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

Justin, BergmannLund University,Lunds universitet,Beräkningskemi,Enheten för fysikalisk och teoretisk kemi,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Computational Chemistry,Physical and theoretical chemistry,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH (författare)

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.

Davidson, MaxUniversity of Western Australia, Crawley (författare)
Oksanen, EskoEuropean Spallation Source ESS ERIC(Swepub:lu)esss-eoe (författare)
Ryde, UlfLund University,Lunds universitet,Beräkningskemi,Enheten för fysikalisk och teoretisk kemi,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Computational Chemistry,Physical and theoretical chemistry,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH(Swepub:lu)teok-ury (författare)
Jayatilaka, DylanUniversity of Western Australia, Crawley (författare)
BeräkningskemiEnheten för fysikalisk och teoretisk kemi (creator_code:org_t)

Av författaren/redakt...: Justin, Bergmann; Davidson, Max; Oksanen, Esko; Ryde, Ulf; Jayatilaka, Dyla ...

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