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

Author

Viktor Ahlberg Gagnér

University of Gothenburg

Ida Lundholm

University of Gothenburg

Maria-Jose Garcia-Bonete

University of Gothenburg

Helena Rodilla

Chalmers, Microtechnology and Nanoscience (MC2), Terahertz and Millimetre Wave Laboratory

Ran Friedman

Linnaeus University

Vitali Zhaunerchyk

University of Gothenburg, Department of Physics

Gleb Bourenkov

European Molecular Biology Laboratory Hamburg

Thomas Schneider

European Molecular Biology Laboratory Hamburg

Jan Stake

Chalmers, Microtechnology and Nanoscience (MC2), Terahertz and Millimetre Wave Laboratory

Gergely Katona

University of Gothenburg

Scientific Reports

2045-2322 (ISSN)

Vol. 9 1 19281

Areas of Advance

Information and Communication Technology

Life Science Engineering (2010-2018)

Infrastructure

Kollberg Laboratory

Subject Categories

Biochemistry and Molecular Biology

Cell and Molecular Biology

Biophysics

Other Electrical Engineering, Electronic Engineering, Information Engineering

DOI

10.1038/s41598-019-55777-5

More information

Latest update

4/20/2020