Targeted mutations and MD simulations of a methanol-stable lipase YLIP9 from Yarrowia lipolytica MSR80 to develop a biodiesel enzyme

Syal, Poonam; Verma, Ved Vrat; Gupta, Rani

doi:10.1016/j.ijbiomac.2017.06.003

Cited by 15 publications

(10 citation statements)

References 39 publications

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“…The conformational change is seen in simulations where BCL lid closure begins to include burial of the hydrophobic or nonpolar residues that are surface-accessible in the crystal structure, as has been seen previously. 14,39,43,56 Notably, the mechanism of lid closure indicated here is different than what has been seen in previous simulations of BCL performed in pure water environments. 38,39 Previous results described lid closure within two replicates of 20 ns of MD simulations, caused by unfolding of α5 and a concerted fluctuation of α5 and α9, whereas in the significantly longer time scale MD simulations performed at the bulk-solvent/lipid interface presented here, α5 motion and α9 are not concerted and α5 movement associated with lid closure occurs over 110 ns in three of five replicates.…”

Section: The Journal Of Physical Chemistry Letterscontrasting

confidence: 77%

“…In the context of protein dynamics, our findings suggest that (1) BCL dynamics sequester into two sets of residue fluctuations only in a negatively charged lipid environment, (2) changes in concentration of neutral lipids do not greatly impact BCL activity-related dynamics, and (3) charged lipid bilayers decrease the number of unique conformational states of BCL. The conformational change is seen in simulations where BCL lid closure begins to include burial of the hydrophobic or nonpolar residues that are surface-accessible in the crystal structure, as has been seen previously. ,,, Notably, the mechanism of lid closure indicated here is different than what has been seen in previous simulations of BCL performed in pure water environments. , Previous results described lid closure within two replicates of 20 ns of MD simulations, caused by unfolding of α5 and a concerted fluctuation of α5 and α9, whereas in the significantly longer time scale MD simulations performed at the bulk-solvent/lipid interface presented here, α5 motion and α9 are not concerted and α5 movement associated with lid closure occurs over 110 ns in three of five replicates. This suggests that the mechanism of lid closure could be different depending on the chemical environment and thus that MD simulations of membrane-embedded proteins should take into consideration realistic interfacial environments.…”

supporting

confidence: 45%

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Impacts of Lipase Enzyme on the Surface Properties of Marine Aerosols

Schiffer

Luo

Dommer

et al. 2018

J. Phys. Chem. Lett.

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Triacylglycerol lipases have recently been shown to be transferred from the ocean to the atmosphere in atmospheric sea spray aerosol (SSA). Lipases have the potential to alter the composition of SSA; however, the structure and properties of enzymes in the high salt, high ionic strength, and low pH conditions found in SSA have never been explored. Here, we study the dynamics of Burkholderia cepacia triacylglycerol lipase (BCL) at SSA model surfaces comprised of palmitic acid and dipalmitoylphosphatidic acid (DPPA), two commonly found lipids at SSA surfaces. Surface adsorption Langmuir isotherm experiments and all-atom explicit solvent molecular dynamics simulations together illuminate how and why BCL expands the ordering of lipids at palmitic acid surfaces the most at pH < 4 and the least in DPPA surfaces at pH 6. Taken together, these results represent a first glimpse into the complex interplay between lipid surface structure and protein dynamics within enzyme-containing aerosols.

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Section: The Journal Of Physical Chemistry Letterscontrasting

confidence: 77%

supporting

confidence: 45%

Impacts of Lipase Enzyme on the Surface Properties of Marine Aerosols

Schiffer

Luo

Dommer

et al. 2018

J. Phys. Chem. Lett.

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“…The wildtype HT1 had a half-life time of 540, 85 and 16 min at 60, 70, and 80 °C, respectively, with a melting temperature at 70.9 °C [ 16 ]. A previous study by Syal et al [ 24 ] demonstrated that YLIPL1 and YLIP9L1Bp3 lipases exhibited better thermostability compared to their wildtype, YLIP9 lipase. Similarly, a directed evolution on Bacillus licheniformis lipase resulted in an increase of lipase thermostability [ 25 ].…”

