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Miller FS, Crone KK, Jensen MR, Shaw S, Harcombe WR, Elias MH, Freeman MF. Conformational rearrangements enable iterative backbone N-methylation in RiPP biosynthesis. Nat Commun 2021; 12:5355. [PMID: 34504067 PMCID: PMC8429565 DOI: 10.1038/s41467-021-25575-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 08/18/2021] [Indexed: 11/10/2022] Open
Abstract
Peptide backbone α-N-methylations change the physicochemical properties of amide bonds to provide structural constraints and other favorable characteristics including biological membrane permeability to peptides. Borosin natural product pathways are the only known ribosomally encoded and posttranslationally modified peptides (RiPPs) pathways to incorporate backbone α-N-methylations on translated peptides. Here we report the discovery of type IV borosin natural product pathways (termed 'split borosins'), featuring an iteratively acting α-N-methyltransferase and separate precursor peptide substrate from the metal-respiring bacterium Shewanella oneidensis. A series of enzyme-precursor complexes reveal multiple conformational states for both α-N-methyltransferase and substrate. Along with mutational and kinetic analyses, our results give rare context into potential strategies for iterative maturation of RiPPs.
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Affiliation(s)
- Fredarla S Miller
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, St. Paul, MN, USA
| | - Kathryn K Crone
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, St. Paul, MN, USA
| | - Matthew R Jensen
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, MN, USA
- Science Department, Concordia University-St. Paul, St. Paul, MN, USA
| | - Sudipta Shaw
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, St. Paul, MN, USA
| | - William R Harcombe
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, MN, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota-Twin Cities, St. Paul, MN, USA
| | - Mikael H Elias
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, St. Paul, MN, USA.
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, MN, USA.
| | - Michael F Freeman
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, St. Paul, MN, USA.
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, MN, USA.
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Haack M, Enck S, Seger H, Geyer A, Beck-Sickinger AG. Pyridone dipeptide backbone scan to elucidate structural properties of a flexible peptide segment. J Am Chem Soc 2008; 130:8326-36. [PMID: 18529062 DOI: 10.1021/ja8004495] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Whereas the C-terminal fragment of neuropeptide Y (NPY) has been structurally well-defined both in solution and as membrane-bound, detailed structural information regarding the proline-rich N-terminus is still missing. The systematic variation of each position by a conformationally constrained pyridone dipeptide building block within the amino terminal segment of NPY leads to a systematic receptor subtype selectivity of the neuropeptide. Thereby, the systematic dipeptide scan proved superior to the traditional L-Ala scan because it showed how to modify the N-terminus in order to obtain increasingly more Y1 or Y5 receptor selective ligands. NMR and CD spectroscopic analyses were used to characterize the stepwise rigidification of the N-terminus of NPY when up to three dipeptide building blocks were incorporated by solid-phase peptide synthesis. The pyridone dipeptide increases the hydrophobicity of the amino terminus of NPY, and this allows the tuning of the membrane affinity of NPY. The amphiphilic C-terminal helix of 3-fold-substituted NPY thus becomes visible by selective line broadening in the (1)H NMR. Accordingly, we could structurally characterize protein segments that are too flexible for other methods.
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Affiliation(s)
- Michael Haack
- Institute of Biochemistry, Universität Leipzig, Brüderstr. 34, D-04103 Leipzig, Germany
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