Controlling protein crystallization by free energy guided design of interactions at crystal contacts
| Autor: | Dariusch Hekmat, Robert Janowski, Dierk Niessing, Johannes Hermann, Daniel Bischoff, Martin Zacharias, Dirk Weuster-Botz, Phillip Grob |
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| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Materials science
General Chemical Engineering Molekularbewegung Molecular dynamics 01 natural sciences law.invention Inorganic Chemistry Hydrophobic effect Dry contact 03 medical and health sciences DDC 570 / Life sciences law ddc:570 0103 physical sciences free energy calculation Proteindesign General Materials Science Crystallization technical protein crystallization 030304 developmental biology 0303 health sciences Crystallography 010304 chemical physics Hydrogen bond Intermolecular force protein engineering Protein engineering Condensed Matter Physics molecular dynamics crystal nucleation and growth QD901-999 Chemical physics Protein crystallization Crystal Nucleation And Growth Free Energy Calculation Molecular Dynamics Protein Engineering Technical Protein Crystallization |
| Zdroj: | Crystals 11:588 (2021) Crystals Volume 11 Issue 6 Crystals, Vol 11, Iss 588, p 588 (2021) |
| Popis: | 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 crystallizability. 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. publishedVersion |
| Databáze: | OpenAIRE |
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