Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase

Trodler, Peter; Schmid, Rolf D.; Pleiss, Jürgen

doi:10.1186/1472-6807-9-38

Cited by 77 publications

(113 citation statements)

References 76 publications

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“…[34,35] Another important consideration is that for both PcL and PaL only crystal structures corresponding to the open conformations are available, whereas for other highly homologous lipases crystal structures of the closed conformations were obtained in water after removing inhibitors from the active sites. [36,37] Humicola lanuginosa lipase (HlL) was selected as a representative case of a fungus taxon for a more detailed investigation of the activation/inactivation mechanism.…”

Section: Global Assessment Of Superficial Properties Of Lipasesmentioning

confidence: 99%

Conformational Changes of Lipases in Aqueous Media: A Comparative Computational Study and Experimental Implications

Ferrario¹,

Ebert²,

Knapic³

et al. 2011

Adv Synth Catal

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Conformational changes occurring to the open form of five different lipases were studied by means of molecular dynamic simulations in explicit water. The conformational changes indicate remarkable differences among the lipases considered, not only in terms of accessibility of the active site but also of modification of the geometry of the catalytic machinery. Lipase B from Candida antarctica undergoes minor conformational change at either level, so that it appears to be the most suitable lipase for being applied and formulated in aqueous environments or other hydrophilic media. On the other side, lipase from Pseudomonas cepacia undergoes the most relevant conformational variations both at the level of the catalytic triad and the residues involved in the oxyanion stabilization, suggesting that its "interfacial activation" is not simply related to a variation of the accessibility of the active site. Indeed, preliminary experimental data here reported indicate that covalent immobilization of lipase from Pseudomonas cepacia performed in the presence of hydrophobic solvent allows one to achieve a more than 10-fold increase in immobilization yield as compared to similar protocols performed in simple aqueous buffer. On the contrary, the benefit coming from immobilizing lipase B from Candida antarctica in hydrophobic solvent appears more limited (two-fold higher immobilization yield).

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Section: Global Assessment Of Superficial Properties Of Lipasesmentioning

confidence: 99%

Conformational Changes of Lipases in Aqueous Media: A Comparative Computational Study and Experimental Implications

Ferrario¹,

Ebert²,

Knapic³

et al. 2011

Adv Synth Catal

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“…Pleiss and coworkers. [83,84] The saturated framework of 3 makes it more difficult to form sandwich-like interactions with 4 than for 1. There is a smaller volume available for the diene to move in to form NACs with 3, and this volume is often occupied by surrounding residues, most dominantly I285, T40 and Val140.…”

Section: Further Optimizationmentioning

confidence: 99%

Computational design of a lipase for catalysis of the Diels-Alder reaction

et al. 2010

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Combined molecular docking, molecular dynamics (MD) and density functional theory (DFT) studies have been employed to study catalysis of the Diels-Alder reaction by a modified lipase. Six variants of the versatile enzyme {\em Candida Antarctica} lipase B (CALB) have been rationally engineered {\em in silico} based on the specific characteristics of the pericyclic addition. A kinetic analysis reveals that hydrogen bond stabilization of the transition state and substrate binding are key components of the catalytic process. In the case of substrate binding, which has the greater potential for optimization, both binding strength and positioning of the substrates are important for catalytic efficiency. The binding strength is determined by hydrophobic interactions and can be tuned by careful selection of solvent and substrates. The MD simulations show that substrate positioning is sensitive to cavity shape and size, and can be controlled by a few rational mutations. The well-documented S105A mutation is essential to enable sufficient space in the vicinity of the oxyanion hole. Moreover, bulky residues on the edge of the active site hinders the formation of a sandwich-like near-attack conformer (NAC), and the I189A mutation is needed to obtain enough space above the face of the $\alpha$,$\beta$-double bond on the dienophile. The double mutant S105A/I189A performs quite well for two of three dienophiles. Based on binding constants and NAC energies obtained from MD simulations combined with activation energies from DFT computations, relative catalytic rates ($v_{cat}/v_{uncat}$) of up to $10^3$ are predicted.Response to Reviewers: We are happy with the favorable comments by the reviewers. We have have corrected the manuscript as suggested by reviewer 1 1. A sentence explaining catalytic promiscuity has been added. 2. A paragraph discussing the relationship between the NAC concept and the Reaction Force has been added.We have shortened the manuscript as suggested by reviewer 2. In particular, we have moved information regarding the structural relaxation of protein structure in MD simulations to the supplementary material. Abstract Combined molecular docking, molecular dynamics (MD) and density functional theory (DFT) studies have been employed to study catalysis of the DielsAlder reaction by a modified lipase. Six variants of the versatile enzyme Candida Antarctica lipase B (CALB) have been rationally engineered in silico based on the specific characteristics of the pericyclic addition. A kinetic analysis reveals that hydrogen bond stabilization of the transition state and substrate binding are key components of the catalytic process. In the case of substrate binding, which has the greater potential for optimization, both binding strength and positioning of the substrates are important for catalytic efficiency. The binding strength is determined by hydrophobic interactions and can be tuned by careful selection of solvent and substrates. The MD simulations show that substrate positioning is sensitive to cavity s...

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“…[5,[9][10][11][12][13][14][15][16][17][18][19][20] Water is known to have a crucial role in protein structure, flexibility, and activity. [21][22][23][24][25] Water molecules bind via hydrogen bonds to the side chain and backbone atoms of proteins, [26] to polar atoms of substrates and ligands, [27] as well as to other water molecules. This enables water to mediate protein-protein and proteinligand contacts, and to take part in enzyme catalysis.…”

Section: Introductionmentioning

confidence: 99%

Molecular Mechanism of the Hydration of Candida antarctica Lipase B in the Gas Phase: Water Adsorption Isotherms and Molecular Dynamics Simulations

Branco¹,

Graber²,

Denis³

et al. 2009

ChemBioChem

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Hydration is a major determinant of activity and selectivity of enzymes in organic solvents or in gas phase. The molecular mechanism of the hydration of Candida antarctica lipase B (CALB) and its dependence on the thermodynamic activity of water (a(w)) was studied by molecular dynamics simulations and compared to experimentally determined water sorption isotherms. Hydration occurred in two phases. At low water activity, single water molecules bound to specific water binding sites at the protein surface. As the water activity increased, water networks gradually developed. The number of protein-bound water molecules increased linearly with a(w), until at a(w)=0.5 a spanning water network was formed consisting of 311 water molecules, which covered the hydrophilic surface of CALB, with the exception of the hydrophobic substrate-binding site. At higher water activity, the thickness of the hydration shell increased up to 10 A close to a(w)=1. Above a limit of 1600 protein-bound water molecules the hydration shell becomes unstable and the formation of pure water droplets occurs in these oversaturated simulation conditions. While the structure and the overall flexibility of CALB was independent of the hydration state, the flexibility of individual loops was sensitive to hydration: some loops, such as those part of the substrate-binding site, became more flexible, while other parts of the protein became more rigid upon hydration. However, the molecular mechanism of how flexibility is related to activity and selectivity is still elusive.

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Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase

Cited by 77 publications

References 76 publications

Conformational Changes of Lipases in Aqueous Media: A Comparative Computational Study and Experimental Implications

Conformational Changes of Lipases in Aqueous Media: A Comparative Computational Study and Experimental Implications

Computational design of a lipase for catalysis of the Diels-Alder reaction

Molecular Mechanism of the Hydration of Candida antarctica Lipase B in the Gas Phase: Water Adsorption Isotherms and Molecular Dynamics Simulations

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