The most abundant member of the collagen protein family, collagen I (also known as type I collagen; COL1), is composed of one unique (chain B) and two similar (chain A) polypeptides that self-assemble with one amino acid offset into a heterotrimeric triple helix. Given the offset, chain B can occupy either the leading (BAA), middle (ABA) or trailing (AAB) position of the triple helix, yielding three isomeric biomacromolecules with different protein recognition properties. Despite five decades of intensive research, there is no consensus on the position of chain B in COL1. Here, three triple-helical heterotrimers that each contain a putative von Willebrand factor (VWF) and discoidin domain receptor (DDR) recognition sequence from COL1 were designed with chain B permutated in all three positions. AAB demonstrated a strong preference for both VWF and DDR, and also induced higher levels of cellular DDR phosphorylation. Thus, we resolve this long-standing mystery and show that COL1 adopts an AAB register.
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The code for computational design of heterotrimers may be requested from the corresponding author.
Leitinger, B. Transmembrane collagen receptors. Annu. Rev. Cell Dev. Biol. 27, 265–290 (2011).
Rosini, S. et al. Thrombospondin-1 promotes matrix homeostasis by interacting with collagen and lysyl oxidase precursors and collagen cross-linking sites. Sci. Signal. 11, eaar2566 (2018).
Lankhof, H. et al. A3 domain is essential for interaction of von Willebrand factor with collagen type III. Thromb. Haemost. 75, 950–958 (1996).
Santoro, S. A. Preferential binding of high molecular weight forms of von Willebrand factor to fibrillar collagen. Biochim. Biophys. Acta 756, 123–126 (1983).
De Meyer, S. F., Stoll, G., Wagner, D. D. & Kleinschnitz, C. von Willebrand factor: an emerging target in stroke therapy. Stroke 43, 599–606 (2012).
Fu, H. L. et al. Discoidin domain receptors: unique receptor tyrosine kinases in collagen-mediated signaling. J. Biol. Chem. 288, 7430–7437 (2013).
Gross, O. et al. DDR1-deficient mice show localized subepithelial GBM thickening with focal loss of slit diaphragms and proteinuria. Kidney Int. 66, 102–111 (2004).
Vogel, W. F. et al. Discoidin domain receptor 1 tyrosine kinase has an essential role in mammary gland development. Mol. Cell. Biol. 21, 2906–2917 (2001).
Hou, G., Vogel, W. & Bendeck, M. P. The discoidin domain receptor tyrosine kinase DDR1 in arterial wound repair. J. Clin. Invest. 107, 727–735 (2001).
Labrador, J. P. et al. The collagen receptor DDR2 regulates proliferation and its elimination leads to dwarfism. EMBO Rep. 2, 446–452 (2001).
Valiathan, R. R. et al. Discoidin domain receptor tyrosine kinases: new players in cancer progression. Cancer Metastasis Rev. 31, 295–321 (2012).
Raynal, N. et al. Use of synthetic peptides to locate novel integrin α2β1-binding motifs in human collagen III. J. Biol. Chem. 281, 3821–3831 (2006).
Farndale, R. W. et al. Cell–collagen interactions: the use of peptide Toolkits to investigate collagen–receptor interactions. Biochem. Soc. Trans. 36, 241–250 (2008).
Kim, J. K. et al. A novel binding site in collagen type III for integrins α1β1 and α2β1. J. Biol. Chem. 280, 32512–32520 (2005).
Emsley, J., Knight, C. G., Farndale, R. W., Barnes, M. J. & Liddington, R. C. Structural basis of collagen recognition by integrin α2β1. Cell 101, 47–56 (2000).
Hamaia, S. W. et al. Unique charge-dependent constraint on collagen recognition by integrin α10β1. Matrix Biol. 59, 80–94 (2017).
Brondijk, T. H. C., Bihan, D., Farndale, R. W. & Huizinga, E. G. Implications for collagen I chain registry from the structure of the collagen von Willebrand factor A3 domain complex. Proc. Natl Acad. Sci. USA 109, 5253–5258 (2012).
