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TitleDe novo macrocyclic peptides for inhibiting, stabilizing, and probing the function of the retromer endosomal trafficking complex.
Journal, issue, pagesSci Adv, Vol. 7, Issue 49, Page eabg4007, Year 2021
Publish dateDec 3, 2021
AuthorsKai-En Chen / Qian Guo / Timothy A Hill / Yi Cui / Amy K Kendall / Zhe Yang / Ryan J Hall / Michael D Healy / Joanna Sacharz / Suzanne J Norwood / Sachini Fonseka / Boyang Xie / Robert C Reid / Natalya Leneva / Robert G Parton / Rajesh Ghai / David A Stroud / David P Fairlie / Hiroaki Suga / Lauren P Jackson / Rohan D Teasdale / Toby Passioura / Brett M Collins /
PubMed AbstractThe retromer complex (Vps35-Vps26-Vps29) is essential for endosomal membrane trafficking and signaling. Mutation of the retromer subunit Vps35 causes late-onset Parkinson’s disease, while viral and ...The retromer complex (Vps35-Vps26-Vps29) is essential for endosomal membrane trafficking and signaling. Mutation of the retromer subunit Vps35 causes late-onset Parkinson’s disease, while viral and bacterial pathogens can hijack the complex during cellular infection. To modulate and probe its function, we have created a novel series of macrocyclic peptides that bind retromer with high affinity and specificity. Crystal structures show that most of the cyclic peptides bind to Vps29 via a Pro-Leu–containing sequence, structurally mimicking known interactors such as TBC1D5 and blocking their interaction with retromer in vitro and in cells. By contrast, macrocyclic peptide RT-L4 binds retromer at the Vps35-Vps26 interface and is a more effective molecular chaperone than reported small molecules, suggesting a new therapeutic avenue for targeting retromer. Last, tagged peptides can be used to probe the cellular localization of retromer and its functional interactions in cells, providing novel tools for studying retromer function.
External linksSci Adv / PubMed:34851660 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.58 - 5.9 Å
Structure data

EMDB-24963:
Mouse retromer (VPS26/VPS35/VPS29) heterotrimer in the presence of cyclic peptide RTL4
Method: EM (single particle) / Resolution: 5.9 Å

EMDB-24964:
Mouse retromer (VPS26/VPS35/VPS29) heterotrimer
Method: EM (single particle) / Resolution: 4.9 Å

PDB-6xs5:
Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-D1
Method: X-RAY DIFFRACTION / Resolution: 2.01 Å

PDB-6xs7:
Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-D2
Method: X-RAY DIFFRACTION / Resolution: 1.58 Å

PDB-6xs8:
Crystal structure of Chaetomium thermophilum Vps29 complexed with RaPID-derived cyclic peptide RT-D3
Method: X-RAY DIFFRACTION / Resolution: 1.95009854987 Å

PDB-6xs9:
Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L1
Method: X-RAY DIFFRACTION / Resolution: 2.69 Å

PDB-6xsa:
Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L2
Method: X-RAY DIFFRACTION / Resolution: 1.83 Å

Chemicals

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-FMT:
FORMIC ACID / Formic acid

ChemComp-HOH:
WATER / Water

ChemComp-MLI:
MALONATE ION / Malonic acid

ChemComp-O4B:
1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / 18-Crown-6

ChemComp-SO4:
SULFATE ION / Sulfate

Source
  • Mus musculus (house mouse)
  • homo sapiens (human)
  • synthetic construct (others)
  • chaetomium thermophilum (fungus)
KeywordsPROTEIN TRANSPORT/INHIBITOR / Vps29 / Retromer / Endosome / Protein transport / cyclic peptide / inhibitor / PROTEIN TRANSPORT-INHIBITOR complex

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