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Kissmann AK, Bolotnikov G, Li R, Müller F, Xing H, Krämer M, Gottschalk KE, Andersson J, Weil T, Rosenau F. IMPATIENT-qPCR: monitoring SELEX success during in vitro aptamer evolution. Appl Microbiol Biotechnol 2024; 108:284. [PMID: 38573322 PMCID: PMC10995058 DOI: 10.1007/s00253-024-13085-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/07/2024] [Accepted: 02/19/2024] [Indexed: 04/05/2024]
Abstract
SELEX (Systematic Evolution of Ligands by Exponential enrichment) processes aim on the evolution of high-affinity aptamers as binding entities in diagnostics and biosensing. Aptamers can represent game-changers as constituents of diagnostic assays for the management of instantly occurring infectious diseases or other health threats. Without in-process quality control measures SELEX suffers from low overall success rates. We present a quantitative PCR method for fast and easy quantification of aptamers bound to their targets. Simultaneous determination of melting temperatures (Tm) of each SELEX round delivers information on the evolutionary success via the correlation of increasing GC content and Tm alone with a round-wise increase of aptamer affinity to the respective target. Based on nine successful and published previous SELEX processes, in which the evolution/selection of aptamer affinity/specificity was demonstrated, we here show the functionality of the IMPATIENT-qPCR for polyclonal aptamer libraries and resulting individual aptamers. Based on the ease of this new evolution quality control, we hope to introduce it as a valuable tool to accelerate SELEX processes in general. IMPATIENT-qPCR SELEX success monitoring. Selection and evolution of high-affinity aptamers using SELEX technology with direct aptamer evolution monitoring using melting curve shifting analyses to higher Tm by quantitative PCR with fluorescence dye SYBR Green I. KEY POINTS: • Fast and easy analysis. • Universal applicability shown for a series of real successful projects.
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Affiliation(s)
- Ann-Kathrin Kissmann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128, Mainz, Germany
| | - Grigory Bolotnikov
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Runliu Li
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Franziska Müller
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Hu Xing
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Markus Krämer
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Kay-E Gottschalk
- Institute of Experimental Physics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Jakob Andersson
- AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210, Vienna, Austria
| | - Tanja Weil
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128, Mainz, Germany
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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Hageb A, Thalheim T, Nattamai KJ, Möhrle B, Saçma M, Sakk V, Thielecke L, Cornils K, Grandy C, Port F, Gottschalk KE, Mallm JP, Glauche I, Galle J, Mulaw MA, Geiger H. Reduced adhesion of aged intestinal stem cells contributes to an accelerated clonal drift. Life Sci Alliance 2022; 5:5/8/e202201408. [PMID: 35487692 PMCID: PMC9057243 DOI: 10.26508/lsa.202201408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022] Open
Abstract
Analysis of clonal dynamics of intestinal stem cells supports an accelerated clonal drift upon aging, likely because of reduced adhesion of aged ISCs because of reduced canonical Wnt signaling. Upon aging, the function of the intestinal epithelium declines with a concomitant increase in aging-related diseases. ISCs play an important role in this process. It is known that ISC clonal dynamics follow a neutral drift model. However, it is not clear whether the drift model is still valid in aged ISCs. Tracking of clonal dynamics by clonal tracing revealed that aged crypts drift into monoclonality substantially faster than young ones. However, ISC tracing experiments, in vivo and ex vivo, implied a similar clonal expansion ability of both young and aged ISCs. Single-cell RNA sequencing for 1,920 high Lgr5 ISCs from young and aged mice revealed increased heterogeneity among subgroups of aged ISCs. Genes associated with cell adhesion were down-regulated in aged ISCs. ISCs of aged mice indeed show weaker adhesion to the matrix. Simulations applying a single cell–based model of the small intestinal crypt demonstrated an accelerated clonal drift at reduced adhesion strength, implying a central role for reduced adhesion for affecting clonal dynamics upon aging.
