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Sandoval-Pérez A, Berger RML, Garaizar A, Farr SE, Brehm MA, König G, Schneider SW, Collepardo-Guevara R, Huck V, Rädler JO, Aponte-Santamaría C. DNA binds to a specific site of the adhesive blood-protein von Willebrand factor guided by electrostatic interactions. Nucleic Acids Res 2020; 48:7333-7344. [PMID: 32496552 PMCID: PMC7367192 DOI: 10.1093/nar/gkaa466] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 05/07/2020] [Accepted: 05/27/2020] [Indexed: 02/07/2023] Open
Abstract
Neutrophils release their intracellular content, DNA included, into the bloodstream to form neutrophil extracellular traps (NETs) that confine and kill circulating pathogens. The mechanosensitive adhesive blood protein, von Willebrand Factor (vWF), interacts with the extracellular DNA of NETs to potentially immobilize them during inflammatory and coagulatory conditions. Here, we elucidate the previously unknown molecular mechanism governing the DNA–vWF interaction by integrating atomistic, coarse-grained, and Brownian dynamics simulations, with thermophoresis, gel electrophoresis, fluorescence correlation spectroscopy (FCS), and microfluidic experiments. We demonstrate that, independently of its nucleotide sequence, double-stranded DNA binds to a specific helix of the vWF A1 domain, via three arginines. This interaction is attenuated by increasing the ionic strength. Our FCS and microfluidic measurements also highlight the key role shear-stress has in enabling this interaction. Our simulations attribute the previously-observed platelet-recruitment reduction and heparin-size modulation, upon establishment of DNA–vWF interactions, to indirect steric hindrance and partial overlap of the binding sites, respectively. Overall, we suggest electrostatics—guiding DNA to a specific protein binding site—as the main driving force defining DNA–vWF recognition. The molecular picture of a key shear-mediated DNA–protein interaction is provided here and it constitutes the basis for understanding NETs-mediated immune and hemostatic responses.
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Affiliation(s)
- Angélica Sandoval-Pérez
- Max Planck Tandem Group in Computational Biophysics, University of Los Andes, Cra. 1, 18A-12, 111711, Bogotá, Colombia
| | - Ricarda M L Berger
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Adiran Garaizar
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, UK
| | - Stephen E Farr
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, UK
| | - Maria A Brehm
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Gesa König
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Stefan W Schneider
- Department of Dermatology, Center for Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Rosana Collepardo-Guevara
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, UK.,Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.,Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Volker Huck
- Department of Dermatology, Center for Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Joachim O Rädler
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Camilo Aponte-Santamaría
- Max Planck Tandem Group in Computational Biophysics, University of Los Andes, Cra. 1, 18A-12, 111711, Bogotá, Colombia.,Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
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Grässle S, Huck V, Pappelbaum KI, Gorzelanny C, Aponte-Santamaría C, Baldauf C, Gräter F, Schneppenheim R, Obser T, Schneider SW. von Willebrand factor directly interacts with DNA from neutrophil extracellular traps. Arterioscler Thromb Vasc Biol 2014; 34:1382-9. [PMID: 24790143 DOI: 10.1161/atvbaha.113.303016] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Inflammatory conditions provoke essential processes in the human vascular system. It leads to the formation of ultralarge von Willebrand factor (VWF) fibers, which are immobilized on the endothelial cell surface and transform to highly adhesive strings under shear conditions. Furthermore, leukocytes release a meshwork of DNA (neutrophil extracellular traps) during the process of the recently discovered cell death program NETosis. In the present study, we characterized the interaction between VWF and DNA and possible binding sites to underline the role of VWF in thrombosis and inflammation besides its function in platelet adhesion. APPROACH AND RESULTS Both functionalized surfaces and intact cell layers of human umbilical vein endothelial cells were perfused with isolated, protein-free DNA or leukocytes from whole blood at distinct shear rates. DNA-VWF interaction was monitored using fluorescence microscopy, ELISA-based assays, molecular dynamics simulations, and electrostatic potential calculations. Isolated DNA, as well as DNA released by stimulated leukocytes, was able to bind to shear-activated, but not inactivated, VWF. However, DNA-VWF binding does not alter VWF degradation by a disintegrin and metalloproteinase with a thrombospondin type 1 motif, member 13. Moreover, DNA-VWF interaction can be blocked using unfractionated and low-molecular-weight heparin, and DNA-VWF complexes attenuate platelet binding to VWF. These findings were supported using molecular dynamics simulations and electrostatic calculations of the A1- and A2-domains. CONCLUSIONS Our findings suggest that VWF directly binds and immobilizes extracellular DNA released from leukocytes. Therefore, we hypothesize that VWF might act as a linker for leukocyte adhesion to endothelial cells, supporting leukocyte extravasation and inflammation.
