TY - JOUR
T1 - fragHAR: towards ab initio quantum crystallographic X-ray structure refinement for polypeptides and proteins
AU - Bergmann, Justin
AU - Davidson, Max
AU - Oksanen, Esko
AU - Ryde, Ulf
AU - Jayatilaka, Dylan
PY - 2020/3/1
Y1 - 2020/3/1
N2 - We describe 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, and thereby speed up quantum-crystallographic Hirshfeld atom refinement (HAR) calculations. We find that the geometric and atomic displacement parameters from the new fragHAR method are essentially unchanged from a HAR refinement on the complete unfragmented system when tested on di-, tri- and hexapeptides. The largest changes are for parameters describing hydrogen atoms involved in hydrogen-bond interactions, but we show that these discrepancies can be removed by including the interacting fragments as a single larger fragment in the fragmentation scheme. Significant speedups are observed for the larger systems. With this approach we are able to perform a highly parallelized HAR in reasonable times for large systems. The method is implemented in the TONTO software.
AB - We describe 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, and thereby speed up quantum-crystallographic Hirshfeld atom refinement (HAR) calculations. We find that the geometric and atomic displacement parameters from the new fragHAR method are essentially unchanged from a HAR refinement on the complete unfragmented system when tested on di-, tri- and hexapeptides. The largest changes are for parameters describing hydrogen atoms involved in hydrogen-bond interactions, but we show that these discrepancies can be removed by including the interacting fragments as a single larger fragment in the fragmentation scheme. Significant speedups are observed for the larger systems. With this approach we are able to perform a highly parallelized HAR in reasonable times for large systems. The method is implemented in the TONTO software.
UR - http://www.scopus.com/inward/record.url?scp=85081533622&partnerID=8YFLogxK
U2 - 10.1107/S2052252519015975
DO - 10.1107/S2052252519015975
M3 - Article
C2 - 32148844
SN - 2052-2525
VL - 7
SP - 158
EP - 165
JO - IUCrJ
JF - IUCrJ
IS - Part 2
ER -