The relationship between enhanced enzyme activity and structural dynamics in ionic liquids: a combined computational and experimental study.

Candida antarctica lipase B (CALB) is an efficient biocatalyst for hydrolysis, esterification, and polymerization reactions. In order to understand how to control enzyme activity and stability we performed a combined experimental and molecular dynamics simulation study of CALB in organic solvents and ionic liquids (ILs). Our results demonstrate that the conformational changes of the active site cavity are directly related to enzyme activity and decrease in the following order: [Bmim][TfO] > tert-butanol > [Bmim][Cl]. The entrance to the cavity is modulated by two isoleucines, ILE-189 and ILE-285, one of which is located on the α-10 helix. The α-10 helix can substantially change its conformation due to specific interactions with solvent molecules. This change is acutely evident in [Bmim][Cl] where interactions of LYS-290 with chlorine anions caused a conformational switch between α-helix and turn. Disruption of the α-10 helix structure results in a narrow cavity entrance and, thus, reduced the activity of CALB in [Bmim][Cl]. Finally, our results show that the electrostatic energy between solvents in this study and CALB is correlated with the structural changes leading to differences in enzyme activity.

[1]  Yaroslava G. Yingling,et al.  The role of hydrogen bonding in water-mediated glucose solubility in ionic liquids , 2012 .

[2]  J. Dunn,et al.  Enzyme activity in dialkyl phosphate ionic liquids. , 2011, Bioresource technology.

[3]  G. S. Lim,et al.  How ion properties determine the stability of a lipase enzyme in ionic liquids: a molecular dynamics study. , 2011, Physical chemistry chemical physics : PCCP.

[4]  Jing-Qi Lai,et al.  Specific ion effects of ionic liquids on enzyme activity and stability , 2011 .

[5]  Oliver May,et al.  Application of designed enzymes in organic synthesis. , 2011, Chemical reviews.

[6]  G. S. Lim,et al.  On the different roles of anions and cations in the solvation of enzymes in ionic liquids. , 2011, Physical chemistry chemical physics : PCCP.

[7]  F. Hernández‐Fernández,et al.  Biocatalytic ester synthesis in ionic liquid media , 2010 .

[8]  F. V. Rantwijk,et al.  Selective lipase-catalyzed 6-O-acylation of alkyl α-D-glucopyranosides using functionalized ethyl esters , 2010 .

[9]  T. Tan,et al.  Analysis of the Conformational Stability and Activity of Candida antarctica Lipase B in Organic Solvents , 2010, The Journal of Biological Chemistry.

[10]  J. Saraiva,et al.  Effect of the ionic liquid [bmim]Cl and high pressure on the activity of cellulase , 2010 .

[11]  F. Srienc,et al.  Toward advanced ionic liquids. Polar, enzyme-friendly solvents for biocatalysis , 2010, Biotechnology and bioprocess engineering : BBE.

[12]  Yaroslava G. Yingling,et al.  The Sequence of HIV-1 TAR RNA Helix Controls Cationic Distribution† , 2010 .

[13]  Jiali Gu,et al.  Enzymatic synthesis of (S)-glutaric acid monoesters aided by molecular docking , 2010 .

[14]  R. J. Branco,et al.  Molecular Mechanism of the Hydration of Candida antarctica Lipase B in the Gas Phase: Water Adsorption Isotherms and Molecular Dynamics Simulations , 2009, Chembiochem : a European journal of chemical biology.

[15]  I. André,et al.  Insights into lid movements of Burkholderia cepacia lipase inferred from molecular dynamics simulations , 2009, Proteins.

[16]  K. Driesen,et al.  Luminescence of LaF3:Ln3+ Nanocrystal Dispersions in Ionic Liquids , 2009 .

[17]  Orlando Acevedo,et al.  Development of OPLS-AA Force Field Parameters for 68 Unique Ionic Liquids. , 2009, Journal of chemical theory and computation.

