Effects of Organic Solvent and Crystal Water on γ-Chymotrypsin in Acetonitrile Media: Observations from Molecular Dynamics Simulation and DFT Calculation

Zhu, Lijuan; Yang, Wei; Yan, Meng; Xiao, Xincai; Guo, Yanzhi; Pu, Xuemei; Li, Menglong

doi:10.1021/jp3002405

Cited by 22 publications

(20 citation statements)

References 90 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The observation implies that the adsorption of CNT would not significantly influence the specificity of α-ChT in aqueous solution. However, the S1 pocket of the free enzyme in heptane solvent is almost fully closed and distinctly different from those in aqueous solution, implying a change in the specificity of the enzyme, consistent with the experiment finding 38 49 . In contrast, the shape of the S1 pocket for the immobilized enzyme in heptane solvent still presents relative “open” state, similar to those in aqueous solution.…”

Section: Resultssupporting

confidence: 88%

“…Heptane was chosen in this work since it is one of the most common nonpolar organic media for non-aqueous enzymatic catalysis 35 36 . In previous work 37 38 , we already used MD simulation to study the effects of the organic solvent and water content on the structure and function of the chymotrypsin. In the work, we further revealed the molecular mechanism concerning the effect of the immobilization of CNT on its structure and stability in the non-polar heptane media, in order to provide valuable information for improving its catalytic properties and advancing its application in non-aqueous media.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Probing Immobilization Mechanism of alpha-chymotrypsin onto Carbon Nanotube in Organic Media by Molecular Dynamics Simulation

Zhang

Xiao

Yuan

et al. 2015

Sci Rep

Self Cite

View full text Add to dashboard Cite

The enzyme immobilization has been adopted to enhance the activity and stability of enzymes in non-aqueous enzymatic catalysis. However, the activation and stabilization mechanism has been poorly understood on experiments. Thus, we used molecular dynamics simulation to study the adsorption of a-chymotrypsin (a-ChT) on carbon nanotube (CNT) in aqueous solution and heptane media. The results indicate that a-ChT has stronger affinity with CNT in aqueous solution than in heptane media, as confirmed by more adsorption atoms, larger contact area and higher binding free energies. Although the immobilization causes significant structure deviations from the crystal one, no significant changes in secondary structure of the enzyme upon adsorption are observed in the two media. Different from aqueous solution, the stabilization effects on some local regions far from the surface of CNT were observed in heptane media, in particular for S1 pocket, which should contribute to the preservation of specificity reported by experiments. Also, CNT displays to some extent stabilization role in retaining the catalytic H-bond network of the active site in heptane media, which should be associated with the enhanced activity of enzymes. The observations from the work can provide valuable information for improving the catalytic properties of enzymes in non-aqueous media.O ver the past two decades, non-aqueous enzymatic catalysis has attracted considerable interests from experiments and theories since it can provide numerous synthetic and processing advantages compared to aqueous environment, for example, higher selectivity, thermo-stability, lower side reactions 1-3 . Thus, it could allow the syntheses of some compounds that are difficult to obtain in aqueous solution. Nevertheless, the enzyme in non-aqueous solution exhibits very low activity and lacks of long-term operational stability, which significantly limited its applications in industry. To tackle these problems, considerable experimental efforts have been devoted to activate enzymes in non-aqueous media, for example, salt activation, chemical modification and enzyme immobilization 4 . As known, the immobilization has been prevalently used in the classical enzymatic catalysis in aqueous media to improve the catalytic properties of enzymes [5][6][7][8] . Also, the method was adopted in the enzymatic catalysis in non-aqueous media, and the enhanced enzyme activity, stability and recyclability 4,9-12 were reported. For example, glass-adsorbed chymotrypsin exhibited much higher activity than the suspended enzyme (by 1-2 orders of magnitude) in some polar and nonpolar organic media 10 . Subtilisin Carlsberg and a-chymotrypsin adsorbed onto silica support led to a significant increase in their activity in acetonitrile media with respect to the native enzyme preparation 11 . Lipases immobilized on poly(acrylonitrile-co-maleic acid) ultrafiltration hollow fiber membrane were observed to have higher hydrolytic activity and the operational stability than its free ones in heptane media 12 . Fo...

show abstract

Section: Resultssupporting

confidence: 88%

mentioning

confidence: 99%

Probing Immobilization Mechanism of alpha-chymotrypsin onto Carbon Nanotube in Organic Media by Molecular Dynamics Simulation

Zhang

Xiao

Yuan

et al. 2015

Sci Rep

Self Cite

View full text Add to dashboard Cite

show abstract

“…Similar phenomena were observed in organic solvents with C=O (e.g., acetone and N,N-dimethylformamide), C"N (e.g., acetonitrile), and cyclic molecules (e.g., benzene, dioxane and tetrahydrofuran) as in alcohols [37,38]. Through MD simulation, acetonitrile molecules were found to penetrate into the active site of lipase, leading to structure variation of the active site and therefore the drop in the enzymatic activity in acetonitrile aqueous solution [38]; acetone, acetonitrile, and 1,4-dioxane could bind to the active site of subtilis and disturb its structure [21,34].…”

