Journal of Biological Chemistry · 2010 · 156 citations · 26 references
Natural SciencesBiochemistryChemistryBiocatalysisEnzymologyPhysical ChemistryConformational AnalysisConformational ChangeEnzyme BiophysicsEnzyme KineticsMolecular DynamicsProtein DynamicsActive SitesConformational StabilityEnzyme Conformational StabilityMolecular Mechanics ModelingNonpolar SolventsProtein Conformation ChangeSolvent Effects On Conformational StabilitySolvent Effects On Enzyme Activity
The conformational stability and activity of Candida antarctica lipase B (CALB) in the polar and nonpolar organic solvents were investigated by molecular dynamics and quantum mechanics/molecular mechanics simulations. The conformation change of CALB in the polar and nonpolar solvents was examined in two aspects: the overall conformation change of CALB and the conformation change of the active site. The simulation results show that the overall conformation of CALB is stable in the organic solvents. In the nonpolar solvents, the conformation of the active site keeps stable, whereas in the polar solvents, the solvent molecules reach into the active site and interact intensively with the active site. This interaction destroys the hydrogen bonding between Ser105 and His224. In the solvents, the activation energy of CALB and that of the active site region were further simulated by quantum mechanics/molecular mechanics simulation. The results indicate that the conformation change in the region of active sites is the main factor that influences the activity of CALB. The conformational stability and activity of Candida antarctica lipase B (CALB) in the polar and nonpolar organic solvents were investigated by molecular dynamics and quantum mechanics/molecular mechanics simulations. The conformation change of CALB in the polar and nonpolar solvents was examined in two aspects: the overall conformation change of CALB and the conformation change of the active site. The simulation results show that the overall conformation of CALB is stable in the organic solvents. In the nonpolar solvents, the conformation of the active site keeps stable, whereas in the polar solvents, the solvent molecules reach into the active site and interact intensively with the active site. This interaction destroys the hydrogen bonding between Ser105 and His224. In the solvents, the activation energy of CALB and that of the active site region were further simulated by quantum mechanics/molecular mechanics simulation. The results indicate that the conformation change in the region of active sites is the main factor that influences the activity of CALB. IntroductionBecause of its high enantioselectivity and catalytic activity, wide range of substrates, and thermal stability, Candida antarctica lipase B (CALB) 3The abbreviations used are: CALBC. antarctica lipase BQMquantum mechanicsMMmolecular mechanicsRMSDroot mean square deviation. is widely used in many industrial applications and scientific researches (1Rotticci D. Rotticci-Mulder J.C. Denman S. Norin T. Hult K. Chembiochem. 2001; 2: 766-770Crossref PubMed Scopus (106) Google Scholar). CALB is composed of 317 amino acid residues and has a molecular mass of 33 K (2Uppenberg J. Hansen M.T. Patkar S. Jones T.A. Structure. 1994; 2: 293-308Abstract Full Text Full Text PDF PubMed Scopus (763) Google Scholar). Similar to other serine hydrolyzes, a serine-histidine-asparate catalytic triad is responsible for the catalytic activity of CALB. The mechanism is outlined in Fig. 1. It is a two-step mechanism with an acylation step and a deacylation step separated by a covalent acyl-enzyme intermediate (3Ottosson J. Enthalpy and Entropy in Enzyme-catalysis: A Study of Lipase Enantioselectivity. Royal Institute of Technology, Stockholm, Sweden2001: P12Google Scholar).The activity of the enzymes is strongly affected by the choice of solvent (4Zaks A. Klibanov A.M. Proc. Natl. Acad. Sci. U.S.A. 1985; 82: 3192-3196Crossref PubMed Scopus (1264) Google Scholar, 5Wescott C.R. Klibanov A.M. Biochim. Biophys. Acta. 1994; 1206: 1-9Crossref PubMed Scopus (312) Google Scholar, 6Russell A.J. Klibanov A.M. Biochem. Soc. Trans. 