Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties
Artikel i vetenskaplig tidskrift, 2019

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. © 2019, The Author(s).

Författare

Viktor Ahlberg Gagnér

Göteborgs universitet

Ida Lundholm

Göteborgs universitet

Maria-Jose Garcia-Bonete

Göteborgs universitet

Helena Rodilla

Chalmers, Mikroteknologi och nanovetenskap (MC2), Terahertz- och millimetervågsteknik

Ran Friedman

Linnéuniversitetet: Kalmar

Vitali Zhaunerchyk

Göteborgs universitet, Institutionen för fysik

Gleb Bourenkov

European Molecular Biology Laboratory Hamburg

Thomas Schneider

European Molecular Biology Laboratory Hamburg

Jan Stake

Chalmers, Mikroteknologi och nanovetenskap (MC2), Terahertz- och millimetervågsteknik

Gergely Katona

Göteborgs universitet

Scientific Reports

2045-2322 (ISSN)

Vol. 9 1 19281

Styrkeområden

Informations- och kommunikationsteknik

Livsvetenskaper och teknik (2010-2018)

Infrastruktur

Kollberglaboratoriet

Ämneskategorier

Biokemi och molekylärbiologi

Cell- och molekylärbiologi

Biofysik

Annan elektroteknik och elektronik

DOI

10.1038/s41598-019-55777-5

Mer information

Senast uppdaterat

2020-01-13