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Structural basis for ligand reception by anaplastic lymphoma kinase

Abstract

The proto-oncogene ALK encodes anaplastic lymphoma kinase, a receptor tyrosine kinase that is expressed primarily in the developing nervous system. After development, ALK activity is associated with learning and memory1 and controls energy expenditure, and inhibition of ALK can prevent diet-induced obesity2. Aberrant ALK signalling causes numerous cancers3. In particular, full-length ALK is an important driver in paediatric neuroblastoma4,5, in which it is either mutated6 or activated by ligand7. Here we report crystal structures of the extracellular glycine-rich domain (GRD) of ALK, which regulates receptor activity by binding to activating peptides8,9. Fusing the ALK GRD to its ligand enabled us to capture a dimeric receptor complex that reveals how ALK responds to its regulatory ligands. We show that repetitive glycines in the GRD form rigid helices that separate the major ligand-binding site from a distal polyglycine extension loop (PXL) that mediates ALK dimerization. The PXL of one receptor acts as a sensor for the complex by interacting with a ligand-bound second receptor. ALK activation can be abolished through PXL mutation or with PXL-targeting antibodies. Together, these results explain how ALK uses its atypical architecture for its regulation, and suggest new therapeutic opportunities for ALK-expressing cancers such as paediatric neuroblastoma.

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Fig. 1: Structure of the ALK–ALKAL complex and the ALK GRD.
Fig. 2: Ligand binding is directed by the C-terminal loop of ALK.
Fig. 3: Dimerization of ALK is directed by the PXL.
Fig. 4: Antibodies to the C-terminal loop or PXL prevent ALK activation.

Data availability

The refined structural protein models and corresponding structure–factor amplitudes have been deposited under PDB accession codes 7LS0 (human ALK GRD–ALKAL fusion complex), 7LRZ (human ALK GRD), 7LIR (worm ALK GRD) and 7MK7 (ALKAL2-AD).

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Acknowledgements

We thank C. Alarcon, Y. Liu, J. Abraham and their laboratories for valuable discussions, as well as members of the Klein, Lemmon and Schlessinger laboratories; A. Reshetnyak, D. Puleo and J. Mohanty for their contributions. This work was supported by the NIH, NIGMS grant R35 GM122485 (to M.A.L.), and NCI grant R01 CA248532 (to D.E.K.). This work is based in part on research conducted at the Northeastern Collaborative Access Team beamlines, which are funded by the National Institute of General Medical Sciences from the National Institutes of Health (P30 GM124165). The Pilatus 6M detector on 24-ID-C beam line is funded by a NIH-ORIP HEI grant (S10 RR029205). This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under contract no. DE-AC02-06CH11357. GM/CA@APS has been funded in whole or in part with Federal funds from the National Cancer Institute (ACB-12002) and the National Institute of General Medical Sciences (AGM-12006). This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. The Eiger 16M detector at GM/CA-XSD was funded by NIH grant S10 OD012289.

Author information

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Authors

Contributions

D.E.K. designed the overall project, with input from M.A.L. and J.S. D.E.K. wrote the manuscript assisted by T.L., with input from all authors. T.L. generated all materials (assisted by J.Z., O.B. and I.X.W.) and performed all solution biophysical studies. T.L., S.E.S. and D.E.K. analysed ALK structures. T.L. performed cell assays (assisted by Y.W. and H.L.). T.L. and Y.T. carried out HDX-MS studies, supervised by M.A.L. T.L. and K.C.M. performed fluorescence studies in membranes, supervised by M.A.L. I.L. carried out full length ALK studies with help from M.A. and Y.S. ALKAL1 AD–MBP structural studies and analysis was performed by S.G.K., supervised by J.S. Purified CDX antibodies were provided by A.P. and D.A.

Corresponding author

Correspondence to Daryl E. Klein.

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Competing interests

J.S. is a member of the scientific advisory board of Celldex. D.A. is an employee of Celldex Therapeutics.

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Peer review information Nature thanks the anonymous reviewer(s) for their contribution to the peer review of this work.

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Extended data figures and tables

Extended Data Fig. 1 Structural comparison of human and invertebrate ALK.

a, Size exclusion chromatography of each protein was carried out using a Superdex 75 Increase 10/300 GL column. The non-glycosylated mass was calculated from the protein sequence. The mass corresponding to each SEC peak was determined based on the log (MW) versus elution volume plot of standards for the column. The SEC peak mass of each protein is consistent with a glycosylated monomer. b, ALK’s glycine helices project downward from the TNF-α like region. Unique to ALK, strand 10 crosses over strands 4 and 5 to terminate the fold, producing a surface terminal loop, “C-term loop”. The GRD has a distinct topology, and does not form the jelly-roll characteristic of TNF-α domains c, The GRD of human ALK. d, The hexagonal array of the Pole, and e, the order and topology of the Pole (red circles into the page, black out of the page). f, C. elegans ALK adopts a similar overall architecture to the human GRD. However, the invertebrate PXL is structurally different, forming a β-hairpin rather than helices (orange). g, The Pole of invertebrate ALK is also smaller, with 11 glycine helices that form 2 complete hexagons. h, The helical strands are in the same order and topology as in human ALK. Interestingly, the missing glycine helices of the invertebrate Pole are partially matched by non PG-II loops that interact with the hexagonal array (dashed circles). The invertebrate GRD structure additionally includes a C-terminal cysteine-rich region that leads up to the transmembrane domain. This region has 10 cysteines and forms 2 EGF-like domains (f, blue).

