Lipases molecular modeling

VAN Tilbeurgh, H., Roussel, A., La-LOUEL, J.M., and Cambiliau, C. lipoprotein lipase. Molecular model based on the pancreatic lipase x-ray structure consequences for heparin binding and catalysis. J. Biol. Chem., 1994, 269, 4626-4633. 

Studies of the ability of the lipase B from Candida antarctica (CAL-B) to catalyse the enantioselective aminolysis of esters by cis- and firms-2-phenylcycloalkanamines (54 n = 1, 3, 4) have been followed up by molecular modelling approaches in order to probe the lipase-catalysed aminolysis mechanism. CAL-B possesses a typical serine-dependent triad, so it was possible, with access to an X-ray crystal structure of CAL-B, to model a series of phosphonamidates (55 n = 1, 3, 4) as analogues of the tetrahedral intermediate (TI) resulting from attack of the amine on the carbonyl of the acyl-enzyme. The results suggested as the most plausible intermediate for the CAL-B-catalysed aminolysis a zwitterionic TI resulting from the direct His-assisted attack of the amine on to a C=0 group of the acyl-enzyme.80... 

Enzymatic enantioselectivity in organic solvents can be markedly enhanced by temporarily enlarging the substrate via salt formation (Ke, 1999). In addition to its size, the stereochemistry of the counterion can greatly affect the enantioselectivity enhancement (Shin, 2000). In the Pseudomonas cepacia lipase-catalyzed propanolysis of phenylalanine methyl ester (Phe-OMe) in anhydrous acetonitrile, the E value of 5.8 doubled when the Phe-OMe/(S)-mandelate salt was used as a substrate instead of the free ester, and rose sevenfold with (K)-maridelic acid as a Briansted-Lewis acid. Similar effects were observed with other bulky, but not with petite, counterions. The greatest enhancement was afforded by 10-camphorsulfonic acid the E value increased to 18 2 for a salt with its K-enanliomer and jumped to 53 4 for the S. These effects, also observed in other solvents, were explained by means of structure-based molecular modeling of the lipase-bound transition states of the substrate enantiomers and their diastereomeric salts. 

Muscarinic receptors are glycoproteins with molecular weights of approximately 80,000. They are located on the outer surface of the cell membrane, and they are of the G-protein-linked type M, Mg, and Mg receptors couple with proteins to stimulate phospho-lipase-C, whereas Mg and M4 receptors couple with Gi proteins to inhibit adenylate cyclase (25). The molecular basis of muscarinic receptor function has been reviewed (26). Nordvall and Hacksell (27) proposed a molecular model of the transmembrane domains of the receptor, to explain the three-dimensional interaction of the receptor with its ligands. However, the authors specified that the model is "primarily of qualitative value". 

Derewenda, Z. S. and Cambillau, C. (1991) Effects of gene mutations in lipoprotein and hepatic lipases as interpreted by a molecular model of the pancreatic triglyceride lipase. J. Biol. Chem. 266, 23112-23119... 

Ke, T., Tidor, B., and Klibanov, A. M., Molecular-modeling calculations for enzymatic enantioselectivity taking hydration into account, Biotechnol. Bioeng., 57,741-745,1998. Haeffner, F., Norin, T., and Hull, K., Molecular modeling of the enantioselectivity in lipase-catalyzed transesterification reactions, Biophys. J., 74, 1251-1262, 1998. Bernstein, F. C., Koetzle, T. R, WiUiams, G. J. B., Meyer, E. F. J., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., and Tasumi, M., The protein data bank a computer-based archival file for macromolecular structures, J. Mol. Biol., 112, 535-542, 1977. Parida, S. and Dordick, J. S., Tailoring lipase specificity by solvent and substrate chemistries, J. Org. Chem., 58, 3238-3244, 1993. 

Lipases are usually active in aqueous systems as well as in organic solvents which makes them applicable not only for hydrolytic reactions but also for esterifications and transesterifications or for the formation of amides. These enzymes are known to accept a wide variety of substrates quite often with high enantioselectivity which makes them useful for chiral organic substrates. Numerous molecular modeling studies during the last decade describe these phenomena and provide us today with a clear picture of the mechanisms behind the enzymatic reaction particularly of CALB. Vicente Gotor, Karl Hult, and Romas J. Kazlauskas are three of the most cited names in this regard who have contributed fantastic work in this field. 

Zhou, Y, Oostenbrink, C., van Maanen, E.M.T., Hagen, W.R., de Leeuw, S.W., Jongejan, J.A. Molecular modeling of the enantioselectivity of Candida antartica lipase b— free energy calculation, J. Comp. Chem, in press. 

Krasinski G, Cypryk M, Kwiatkowska M, Mikotajczyk M, Kietbasinski P (2012) Molecular modeling of the lipase-catalyzed hydrolysis of acetoxymethyl(i-propoxy)phenylphosphine oxide and its P-btuane analogue. J Mol Graph Model 38 290-297... 

Klein, R., G. King, R. Moreau, and M. Haas. 1997. Altered Acyl Chain Length Specificity of Rhizopus Delemar Lipase through Mutagenesis and Molecular Modeling. Lipids 32 (2) 123-130. 

Haeffner F, Norm T. 1999. Molecular modeling of lipase-catalyzed reactions. Prediction of enantioselectivity. Chem Pharm Bull 47 591-600. 

C. rugosa lipase [9]. Molecular modeling studies of the two ester enantiomers bound to the active site of the lipase revealed the presence of two different modes of binding the... 

Crystallographic and molecular modelling smdies of lipase B from Candida antarctica reveal a stereospecffidty pocket for secondary alcohols. Biochemistry, 34,16838 51. 

Detailed studies on the lipase-catalyzed polymerization of divinyl adipate and 1,4-butanediol were performed [41-44]. Bulk polymerization increased the reaction rate and molecular weight of the polymer however, the hydrolysis of the terminal vinyl ester significantly limited the formation of the polyester with high molecular weight. A mathematical model describing the kinetics of this polymerization was proposed, which effectively predicts the composition (terminal structure) of the polyester. 

A second example of the use of directed molecular evolution for natural product synthesis is the use of lipases by Reetz and colleagues. This work is based on the kinetic hydrolytic resolution of racemic mixtures, in which one enantiomer is preferentially hydrolyzed and the chiral product is thus enriched. Utilizing both random mutagenesis and directed techniques such as CAST,64 they have improved the stereoselectivity of a lipase from Pseudomonas aeruginosa (PAL) on a number of occasions with different substrates. One of the first examples utilized the model substrate 2-methyldecanoic acid /xnitrophenyl ester, for which the wild-type enzyme has an enantioselectivity of E= 1.1. As a consequence of five mutations accumulated through random mutagenesis, followed by saturation mutagenesis, the enantioselectivity was increased to 25.8.123 More... 

These results showed the benefits of systematic investigations of immobilization parameters to achieve enhanced enzyme-catalyst activities. However, much work remains to understand on a molecular level how, for example, changes in enzyme loading influences the fraction of active lipase. Details of enzyme conformation and orientation as function of surface chemistry and morphology on model systems taken together with better control of surface... 

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