Structural basis of divergent substrate recognition and inhibition of human neurolysin.
Crystal structure
Dynorphin A
Enzyme inhibition
Metalloprotease
Neurolysin
Neuropeptide
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
08 Aug 2024
08 Aug 2024
Historique:
received:
02
04
2024
accepted:
15
07
2024
medline:
9
8
2024
pubmed:
9
8
2024
entrez:
8
8
2024
Statut:
epublish
Résumé
A zinc metallopeptidase neurolysin (Nln) processes diverse bioactive peptides to regulate signaling in the mammalian nervous system. To understand how Nln interacts with various peptides with dissimilar sequences, we determined crystal structures of Nln in complex with diverse peptides including dynorphins, angiotensin, neurotensin, and bradykinin. The structures show that Nln binds these peptides in a large dumbbell-shaped interior cavity constricted at the active site, making minimal structural changes to accommodate different peptide sequences. The structures also show that Nln readily binds similar peptides with distinct registers, which can determine whether the peptide serves as a substrate or a competitive inhibitor. We analyzed the activities and binding of Nln toward various forms of dynorphin A peptides, which highlights the promiscuous nature of peptide binding and shows how dynorphin A (1-13) potently inhibits the Nln activity while dynorphin A (1-8) is efficiently cleaved. Our work provides insights into the broad substrate specificity of Nln and may aid in the future design of small molecule modulators for Nln.
Identifiants
pubmed: 39117724
doi: 10.1038/s41598-024-67639-w
pii: 10.1038/s41598-024-67639-w
doi:
Substances chimiques
neurolysin
EC 3.4.24.16
Dynorphins
74913-18-1
Neurotensin
39379-15-2
Metalloendopeptidases
EC 3.4.24.-
Bradykinin
S8TIM42R2W
Angiotensins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
18420Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM118047
Pays : United States
Organisme : NIH HHS
ID : R01NS106879
Pays : United States
Organisme : NIH HHS
ID : R35GM118047
Pays : United States
Informations de copyright
© 2024. The Author(s).
Références
Checler, F. & Ferro, E. S. Neurolysin: From initial detection to latest advances. Neurochem. Res. 43, 2017–2024 (2018).
doi: 10.1007/s11064-018-2624-6
pubmed: 30159819
Shrimpton, C. N., Smith, A. I. & Lew, R. A. Soluble metalloendopeptidases and neuroendocrine signaling. Endocr. Rev. 23, 647–664 (2002).
doi: 10.1210/er.2001-0032
pubmed: 12372844
Checler, F., Vincent, J. P. & Kitabgi, P. Purification and characterization of a novel neurotensin-degrading peptidase from rat brain synaptic membranes. J. Biol. Chem. 261, 11274–11281 (1986).
doi: 10.1016/S0021-9258(18)67379-X
pubmed: 3525564
Dauch, P., Vincent, J. P. & Checler, F. Molecular cloning and expression of rat brain endopeptidase 3.4.24.16. J. Biol. Chem. 270, 27266–27271 (1995).
doi: 10.1074/jbc.270.45.27266
pubmed: 7592986
Checler, F. Experimental stroke: Neurolysin back on stage. J. Neurochem. 129, 1–3 (2014).
doi: 10.1111/jnc.12635
pubmed: 24386939
Karamyan, V. T. The role of peptidase neurolysin in neuroprotection and neural repair after stroke. Neural Regen. Res. 16, 21–25 (2021).
doi: 10.4103/1673-5374.284904
pubmed: 32788443
Mirali, S. et al. The mitochondrial peptidase, neurolysin, regulates respiratory chain supercomplex formation and is necessary for AML viability. Sci. Transl. Med. https://doi.org/10.1126/scitranslmed.aaz8264 (2020).
doi: 10.1126/scitranslmed.aaz8264
pubmed: 32269163
Teixeira, P. F. et al. Mechanism of peptide binding and cleavage by the human mitochondrial peptidase neurolysin. J. Mol. Biol. 430, 348–362 (2018).
doi: 10.1016/j.jmb.2017.11.011
pubmed: 29183787
Rioli, V. et al. Novel natural peptide substrates for endopeptidase 24.15, neurolysin, and angiotensin-converting enzyme. J. Biol. Chem. 278, 8547–8555 (2003).
doi: 10.1074/jbc.M212030200
pubmed: 12500972
Brown, C. K. et al. Structure of neurolysin reveals a deep channel that limits substrate access. Proc. Natl. Acad. Sci. U. S. A. 98, 3127–3132 (2001).
doi: 10.1073/pnas.051633198
pubmed: 11248043
pmcid: 30618
Hines, C. S. et al. Allosteric inhibition of the neuropeptidase neurolysin. J. Biol. Chem. 289, 35605–35619 (2014).
doi: 10.1074/jbc.M114.620930
pubmed: 25378390
pmcid: 4271243
Uyar, A., Karamyan, V. T. & Dickson, A. Long-range changes in neurolysin dynamics upon inhibitor binding. J. Chem. Theory Comput. 14, 444–452 (2018).
