Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD

Diego F. Gauto; Olga O. Lebedenko; Lea Marie Becker; Isabel Ayala; Roman Lichtenecker; Nikolai R. Skrynnikov; Paul Schanda

doi:10.1016/j.yjsbx.2022.100079

Titel

Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD

Autor*in

Diego F. Gauto

Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes

Olga O. Lebedenko

Laboratory of Biomolecular NMR, St. Petersburg State University

Lea Marie Becker

Institute of Science and Technology Austria

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Abstract

Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein’s hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine ¹H-¹³C/²H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.

Stichwort

NERRD relaxation dispersionDipolar coupling measurementsMolecular dynamics simulations¹H relaxation¹³C relaxation

Objekt-Typ

journal article

Sprache

Englisch [eng]

Persistent identifier

phaidra.univie.ac.at/o:2060187

DOI

10.1016/j.yjsbx.2022.100079

Erschienen in

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