Systematic enhancement of protein crystallization efficiency by bulk lysine-to-arginine (KR) substitution.
circular dichroism spectroscopy
homology analysis
protein crystallization
protein engineering
protein solubility
protein thermodynamics
x-ray crystallography
Journal
Protein science : a publication of the Protein Society
ISSN: 1469-896X
Titre abrégé: Protein Sci
Pays: United States
ID NLM: 9211750
Informations de publication
Date de publication:
Mar 2024
Mar 2024
Historique:
revised:
01
01
2024
received:
18
06
2023
accepted:
02
01
2024
medline:
15
2
2024
pubmed:
15
2
2024
entrez:
15
2
2024
Statut:
ppublish
Résumé
Structural genomics consortia established that protein crystallization is the primary obstacle to structure determination using x-ray crystallography. We previously demonstrated that crystallization propensity is systematically related to primary sequence, and we subsequently performed computational analyses showing that arginine is the most overrepresented amino acid in crystal-packing interfaces in the Protein Data Bank. Given the similar physicochemical characteristics of arginine and lysine, we hypothesized that multiple lysine-to-arginine (KR) substitutions should improve crystallization. To test this hypothesis, we developed software that ranks lysine sites in a target protein based on the redundancy-corrected KR substitution frequency in homologs. This software can be run interactively on the worldwide web at https://www.pxengineering.org/. We demonstrate that three unrelated single-domain proteins can tolerate 5-11 KR substitutions with at most minor destabilization, and, for two of these three proteins, the construct with the largest number of KR substitutions exhibits significantly enhanced crystallization propensity. This approach rapidly produced a 1.9 Å crystal structure of a human protein domain refractory to crystallization with its native sequence. Structures from Bulk KR-substituted domains show the engineered arginine residues frequently make hydrogen-bonds across crystal-packing interfaces. We thus demonstrate that Bulk KR substitution represents a rational and efficient method for probabilistic engineering of protein surface properties to improve crystallization.
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e4898Subventions
Organisme : NIH HHS
Pays : United States
Informations de copyright
© 2024 The Protein Society.
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