Coarse-Grained Diffraction Template Matching Model to Retrieve Multiconformational
Models for Biomolecule Structures from Noisy Diffraction Patterns
Posted on 2020-06-12 - 19:09
Biomolecular
imaging using X-ray free-electron lasers (XFELs) has
been successfully applied to serial femtosecond crystallography. However,
the application of single-particle analysis for structure determination
using XFELs with 100 nm or smaller biomolecules has two practical
problems: the incomplete diffraction data sets for reconstructing
3D assembled structures and the heterogeneous conformational states
of samples. A new diffraction template matching method is thus presented
here to retrieve a plausible 3D structural model based on single noisy
target diffraction patterns, assuming candidate structures. Two concepts
are introduced here: prompt candidate diffraction, generated by enhanced
sampled coarse-grain (CG) candidate structures, and efficient molecular
orientation searching for matching based on Bayesian optimization.
A CG model-based diffraction-matching protocol is proposed that achieves
a 100-fold speed increase compared to exhaustive diffraction matching
using an all-atom model. The conditions that enable multiconformational
analysis were also investigated by simulated diffraction data for
various conformational states of chromatin and ribosomes. The proposed
method can enable multiconformational analysis, with a structural
resolution of at least 20 Å for 270–800 Å flexible
biomolecules, in experimental single-particle structure analyses that
employ XFELs.
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Tokuhisa, Atsushi; Kanada, Ryo; Chiba, Shuntaro; Terayama, Kei; Isaka, Yuta; Ma, Biao; et al. (2020). Coarse-Grained Diffraction Template Matching Model to Retrieve Multiconformational
Models for Biomolecule Structures from Noisy Diffraction Patterns. ACS Publications. Collection. https://doi.org/10.1021/acs.jcim.0c00131
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AUTHORS (8)
AT
Atsushi Tokuhisa
RK
Ryo Kanada
SC
Shuntaro Chiba
KT
Kei Terayama
YI
Yuta Isaka
BM
Biao Ma
NK
Narutoshi Kamiya
YO
Yasushi Okuno
KEYWORDS
Noisy Diffraction Patterns Biomolec...CG model-based diffraction-matching...XFELX-ray free-electron laserssingle-particle structure analysescandidate structures3 DCoarse-Grained Diffraction TemplateRetrieve Multiconformational Modelstarget diffraction patternsdiffraction data setsmulticonformational analysis