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Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties.

Journal article
Authors Viktor Ahlberg Gagnér
Ida Lundholm
Maria-Jose Garcia-Bonete
Helena Rodilla
Vitali Zhaunerchyk
Gleb Bourenkov
Thomas Schneider
Jan Stake
Gergely Katona
Published in Scientific reports
Volume 9
Issue 1
Pages 19281
ISSN 2045-2322
Publication year 2019
Published at Department of Chemistry and Molecular Biology
Department of Physics (GU)
Pages 19281
Language en
Links dx.doi.org/10.1038/s41598-019-55777...
www.ncbi.nlm.nih.gov/entrez/query.f...
Subject categories Structural and vibration physics, Structural Biology, Biological physics, Biochemistry and Molecular Biology, Biochemistry, Condensed Matter Physics

Abstract

Low-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increased upon terahertz irradiation. Atomic displacement similarities developed between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arises from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. The displacement correlation between these atoms were detected by a hierarchical clustering method, which can assist the analysis of other ultra-high resolution crystal structures. These experimental and analytical tools provide a detailed description of protein dynamics to complement the structural information from static diffraction experiments.

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