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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 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
2020-04-03 03:00:03
@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},
  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},
}