[18]  L. De Maria,et al.  Understanding the Plasticity of the α/β Hydrolase Fold: Lid Swapping on the Candida antarctica Lipase B Results in Chimeras with Interesting Biocatalytic Properties , 2009, Chembiochem : a European journal of chemical biology.

[19]  Sang Hyun Lee,et al.  Influence of ionic liquids under controlled water activity and low halide content on lipase activity , 2008 .

[20]  F. Hernández‐Fernández,et al.  Synthesis of flavour esters using free Candida antarctica lipase B in ionic liquids , 2008 .

[21]  N. Micaêlo,et al.  Protein structure and dynamics in ionic liquids. Insights from molecular dynamics simulation studies. , 2008, The journal of physical chemistry. B.

[22]  C. Herrmann,et al.  Protein denaturation by ionic liquids and the Hofmeister series: a case study of aqueous solutions of ribonuclease A. , 2007, Angewandte Chemie.

[23]  P. Villeneuve.  Lipases in lipophilization reactions. , 2007, Biotechnology advances.

[24]  Sung Ho Ha,et al.  Lipase-catalyzed biodiesel production from soybean oil in ionic liquids. , 2007 .

[25]  Zhi-Gang Wang,et al.  Revealing long-range density fluctuations in dialkylimidazolium chloride ionic liquids by dynamic light scattering. , 2007, The journal of physical chemistry. B.

[26]  Y. Pyun,et al.  In vitro evolution of lipase B from Candida antarctica using surface display in hansenula polymorpha. , 2007, Journal of microbiology and biotechnology.

[27]  M. Ueda,et al.  Preparation of a whole-cell biocatalyst of mutated Candida antarctica lipase B (mCALB) by a yeast molecular display system and its practical properties , 2007, Applied Microbiology and Biotechnology.

[28]  V. Hornak,et al.  Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.

[29]  S. Ha,et al.  Enzyme-catalyzed reactions in ionic liquids , 2006 .

[30]  Michiel Janssen,et al.  Room-temperature ionic liquids that dissolve carbohydrates in high concentrations , 2005 .

[31]  Hua Zhao.  Effect of ions and other compatible solutes on enzyme activity, and its implication for biocatalysis using ionic liquids , 2005 .

[32]  R. Gross,et al.  Dynamics of Proteins in Hydrated State and in Solution As Studied by Dielectric Relaxation Spectroscopy , 2005 .

[33]  Zhen Qian,et al.  Improving the catalytic activity of Candida antarctica lipase B by circular permutation. , 2005, Journal of the American Chemical Society.

[34]  J. V. Gerpen,et al.  Biodiesel processing and production , 2005 .

[35]  A. Mattevi,et al.  Demonstration of Isoleucine 199 as a Structural Determinant for the Selective Inhibition of Human Monoamine Oxidase B by Specific Reversible Inhibitors* , 2005, Journal of Biological Chemistry.

[36]  N. V. D. van der Vegt,et al.  A new force field for atomistic simulations of aqueous tertiary butanol solutions. , 2005, The Journal of chemical physics.

[37]  J. Iborra,et al.  Understanding structure-stability relationships of Candida antartica lipase B in ionic liquids. , 2005, Biomacromolecules.

[38]  J. Iborra,et al.  Dynamic structure–function relationships in enzyme stabilization by ionic liquids , 2005 .

[39]  Roger A. Sheldon,et al.  Dissolution of Candida antarctica lipase B in ionic liquids: effects on structure and activity , 2004 .

[40]  B. Hammock,et al.  Biocatalysis in ionic liquids: the stereoconvergent hydrolysis of trans-β-methylstyrene oxide catalyzed by soluble epoxide hydrolase , 2004 .

[41]  W. Suen,et al.  Improved activity and thermostability of Candida antarctica lipase B by DNA family shuffling. , 2004, Protein engineering, design & selection : PEDS.

