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

Bergmann Justin, Max Davidson, Esko Oksanen, Ulf Ryde, Dylan Jayatilaka

Research output: Contribution to journalArticlepeer-review

7 Citations (SciVal)

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 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.

Original languageEnglish
Pages (from-to)158-165
Number of pages8
JournalIUCrJ
Volume7
Issue number2
DOIs
Publication statusPublished - 2020 Mar

Subject classification (UKÄ)

  • Theoretical Chemistry
  • Structural Biology

Keywords

  • H atoms
  • Hirshfeld atom refinement
  • Peptides
  • Quantum crystallography

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