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Affiliation(s)
- Sandra Grässle
- From the Experimental Dermatology Division, Department of Dermatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany (S.G., V.H., K.I.P., C.G., S.W.S.); Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany (C.A.-S., F.G.); Theory Department, Fritz Haber Institute of the Max Planck Society, Berlin, Germany (C.B.); and Department of Pediatric Hematology and Oncology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany (R.S., T.O.)
| | - Volker Huck
- From the Experimental Dermatology Division, Department of Dermatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany (S.G., V.H., K.I.P., C.G., S.W.S.); Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany (C.A.-S., F.G.); Theory Department, Fritz Haber Institute of the Max Planck Society, Berlin, Germany (C.B.); and Department of Pediatric Hematology and Oncology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany (R.S., T.O.)
| | - Karin I Pappelbaum
- From the Experimental Dermatology Division, Department of Dermatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany (S.G., V.H., K.I.P., C.G., S.W.S.); Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany (C.A.-S., F.G.); Theory Department, Fritz Haber Institute of the Max Planck Society, Berlin, Germany (C.B.); and Department of Pediatric Hematology and Oncology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany (R.S., T.O.)
| | - Christian Gorzelanny
- From the Experimental Dermatology Division, Department of Dermatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany (S.G., V.H., K.I.P., C.G., S.W.S.); Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany (C.A.-S., F.G.); Theory Department, Fritz Haber Institute of the Max Planck Society, Berlin, Germany (C.B.); and Department of Pediatric Hematology and Oncology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany (R.S., T.O.)
| | - Camilo Aponte-Santamaría
- From the Experimental Dermatology Division, Department of Dermatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany (S.G., V.H., K.I.P., C.G., S.W.S.); Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany (C.A.-S., F.G.); Theory Department, Fritz Haber Institute of the Max Planck Society, Berlin, Germany (C.B.); and Department of Pediatric Hematology and Oncology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany (R.S., T.O.)
| | - Carsten Baldauf
- From the Experimental Dermatology Division, Department of Dermatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany (S.G., V.H., K.I.P., C.G., S.W.S.); Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany (C.A.-S., F.G.); Theory Department, Fritz Haber Institute of the Max Planck Society, Berlin, Germany (C.B.); and Department of Pediatric Hematology and Oncology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany (R.S., T.O.)
| | - Frauke Gräter
- From the Experimental Dermatology Division, Department of Dermatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany (S.G., V.H., K.I.P., C.G., S.W.S.); Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany (C.A.-S., F.G.); Theory Department, Fritz Haber Institute of the Max Planck Society, Berlin, Germany (C.B.); and Department of Pediatric Hematology and Oncology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany (R.S., T.O.)
| | - Reinhard Schneppenheim
- From the Experimental Dermatology Division, Department of Dermatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany (S.G., V.H., K.I.P., C.G., S.W.S.); Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany (C.A.-S., F.G.); Theory Department, Fritz Haber Institute of the Max Planck Society, Berlin, Germany (C.B.); and Department of Pediatric Hematology and Oncology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany (R.S., T.O.)
| | - Tobias Obser
- From the Experimental Dermatology Division, Department of Dermatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany (S.G., V.H., K.I.P., C.G., S.W.S.); Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany (C.A.-S., F.G.); Theory Department, Fritz Haber Institute of the Max Planck Society, Berlin, Germany (C.B.); and Department of Pediatric Hematology and Oncology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany (R.S., T.O.)
| | - Stefan W Schneider
- From the Experimental Dermatology Division, Department of Dermatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany (S.G., V.H., K.I.P., C.G., S.W.S.); Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany (C.A.-S., F.G.); Theory Department, Fritz Haber Institute of the Max Planck Society, Berlin, Germany (C.B.); and Department of Pediatric Hematology and Oncology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany (R.S., T.O.).
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