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DIADECOMP: a new approach to analyze decompositions from projection spectroscopy

Journal article
Authors Jonas Fredriksson
Viviane de Paula
Ana Paula Valente
Fabio Almeida
Martin Billeter
Published in Journal of magnetic resonance
Volume 273
Pages 1-8
ISSN 1090-7807
Publication year 2016
Published at Department of Chemistry and Molecular Biology
Pages 1-8
Language en
Links dx.doi.org/10.1016/j.jmr.2016.10.00...
Keywords NMR; proteins; projection spectroscopy; decompositions; defensins
Subject categories Structural Biology, Molecular biophysics

Abstract

We demonstrate for the first time a complete small protein characterization with the projection-decomposition approach, including full assignments as well as determination of the 3D fold. In TOCSY- and NOESY-type 4D experiments, pairing of signals from hydrogens and from their respective heavy atoms in decompositions represents a new problem. An approach, referred to as “DIADECOMP” (diagonal decomposition), is introduced to solve this problem; it consists of two separate decompositions of the input projections, differing in a 45° rotation of the spectral axes. While DIADECOMP requires a somewhat complex formulation, in practice it results in observing signals in the rotated decompositions that correspond to sums or differences of frequencies. When applied to a small protein, human defensin β6, the analysis of a HCC(CO)NH-TOCSY with DIADECOMP results in largely unambiguous assignments of the aliphatic side chain groups. Furthermore, DIADECOMP applied to a 15N-HSQC-NOESY-15N-HSQC provides all expected short distances between amide groups (defined as all HN-HN distances <3.5 Å in a reference structure). It is worth noting that short HN-HN distances unambiguously define α-helices, the alignment of β-strands in sheets, as well as the presence of β-bulges. This approach of using a minimal amount of NMR data, namely four projection experiments recorded in ~2.5 days, resulted for the human defensin β6 in complete assignments and a backbone fold with a RMSD of the non-flexible structure of 0.6 Å. Uniqueness of decompositions specifically from TOCSY- and NOESY-type 4D experiments is discussed

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