Section: Effect Of the Functional Groups Of Organic Solventsupporting

confidence: 60%

“…Through MD simulation, acetonitrile molecules were found to penetrate into the active site of lipase, leading to structure variation of the active site and therefore the drop in the enzymatic activity in acetonitrile aqueous solution [38]; acetone, acetonitrile, and 1,4-dioxane could bind to the active site of subtilis and disturb its structure [21,34]. Gupta et al [39] observed that the activity of polyphenol oxidase and trypsin reduced to different extents by 50% of tetrahydrofuran, dioxane, acetone, and acetonitrile.…”

Section: Effect Of the Functional Groups Of Organic Solventmentioning

confidence: 99%

Enzyme Stability and Activity in Non-Aqueous Reaction Systems: A Mini Review

et al. 2016

View full text Add to dashboard Cite

Abstract:Enormous interest in biocatalysis in non-aqueous phase has recently been triggered due to the merits of good enantioselectivity, reverse thermodynamic equilibrium, and no water-dependent side reactions. It has been demonstrated that enzyme has high activity and stability in non-aqueous media, and the variation of enzyme activity is attributed to its conformational modifications. This review comprehensively addresses the stability and activity of the intact enzymes in various non-aqueous systems, such as organic solvents, ionic liquids, sub-/super-critical fluids and their combined mixtures. It has been revealed that critical factors such as Log P, functional groups and the molecular structures of the solvents define the microenvironment surrounding the enzyme molecule and affect enzyme tertiary and secondary structure, influencing enzyme catalytic properties. Therefore, it is of high importance for biocatalysis in non-aqueous media to elucidate the links between the microenvironment surrounding enzyme surface and its stability and activity. In fact, a better understanding of the correlation between different non-aqueous environments and enzyme structure, stability and activity can contribute to identifying the most suitable reaction medium for a given biotransformation.

show abstract

“…Molecular dynamics (MD) simulations have been used successfully to study the structure and function of proteins to obtain microscopic information at the molecular level and to supplement experimental investigations [18][19][20][21][22], including study of GPCRs [23,24]. Previous MD studies on GPCRs have focused largely on the effects of ligand binding.…”

Section: Introductionmentioning

confidence: 99%

Understanding the effects on constitutive activation and drug binding of a D130N mutation in the β2 adrenergic receptor via molecular dynamics simulation

et al. 2014

Self Cite

View full text Add to dashboard Cite

G-protein-coupled receptors (GPCRs) are currently one of the largest families of drug targets. The constitutive activation induced by mutation of key GPCR residues is associated closely with various diseases. However, the structural basis underlying such activation and its role in drug binding has remained unclear. Herein, we used all-atom molecular dynamics simulations and free energy calculations to study the effects of a D130N mutation on the structure of β2 adrenergic receptor (β2AR) and its binding of the agonist salbutamol. The results indicate that the mutation caused significant changes in some key helices. In particular, the mutation leads to the departure of transmembrane 3 (TM3) from transmembrane 6 (TM6) and marked changes in the NPxxY region as well as the complete disruption of a key ionic lock, all of which contribute to the observed constitutive activation. In addition, the D130N mutation weakens some important H-bonds, leading to structural changes in these regions. Binding free energy calculations indicate that van der Waals and electrostatic interactions are the main driving forces in binding salbutamol; however, binding strength in the mutant β2AR is significantly enhanced mainly through modifying electrostatic interactions. Further analysis revealed that the increase in binding energy upon mutation stems mainly from the H-bonds formed between the hydroxyl group of salbutamol and the serine residues of TM5. This observation suggests that modifications of the H-bond groups of this drug could significantly influence drug efficacy in the treatment of diseases associated with this mutation.

show abstract

Effects of Organic Solvent and Crystal Water on γ-Chymotrypsin in Acetonitrile Media: Observations from Molecular Dynamics Simulation and DFT Calculation

Cited by 22 publications

References 90 publications

Probing Immobilization Mechanism of alpha-chymotrypsin onto Carbon Nanotube in Organic Media by Molecular Dynamics Simulation

Probing Immobilization Mechanism of alpha-chymotrypsin onto Carbon Nanotube in Organic Media by Molecular Dynamics Simulation

Enzyme Stability and Activity in Non-Aqueous Reaction Systems: A Mini Review

Understanding the effects on constitutive activation and drug binding of a D130N mutation in the β2 adrenergic receptor via molecular dynamics simulation

Contact Info

Product

Resources

About