Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data.
Acta Crystallogr D Struct Biol
; 75(Pt 4): 368-380, 2019 Apr 01.
Article
in En
| MEDLINE
| ID: mdl-30988254
ABSTRACT
Neutron crystallography is a powerful method to determine the positions of H atoms in macromolecular structures. However, it is sometimes hard to judge what would constitute a chemically reasonable model, and the geometry of H atoms depends more on the surroundings (for example the formation of hydrogen bonds) than heavy atoms, so that the empirical geometry information for the H atoms used to supplement the experimental data is often less accurate. These problems may be reduced by using quantum-mechanical calculations. A method has therefore been developed to combine quantum-mechanical calculations with joint crystallographic refinement against X-ray and neutron data. A first validation of this method is provided by re-refining the structure of the galectin-3 carbohydrate-recognition domain in complex with lactose. The geometry is improved, in particular for water molecules, for which the method leads to better-resolved hydrogen-bonding interactions. The method has also been applied to the active copper site of lytic polysaccharide monooxygenase and shows that the protonation state of the amino-terminal histidine residue can be determined.
Key words
Full text:
1
Database:
MEDLINE
Main subject:
Polysaccharides
/
Protein Conformation
/
Crystallography, X-Ray
/
Galectin 3
/
Mixed Function Oxygenases
/
Neutrons
Language:
En
Journal:
Acta Crystallogr D Struct Biol
Year:
2019
Type:
Article
Affiliation country:
Sweden