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Relevant bibliographies by topics / Protein binding

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Academic literature on the topic 'Protein binding'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 August 2024

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Journal articles on the topic "Protein binding"

1

Sawicka, Kirsty, Martin Bushell, Keith A. Spriggs, and Anne E. Willis. "Polypyrimidine-tract-binding protein: a multifunctional RNA-binding protein." Biochemical Society Transactions 36, no. 4 (July 22, 2008): 641–47. http://dx.doi.org/10.1042/bst0360641.

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PTB (polypyrimidine-tract-binding protein) is a ubiquitous RNA-binding protein. It was originally identified as a protein with a role in splicing but it is now known to function in a large number of diverse cellular processes including polyadenylation, mRNA stability and translation initiation. Specificity of PTB function is achieved by a combination of changes in the cellular localization of this protein (its ability to shuttle from the nucleus to the cytoplasm is tightly controlled) and its interaction with additional proteins. These differences in location and trans-acting factor requirements account for the fact that PTB acts both as a suppressor of splicing and an activator of translation. In the latter case, the role of PTB in translation has been studied extensively and it appears that this protein is required for an alternative form of translation initiation that is mediated by a large RNA structural element termed an IRES (internal ribosome entry site) that allows the synthesis of picornaviral proteins and cellular proteins that function to control cell growth and cell death. In the present review, we discuss how PTB regulates these disparate processes.

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Viswanathan, Raji, Eduardo Fajardo, Gabriel Steinberg, Matthew Haller, and Andras Fiser. "Protein—protein binding supersites." PLOS Computational Biology 15, no. 1 (January 7, 2019): e1006704. http://dx.doi.org/10.1371/journal.pcbi.1006704.

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Wilkins, Anna L., Yiming Ye, Wei Yang, Hsiau-Wei Lee, Zhi-ren Liu, and Jenny J. Yang. "Metal-binding studies for a de novo designed calcium-binding protein." Protein Engineering, Design and Selection 15, no. 7 (July 2002): 571–74. http://dx.doi.org/10.1093/protein/15.7.571.

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NAKANO, Akihiko. "Protein Secretion and GTP-binding Proteins." Seibutsu Butsuri 31, no. 2 (1991): 53–57. http://dx.doi.org/10.2142/biophys.31.53.

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Guo, Ting, Yanxin Shi, and Zhirong Sun. "A novel statistical ligand-binding site predictor: application to ATP-binding sites." Protein Engineering, Design and Selection 18, no. 2 (February 1, 2005): 65–70. http://dx.doi.org/10.1093/protein/gzi006.

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Rodilla-Sala, E., G. C. Lunazzi, W. Stremmel, and C. Tiribelli. "BSP-bilirubin binding protein, fatty acid binding protein and bilitranslocase are immunological distinct proteins." Journal of Hepatology 11 (January 1990): S53. http://dx.doi.org/10.1016/0168-8278(90)91545-8.

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Lipovsek, D. "Adnectins: engineered target-binding protein therapeutics." Protein Engineering Design and Selection 24, no. 1-2 (November 10, 2010): 3–9. http://dx.doi.org/10.1093/protein/gzq097.

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Hisatomi, Osamu, Mari Kotoura, Daisuke Kitano, Tatsushi Goto, Akiyuki Hasegawa, Eiri Ono, and Fumio Tokunaga. "1P210 DNA-binding proteins expressed in regenerating newt retina(7. Nucleic acid binding protein,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S199. http://dx.doi.org/10.2142/biophys.46.s199_2.

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Nelson, R. M., and G. L. Long. "Binding of protein S to C4b-binding protein. Mutagenesis of protein S." Journal of Biological Chemistry 267, no. 12 (April 1992): 8140–45. http://dx.doi.org/10.1016/s0021-9258(18)42418-0.

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Fischer, B. E., U. Schlokat, M. Himmelspach, and F. Dorner. "Binding of hirudin to meizothrombin." Protein Engineering Design and Selection 11, no. 8 (August 1, 1998): 715–21. http://dx.doi.org/10.1093/protein/11.8.715.

