Automated orientation of water molecules in neutron crystallographic structures of proteins
Eriksson, Axl ; Caldararu, Octav LU ; Ryde, Ulf LU
and Oksanen, Esko
LU
(2020)
In Acta Crystallographica Section D: Structural Biology
76.
p.1025-1032
- Abstract
The structure and function of proteins are strongly affected by the surrounding solvent water, for example through hydrogen bonds and the hydrophobic effect. These interactions depend not only on the position, but also on the orientation, of the water molecules around the protein. Therefore, it is often vital to know the detailed orientations of the surrounding ordered water molecules. Such information can be obtained by neutron crystallography. However, it is tedious and time-consuming to determine the correct orientation of every water molecule in a structure (there are typically several hundred of them), which is presently performed by manual evaluation. Here, a method has been developed that reliably automates the orientation of a... (More)
The structure and function of proteins are strongly affected by the surrounding solvent water, for example through hydrogen bonds and the hydrophobic effect. These interactions depend not only on the position, but also on the orientation, of the water molecules around the protein. Therefore, it is often vital to know the detailed orientations of the surrounding ordered water molecules. Such information can be obtained by neutron crystallography. However, it is tedious and time-consuming to determine the correct orientation of every water molecule in a structure (there are typically several hundred of them), which is presently performed by manual evaluation. Here, a method has been developed that reliably automates the orientation of a water molecules in a simple and relatively fast way. Firstly, a quantitative quality measure, the real-space correlation coefficient, was selected, together with a threshold that allows the identification of water molecules that are oriented. Secondly, the refinement procedure was optimized by varying the refinement method and parameters, thus finding settings that yielded the best results in terms of time and performance. It turned out to be favourable to employ only the neutron data and a fixed protein structure when reorienting the water molecules. Thirdly, a method has been developed that identifies and reorients inadequately oriented water molecules systematically and automatically. The method has been tested on three proteins, galectin-3C, rubredoxin and inorganic pyrophosphatase, and it is shown that it yields improved orientations of the water molecules for all three proteins in a shorter time than manual model building. It also led to an increased number of hydrogen bonds involving water molecules for all proteins.
(Less)
- author
- Eriksson, Axl
; Caldararu, Octav
LU
; Ryde, Ulf
LU
and Oksanen, Esko
LU
- organization
- publishing date
- 2020
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- automatic model building, automatic water orientation, hydrogen bonds, neutron crystallography, real-space correlation coefficient, solvent structure, water molecules
- in
- Acta Crystallographica Section D: Structural Biology
- volume
- 76
- pages
- 8 pages
- publisher
- John Wiley & Sons Inc.
- external identifiers
-
- scopus:85092652487
- pmid:33021504
- ISSN
- 2059-7983
- DOI
- 10.1107/S2059798320011729
- language
- English
- LU publication?
- yes
- id
- 2570b1da-bab1-4e53-b4e9-a767d34ce5b6
- date added to LUP
- 2020-11-09 09:35:20
- date last changed
- 2024-04-03 17:02:59
@article{2570b1da-bab1-4e53-b4e9-a767d34ce5b6,
abstract = {{<p>The structure and function of proteins are strongly affected by the surrounding solvent water, for example through hydrogen bonds and the hydrophobic effect. These interactions depend not only on the position, but also on the orientation, of the water molecules around the protein. Therefore, it is often vital to know the detailed orientations of the surrounding ordered water molecules. Such information can be obtained by neutron crystallography. However, it is tedious and time-consuming to determine the correct orientation of every water molecule in a structure (there are typically several hundred of them), which is presently performed by manual evaluation. Here, a method has been developed that reliably automates the orientation of a water molecules in a simple and relatively fast way. Firstly, a quantitative quality measure, the real-space correlation coefficient, was selected, together with a threshold that allows the identification of water molecules that are oriented. Secondly, the refinement procedure was optimized by varying the refinement method and parameters, thus finding settings that yielded the best results in terms of time and performance. It turned out to be favourable to employ only the neutron data and a fixed protein structure when reorienting the water molecules. Thirdly, a method has been developed that identifies and reorients inadequately oriented water molecules systematically and automatically. The method has been tested on three proteins, galectin-3C, rubredoxin and inorganic pyrophosphatase, and it is shown that it yields improved orientations of the water molecules for all three proteins in a shorter time than manual model building. It also led to an increased number of hydrogen bonds involving water molecules for all proteins.</p>}},
author = {{Eriksson, Axl and Caldararu, Octav and Ryde, Ulf and Oksanen, Esko}},
issn = {{2059-7983}},
keywords = {{automatic model building; automatic water orientation; hydrogen bonds; neutron crystallography; real-space correlation coefficient; solvent structure; water molecules}},
language = {{eng}},
pages = {{1025--1032}},
publisher = {{John Wiley & Sons Inc.}},
series = {{Acta Crystallographica Section D: Structural Biology}},
title = {{Automated orientation of water molecules in neutron crystallographic structures of proteins}},
url = {{http://dx.doi.org/10.1107/S2059798320011729}},
doi = {{10.1107/S2059798320011729}},
volume = {{76}},
year = {{2020}},
}