1989; 17 (1145): 1145Crossref PubMed Scopus (12) Google Scholar, 7Stahl M. Jeppssonwistrand U. Mansson M.O. Mosbach K. J. Am. Chem. Soc. 1991; 113: 9366-9368Crossref Scopus (115) Google Scholar). As a matter of fact, even reversal of substrate specificity (8Wescott C.R. Klibanov A.M. J. Am. Chem. Soc. 1993; 115: 1629-1631Crossref Scopus (138) Google Scholar, 9Zaks A. Klibanov A.M. J. Am. Chem. Soc. 1986; 108: 2767-2768Crossref Scopus (237) Google Scholar) and enantiopreference (10Wescott C.R. Klibanov A.M. Biotechnol. Bioeng. 1997; 56: 340-344Crossref PubMed Scopus (27) Google Scholar, 11Tawaki S. Klibanov A.M. J. Am. Chem. Soc. 1992; 114: 1882-1884Crossref Scopus (180) Google Scholar) has been reported. A higher thermostability and altered stereoselectivity for CALB in organic solvents have also been observed (12Kirk O. Christensen M.W. Org. Process. Res. Dev. 2002; 6: 446-451Crossref Scopus (324) Google Scholar, 13Magnusson A.O. Rotticci-Mulder J.C. Santagostino A. Hult K. Chembiochem. 2005; 6: 1051-1056Crossref PubMed Scopus (108) Google Scholar). Many researchers have put effort into elucidating the underlying mechanisms responsible for the observed solvent effects. The most widely accepted model was described by Laane (14Laane C. Boeren S. Vos K. Veeger C. Biotechnol. Bioeng. 1987; 30: 81-87Crossref PubMed Scopus (1490) Google Scholar), who summarized the influence of organic solvents on the enzymatic reactions and concluded that the enzyme activity is higher in the environment surrounded by nonpolar and mid-polar solvents, whereas the lowest activity is expressed in polar solvents. The Laane model has been widely used in solvent selection in enzymatic reactions. However, the Laane model does not describe the mechanisms of solvent effect on a molecular level.Molecular dynamics simulations have been proven to be a useful tool in understanding protein structure and have been used to get insights into the structure and behavior of the enzymes (15Tejo B.A. Salleh A.B. Pleiss J. J. Mol. Model. 2004; 10: 358-366Crossref PubMed Scopus (46) Google Scholar, 16Lee J. Suh S.W. Shin S. J. Biomol. Struct. Dyn. 2000; 18: 297-309Crossref PubMed Scopus (13) Google Scholar, 17Cherukuvada S.L. Seshasayee A.S. Raghunathan K. Anishetty S. Pennathur G. PLOS Comput. Biol. 2005; 1: e28Crossref PubMed Google Scholar, 18Norin M. Haeffner F. Hult K. Edholm O. Biophys. J. 1994; 67: 548-559Abstract Full Text PDF PubMed Scopus (89) Google Scholar). The effect of solvents on the activity of CALB might be the results of the conformational change around the activity site or some particular area. In this work, the overall conformational change of CALB and the local conformational change around the active site in polar and nonpolar organic solvents were investigated through molecular dynamics simulation. Through constructing the tetrahedral intermediate model, the solvent effect of the conformation change on the activity of CALB was investigated by quantum mechanics (QM)/molecular mechanics (MM) simulation. IntroductionBecause of its high enantioselectivity and catalytic activity, wide range of substrates, and thermal stability, Candida antarctica lipase B (CALB) 3The abbreviations used are: CALBC. antarctica lipase BQMquantum mechanicsMMmolecular mechanicsRMSDroot mean square deviation. is widely used in many industrial applications and scientific researches (1Rotticci D. Rotticci-Mulder J.C. Denman S. Norin T. Hult K. Chembiochem. 2001; 2: 766-770Crossref PubMed Scopus (106) Google Scholar). CALB is composed of 317 amino acid residues and has a molecular mass of 33 K (2Uppenberg J. Hansen M.T. Patkar S. Jones T.A. Structure. 