Xu, H. et al. Collagen binding specificity of the discoidin domain receptors: binding sites on collagens II and III and molecular determinants for collagen IV recognition by DDR1. Matrix Biol. 30, 16–26 (2011).
Konitsiotis, A. D. et al. Characterization of high affinity binding motifs for the discoidin domain receptor DDR2 in collagen. J. Biol. Chem. 283, 6861–6868 (2008).
Manka, S. W. et al. Structural insights into triple-helical collagen cleavage by matrix metalloproteinase 1. Proc. Natl Acad. Sci. USA 109, 12461–12466 (2012).
Hohenester, E., Sasaki, T., Giudici, C., Farndale, R. W. & Bächinger, H. P. Structural basis of sequence-specific collagen recognition by SPARC. Proc. Natl Acad. Sci. USA 105, 18273–18277 (2008).
Zhou, L. et al. Structural basis for collagen recognition by the immune receptor OSCAR. Blood 127, 529–537 (2016).
Munnix, I. C. A. et al. Collagen-mimetic peptides mediate flow-dependent thrombus formation by high- or low-affinity binding of integrin α2β1 and glycoprotein VI. J. Thromb. Haemost. 6, 2132–2142 (2008).
Lebbink, R. J. et al. Identification of multiple potent binding sites for human leukocyte associated Ig-like receptor LAIR on collagens II and III. Matrix Biol. 28, 202–210 (2009).
Piez, K. A., Eigner, E. A. & Lewis, M. S. The chromatographic separation and amino acid composition of the subunits of several collagens. Biochemistry 2, 58–66 (1963).
Piez, K. A. & Trus, B. L. Sequence regularities and packing of collagen molecules. J. Mol. Biol. 122, 419–432 (1978).
Traub, W. & Fietzek, P. P. Contribution of the α2 chain to the molecular stability of collagen. FEBS Lett. 68, 245–249 (1976).
Bender, E., Silver, H., Hayashi, K. & Trelstad, R. L. Type I collagen segment long spacing banding patterns. J. Biol. Chem. 257, 9653–9657 (1982).
Orgel, J. P. R. O., Irving, T. C., Miller, A. & Wess, T. J. Microfibrillar structure of type I collagen in situ. Proc. Natl Acad. Sci. USA 103, 9001–9005 (2006).
Lisman, T. et al. A single high-affinity binding site for von Willebrand factor in collagen III, identified using synthetic triple-helical peptides. Blood 108, 3753–3756 (2006).
Jalan, A. A. & Hartgerink, J. D. Simultaneous control of composition and register of an AAB-type collagen heterotrimer. Biomacromolecules 14, 179–185 (2013).
Xu, F., Zhang, L., Koder, R. L. & Nanda, V. De novo self-assembling collagen heterotrimers using explicit positive and negative design. Biochemistry 49, 2307–2316 (2010).
Zheng, H. et al. How electrostatic networks modulate specificity and stability of collagen. Proc. Natl Acad. Sci. USA 115, 6207–6212 (2018).
Gauba, V. & Hartgerink, J. D. Self-assembled heterotrimeric collagen triple helices directed through electrostatic interactions. J. Am. Chem. Soc. 129, 2683–2690 (2007).
Fallas, J. A. & Hartgerink, J. D. Computational design of self-assembling register-specific collagen heterotrimers. Nat. Commun. 3, 1087–1088 (2012).
Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996).
Carafoli, F. et al. Crystallographic insight into collagen recognition by discoidin domain receptor 2. Structure 17, 1573–1581 (2009).
Jalan, A. A., Demeler, B. & Hartgerink, J. D. Hydroxyproline-free single composition ABC collagen heterotrimer. J. Am. Chem. Soc. 135, 6014–6017 (2013).
Li, I.-C. et al. Org. Lett. 21(14), 5480–5484 (2019). https://doi.org/10.1021/acs.orglett.9b01771.
Persikov, A. V., Ramshaw, J. A. M., Kirkpatrick, A. & Brodsky, B. Amino acid propensities for the collagen triple-helix. Biochemistry 39, 14960–14967 (2000).
