SEQUENCE SLIDER: integration of structural and genetic data to characterize isoforms from natural source

Abstract

ABSTRACTProteins isolated from natural source can be composed of a mixture of isoforms with similar physicochemical properties that coexists in final steps of purification, toxins being prominent examples. Sequence composition is enforced throughout structural studies even when unsubstantiated. Herein, we propose a novel perspective to address the usually neglected heterogeneity of natural products by integrating biophysical, genetic and structural data in our program SEQUENCE SLIDER.The aim is to assess the evidence supporting chemical composition in structure determination. Locally, we interrogate the experimental map to establish which side chains are supported by the structural data and the genetic information relating sequence conservation is integrated in this statistic. Hence, we build a constrained peptide database, containing most probable sequences to interpret mass spectrometry data (MS). In parallel, we perform MS de novo sequencing with genomic-based algorithms that foresee point mutations.We calibrated SLIDER with Gallus gallus lysozyme, for which sequence is unequivocally established and numerous natural isoforms are reported. We used SLIDER to characterise a metalloproteinase and a phospholipase A2-like protein from the venom of Bothrops moojeni and a crotoxin from Crotalus durissus collilineatus. This integrated approach offers a more realistic structural descriptor to characterize macromolecules isolated from natural source.Key pointsThe method SEQUENCE SLIDER integrates biophysical, genetic and structural data to assign sequence.It joins crystallography, mass spectrometry and phylogenetic data to characterize isoforms.Sequence heterogeneity of four proteins purified directly from snake venom was established.