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Affiliation(s)
- Ali Hageb
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Torsten Thalheim
- Interdisciplinary Centre for Bioinformatics, University Leipzig, Leipzig, Germany
| | - Kalpana J Nattamai
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA
| | - Bettina Möhrle
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Mehmet Saçma
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Vadim Sakk
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Lars Thielecke
- Institute for Medical Informatics and Biometry, Technische Universität Dresden, Dresden, Germany
| | - Kerstin Cornils
- Clinic of Pediatric Hematology and Oncology, Division of Pediatric Stem Cell Transplantation and Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Carolin Grandy
- Institute for Experimental Physics, Ulm University, Ulm, Germany
| | - Fabian Port
- Institute for Experimental Physics, Ulm University, Ulm, Germany
| | - Kay-E Gottschalk
- Institute for Experimental Physics, Ulm University, Ulm, Germany
| | - Jan-Philipp Mallm
- Division of Chromatin Networks, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry, Technische Universität Dresden, Dresden, Germany
| | - Jörg Galle
- Interdisciplinary Centre for Bioinformatics, University Leipzig, Leipzig, Germany
| | - Medhanie A Mulaw
- Central Unit Single Cell Sequencing, Medical Faculty, Ulm University, Ulm, Germany
| | - Hartmut Geiger
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
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Khalaji S, Zondler L, KleinJan F, Nolte U, Mulaw MA, Danzer KM, Weishaupt JH, Gottschalk KE. Age Increases Monocyte Adhesion on Collagen. Sci Rep 2017; 7:46532. [PMID: 28513618 PMCID: PMC5434452 DOI: 10.1038/srep46532] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 03/16/2017] [Indexed: 01/17/2023] Open
Abstract
Adhesion of monocytes to micro-injuries on arterial walls is an important early step in the occurrence and development of degenerative atherosclerotic lesions. At these injuries, collagen is exposed to the blood stream. We are interested whether age influences monocyte adhesion to collagen under flow, and hence influences the susceptibility to arteriosclerotic lesions. Therefore, we studied adhesion and rolling of human peripheral blood monocytes from old and young individuals on collagen type I coated surface under shear flow. We find that firm adhesion of monocytes to collagen type I is elevated in old individuals. Pre-stimulation by lipopolysaccharide increases the firm adhesion of monocytes homogeneously in older individuals, but heterogeneously in young individuals. Blocking integrin αx showed that adhesion of monocytes to collagen type I is specific to the main collagen binding integrin αxβ2. Surprisingly, we find no significant age-dependent difference in gene expression of integrin αx or integrin β2. However, if all integrins are activated from the outside, no differences exist between the age groups. Altered integrin activation therefore causes the increased adhesion. Our results show that the basal increase in integrin activation in monocytes from old individuals increases monocyte adhesion to collagen and therefore the risk for arteriosclerotic plaques.
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Affiliation(s)
- Samira Khalaji
- Institute for Experimental Physics, Ulm University, Ulm, Germany
| | - Lisa Zondler
- Department of Neurology, Ulm University, Ulm, Germany
| | - Fenneke KleinJan
- Institute for Experimental Physics, Ulm University, Ulm, Germany
| | - Ulla Nolte
- Institute for Experimental Physics, Ulm University, Ulm, Germany
| | - Medhanie A Mulaw
- Institute for Experimental Cancer Research, Ulm University, Ulm, Germany
| | | | | | - Kay-E Gottschalk
- Institute for Experimental Physics, Ulm University, Ulm, Germany
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4
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Brandt S, Krauel K, Gottschalk KE, Renné T, Helm CA, Greinacher A, Block S. Characterisation of the conformational changes in platelet factor 4 induced by polyanions: towards in vitro prediction of antigenicity. Thromb Haemost 2014; 112:53-64. [PMID: 24671506 DOI: 10.1160/th13-08-0634] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 01/20/2014] [Indexed: 11/05/2022]
Abstract
Heparin-induced thrombocytopenia (HIT) is the most frequent drug-induced immune reaction affecting blood cells. Its antigen is formed when the chemokine platelet factor 4 (PF4) complexes with polyanions. By assessing polyanions of varying length and degree of sulfation using immunoassay and circular dichroism (CD)-spectroscopy, we show that PF4 structural changes resulting in antiparallel β-sheet content >30% make PF4/polyanion complexes antigenic. Further, we found that polyphosphates (polyP-55) induce antigenic changes on PF4, whereas fondaparinux does not. We provide a model suggesting that conformational changes exposing antigens on PF4/polyanion complexes occur in the hairpin involving AA 32-38, which form together with C-terminal AA (66-70) of the adjacent PF4 monomer a continuous patch on the PF4 tetramer surface, explaining why only tetrameric PF4 molecules express "HIT antigens". The correlation of antibody binding in immunoassays with PF4 structural changes provides the intriguing possibility that CD-spectroscopy could become the first antibody-independent, in vitro method to predict potential immunogenicity of drugs. CD-spectroscopy could identify compounds during preclinical drug development that induce PF4 structural changes correlated with antigenicity. The clinical relevance can then be specifically addressed during clinical trials. Whether these findings can be transferred to other endogenous proteins requires further studies.