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Dissertations / Theses on the topic "Protein binding"

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Jones, Marc. "Folate binding protein : partial characterisation of bovine milk folate binding protein, includings its ligand binding /." [St. Lucia, Qld], 2004. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe18263.pdf.

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Zeng, Bin. "Functional characterization of acyl-CoA binding protein (ACBP) and oxysterol binding protein-related proteins (ORPS) from Cryptosporidium parvum." Thesis, [College Station, Tex. : Texas A&M University, 2006. http://hdl.handle.net/1969.1/ETD-TAMU-1211.

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Tse, Muk-hei. "Investigations on recombinant Arabidopsis acyl-coenzyme A binding protein 1." View the Table of Contents & Abstract, 2005. http://sunzi.lib.hku.hk/hkuto/record/B36427664.

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Crombie, Catriona Ann. "Histone hairpin binding protein, an RNA binding protein, essential for development." Thesis, University of Aberdeen, 2003. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU602058.

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Histones are proteins found in the nuclei of eukaryotic cells where they are complexed to DNA in chromatin. Rephcation-dependent histones are expressed only during S-phase. Regulation of expression of replication-dependent histone genes requires a highly conserved hairpin RNA element in the 3' untranslated region of histone mRNAs. Replication-dependent histone mRNAs are not polyadenylated; their 3' end is formed by an endonucleolytic cleavage event, 3' of a hairpin element, which is recognised by the Hairpin Binding Protein, HBP (also known as Stem-Loop Binding Protein, SLBP). This protein-RNA interaction is important for the endonucleolytic cleavage that generates the mature mRNA 3' end. The 3' hairpin, and presumably HBP, are also required for nucleocytoplasmic transport, translation and stability of histone mRNAs. It is therefore important to understand this interaction. The hairpin is highly conserved and I have demonstrated that residues in the hairpin loop are important for binding the HBP. This complimented structural studies that showed that the same residues are involved in stacking interactions in the RNA loop. In cell culture, expression of replication-dependent histone genes is S phase specific as is the expresion of HBP. Here I demonstrated that in Caenorhabditis elegans the HBP promoter is active in dividing cells during embryonic and postembryonic development. Depletion of HBP by RNAi leads to an embryonic lethal phenotype associated with defects in chromosome condensation. Postembryonic depletion of HBP results in defects in cell fate during late larval development, specifically in vulval development. A similar phenotype was obtained when histone H3 and H2A were depleted by RNAi suggesting that the phenotype of the hbp (RNAi) worms was due to a lack of histone proteins. I have confirmed this by showing that histone proteins are indeed reduced in hbp (RNAi) worms. I have also shown that depletion of HBP leads to a change in expression of a number of other proteins and specifically an up-regulation of a histone H3 like protein with an apparent molecular mass of 34 kDa. I have evidence that suggests that this protein is the centromer specific protein, CENP-A. As this protein was up-regulated when RNAi was used to deplete histones proteins, this suggests that there could be a compensatory mechanism that helps the animal to deal with the shortage of histone proteins.

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Prigge, Justin Robert. "Identification and characterization of novel protein-protein interactions with the basal transcription factor, TATA-binding protein." Diss., Montana State University, 2006. http://etd.lib.montana.edu/etd/2006/prigge/PriggeJ0506.pdf.

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Wei, Heng. "Split PH domain identification & redundancy analyses in the classification of PDZ domains /." View abstract or full-text, 2006. http://library.ust.hk/cgi/db/thesis.pl?BICH%202006%20WEI.

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Fang, Lin. "Mechanism of client protein binding by heat shock protein 90 /." view abstract or download file of text, 2006. http://proquest.umi.com/pqdweb?did=1251819301&sid=2&Fmt=2&clientId=11238&RQT=309&VName=PQD.

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Thesis (Ph. D.)--University of Oregon, 2006.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 115-121). Also available for download via the World Wide Web; free to University of Oregon users.

