The open lid conformation of the lipase is explored in the compressed gas: New insights from molecular dynamic simulation

Housaindokht, Mohammad Reza; Monhemi, Hassan

doi:10.1016/j.molcatb.2012.11.003

Cited by 22 publications

(7 citation statements)

References 46 publications

(54 reference statements)

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“…MD simulations have helped to reveal the influence of high pressure on the enzymes from the viewpoint that changes in their conformation upon treatment dominate the properties of proteins. For example, MD simulations have revealed that, in some cases, high-pressure condition can open the lid of enzymes such as lipases, which controls the substrate-accessible channel to the catalytic site (Housaindokht & Monhemi, 2013;Johnson, Lindsay, Nellas, & Shen, 2016). found that the position of Trp residue was modified by high pressure, which dominated the change in fluorescence intensity of R. chinesis lipase.…”

Section: Influences Of Processing Conditions (Pressure and Temperaturmentioning

confidence: 99%

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Chen

Huang

Miao

et al. 2018

Comp Rev Food Sci Food Safe

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Molecular dynamics (MD) simulation is a useful technique to study the interaction between molecules and how they are affected by various processes and processing conditions. This review summarizes the application of MD simulations in food processing and safety, with an emphasis on the effects that emerging nonthermal technologies (for example, high hydrostatic pressure, pulsed electric field) have on the molecular and structural characteristics of foods and biomaterials. The advances and potential projection of MD simulations in the science and engineering aspects of food materials are discussed and focused on research work conducted to study the effects of emerging technologies on food components. It is expected by showing key case studies that it will stir novel developments as a valuable tool to study the effects of emerging food technologies on biomaterials. This review is useful to food researchers and the food industry, as well as researchers and practitioners working on flavor and nutraceutical encapsulations, dietary carbohydrate product developments, modified starches, protein engineering, and other novel food applications.

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Section: Influences Of Processing Conditions (Pressure and Temperaturmentioning

confidence: 99%

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Chen

Huang

Miao

et al. 2018

Comp Rev Food Sci Food Safe

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“…Recently we also explored that lipase can be activated by an interfacial activation mechanism in near-critical propane. 34 To continue our studies on the structure and dynamics of the enzyme in non-aqueous media, here we show how an enzyme is stabilized in green DESs including high amounts of urea.…”

Section: Introductionmentioning

confidence: 96%

How a protein can remain stable in a solvent with high content of urea: insights from molecular dynamics simulation of Candida antarctica lipase B in urea : choline chloride deep eutectic solvent

Monhemi

Housaindokht

Moosavi-Movahedi

et al. 2014

Phys. Chem. Chem. Phys.

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210

149

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Deep eutectic solvents (DESs) are utilized as green and inexpensive alternatives to classical ionic liquids. It has been known that some of DESs can be used as solvent in the enzymatic reactions to obtain very green chemical processes. DESs are quite poorly understood at the molecular level. Moreover, we do not know much about the enzyme microstructure in such systems. For example, how some hydrolase can remain active and stable in a deep eutectic solvent including 9 M of urea? In this study, the molecular dynamics of DESs as a liquid was simulated at the molecular level. Urea : choline chloride as a well-known eutectic mixture was chosen as a model DES. The behavior of the lipase as a biocatalyst was studied in this system. For comparison, the enzyme structure was also simulated in 8M urea. The thermal stability of the enzyme was also evaluated in DESs, water, and 8M urea. The enzyme showed very good conformational stability in the urea : choline chloride mixture with about 66% urea (9 M) even at high temperatures. The results are in good agreement with recent experimental observations. In contrast, complete enzyme denaturation occurred in 8M urea with only 12% urea in water. It was found that urea molecules denature the enzyme by interrupting the intra-chain hydrogen bonds in a "direct denaturation mechanism". However, in a urea : choline chloride deep eutectic solvent, as a result of hydrogen bonding with choline and chloride ions, urea molecules have a low diffusion coefficient and cannot reach the protein domains. Interestingly, urea, choline, and chloride ions form hydrogen bonds with the surface residues of the enzyme which, instead of lipase denaturation, leads to greater enzyme stability. To the best of our knowledge, this is the first study in which the microstructural properties of a macromolecule are examined in a deep eutectic solvent.

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“…To date, a few MD studies have been performed to gain some insights into the conformation changes of the lid and the role played by the surrounding environment (solvent, pH, ionic liquids, and temperature) on the dynamic properties of several lipases. [33][34][35][36][37][38][39][40][41][42] For example, Barbe et al 37 studied the molecular mechanism by which the lid of Burkholderia cepacia lipase might operate in different explicit solvent environments (water, octane, and water/octane interface). In aqueous media, the lid switches from an open conformation to a closed one while the reverse motion occurs in an organic environment.…”

Section: Introductionmentioning

confidence: 99%

“…Other similar simulations were also performed to gain insight into the lid interconversion from either closedto-open or open-to-closed. 34,35,[39][40][41][42] The interactions between enzymes and carrier surfaces strongly influence the orientation of the immobilised enzymes and thereby their catalytic efficiency. Little is known about the This journal is © the Owner Societies 2015 effect of differently charged and hydrophilic/hydrophobic solidliquid interfaces on lipase activity and adsorption orientation.…”

Section: Introductionmentioning

confidence: 99%

Lipase adsorption on different nanomaterials: a multi-scale simulation study

Zhao

Chen

Jian

2015

Phys. Chem. Chem. Phys.

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Candida antarctica lipase B (CalB) is an efficient biocatalyst for hydrolysis and esterification, which plays an important role in the production of biodiesel in the bioenergy industries. The ordered immobilisation of lipases on different supports would be significant for its enzymatic catalysis in some biodiesel production processes; however, the underlying mechanisms and the preferred lipase orientation are not well understood yet. In this work, a fundamental understanding of the orientation and adsorption mechanism of lipase on four different nanomaterial surfaces with different surface chemistry are explored in detail by a combination of parallel tempering Monte Carlo (PTMC) and molecular dynamics (MD) simulations. Simulation results show that lipase is strongly adsorbed onto the hydrophobic graphite surface, as reflected by the large contact area and interaction energy; while the adsorption onto the hydrophilic TiO2 surface is weak due to two strongly adhered water layers; meanwhile lipase undergoes desorption and reorientation processes. For CalB adsorption on positively and negatively charged surfaces (NH2-SAM and COOH-SAM), the orientation distributions of lipase are narrow, and opposite orientations are obtained. CalB adsorbed on NH2-SAM has its catalytic centre oriented towards the surface, which is not conducive to the substrate binding; while the catalytic centre faces toward the solution when it is adsorbed on the COOH-SAM. Besides, the native structures of CalB adsorbed on different surfaces are preserved, which indicates lipase as a robust enzyme. The simulation results will promote our understanding on how surface properties of nanomaterials, such as charge or hydrophobicity, will affect lipase immobilisation, and help us in the rational design and development of immobilised lipase carriers.

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The open lid conformation of the lipase is explored in the compressed gas: New insights from molecular dynamic simulation

Cited by 22 publications

References 46 publications

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

How a protein can remain stable in a solvent with high content of urea: insights from molecular dynamics simulation of Candida antarctica lipase B in urea : choline chloride deep eutectic solvent

Lipase adsorption on different nanomaterials: a multi-scale simulation study

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