1994; 2: 293-308Abstract Full Text Full Text PDF PubMed Scopus (763) Google Scholar). Similar to other serine hydrolyzes, a serine-histidine-asparate catalytic triad is responsible for the catalytic activity of CALB. The mechanism is outlined in Fig. 1. It is a two-step mechanism with an acylation step and a deacylation step separated by a covalent acyl-enzyme intermediate (3Ottosson J. Enthalpy and Entropy in Enzyme-catalysis: A Study of Lipase Enantioselectivity. Royal Institute of Technology, Stockholm, Sweden2001: P12Google Scholar).The activity of the enzymes is strongly affected by the choice of solvent (4Zaks A. Klibanov A.M. Proc. Natl. Acad. Sci. U.S.A. 1985; 82: 3192-3196Crossref PubMed Scopus (1264) Google Scholar, 5Wescott C.R. Klibanov A.M. Biochim. Biophys. Acta. 1994; 1206: 1-9Crossref PubMed Scopus (312) Google Scholar, 6Russell A.J. Klibanov A.M. Biochem. Soc. Trans. 1989; 17 (1145): 1145Crossref PubMed Scopus (12) Google Scholar, 7Stahl M. Jeppssonwistrand U. Mansson M.O. Mosbach K. J. Am. Chem. Soc. 1991; 113: 9366-9368Crossref Scopus (115) Google Scholar). As a matter of fact, even reversal of substrate specificity (8Wescott C.R. Klibanov A.M. J. Am. Chem. Soc. 1993; 115: 1629-1631Crossref Scopus (138) Google Scholar, 9Zaks A. Klibanov A.M. J. Am. Chem. Soc. 1986; 108: 2767-2768Crossref Scopus (237) Google Scholar) and enantiopreference (10Wescott C.R. Klibanov A.M. Biotechnol. Bioeng. 1997; 56: 340-344Crossref PubMed Scopus (27) Google Scholar, 11Tawaki S. Klibanov A.M. J. Am. Chem. Soc. 1992; 114: 1882-1884Crossref Scopus (180) Google Scholar) has been reported. A higher thermostability and altered stereoselectivity for CALB in organic solvents have also been observed (12Kirk O. Christensen M.W. Org. Process. Res. Dev. 2002; 6: 446-451Crossref Scopus (324) Google Scholar, 13Magnusson A.O. Rotticci-Mulder J.C. Santagostino A. Hult K. Chembiochem. 2005; 6: 1051-1056Crossref PubMed Scopus (108) Google Scholar). Many researchers have put effort into elucidating the underlying mechanisms responsible for the observed solvent effects. The most widely accepted model was described by Laane (14Laane C. Boeren S. Vos K. Veeger C. Biotechnol. Bioeng. 1987; 30: 81-87Crossref PubMed Scopus (1490) Google Scholar), who summarized the influence of organic solvents on the enzymatic reactions and concluded that the enzyme activity is higher in the environment surrounded by nonpolar and mid-polar solvents, whereas the lowest activity is expressed in polar solvents. The Laane model has been widely used in solvent selection in enzymatic reactions. However, the Laane model does not describe the mechanisms of solvent effect on a molecular level.Molecular dynamics simulations have been proven to be a useful tool in understanding protein structure and have been used to get insights into the structure and behavior of the enzymes (15Tejo B.A. Salleh A.B. Pleiss J. J. Mol. Model. 2004; 10: 358-366Crossref PubMed Scopus (46) Google Scholar, 16Lee J. Suh S.W. Shin S. J. Biomol. Struct. Dyn. 2000; 18: 297-309Crossref PubMed Scopus (13) Google Scholar, 17Cherukuvada S.L. Seshasayee A.S. Raghunathan K. Anishetty S. Pennathur G. PLOS Comput. Biol. 2005; 1: e28Crossref PubMed Google Scholar, 18Norin M. Haeffner F. Hult K. Edholm O. Biophys. J. 1994; 67: 548-559Abstract Full Text PDF PubMed Scopus (89) Google Scholar). The effect of solvents on the activity of CALB might be the results of the conformational change around the activity site or some particular area. In this work, the overall conformational change of CALB and the local conformational change around the active site in polar and nonpolar organic solvents were investigated through molecular dynamics simulation. Through constructing the tetrahedral intermediate model, the solvent effect of the conformation change on the activity of CALB was investigated by quantum mechanics (QM)/molecular mechanics (MM) simulation.
26
Molecular dynamics with coupling to an external bath
Herman J. C. Berendsen, Johan P. M. Postma, Wilfred F. van Gunsteren et al. · The Journal of Chemical Physics · 1984 · 31K citations · Full text
Natural Sciences, Chemistry, Physics +17
Rules for optimization of biocatalysis in organic solvents
Colja Laane, Sjef Boeren, Kees Vos et al. · Biotechnology and Bioengineering · 1987 · 1.6K citations · Full text