Houdijk, W. P. M., Sakariassen, K. S., Nievelstein, P. F. E. M. & Sixma, J. J. Role of factor VIII-von Willebrand factor and fibronectin in the interaction of platelets in flowing blood with monomeric and fibrillar human collagen types I and III. J. Clin. Invest. 75, 531–540 (1985).
Vogel, W., Gish, G. D., Alves, F. & Pawson, T. The discoidin domain receptor tyrosine kinases are activated by collagen. Mol. Cell 1, 13–23 (1997).
Bodian, D. L., Madhan, B., Brodsky, B. & Klein, T. E. Predicting the clinical lethality of osteogenesis imperfecta from collagen glycine mutations. Biochemistry 47, 5424–5432 (2008).
Leitinger, B. Molecular analysis of collagen binding by the human discoidin domain receptors, DDR1 and DDR2. J. Biol. Chem. 278, 16761–16769 (2003).
Vonrhein, C. et al. Data processing and analysis with the autoPROC toolbox. Acta Crystallogr. D. 67, 293–302 (2011).
Winter, G. et al. DIALS: implementation and evaluation of a new integration package. Acta Crystallogr. D. 74, 85–97 (2018).
Evans, P. Scaling and assessment of data quality. Acta Crystallogr. D. 62, 72–82 (2006).
Evans, P. R. An introduction to data reduction: space-group determination, scaling and intensity statistics. Acta Crystallogr. D. 67, 282–292 (2011).
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).
Rainey, J. K. & Goh, M. C. An interactive triple-helical collagen builder. Bioinformatics 20, 2458–2459 (2004).
Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D. 53, 240–255 (1997).
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D. 60, 2126–2132 (2004).
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D. 66, 213–221 (2010).
Liebschner, D. et al. Polder maps: improving OMIT maps by excluding bulk solvent. Acta Crystallogr. D. 73, 148–157 (2017).
Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D. 66, 12–21 (2010).
Merritt, E. A. Comparing anisotropic displacement parameters in protein structures. Acta Crystallogr. D. 55, 1997–2004 (1999).
Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277–293 (1995).
Fogh, R. et al. The ccpn project: an interim report on a data model for the nmr community. Nat. Struct. Biol. 9, 416–418 (2002).
Schlick, T. L., Ding, Z., Kovacs, E. W. & Francis, M. B. Dual-surface modification of the tobacco mosaic virus. J. Am. Chem. Soc. 127, 3718–3723 (2005).
Xu, H. et al. Normal activation of discoidin domain receptor 1 mutants with disulfide cross-links, insertions, or deletions in the extracellular juxtamembrane region: mechanistic implications. J. Biol. Chem. 289, 13565–13574 (2014).
Juskaite, V., Corcoran, D. S. & Leitinger, B. Collagen induces activation of DDR1 through lateral dimer association and phosphorylation between dimers. elife 6, e25716 (2017).
A.A.J. was supported by Newton International Fellowship (NF140721) granted jointly by the Royal Society, the British Academy and the Academy of Medical Sciences. D.S. was supported by a PhD studentship from the Imperial College London–Royal Holloway BBSRC Doctoral Training Partnership. J.D.H. and D.R.W. were supported in part by the Welch Foundation (C1557) and the National Science Foundation (CHE1709631). R.W.F. was supported by a British Heart Foundation programme grant (RG/15/4/31268). The authors thank D. Chirgadze and M. Hyvonen in the Department of Biochemistry at the University of Cambridge for X-ray crystallography support and crystallographic data refinement, respectively; E. Hohenester in the Department of Life Sciences at Imperial College London for helpful discussion on solid-phase binding assays; and J.-D. Malcor and A. Bonna in the Department of Biochemistry at the University of Cambridge for support in peptide synthesis. The authors also thank Diamond Light Source for beamtime (proposal mx14043) and the staff of beamlines I03, I04 and I24 for assistance with crystal testing and data collection.
The authors declare no competing interests.
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Jalan, A.A., Sammon, D., Hartgerink, J.D. et al. Chain alignment of collagen I deciphered using computationally designed heterotrimers. Nat Chem Biol 16, 423–429 (2020). https://doi.org/10.1038/s41589-019-0435-y