[42]  R. Kazlauskas,et al.  Biocatalysis in ionic liquids - advantages beyond green technology. , 2003, Current opinion in biotechnology.

[43]  R. Rogers,et al.  Ionic liquid salt-induced inactivation and unfolding of cellulase from Trichoderma reesei , 2003 .

[44]  R. Bogel-Łukasik,et al.  1‐Octanol/Water Partition Coefficients of 1Alkyl‐3‐methylimidazolium Chloride , 2003 .

[45]  U. Bornscheuer,et al.  Increased stability of an esterase from Bacillus stearothermophilus in ionic liquids as compared to organic solvents , 2003 .

[46]  Alan J Russell,et al.  Impact of ionic liquid physical properties on lipase activity and stability. , 2003, Journal of the American Chemical Society.

[47]  V. V. Mozhaev,et al.  Oxidative enzymes possess catalytic activity in systems with ionic liquids , 2002, Biotechnology Letters.

[48]  Ole Kirk,et al.  Lipases from Candida antarctica: Unique Biocatalysts from a Unique Origin , 2002 .

[49]  H. Olivier-Bourbigou,et al.  Ionic liquids: perspectives for organic and catalytic reactions , 2002 .

[50]  Roger A. Sheldon,et al.  Biocatalysis in ionic liquids. , 2002, Chemical reviews.

[51]  J. Iborra,et al.  Stabilization of α‐chymotrypsin by ionic liquids in transesterification reactions , 2001 .

[52]  K. Hult,et al.  Improved Enantioselectivity of a Lipase by Rational Protein Engineering , 2001, Chembiochem : a European journal of chemical biology.

[53]  J. Iborra,et al.  Over-stabilization of Candida antarctica lipase B by ionic liquids in ester synthesis , 2001, Biotechnology Letters.

[54]  R D Schmid,et al.  Anatomy of lipase binding sites: the scissile fatty acid binding site. , 1998, Chemistry and physics of lipids.

[55]  K. Merz,et al.  The Concept of Solvent Compatibility and Its Impact on Protein Stability and Activity Enhancement in Nonaqueous Solvents , 1997 .

[56]  K. R. Seddon.  Ionic Liquids for Clean Technology , 1997 .

[57]  B. Wallace,et al.  HOLE: a program for the analysis of the pore dimensions of ion channel structural models. , 1996, Journal of molecular graphics.

[58]  M. Grätzel,et al.  Hydrophobic, Highly Conductive Ambient-Temperature Molten Salts. , 1996, Inorganic chemistry.

[59]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[60]  G J Kleywegt,et al.  Crystallographic and molecular-modeling studies of lipase B from Candida antarctica reveal a stereospecificity pocket for secondary alcohols. , 1995, Biochemistry.

[61]  A. Klibanov,et al.  The solvent dependence of enzyme specificity. , 1994, Biochimica et biophysica acta.

[62]  T A Jones,et al.  The sequence, crystal structure determination and refinement of two crystal forms of lipase B from Candida antarctica. , 1994, Structure.

[63]  B. Wallace,et al.  The pore dimensions of gramicidin A. , 1993, Biophysical journal.

[64]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[65]  Joel L. Sussman,et al.  The α/β hydrolase fold , 1992 .

[66]  J. Dordick,et al.  Organic solvents strip water off enzymes , 1992, Biotechnology and bioengineering.

[67]  A. Klibanov,et al.  Enzymatic catalysis in nonaqueous solvents. , 1988, The Journal of biological chemistry.

[68]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[69]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[70]  Debra L. Fulton,et al.  Additional file 5 , 2009 .

[71]  A. Russell,et al.  Enzymatic Catalysis of Formation of Z‐Aspartame in Ionic Liquid − An Alternative to Enzymatic Catalysis in Organic Solvents , 2000, Biotechnology progress.

[72]  Ole Kirk,et al.  One Biocatalyst–Many Applications: The Use of Candida Antarctica B-Lipase in Organic Synthesis , 1998 .