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PDBsum entry 6svb
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References listed in PDB file
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Key reference
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Title
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Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties.
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Authors
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V.A.Gagnér,
I.Lundholm,
M.J.Garcia-Bonete,
H.Rodilla,
R.Friedman,
V.Zhaunerchyk,
G.Bourenkov,
T.Schneider,
J.Stake,
G.Katona.
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Ref.
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Sci Rep, 2019,
9,
19281.
[DOI no: ]
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PubMed id
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Abstract
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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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