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Ranganathan, Anirudh. "Protein – Ligand Binding: Estimation of Binding Free Energies." Thesis, KTH, Skolan för kemivetenskap (CHE), 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-147527.

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Accurate prediction of binding free energies of protein-ligand system has long been a focus area for theoretical and computational studies; with important implications in fields like pharmaceuticals, enzyme-redesign, etc. The aim of this project was to develop such a predictive model for calculating binding free energies of protein-ligand systems based on the LIE-SASA methods. Many models have been successfully fit to experimental data, but a general predictive model, not reliant on experimental values, would make LIE-SASA a more powerful and widely applicable method. The model was developed such that There is no significant increase in computational time No increase in complexity of system setup No increase in the number of empirical parameters. The method was tested on a small number of protein-ligand systems, selected with certain constraints. This was our training set, from which we obtain the complete expression for binding free energy. Expectedly, there was good agreement with experimental values for the training set On applying our model to a similar sized validation set, with the same selection constraints as for the training set, we achieved even better agreement with experimental results, with lower standard errors. Finally, the model was tested by applying it to a set of systems without such selection constraints, and again found good agreement with experimental values. In terms of accuracy, the model was comparable to a system specific empirical fit that was performed on this set. These encouraging results could be an indicator of generality.

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Gao, Wei, and 高威. "Characterization of protein interactors of Arabidopsis acyl-coenzymea-binding protein 2." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B43223837.

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Chung, Jo-Lan. "Identifying protein-protein binding sites and binding partners using sequence and structure information /." Diss., Connect to a 24 p. preview or request complete full text in PDF formate. Access restricted to UC campuses, 2007. http://wwwlib.umi.com/cr/ucsd/fullcit?p3244170.

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Books on the topic "Protein binding"

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Symposium, Fundación Dr Antonio Esteve. Drug-protein binding. New York: Praeger, 1986.

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Symposium, Esteve Foundation. Drug-protein binding. New York: Praeger, 1985.

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1934-, Reidenberg M. M., and Erill Sergio, eds. Drug-protein binding. New York: Praeger, 1985.

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Colin, Kleanthous, ed. Protein-protein recognition. Oxford: Oxford University Press, 2000.

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Pauls, Thomas Lawrence. Metal-binding properties and cation-dependent conformational changes in rat parvalbumin wild-type and mutant proteins. Konstanz: Hartung-Gorre, 1995.

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Vogel, Hans J. Calcium-Binding Protein Protocols. New Jersey: Humana Press, 2002. http://dx.doi.org/10.1385/1592591833.

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Vogel, Hans J. Calcium-Binding Protein Protocols. New Jersey: Humana Press, 2002. http://dx.doi.org/10.1385/1592591841.

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J, Vogel Hans, ed. Calcium-binding protein protocols. Totowa, NJ: Humana Press, 2002.

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M, Thornton Janet, ed. Atlas of protein side-chain interactions. Oxford: IRL Press at Oxford University Press, 1992.

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Singh, Juswinder. Atlas of protein side-chain interactions. Oxford: IRL Press at Oxford University Press, 1992.

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Book chapters on the topic "Protein binding"

1

Kangueane, Pandjassarame, and Christina Nilofer. "Protein-Protein Binding." In Protein-Protein and Domain-Domain Interactions, 15–33. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-10-7347-2_2.

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Nahler, Gerhard. "protein binding." In Dictionary of Pharmaceutical Medicine, 149. Vienna: Springer Vienna, 2009. http://dx.doi.org/10.1007/978-3-211-89836-9_1151.

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Sparreboom, Alex, and Walter J. Loos. "Protein Binding." In Cancer Drug Discovery and Development, 209–27. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-9135-4_13.

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Mohler, Marjorie A., Jennifer E. Cook, and Gerhard Baumann. "Binding Proteins of Protein Therapeutics." In Pharmaceutical Biotechnology, 35–71. Boston, MA: Springer US, 1992. http://dx.doi.org/10.1007/978-1-4899-2329-5_2.

