High accuracy achieved predicting stabilizing surface mutations in UBA(1)

Rothfuss, Mike T.; Becht, Dustin C.; Zeng, Baisen; McClelland, Levi J.; Yates-Hansen, Cindee; Bowler, Bruce E.

doi:10.1016/j.bpj.2021.11.2492

Cited by 1 publication

(1 citation statement)

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“…For instance, EmCAST, which relies on an empirical potential related to C α dihedral angle preferences, has been developed to predict stabilizing mutations, particularly those involving surface hydrophilic residues in monomeric proteins. 46 However, accurately assessing the interactions between surface hydrophobic residues, especially aromatic ones, and solvent molecules remains a challenging task in computation protein redesign. It's imperative to acknowledge that urea and Gnd + ions can interact not only with hydrophilic but also hydrophobic side chains.…”

Section: Discussionmentioning

confidence: 99%

Computational Enzyme Redesign Enhances Tolerance to Denaturants for Peptide C-Terminal Amidation

Zhu,

Sun,

Pang

et al. 2024

JACS Au

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The escalating demand for biocatalysts in pharmaceutical and biochemical applications underscores the critical imperative to enhance enzyme activity and durability under high denaturant concentrations. Nevertheless, the development of a practical computational redesign protocol for improving enzyme tolerance to denaturants is challenging due to the limitations of relying solely on model-driven approaches to adequately capture denaturant−enzyme interactions. In this study, we introduce an enzyme redesign strategy termed GRAPE_DA, which integrates multiple data-driven and model-driven computational methods to mitigate the sampling biases inherent in a single approach and comprehensively predict beneficial mutations on both the protein surface and backbone. To illustrate the methodology's effectiveness, we applied it to engineer a peptidylamidoglycolate lyase, resulting in a variant exhibiting up to a 24-fold increase in peptide C-terminal amidation activity under 2.5 M guanidine hydrochloride. We anticipate that this integrated engineering strategy will facilitate the development of enzymatic peptide synthesis and functionalization under denaturing conditions and highlight the role of engineering surface residues in governing protein stability.

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Section: Discussionmentioning

confidence: 99%