Extended Data Fig. 2 Structure of invertebrate ALK’s EGF-like domains.

a, The first EGF-like domain has canonical disulfide pairing. b, The second EGF-like domain is atypical in that it lacks the first 1-3 disulfide bond, the stabilizing role of which is replaced by hydrophobic interactions involving Y871 and F859. c, The EGF-like domains pack tightly to the TNF-α like domain with hydrophobic interactions. Y836 and F837 of the first EGF domain bind to the proximal C-terminal loop. F874 of the second EGF like domain is buried in a hydrophobic cavity.

Extended Data Fig. 3 HDX analysis of ALKAL binding to ALK.

HDX-MS percent exchange butterfly plot for ALKAL2-AD binding to human ALK GRD. Each peptide is assigned a peptide ID number (Extended Data Table 2) from the N- (left) to the C-terminus (right). Each grey bar shows the sum of ∆%Exchange at all labeling timepoints (∆%sum) for each peptide. The dotted purple line corresponds to statistically significant ∆%sum (16%, or ± 0.77 Da difference in deuterium uptake between unliganded and ALKAL-bound GRD) with 98 % confidence limit calculated based on the measured standard deviation of deuterium uptake for each peptide. Regions with positive or negative ∆%Exchange become more stable or flexible, respectively, upon ALKAL binding. Statistics were derived from two independent biological repeats, each with three technical repeats. Data represent mean ± SD.

Extended Data Fig. 4 ALK binding and signaling by ALKAL2-AD.

a, Representative BLI sensograms traces (black) and kinetic fittings (red). Fitting was carried out using ForteBio Data Analysis 10.0 software using 1:1 model with Rmax linked global fitting. Where appropriate, kinetic fit parameters are included. b, c, NIH 3T3 cells stably expressing wild type (WT) or mutated full length ALK, stimulated with high concentrations (10 nM) of ALKAL2 to assess residual signaling ability. b, Single point mutations of conserved binding-site residues. E978R has the greatest impact on ALKAL induced ALK signaling in agreement with binding data. c, C-terminal conserved glutamates mutated to the residues found at the same position in invertebrate ALK. The double (E974L/E978Y) mutant fails to signal, consistent with it being the only mutation shown here that completely abolished ligand binding in (a) (Extended Data Table 3). For gel source data, see Supplementary Fig. 2. The stimulation experiment was repeated three times with similar results.

Extended Data Fig. 5 Ligand binding and receptor dimerization are coupled to Pole rotation and PXL changes.

a, View looking down the long axis of the Pole with apo ALK (gray) aligned to the complex structure (color). Compared to unliganded ALK, the ligand-bound ALK dimer undergoes a clockwise rotation of the Pole about the central glycine helix (number 4). b, Unliganded ALK (gray) aligned to both protomers of the complex dimer (color). The PXL residues surrounding Q788 adopt a helical structure upon ligand binding and dimerization. c, Upon ligand binding, two additional peptides – not directly involved in ligand binding and discussed in Fig. 2 – are significantly protected. Statistics were derived from two independent biological repeats, each with three technical repeats. Data represent mean ± SD. d, these peptides (cyan) (peptide #1 and #21, Extended Data Fig. 3) correspond to the dimer interface including the disulfide linked helix of the PXL (#21) and the helix on the TNF-α like domain it forms a bond with (#1). e, The core helix-turn-helix of the AD is largely unaltered upon binding. ALKAL2 from the ALK-ALKAL fusion complex structure (green) is aligned to an un-complexed ALKAL1-AD MBP (Maltose Binding Protein) fusion (cyan).

Extended Data Fig. 6 The PXL region is necessary for ALK signaling.

a, Binding of ALKAL2-AD to GRD PXL mutations detected by BLI. The sensors were loaded with ALKAL2-AD. REQ is a mutant that alters the interface residues 795-“IGE”-797 (shown in Fig. 3b, c) to REQ. ΔPXL is a mutant that removes the entire “disulfided helix” 783-797 (shown in Fig. 3b, c). The relative binding is the binding normalized to the maximum responses. Data represent mean ± SD of four measurements. b, Expression of Halo-ALK on NIH/3T3 cell membranes. NIH/3T3 cells were untransfected, transfected with wildtype Halo-ALK or ALK mutants. Cells were stained with membrane impermeable dye, JF549i, before imaging. For each construct fluorescence (top row), brightfield (middle row), and a merge (bottom row) were shown. Scale bar 5 µm. The experiment was repeated two times with similar results. c, Binding of CDX123 or CDX125 to GRD or GRDΔPXL detected by BLI. Data represent mean ± SD from three independent experiments.

Extended Data Fig. 7 Implications for GRD mutation and evolution.

a, Invertebrate ALK GRD structure with known glycine-to-acidic residue (D/E) mutations highlighted (purple spheres)9. b, Human ALK GRD structure with all of glycine-to-acidic residue mutations found in the COSMIC database (https://cancer.sanger.ac.uk) highlighted (purple spheres). c, Invertebrate ALK GRD does not bind to human ALKAL2-AD. The relative binding is the binding normalized to the maximum responses. Data represent mean ± SD of three measurements. d, The EGF-like domain of invertebrate ALK occupies a region of the C-terminal loop required for ALKAL binding. This would prevent binding of any similar helix-loop-helix like ligand.

Extended Data Table 1 Data collection and refinement statistics
Extended Data Table 2 HDX peptides
Extended Data Table 3 Binding analysis of GRD and ALKAL mutants

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Li, T., Stayrook, S.E., Tsutsui, Y. et al. Structural basis for ligand reception by anaplastic lymphoma kinase. Nature (2021). https://doi.org/10.1038/s41586-021-04141-7

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