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Evtushenko, Vladimir I. "Protein Binding Matrices." In Manufacturing of Gene Therapeutics, 99–133. Boston, MA: Springer US, 2002. http://dx.doi.org/10.1007/978-1-4615-1353-7_6.

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McAllister-Williams, R. Hamish, Daniel Bertrand, Hans Rollema, Raymond S. Hurst, Linda P. Spear, Tim C. Kirkham, Thomas Steckler, et al. "Protein-Binding Microarray." In Encyclopedia of Psychopharmacology, 1075. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-540-68706-1_4483.

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Shoff, William H., Catherine T. Shoff, Suzanne M. Shepherd, Jonathan L. Burstein, Calvin A. Brown, Ashita J. Tolwani, Bala Venkatesh, et al. "Retinol-Binding Protein." In Encyclopedia of Intensive Care Medicine, 1999. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-00418-6_2154.

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Ward, Tony Milford. "Retinol Binding Protein." In Proteins and Tumour Markers May 1995, 1366–68. Dordrecht: Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-0681-8_74.

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Penalva, Luiz O. F. "RNA-binding Protein." In Encyclopedia of Systems Biology, 1875–76. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_313.

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Schumann, R. R., and E. Latz. "Lipopolysaccharide-Binding Protein." In CD14 in the Inflammatory Response, 42–60. Basel: KARGER, 1999. http://dx.doi.org/10.1159/000058760.

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Conference papers on the topic "Protein binding"

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Walker, F. J. "REGULATION OF THE ANTICOAGULANT ACTIVITY OF ACTIVATED PROTEIN C BY PROTEIN S AND PROTEIN S BINDING PROTEIN." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642964.

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Protein S is a vitamin K-dependent protein that acts as a cofactor for the anticoagulant activity of activated protein C both in the proteolytic inactivation of factor V and VIII. Protein S is a single chain protein with a molecular weight of approximately 62 kDa. When the molecular weight of protein S in plasma was determined it was found to be much larger than the single chain protein. The molecular weight of functional protein S when measured by sedimentation equilibrium with the air-driven ultracentrifuge was observed to be between 115 and 130 kDa. In high salt or in the presence of copper ions this was observed to be reduced to approximately 62 kDa. Frontal analysis of plasma indicated that the functional protein by exist in as many as three molecular weight foras. Gel filtration of radiolabeled protein S also indicates heterogeneity in the molecular weight. In order to isolate the binding protein, bovine plasma was fractionated first on a column of immobilized iminodiacetic acid that had been equilibrated with copper ions. The proteins that eluted in the 0.6 M NaCl wash were passed over a column of protein S immobilized on agarose beads. A single protein was observed to elute from the protein S agarose at high salt. Fractionation of human plasma indicated the presence of several proteins. One major component isolated was C4-binding protein. A second major component has also been isolated that appears to correspond to protein S-binding protein that has been isolated from bovine plasma. When added to plasma depleted of both protein S and the binding protein, the binding protein was observed to enhance the anticoagulant activity of activated protein C only in the presence of protein S. Protein S-binding protein was also observed to enhance the rate of factor Va inactivation by activated protein C and protein S.

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Suzuki, K., J. Nishioka, H. Kusumoto, and Y. Deyashiki. "BINDING SITE OF VITAMIN K-DEPENDENT PROTEIN S ON C4b-BINDING PROTEIN." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644637.

