Abstract
The stability of enzymes is critical for their application in industrial processes, which generally require different conditions from the natural enzyme environment. Both rational and random protein engineering approaches have been used to increase stability, with the latter requiring extensive experimental effort for the screening of variants. Moreover, some general rules addressing the molecular origin of protein thermostability have been established. Herein, we demonstrate the use of molecular dynamics simulations to gain molecular level understanding of protein thermostability and to engineer stabilizing mutations. Carbonic anhydrase (CA) is an enzyme with a high potential for biotechnological carbon capture applications, provided it can be engineered to withstand the high temperature process environments, inevitable in most gas treatment units. In this study, we used molecular dynamics simulations at 343, 353, and 363 K to study the relationship between structure flexibility and thermostability in bacterial α-CAs and applied this knowledge to the design of mutants with increased stability. The most thermostable α-CA known, TaCA from Thermovibrio ammonificans, had the most rigid structure during molecular dynamics simulations, but also showed regions with high flexibility. The most flexible amino acids in these regions were identified from root mean square fluctuation (RMSF) studies, and stabilizing point mutations were predicted based on their capacity to improve the calculated free energy of unfolding. Disulfide bonds were also designed at sites with suitable geometries and selected based on their location at flexible sites, assessed by B-factor calculation. Molecular dynamics simulations allowed the identification of five mutants with lower RMSF of the overall structure at 400 K, compared to wild-type TaCA. Comparison of free-energy landscapes between wild-type TaCA and the most promising mutants, Pro165Cys-Gln170Cys and Asn140Gly, showed an increased conformational stability of the mutants at 400 K.
Highlights
Carbonic anhydrase (CA; EC 4.2.1.1) catalyzes the reversible hydration of carbon dioxide into hydrogen carbonate and a proton, with one of the fastest reaction rates known so far in nature.Enzymes in this class are encoded by six evolutionarily unrelated gene families (α, β, γ, δ, ξ and η), which all have a divalent metal-dependent mechanism, generally Zn-based, as a common feature.[1]
Molecular dynamics simulations were performed at three different temperatures, to understand which regions of the protein are the most flexible
Stabilizing mutations were subsequently designed in these regions and their ability to reduce flexibility was analyzed by molecular dynamics
Summary
Carbonic anhydrase (CA; EC 4.2.1.1) catalyzes the reversible hydration of carbon dioxide into hydrogen carbonate and a proton, with one of the fastest reaction rates known so far in nature. Enzymes in this class are encoded by six evolutionarily unrelated gene families (α, β, γ, δ, ξ and η), which all have a divalent metal-dependent mechanism, generally Zn-based, as a common feature.[1] One of the most studied CA families are the α-CAs, in which the Zn2+ ion, typically bound by three histidines, activates a hydroxyl group to perform the nucleophilic attack on CO2. Two approaches have been used for the development of stable CAs: isolation and characterization of enzymes from thermophilic bacteria,[5] and stability engineering by directed evolution under high temperature and pH conditions.[6]
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