective)–diffusive forces. Phase shifted AC signal is applied to the alternating electrodes for achieving the mixing of two different colloidal suspensions. The results indicate that the electric field and DEP forces are maximum at the edges of the electrodes and become minimum elsewhere. As compared to curved edges, straight edges of electrodes have lower electric field and DEP forces. The results also indicate that DEP force decays exponentially along the height of the channel. The effect of DEP forces on the concentration profile is studied. It is observed that, the concentration of colloidal particles at the electrodes edges is very less compared to elsewhere. Mixing of two colloidal suspensions due to diffusion is observed at the interface of the two suspensions. The improvement in mixing after applying the repulsive DEP forces on the colloidal suspension is observed. Most of the mixing takes place across the slant edges of the triangular electrodes. The effect of electrode pairs and the mixing length on degree of mixing efficiency are also observed.
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Reports on the topic "Protein folding studies"

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Eliezer, D. Protein folding and protein metallocluster studies using synchrotron small angler X-ray scattering. Office of Scientific and Technical Information (OSTI), June 1994. http://dx.doi.org/10.2172/10194910.

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Chen, Lingling. Studies of protein structure in solution and protein folding using synchrotron small-angle x-ray scattering. Office of Scientific and Technical Information (OSTI), April 1996. http://dx.doi.org/10.2172/510600.

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Bakajin, O. Development of a Fast Microfluidic Mixer for Studies of Protein Folding KineticsFinal Report Cover Page. Office of Scientific and Technical Information (OSTI), February 2005. http://dx.doi.org/10.2172/917494.

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