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Protein S, a cofactor for activated protein C, reversibly complexes with a regulatory complement component C4b-binding protein (C4bp) in plasma. In plasma of patients with congenital protein S deficiency, most protein S exists as a complex with C4bp, which has no cofactor activity. C4bp (Mw 550,000) is composed of approximately seven subunits with Mw 75,000 which are linked by disulfide bonds near the carboxy1-terminus. We report here about the complex formation between protein S and C4bp particularly on the binding site of protein S on C4bp molecule. Protein S and C4bp were purified from human plasma. Seventeen mouse monoclonal antibodies against C4bp were prepared. Chymotrypsin-digested C4bp was separated on gel filtration into a fragment with Mw 160,000 derived from the carboxyl-terminal core of the intact C4bp and fragments with Mw 48,000 from the amino-terminus. The carboxy1-terminal fragment with Mw 160,000 was found to be composed of approximately seven polypeptides with Mw 25,000, which were linked by disulfide bonds.The experiments using these fragments and the monoclonal antibodies showed that: (1) Protein S bound not only to the intact C4bp, but also to the fragment with Mw 160,000. (2) The fragment with Mw 160,000 inhibited the binding of protein S to C4bp, but the fragment with Mw 48,000 did not. (3) One of the seventeen monoclonal antibodies blocked the inhibition of C4bp on the cofactor activity of protein S. (4) This antibody inhibited C4bp binding to protein S. (5) The antibody bound to the fragment with Mw 160,000. Based on these results, protein S was suggested to lose its cofactor activity for activated protein C by binding to the carboxyl-terminal core of C4bp where seven subunits are linked by disulfide bonds.

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Malm, J., R. Bennhagen, L. Holmberg, and B. Dahlbäck. "LOW PLASMA CONCENTRATIONS OF C4b-BINDING PROTEIN AND VITAMIN K-DEPENDENT PROTEIN S IN PRETERM INFANTS WITH DECREASED FORMATION OF PROTEIN S-C4b-BINDING PROTEIN COMPLEXES." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644265.

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Protein S is a vitamin K-dependent plasmaprotein functioning as a non-enzymatic cofactor to the activated form of protein C in the degradation of coagulationfactors Va and VIIa. In the circulation approximately 60% of protein S is complexed to the complement protein C4b-binding protein (C4BP). Only the remaining, free fraction exhibits protein Ca cofactor activity.The plasma concentrations of protein S and C4BP were determined in 25 term and 26 preterm infants. Both proteins werequantified with radioimmunoassays. The free, functionally active form of proteinS and the total protein S concentration were determined separately. The level ofC4BP in preterm infants was found to be very low (mean 6% of the adult level). In term infants the level had increased to a mean of 18%. Also the total concentration of protein S was decreased in preterm as well as in term infants; 18% and 31% of the adult level, respectively. Free protein S was the predominant form in plasma representing 83 % of total protein S in preterm and 68 % in term infants. This was probably due to the very low C4BP levels. In adult controls the corresponding value was 34%. The plasma concentration of free protein S in preterm and term infants, when compared to the adult level, was 44% and 66%, respectively. These results demonstrate that although the total protein S concentration in preterm and term infants was very low when compared to adult levels, the difference in the concentration of free, functionally active protein S between infants and adults was less pronounced.

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SANDER, OLIVER, FRANCISCO S. DOMINGUES, HONGBO ZHU, THOMAS LENGAUER, and INGOLF SOMMER. "STRUCTURAL DESCRIPTORS OF PROTEIN-PROTEIN BINDING SITES." In The 6th Asia-Pacific Bioinformatics Conference. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2007. http://dx.doi.org/10.1142/9781848161092_0011.

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Lapetina, Eduardo G., Bryan R. Reep, and Luis Molina Y. Vedia. "NOVEL GTP-BINDING PROTEINS OF CYTOSOLIC AND MEMBRANE FRACTIONS OF HUMAN PLATELETS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644629.