doi: 10.1021/acs.jctc.7b00944
pubmed: 29179556
Jayaraman, S. et al. Identification and characterization of two structurally related dipeptides that enhance catalytic efficiency of neurolysin. J. Pharmacol. Exp. Ther. 379, 191–202 (2021).
doi: 10.1124/jpet.121.000840
pubmed: 34389655
pmcid: 8626779
Rahman, M. S. et al. Discovery of first-in-class peptidomimetic neurolysin activators possessing enhanced brain penetration and stability. J. Med. Chem. 64, 12705–12722 (2021).
doi: 10.1021/acs.jmedchem.1c00759
pubmed: 34436882
pmcid: 9295256
Esfahani, S. H., Abbruscato, T. J., Trippier, P. C. & Karamyan, V. T. Small molecule neurolysin activators, potential multi-mechanism agents for ischemic stroke therapy. Expert Opin. Ther. Targets 26, 401–404 (2022).
doi: 10.1080/14728222.2022.2077190
pubmed: 35543670
Jayaraman, S. et al. Peptidase neurolysin functions to preserve the brain after ischemic stroke in male mice. J. Neurochem. 153, 120–137 (2020).
doi: 10.1111/jnc.14864
pubmed: 31486527
Barrett, A. J. et al. Thimet oligopeptidase and oligopeptidase M or neurolysin. Methods Enzymol. 248, 529–556 (1995).
doi: 10.1016/0076-6879(95)48034-X
pubmed: 7674943
Schwarzer, C. 30 years of dynorphins—New insights on their functions in neuropsychiatric diseases. Pharmacol. Ther. 123, 353–370 (2009).
doi: 10.1016/j.pharmthera.2009.05.006
pubmed: 19481570
pmcid: 2872771
Dahms, P. & Mentlein, R. Purification of the main somatostatin-degrading proteases from rat and pig brains, their action on other neuropeptides, and their identification as endopeptidases 24.15 and 24.16. Eur. J. Biochem. 208, 145–154 (1992).
doi: 10.1111/j.1432-1033.1992.tb17168.x
pubmed: 1355047
Wangler, N. J. et al. Preparation and preliminary characterization of recombinant neurolysin for in vivo studies. J. Biotechnol. 234, 105–115 (2016).
doi: 10.1016/j.jbiotec.2016.07.007
pubmed: 27496565
Karamyan, V. T., Gadepalli, R., Rimoldi, J. M. & Speth, R. C. Brain AT1 angiotensin receptor subtype binding: importance of peptidase inhibition for identification of angiotensin II as its endogenous ligand. J. Pharmacol. Exp. Ther. 331, 170–177 (2009).
doi: 10.1124/jpet.109.157461
pubmed: 19587313
Karamyan, V. T. & Speth, R. C. Enzymatic pathways of the brain renin-angiotensin system: Unsolved problems and continuing challenges. Regul. Pept. 143, 15–27 (2007).
doi: 10.1016/j.regpep.2007.03.006
pubmed: 17493693
pmcid: 7114358
Machado, M. F. et al. The role of Tyr605 and Ala607 of thimet oligopeptidase and Tyr606 and Gly608 of neurolysin in substrate hydrolysis and inhibitor binding. Biochem. J. 404, 279–288 (2007).
doi: 10.1042/BJ20070060
pubmed: 17313369
pmcid: 1868798
Oliveira, V. et al. Selective neurotensin-derived internally quenched fluorogenic substrates for neurolysin (EC 3.4.24.16): Comparison with thimet oligopeptidase (EC 3.4.24.15) and neprilysin (EC 3.4.24.11). Anal. Biochem. 292, 257–265 (2001).
doi: 10.1006/abio.2001.5083
pubmed: 11355859
Oliveira, V. et al. Substrate specificity characterization of recombinant metallo oligo-peptidases thimet oligopeptidase and neurolysin. Biochemistry 40, 4417–4425 (2001).
doi: 10.1021/bi002715k
pubmed: 11284698
Bar-Even, A. et al. The moderately efficient enzyme: Evolutionary and physicochemical trends shaping enzyme parameters. Biochemistry 50, 4402–4410 (2011).
doi: 10.1021/bi2002289
pubmed: 21506553
Lim, E. J. et al. Swapping the substrate specificities of the neuropeptidases neurolysin and thimet oligopeptidase. J. Biol. Chem. 282, 9722–9732 (2007).
doi: 10.1074/jbc.M609897200
pubmed: 17251185
Ray, K., Hines, C. S. & Rodgers, D. W. Mapping sequence differences between thimet oligopeptidase and neurolysin implicates key residues in substrate recognition. Protein Sci. 11, 2237–2246 (2002).
doi: 10.1110/ps.0216302
pubmed: 12192079
pmcid: 2373592
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).
doi: 10.1107/S0907444910007493
pubmed: 20383002
pmcid: 2852313
Adams, P. D. et al. PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).
doi: 10.1107/S0907444909052925
pubmed: 20124702
pmcid: 2815670