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Affiliation(s)
| | | | | | | | | | - A Greinacher
- Prof. Dr. med. Andreas Greinacher, Institut für Immunologie und Transfusionsmedizin, Sauerbruchstrasse, 17475 Greifswald, Germany, Tel.: +49 3834 865482, Fax: +49 3834 865489, E-mail:
| | - S Block
- Stephan Block, PhD, Applied Physics, Chalmers University of Technology, Fysikgränd 3, S-412 96 Gothenburg, Sweden, E-mail: ,
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Schiller HB, Hermann MR, Polleux J, Vignaud T, Zanivan S, Friedel CC, Sun Z, Raducanu A, Gottschalk KE, Théry M, Mann M, Fässler R. β1- and αv-class integrins cooperate to regulate myosin II during rigidity sensing of fibronectin-based microenvironments. Nat Cell Biol 2013; 15:625-36. [PMID: 23708002 DOI: 10.1038/ncb2747] [Citation(s) in RCA: 324] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 04/04/2013] [Indexed: 12/14/2022]
Abstract
How different integrins that bind to the same type of extracellular matrix protein mediate specific functions is unclear. We report the functional analysis of β1- and αv-class integrins expressed in pan-integrin-null fibroblasts seeded on fibronectin. Reconstitution with β1-class integrins promotes myosin-II-independent formation of small peripheral adhesions and cell protrusions, whereas expression of αv-class integrins induces the formation of large focal adhesions. Co-expression of both integrin classes leads to full myosin activation and traction-force development on stiff fibronectin-coated substrates, with αv-class integrins accumulating in adhesion areas exposed to high traction forces. Quantitative proteomics linked αv-class integrins to a GEF-H1-RhoA pathway coupled to the formin mDia1 but not myosin II, and α5β1 integrins to a RhoA-Rock-myosin II pathway. Our study assigns specific functions to distinct fibronectin-binding integrins, demonstrating that α5β1integrins accomplish force generation, whereas αv-class integrins mediate the structural adaptations to forces, which cooperatively enable cells to sense the rigidity of fibronectin-based microenvironments.
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Affiliation(s)
- Herbert B Schiller
- Department of Molecular Medicine, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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6
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Morfill J, Blank K, Zahnd C, Luginbühl B, Kühner F, Gottschalk KE, Plückthun A, Gaub HE. Affinity-matured recombinant antibody fragments analyzed by single-molecule force spectroscopy. Biophys J 2007; 93:3583-90. [PMID: 17675348 PMCID: PMC2072072 DOI: 10.1529/biophysj.107.112532] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
For many applications, antibodies need to be engineered toward maximum affinity. Strategies are in demand to especially optimize this process toward slower dissociation rates, which correlate with the (un)binding forces. Using single-molecule force spectroscopy, we have characterized three variants of a recombinant antibody single-chain Fv fragment. These variants were taken from different steps of an affinity maturation process. Therefore, they are closely related and differ from each other by a few mutations only. The dissociation rates determined with the atomic force microscope differ by one order of magnitude and agree well with the values obtained from surface plasmon resonance measurements. However, the effective potential width of the binding complexes, which was derived from the dynamic force spectroscopy measurements, was found to be the same for the different mutants. The large potential width of 0.9 nm indicates that both the binding pocket and the peptide deform significantly during the unbinding process.
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Affiliation(s)
- Julia Morfill
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany.
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Abstract
The recently reported crystal structures of the extracellular domains of the alphavbeta3 integrin in its unligated state and in complex with the peptide cyclo(-RGDf[NMe]V-) have dramatically increased our understanding of ligand binding to integrins. Nonetheless, ligand selectivity toward different integrin subtypes is still a challenging problem complicated by the fact that 3D structures of most of the integrin subtypes remain unknown. In this study, a three-dimensional model for the human alphavbeta5 integrin was obtained using homology modeling based on the crystal coordinates of alphavbeta3 in its bound conformation as template. The modeled receptor was refined using energy minimization and molecular dynamics simulations in explicit solvent. The refined alphavbeta5 model was used to explore the interactions between this integrin and alphavbeta3/alphavbeta5 dual and alphavbeta3-selective ligands in the attempt to provide a preliminary rationalization, at the molecular level, of ligand selectivity toward the two alphav integrins. It was found that, in the RGD binding site of the alphavbeta5 receptor, a partial "roof" composed mainly of the SDL residues Tyr179 and Lys180 is present and hampers the binding of compounds containing bulky substituents in the proximity of the carboxylate group. This study provides a testable hypothesis for alphav integrins subtype ligand binding selectivity, in line with both mutagenesis data and SARs studies.
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Affiliation(s)
- Luciana Marinelli
- Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli "Federico II", Via D. Montesano, 49-80131 Napoli, Italy
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8
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Marinelli L, Lavecchia A, Gottschalk KE, Novellino E, Kessler H. Docking studies on alphavbeta3 integrin ligands: pharmacophore refinement and implications for drug design. J Med Chem 2003; 46:4393-404. [PMID: 14521404 DOI: 10.1021/jm020577m] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Starting from the first crystal structure of the extracellular segment of the alpha(v)beta(3) integrin receptor with a cyclic RGD ligand bound to the active site, structural models for the interactions of known ligands with the alpha(v)beta(3) integrin receptor were generated by automated computational docking. The obtained complexes were evaluated for their consistency with structure-activity relationships and site-directed mutagenesis data. A comparison between the calculated interaction free energies and the experimental biological activities was also made. All the possible interactions of the investigated compounds at the active site and the probable ligand binding conformations provide an improved basis for structure-based rational ligand design. Additionally, our docking results allow a further validation and refinement of the pharmacophore model previously postulated by us.