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We have assessed the binding of (α-32P)GTP to platelet proteins from cytosolic and membrane fractions. Proteins were separated by SDS-PAGE and electrophoretically transferred to nitrocellulose. Incubation of the nitrocellulose blots with (α-32p)GTP indicated the presence of specific and distinct GTP-binding proteins in cytosol and membranes. Binding was prevented by 10-100 nM GTP or GTPyS and by 100 nM GDP; binding was unaffected by 1 nM-1 μM ATP. One main GTP-binding protein (29.5 KDa) was detected in the membrane fraction while three others (29, 27, and 21 KDa) were detected in the soluble fraction. Two cytosolic GTP-binding proteins (29 and 27 KDa) were degraded by trypsin; another cytosolic protein (21 KDa) and the membrane-bound protein (29.5 KDa) were resistant to the action of trypsin. Treatment of intact platelets with trypsin or thrombin, followed by lysis and fractionation, did not affect the binding of (α-32P)GTP to the membrane-bound protein. GTPyS still stimulates phospholipase C in permeabilized platelets already preincubated with trypsin. This suggests that trypsin-resistant GTP-binding proteins might regulate phospholipase C stimulated by GTPyS. We have started to purify the membrane-bound, trypsin-resistant, GTP-binding protein. Purification includes 1 M NaCl extraction and the use of an FPLC system with successive phenyl superose and superose 12 columns.

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Timmons, Sheila, and Jack Hawiger. "REGULATION OF PLATELET RECEPTORS FOR FIBRINOGEN AND VON WILLEBRAND FACTOR BY PROTEIN KINASE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644674.

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Positive and negative regulation of platelet receptors for adhesive proteins, fibrinogen (F) and von Willebrand Factor (vWF) determines whether binding of these ligands will or will not take place. We have shown previously that ADP stimulates and cyclic AMP inhibits binding of F and vWF to human platelets. Now we show that positive regulation of F and vWF binding to platelets via the glycoprotein 11b/1111a complex is dependent on platelet Protein Kinase C, a calcium- and phospholipid-dependent enzyme. A potent activator of Protein Kinase C, phorbol-12-myristoyl-13-acetate (PMA) induced saturable and specific binding of F and vWF which was inhibited by synthetic peptides, gamma chain .dodecapeptide (gamma 400-411) and RGDS. The phosphorylation of 47kDa protein (P47), a marker of Protein Kinase C activation in platelets, preceded binding of F and vWF induced with PMA as well as with ADP and thrombin. Sphingosine, an inhibitor of Protein Kinase C, blocked binding of F and vWF to platelets stimulated with PMA, ADP, and thrombin. Inhibition of binding was concentration-dependent and it was accompanied by inhibition of platelet aggregation. Thus, stimulation of Protein Kinase C is required for exposure of platelet receptors for adhesive proteins whereas inhibition of Protein Kinase C prevents receptorexposure. Protein Kinase C fulfills the role of an intraplatelet signal transducer, regulating receptors for adhesive proteins, and constitutes a target for pharmacologic modulation of the adhesive interactions of platelets.

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Melissari, E., M. F. Scully, C. Parker, K. H. Nicolaides, and V. V. Kakkar. "PROTEIN C/PROTEIN S IN THE FOETAL BLOOD. ABSENCE OF BOUND PROTEINS AND C4 BINDING PROTEIN." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644290.

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Protein C, free and bound protein S and C4 binding protein levels (C4bp), were measured by electroimmunoassay in 7 pregnant women aged 22-29 years at 16-18 weeks of gestation, immediately prior to termination of pregnancy for social reasons. Protein C and protein S levels were also measured in their foetuses from blood taken through the umbilical cord. In this group of pregnant women the mean levels for protein C were 104% of normal adult mean (range 80-128%), for C4bp 100% (52-150%), for free protein S 66% (43-89%). In the foetuses the mean value for protein C was 15.3% (10.5-21%) and for free protein S 36.85% (27-47%) of the normal adult mean. Bound protein S and C4bp levels were zero. Conclusions: (1) free protein S is significantly decreased (< 2SD below the normal adult mean) in women after the first trimester of gestation whereas no change is seen in protein C concentration; (2) C4bp levels are at zero in the foetus as also are the levels of bound protein S; (3) foetal blood protein S level is approximately 2.5 times higher than protein C. Since all other vitamin K-dependent factors have been observed to be in the range of 10-20% of normal at this stage of gestation, our findings may be further proof of a non hepatic (endothelial) source of plasma protein S.

