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Controlling protein crystallization by free energy guided design of interactions at crystal contacts.
Crystals 11:588 (2021)
Protein crystallization can function as an effective method for protein purification or formulation. Such an application requires a comprehensive understanding of the intermolecular protein–protein interactions that drive and stabilize protein crystal formation to ensure a reproducible process. Using alcohol dehydrogenase from Lactobacillus brevis (LbADH) as a model system, we probed in our combined experimental and computational study the effect of residue substitutions at the protein crystal contacts on the crystallizability and the contact stability. Increased or decreased contact stability was calculated using molecular dynamics (MD) free energy simulations and showed excellent qualitative correlation with experimentally determined increased or decreased crystalliz-ability. The MD simulations allowed us to trace back the changes to their physical origins at the atomic level. Engineered charge–charge interactions as well as engineered hydrophobic effects could be characterized and were found to improve crystallizability. For example, the simulations revealed a redesigning of a water mediated electrostatic interaction (“wet contact”) into a water depleted hydrophobic effect (“dry contact”) and the optimization of a weak hydrogen bonding contact towards a strong one. These findings explained the experimentally found improved crystallizability. Our study emphasizes that it is difficult to derive simple rules for engineering crystallizability but that free energy simulations could be a very useful tool for understanding the contribution of crystal contacts for stability and furthermore could help guide protein engineering strategies to enhance crystallization for technical purposes.
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
Crystal Nucleation And Growth ; Free Energy Calculation ; Molecular Dynamics ; Protein Engineering ; Technical Protein Crystallization; Brevis Alcohol-dehydrogenase; Particle Mesh Ewald; Molecular-dynamics; Growth; Nucleation; Resolution; Simulations; Refinement; Mechanism; Lysozyme
ISSN (print) / ISBN
2073-4352
e-ISSN
2073-4352
Journal
Crystals
Quellenangaben
Volume: 11,
Issue: 6,
Article Number: 588
Publisher
MDPI
Publishing Place
St Alban-anlage 66, Ch-4052 Basel, Switzerland
Non-patent literature
Publications
Reviewing status
Peer reviewed
Institute(s)
Institute of Structural Biology (STB)
Grants
TUM Graduate School
German Research Foundation (DFG)
German Research Foundation (DFG)