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FragHAR : Towards ab initio quantum-crystallographic X-ray structure refinement for polypeptides and proteins

Justin, Bergmann LU ; Davidson, Max ; Oksanen, Esko LU ; Ryde, Ulf LU orcid and Jayatilaka, Dylan (2020) In IUCrJ 7(2). p.158-165
Abstract

The first ab initio aspherical structure refinement against experimental X-ray structure factors for polypeptides and proteins using a fragmentation approach to break up the protein into residues and solvent, thereby speeding up quantum-crystallographic Hirshfeld atom refinement (HAR) calculations, is described. It it found that the geometric and atomic displacement parameters from the new fragHAR method are essentially unchanged from a HAR on the complete unfragmented system when tested on dipeptides, tripeptides and hexapeptides. The largest changes are for the parameters describing H atoms involved in hydrogen-bond interactions, but it is shown that these discrepancies can be removed by including the interacting fragments as a single... (More)

The first ab initio aspherical structure refinement against experimental X-ray structure factors for polypeptides and proteins using a fragmentation approach to break up the protein into residues and solvent, thereby speeding up quantum-crystallographic Hirshfeld atom refinement (HAR) calculations, is described. It it found that the geometric and atomic displacement parameters from the new fragHAR method are essentially unchanged from a HAR on the complete unfragmented system when tested on dipeptides, tripeptides and hexapeptides. The largest changes are for the parameters describing H atoms involved in hydrogen-bond interactions, but it is shown that these discrepancies can be removed by including the interacting fragments as a single larger fragment in the fragmentation scheme. Significant speed-ups are observed for the larger systems. Using this approach, it is possible to perform a highly parallelized HAR in reasonable times for large systems. The method has been implemented in the TONTO software.

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author
; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
H atoms, Hirshfeld atom refinement, Peptides, Quantum crystallography
in
IUCrJ
volume
7
issue
2
pages
8 pages
publisher
International Union of Crystallography
external identifiers
  • pmid:32148844
  • scopus:85081533622
ISSN
2052-2525
DOI
10.1107/S2052252519015975
language
English
LU publication?
yes
id
d2944f81-cc68-47f6-89d8-4c1b9b72fb15
date added to LUP
2020-04-02 16:01:30
date last changed
2024-09-04 19:35:32
@article{d2944f81-cc68-47f6-89d8-4c1b9b72fb15,
  abstract     = {{<p>The first ab initio aspherical structure refinement against experimental X-ray structure factors for polypeptides and proteins using a fragmentation approach to break up the protein into residues and solvent, thereby speeding up quantum-crystallographic Hirshfeld atom refinement (HAR) calculations, is described. It it found that the geometric and atomic displacement parameters from the new fragHAR method are essentially unchanged from a HAR on the complete unfragmented system when tested on dipeptides, tripeptides and hexapeptides. The largest changes are for the parameters describing H atoms involved in hydrogen-bond interactions, but it is shown that these discrepancies can be removed by including the interacting fragments as a single larger fragment in the fragmentation scheme. Significant speed-ups are observed for the larger systems. Using this approach, it is possible to perform a highly parallelized HAR in reasonable times for large systems. The method has been implemented in the TONTO software.</p>}},
  author       = {{Justin, Bergmann and Davidson, Max and Oksanen, Esko and Ryde, Ulf and Jayatilaka, Dylan}},
  issn         = {{2052-2525}},
  keywords     = {{H atoms; Hirshfeld atom refinement; Peptides; Quantum crystallography}},
  language     = {{eng}},
  number       = {{2}},
  pages        = {{158--165}},
  publisher    = {{International Union of Crystallography}},
  series       = {{IUCrJ}},
  title        = {{FragHAR : Towards ab initio quantum-crystallographic X-ray structure refinement for polypeptides and proteins}},
  url          = {{http://dx.doi.org/10.1107/S2052252519015975}},
  doi          = {{10.1107/S2052252519015975}},
  volume       = {{7}},
  year         = {{2020}},
}