Visualization and edition of polymers with non linear structures

Maude Pupin

Bonsai teamCRIStAL

Lille University

Outline

● Tool design for nonribosomal peptides– Extensible to any complex polymer

● Context– What are nonribosomal peptides ?

● Structure representations● Tools● Conclusion and future work

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What are nonribosomal peptides ?

> 500 monomers(amino acids and others)

complex 2D structures(linear, cycles, branches)

various activities(antibiotic, siderophore...)

synthesized by huge enzymatic complexes

5 main specificitiesfor NRPs

synthesizedby bacteriaand fungi

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What are nonribosomal peptides ?

> 20 amino acidsfatty acids

carbohydratespolyketides

chromophores

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What are nonribosomal peptides ?

linear

cyclic partial cyclic

other

double cyclicbranched

various 2D structures, mainly non linear

ACV

actinomycin Dbacillibactin

vancomycin

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Specific needs for interesting peptides

Biological interest:unusual peptides

Computer science interest:need for specific algorithms

no existingtools

http://bioinfo.lifl.fr/norine/

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Norine: 4 structure representationsMonomeric structure Atomic structure

Textual representation for both structures

D-Pro,Ala,D-Ala,C10:0-NH2(2)-Ep(9)-oxo(8)@1,3@0,2@1,3@0,2CC2NC(=O)C(C)NC(=O)C3CCCN3(C(=O)C(CCCCCC(=O)C1CO1)NC2(=O))

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smiles2monomers

From the chemical structure to the monomeric structure

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Monomeric editor

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Monomeric visualisation

Algorithm for graph drawingSpecific strategies for simple structures

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Conclusion and future work

● Visualization and edition of any polymers● Source code available

– https://github.com/JurMich/EditORINE

– used in Norine

● Extension to edition of atomic structures drawn with monomers

● Interaction with HELM notation + Pistoia Alliance Public resources or BIRD (PDB peptides)

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Bonsai teamCRIStAL

Lille University

S. CabocheY. Dufresne

A. FlissiS. JanotL. Noé

L. Tonon

Collaborators

ProBioGEMInstitut C. Viollette

Lille University

M. ChevalierQ. EsmaeelC. FlahautP. JacquesV. Leclère

BiosustainabilityNovo Nordisk F

Tech Univ DenmarkK. Blin

T. Weber

PIGSwiss Institute of

bioinformaticsF. LisacekM. MullerE. Ricart

bililleLille University

J. Michalik

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What are nonribosomal peptides ?Various activities, several activities for some peptides

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What are nonribosomal peptides ?

Remediation of soils contaminated with

toxic metals

Plant protection against pathogensAvoid transplantation

rejection

Antibiotic

Anti-tumor

Diverse industrial applications

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NRP synthesis: high specificity

a givennonribosomal

peptide synthetase

a specificnonribosomal

peptide