Section: Discussionmentioning

confidence: 99%

Ion-Pair Interaction and Hydrogen Bonds as Main Features of Protein Thermostability in Mutated T1 Recombinant Lipase Originating from Geobacillus zalihae

et al. 2020

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A comparative structure analysis between space- and an Earth-grown T1 recombinant lipase from Geobacillus zalihae had shown changes in the formation of hydrogen bonds and ion-pair interactions. Using the space-grown T1 lipase validated structure having incorporated said interactions, the recombinant T1 lipase was re-engineered to determine the changes brought by these interactions to the structure and stability of lipase. To understand the effects of mutation on T1 recombinant lipase, five mutants were developed from the structure of space-grown T1 lipase and biochemically characterized. The results demonstrate an increase in melting temperature up to 77.4 °C and 76.0 °C in E226D and D43E, respectively. Moreover, the mutated lipases D43E and E226D had additional hydrogen bonds and ion-pair interactions in their structures due to the improvement of stability, as observed in a longer half-life and an increased melting temperature. The biophysical study revealed differences in β-Sheet percentage between less stable (T118N) and other mutants. As a conclusion, the comparative analysis of the tertiary structure and specific residues associated with ion-pair interactions and hydrogen bonds could be significant in revealing the thermostability of an enzyme with industrial importance.

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“…In some cases, there is a need to rebuild the lid by site‐directed mutation for enhancing the catalytic efficiency and tailoring the substrate selectivity of lipase in the reaction system, for example, to design a mutation of lipase from Yarrowia lipolytica with enhanced activity toward long‐chain fatty acids by introducing E116L or S119V in the lid (Syal et al., 2017). In this way, special demands from the reaction in food industry would be satisfied, for example, the production of the medium–long–medium‐structured lipids that typically contain medium‐chain fatty acids at sn‐1,3 and long‐chain fatty acids (C14–C24) at sn‐2 positions.…”

Section: Strategies Of Rebuilding the Lipase Lid For Food Applicationsmentioning

confidence: 99%

Rebuilding the lid region from conformational and dynamic features to engineering applications of lipase in foods: Current status and future prospects

Chen

Khan

He³

et al. 2022

Comp Rev Food Sci Food Safe

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The applications of lipases in esterification, amidation, and transesterification have broadened their potential in the production of fine compounds with high cumulative values. Mostly, the catalytic triad of lipases is covered by either one or two mobile peptides called the “lid” that control the substrate channel to the catalytic center. The lid holds unique conformational allostery via interfacial activation to regulate the dynamics and catalytic functions of lipases, thereby highlighting its importance in redesigning these enzymes for industrial applications. The structural characteristic of lipase, the dynamics of lids, and the roles of lid in lipase catalysis were summarized, providing opportunities for rebuilding lid region by biotechniques (e.g., metagenomic technology and protein engineering) and enzyme immobilization. The review focused on the advantages and disadvantages of strategies rebuilding the lid region. The main shortcomings of biotechnologies on lid rebuilding were discussed such as negative effects on lipase (e.g., a decrease of activity). Additionally, the main shortcomings (e.g., enzyme desorption at high temperatre) in immobilization on hydrophobic supports via interfacial action were presented. Solutions to the mentioned problems were proposed by combinations of computational design with biotechnologies, and improvements of lipase immobilization (e.g., immobilization protocols and support design). Finally, the review provides future perspectives about designing hyperfunctional lipases as biocatalysts in the food industry based on lid conformation and dynamics.

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Targeted mutations and MD simulations of a methanol-stable lipase YLIP9 from Yarrowia lipolytica MSR80 to develop a biodiesel enzyme

Cited by 15 publications

References 39 publications

Impacts of Lipase Enzyme on the Surface Properties of Marine Aerosols

Impacts of Lipase Enzyme on the Surface Properties of Marine Aerosols

Ion-Pair Interaction and Hydrogen Bonds as Main Features of Protein Thermostability in Mutated T1 Recombinant Lipase Originating from Geobacillus zalihae

Rebuilding the lid region from conformational and dynamic features to engineering applications of lipase in foods: Current status and future prospects

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