Understanding domain movements and interactions of Pseudomonas aeruginosa lipase with lipid molecule tristearoyl glycerol: A molecular dynamics approach

Thiruvengadam, Kothai; Baskaran, Sarath Kumar; Pennathur, Gautam

doi:10.1016/j.jmgm.2018.09.005

Cited by 4 publications

(3 citation statements)

References 29 publications

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“…For running MD, C4 was bound in active site using protein-ligand docking before MD run. According to the previous report, the existence of ligand is important for maintaining open structure of lipase during MD [26]. Therefore, we performed protein-ligand docking before running MD.…”

Section: Resultsmentioning

confidence: 99%

Directed Evolution of Lipase to Have Enhanced Activity toward Short Chain Fatty Acids and Elucidation of Structural Features of Mutant

Shin

Seo

2023

KSBB

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Development of lipase having substrate specificity toward short chain fatty acids have industrial importance. Among the various lipase, LipC12 has substrate specificity to long chain fatty acids, good thermostability and tolerance in high concentration of aqueous solutions of polar organic solvents, thereby showing good evolvability. In this study, LipC12 was subjected to random mutation and mutant having activity to short chain fatty acids was identified using p-nitrophenol derivative of various length of fatty acids. Among the mutants, S4T mutant showed similar activity to 4-nitrophenyl acetate and 2-fold increased activity to 4-nitrophenyl butyrate when compared to the activity of wild type. Interestingly, S4T mutant showed 10% reduced activity to 4-nitrophenyl octanoate, 20% reduced activity to 4-nitrophenyl decanoate and 21% reduced activity to 4-nitrophenyl palmitate. To elucidate the reason for changed activities, molecular dynamics simulation was used. As a result, S4T showed higher rigidity in loop close to lid domain and C-terminal region than wild type. In addition, overall movement of S4T mutant showed higher compactness and lower solvent accessible surface area than wild type. All of these analysis results indicates the increased overall rigidity of S4T mutant structure in spite of small increase in some local structures such as lid domain and Cterminal region. Structural rigidity of S4T may be one reason for the increased activity to short chain fatty acids and decreased activity to long chain fatty acids.

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Section: Resultsmentioning

confidence: 99%

Directed Evolution of Lipase to Have Enhanced Activity toward Short Chain Fatty Acids and Elucidation of Structural Features of Mutant

Shin

Seo

2023

KSBB

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“…Molecular dynamics simulations of LipA with the disulfide bridge showed that the two most flexible parts were the helices α5 (residues 125 to 147), α6 (residues 155 to 163), and G2 with connecting loops (residues 251 to 268); together, they are responsible for the opening and closing of the active site (Figure 6a). The helix α5 is considered part of the lid along with α4 and α6 [35], sometimes with the helix α8 (residues 210 to 219) as a second lid [36]. While it is true that the helix α8 shows some level of flexibility during the simulation, it is the helix G2 and its connecting loops that move towards the helix α5.…”

Section: Flexibility Of Lipa With and Without Disulfide Bonds During The Molecular Dynamics Simulationsmentioning

confidence: 99%

“…They are therefore responsible for closing the catalytic cleft, and together with the helix α5, which also moves towards them, they form the actual lid domain that protects the active site in a coordinated movement with the correct orientation (Figure 6c). sometimes with the helix α8 (residues 210 to 219) as a second lid [36]. While it is true that the helix α8 shows some level of flexibility during the simulation, it is the helix G2 and its connecting loops that move towards the helix α5.…”

Section: Flexibility Of Lipa With and Without Disulfide Bonds During The Molecular Dynamics Simulationsmentioning

confidence: 99%

Functional Heterologous Expression of Mature Lipase LipA from Pseudomonas aeruginosa PSA01 in Escherichia coli SHuffle and BL21 (DE3): Effect of the Expression Host on Thermal Stability and Solvent Tolerance of the Enzyme Produced

Pulido

Prieto

Pieffet

et al. 2020

IJMS

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This study aimed to express heterologously the lipase LipA from Pseudomonas aeruginosa PSA01 obtained from palm fruit residues. In previous approaches, LipA was expressed in Escherichia coli fused with its signal peptide and without its disulfide bond, displaying low activity. We cloned the mature LipA with its truncated chaperone Lif in a dual plasmid and overexpressed the enzyme in two E. coli strains: the traditional BL21 (DE3) and the SHuffle® strain, engineered to produce stable cytoplasmic disulfide bonds. We evaluated the effect of the disulfide bond on LipA stability using molecular dynamics. We expressed LipA successfully under isopropyl β-d-1-thio-galactopyranoside (IPTG) and slow autoinducing conditions. The SHuffle LipA showed higher residual activity at 45 °C and a greater hyperactivation after incubation with ethanol than the enzyme produced by E. coli BL21 (DE3). Conversely, the latter was slightly more stable in methanol 50% and 60% (t½: 49.5 min and 9 min) than the SHuffle LipA (t½: 31.5 min and 7.4 min). The molecular dynamics simulations showed that removing the disulfide bond caused some regions of LipA to become less flexible and some others to become more flexible, significantly affecting the closing lid and partially exposing the active site at all times.

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Understanding domain movements and interactions of Pseudomonas aeruginosa lipase with lipid molecule tristearoyl glycerol: A molecular dynamics approach

Cited by 4 publications

References 29 publications

Directed Evolution of Lipase to Have Enhanced Activity toward Short Chain Fatty Acids and Elucidation of Structural Features of Mutant

Directed Evolution of Lipase to Have Enhanced Activity toward Short Chain Fatty Acids and Elucidation of Structural Features of Mutant

Functional Heterologous Expression of Mature Lipase LipA from Pseudomonas aeruginosa PSA01 in Escherichia coli SHuffle and BL21 (DE3): Effect of the Expression Host on Thermal Stability and Solvent Tolerance of the Enzyme Produced

Computational reverse protein engineering of a lipase from Pseudomonas aeruginosa in n-hexane

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