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Affiliation(s)
- Luciana Marinelli
- Institut für Organische Chemie und Biochemie, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
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9
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Abstract
Integrins are pivotal proteins in cell-cell adhesion, signaling and apoptosis. These properties render them attractive targets for drugs, especially those involved in cancer treatment. Recently, the structures of the extracellular domains of one of the integrin subtypes was solved with X-ray crystallography in the free form as well as bound to a ligand. These structures in combination with NMR spectroscopic data, electron microscopy images, and molecular modeling provide deeper insight into the mechanism of integrin-mediated signal transduction. The structures make structure-based rational drug design possible and are certainly hallmarks in integrin research.
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Affiliation(s)
- Kay-E Gottschalk
- Institut für Organische Chemie und Biochemie, Technische Universität München, Germany
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10
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Eastman MA, Pedersen LG, Hiskey RG, Pique M, Koehler KA, Gottschalk KE, Némethy G, Scheraga HA. Conformation of the 18-23 loop region of bovine prothrombin in the absence and presence of a model Ca2+ ion. An energy minimization study. Int J Pept Protein Res 1986; 27:530-53. [PMID: 3733321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The conformation of the cyclic peptide Ac-Cys-Leu-Gla-Gla-Pro-Cys-NHMe, representing the 18-23 disulfide loop of bovine prothrombin, was studied by energy minimization with the ECEPP (Empirical Conformational Energy Program for Peptides) algorithm. Parameters for charge and geometry for the gamma-carboxyglutamic acid (Gla) residue were obtained for inclusion in the ECEPP data set. Construction of the 18-23 cyclic peptide, for which no crystal structure is available, was carried out by using a scheme that took advantage of the constraints imposed by the requirement of disulfide ring closure and utilized known low-energy structures of single residues and dipeptides. Both cis and trans isomers about the Gla 21-Pro 22 peptide bond were considered. The lowest-energy conformation found for the isolated 18-23 cyclic peptide with arbitrary reduction of the charge on the Gla residues (to simulate hydration roughly) is a trans form, differing in energy by 11 kcal-mol-1 from the lowest-energy cis form. However, when the energy calculation includes one model Ca2+ ion, X2+, introduced at a fixed distance of 2.3 A from a single oxygen atom of either of the side-chain carboxyl groups of Gla with the C delta-O-X2+ bond angle fixed at one of three values, the lowest-energy cis conformation is about 1 kcal-mol-1 lower in energy than the lowest-energy trans conformation; i.e. the two structures have similar energies. In these structures, four oxygen atoms, two from each Gla side-chain, approach the model Ca2+ ion closely, in a manner similar to that seen in crystals of calcium alpha-ethylmalonate (Zell, A., Einspahr, H. & Bugg, C.E. (1985) Biochemistry 24, 533-537). It appears that the binding of Ca2+ to the 18-23 cyclic peptide may alter the equilibrium between cis and trans structures such that the fraction of cis isomers is greater in the presence of Ca2+.
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Kabis CW, Sarasua MM, Gottschalk KE, Bourne CD, Pedersen LG, Jackson CM, Hiskey RG, Koehler KA. A kinetic model describing the interaction of bovine prothrombin fragment 1 with calcium ions. Thromb Haemost 1985; 53:19-23. [PMID: 3838826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A kinetic model is derived for the interaction of bovine prothrombin fragment 1 with calcium ions. The model requires binding of a minimum of two calcium ions for induction of the observed biphasic fluorescence decrease as a function of time. The model is shown to be consistent with experimental kinetic and equilibrium data by fitting theoretical curves for the biphasic fluorescence change to the data through exact solution of the nonlinear differential rate equations derived from the model. The rate constants for the binding of these two required calcium ions are calculated from the solutions as best fit parameters. The thermodynamic equilibrium constants, K1 and K2, for the binding of these two calcium ions are calculated from ratios of the forward and reverse rate constants as 0.6 X 10(4) and 5.4 X 10(4), respectively. Thus, the model correctly predicts positively cooperative calcium ion binding for at least the two calcium ions required to induce fluorescence quenching.
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Madar DA, Sarasua MM, Marsh HC, Pedersen LG, Gottschalk KE, Hiskey RG, Koehler KA. The relationship between protein-protein and protein-lipid interactions and the immunological properties of bovine prothrombin and several of its fragments. J Biol Chem 1982; 257:1836-44. [PMID: 6173382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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