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Dahiback, Bjorn, Ake Lundwall, Andreas Hillarp, Johan Malm, and Johan Stenflo. "STRUCTURE AND FUNCTION OF VITAMIN K-DEPENDENT PROTEIN S, a cofactor to activated protein C which also interacts with the complement protein C4b-binding protein." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642960.

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Protein S is a single chain (Mr 75.000) plasma protein. It is a cofactor to activated protein C (APC) in the regulation of coagulation factors Va and Villa. It has high affinity for negatively charged phospolipids and it forms a 1:1 complex with APC on phospholipid surfaces, platelets and on endothelial cells. Patients with heterozygous protein S deficiency have a high incidence of thrombosis. Protein S is cleaved by thrombin, which leads to a loss of calcium binding sites and of APC cofactor activity. Protein S has two to three high affinity (KD 20uM) calcium binding sites - unrelated to the Gla-region - that are unaffected by the thrombin cleavage. In human plasma protein S (25 mg/liter) circulates in two forms; free (approx. 40%) and in a 1:1 noncovalent complex (KD 1× 10-7M) with the complement protein C4b-binding protein (C4BP). C4BP (Mr 570.000) is composed of seven identical 70 kDa subunits that are linked by disulfide bonds. When visualized by electron microscopy, C4BP has a spiderlike structure with the single protein S binding site located close to the central core and one C4b-binding site on each of the seven tentacles. When bound to C4BP, protein S looses its APC cofactor activity, whereas the function-of C4BP is not directly affected by the protein S binding. Chymotrypsin cleaves each of the seven C4BP subunits close to the central core which results in the liberation of multiple 48 kDa “tentacte” fragments and the formation of a 160 kDa central core fragment. We have successfully isolated a 160 kDa central core fragment with essentially intact protein S binding ability.The primary structure of both bovine and human protein S has been determined and found to contain 635 and 634 amino acids, respectively, with 82 % homology to each other. Four different regions were distinguished; the N-terminal Gla-domain (position 1-45) was followed by a region which has two thrombin-sensitive bonds positioned within a disulfide loop. Position 76 to 244 was occupied by four repeats homologous to the epidermal growth factor (EGF) precursor. In the first EGF-domain a modified aspartic acid was identified at position 95, B-hydroxaspartic acid (Hya), and in corresponding positions in the three following EGF-domains (positions 136,178 and 217) we found B-hydroxyasparagine (Hyn). Hyn has not previously been identified in proteins. The C-terminal half of protein S (from position 245) shows no homology to the serine proteases but instead to human Sexual Hormon Binding Globulin (SHBG)(see separate abstract). To study the structure-function relationship we made eighteen monoclonal antibodies to human protein S. The effects of the monoclonals on the C4BP-protein S interaction and on the APC cofactor activity were analysed. Eight of the antibodies were calciumdependent, four of these were against the Gla-domain, two against the thrombin sensitive portion and two against the region bearing the high affinity calcium binding sites. Three of the monoclonals were dependent on the presence of chelating agents, EDTA or EGTA, and were probably directed against the high affinity calcium binding region. Three other monoclonals inhibited the protein S-C4BP interaction. At present, efforts are made to localize the epitopes to gain information about functionally important regions of protein S.

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Buddi, S. P., and T. Taylor. "Estimation of Protein-Ligand Binding Affinity from Protein Microarrays." In IASTED Technology Conferences 2010. Calgary,AB,Canada: ACTAPRESS, 2010. http://dx.doi.org/10.2316/p.2010.728-026.

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Konc, Janez, and Dušanka Janežič. "Algorithms and web servers for protein binding sites detection in drug discovery." In 2nd International Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.014k.

