title: Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins.
abstract: Resonance assignment is a prerequisite for almost any NMR-based study of proteins. It can be very challenging in some cases, however, due to the nature of the protein under investigation. This is the case with intrinsically disordered proteins, for example, whose NMR spectra suffer from low chemical shifts dispersion and generally low resolution. For these systems, sequence specific assignment is highly time-consuming, so the prospect of using automatic strategies for their assignment is very attractive. In this article we present a new version of the automatic assignment program TSAR dedicated to intrinsically disordered proteins. In particular, we demonstrate how the automatic procedure can be improved by incorporating methods for amino acid recognition and information on chemical shifts in selected amino acids. The approach was tested in silico on 16 disordered proteins and experimentally on α-synuclein, with remarkably good results.
authors.affiliation: CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Piai
authors.affiliation: CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Gonnelli
authors.affiliation: CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy.
authors.forename: Isabella C
authors.initials: IC
authors.lastname: Felli
authors.affiliation: CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy.
authors.forename: Roberta
authors.initials: R
authors.lastname: Pierattelli
authors.affiliation: Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland.
authors.forename: Krzysztof
authors.initials: K
authors.lastname: Kazimierczuk
authors.affiliation: Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Grudziąż
authors.affiliation: Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.
authors.forename: Wiktor
authors.initials: W
authors.lastname: Koźmiński
authors.affiliation: Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland. anzaw@chem.uw.edu.pl.
authors.forename: Anna
authors.initials: A
authors.lastname: Zawadzka-Kazimierczuk
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D064267:Intrinsically Disordered Proteins / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods
chemical_list: D000596:Amino Acids; D064267:Intrinsically Disordered Proteins
keywords: 13C direct-detection NMR; Amino acid-selective experiments; Automatic assignment; Compressed sensing; High-dimensional NMR experiment; Intrinsically disordered proteins; Non-uniform sampling; Sparse multidimensional Fourier transform