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Drug discovery is a protracted and demanding process, which can be expedited during its early stages through novel mathematical approaches and modern computing. To tackle this crucial issue, we are developing fresh mathematical solutions aimed at detecting and characterizing protein binding sites, pivotal for new drug discovery. This paper introduces algorithms founded on graph theory which we have devised to scrutinize target biological proteins. These algorithms yield vital data, facilitating the optimization of initial phases in novel drug development. A particular emphasis lies in the creation of pioneering protein binding site prediction algorithms (ProBiS) and innovative web tools for modeling pharmaceutically intriguing molecules—ProBiS tools. These tools have matured into comprehensive graphical resources for the study of proteins in the proteome. ProBiS stands apart from other structural algorithms due to its ability to align proteins with disparate folds, all without prior knowledge of the binding sites. This unique capability enables the identification of analogous binding sites and the prediction of molecular ligands of diverse pharmaceutical relevance. These ligands could potentially progress into drug candidates for treating diseases. Notably, this prediction is based on data sourced from the complete Protein Data Bank (PDB) and the AlphaFold database, encompassing proteins not yet cataloged in the PDB. All ProBiS tools are made available without charge to the academic community through http://insilab.org and https://probis.nih.gov.

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Reports on the topic "Protein binding"

1

Hanke, Andreas. DNA Conforming Dynamics and Protein Binding. Fort Belvoir, VA: Defense Technical Information Center, December 2006. http://dx.doi.org/10.21236/ada461014.

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Chamovitz, Daniel A., and Zhenbiao Yang. Chemical Genetics of the COP9 Signalosome: Identification of Novel Regulators of Plant Development. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7699844.bard.

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This was an exploratory one-year study to identify chemical regulators of the COP9 signalosome. Chemical Genetics uses small molecules to modify or disrupt the function of specific genes/proteins. This is in contrast to classical genetics, in which mutations disrupt the function of genes. The underlying concept is that the functions of most proteins can be altered by the binding of a chemical, which can be found by screening large libraries for compounds that specifically affect a biological, molecular or biochemical process. In addition to screens for chemicals which inhibit specific biological processes, chemical genetics can also be employed to find inhibitors of specific protein-protein interactions. Small molecules altering protein-protein interactions are valuable tools in probing protein-protein interactions. In this project, we aimed to identify chemicals that disrupt the COP9 signalosome. The CSN is an evolutionarily conserved eight-subunit protein complex whose most studied role is regulation of E3 ubiquitinligase activity. Mutants in subunits of the CSN undergo photomorphogenesis in darkness and accumulate high levels of pigments in both dark- and light-grown seedlings, and are defective in a wide range of important developmental and environmental-response pathways. Our working hypothesis was that specific molecules will interact with the CSN7 protein such that binding to its various interacting proteins will be inhibited. Such a molecule would inhibit either CSN assembly, or binding of CSN-interacting proteins, and thus specifically inhibit CSN function. We used an advanced chemical genetic screen for small-molecule-inhibitors of CSN7 protein-protein interactions. In our pilot study, following the screening of ~1200 unique compounds, we isolated four chemicals which reproducibly interfere with CSN7 binding to either CSN8 or CSN6.

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Willmert, Leslie J. Cellular Retinoic Acid Binding Protein and Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, May 2005. http://dx.doi.org/10.21236/ada437738.

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Clarke, Robert. X-Box Binding Protein-1 in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, August 2005. http://dx.doi.org/10.21236/ada446755.

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Donato, Leslie J. Cellular Retinoic Acid Binding Protein and Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, May 2006. http://dx.doi.org/10.21236/ada455778.

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Clarke, Robert R. X-Box Binding Protein-1 in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, August 2004. http://dx.doi.org/10.21236/ada433869.

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Clarke, Robert R. X-Box Binding Protein-1 in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, August 2003. http://dx.doi.org/10.21236/ada421992.

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Willmert, Leslie J. Cellular Retinoic Acid Binding Protein and Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, May 2004. http://dx.doi.org/10.21236/ada425991.

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Clarke, Robert. X-Box Binding Protein-1 in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, August 2006. http://dx.doi.org/10.21236/ada460787.

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Yaswen, Paul. Functional Analysis of BORIS, A Novel DNA Binding Protein. Fort Belvoir, VA: Defense Technical Information Center, April 2006. http://dx.doi.org/10.21236/ada448330.

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