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Computational design of a lipase for catalysis of the Diels-Alder reaction
KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.ORCID iD: 0000-0003-2673-075X
2011 (English)In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 17, no 4, 833-849 p.Article in journal (Refereed) Published
Abstract [en]

Combined molecular docking, molecular dynamics (MD) and density functional theory (DFT) studies have been employed to study catalysis of the Diels-Alder reaction by a modified lipase. Six variants of the versatile enzyme Candida Antarctica lipase B (CALB) have been rationally engineered in silico based on the specific characteristics of the pericyclic addition. A kinetic analysis reveals that hydrogen bond stabilization of the transition state and substrate binding are key components of the catalytic process. In the case of substrate binding, which has the greater potential for optimization, both binding strength and positioning of the substrates are important for catalytic efficiency. The binding strength is determined by hydrophobic interactions and can be tuned by careful selection of solvent and substrates. The MD simulations show that substrate positioning is sensitive to cavity shape and size, and can be controlled by a few rational mutations. The well-documented S105A mutation is essential to enable sufficient space in the vicinity of the oxyanion hole. Moreover, bulky residues on the edge of the active site hinders the formation of a sandwich-like nearattack conformer (NAC), and the I189A mutation is needed to obtain enough space above the face of the alpha,beta-double bond on the dienophile. The double mutant S105A/I189A performs quite well for two of three dienophiles. Based on binding constants and NAC energies obtained from MD simulations combined with activation energies from DFT computations, relative catalytic rates (v (cat) /v (uncat) ) of up to 103 are predicted.

Place, publisher, year, edition, pages
2011. Vol. 17, no 4, 833-849 p.
Keyword [en]
CALB, DFT, Diels-Alder, Molecular dynamics, Rational design
National Category
Other Physics Topics
Identifiers
URN: urn:nbn:se:kth:diva-33221DOI: 10.1007/s00894-010-0775-8ISI: 000289531300021Scopus ID: 2-s2.0-79958143417OAI: oai:DiVA.org:kth-33221DiVA: diva2:416534
Funder
Swedish Research Council
Note
QC 20110512Available from: 2011-05-12 Created: 2011-05-02 Last updated: 2017-12-11Bibliographically approved
In thesis
1. Computational Studies and Design of Biomolecular Diels-Alder Catalysis
Open this publication in new window or tab >>Computational Studies and Design of Biomolecular Diels-Alder Catalysis
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The Diels-Alder reaction is one of the most powerful synthetic tools in organic chemistry, and asymmetric Diels-Alder catalysis allows for rapid construction of chiral carbon scaffolds. For this reason, considerable effort has been invested in developing efficient and stereoselective organo- and biocatalysts. However, Diels-Alder is a virtually unknown reaction in Nature, and to engineer an enzyme into a Diels-Alderase is therefore a challenging task. Despite several successful designs of catalytic antibodies since the 1980’s, their catalytic activities have remained low, and no true artificial ’Diels-Alderase’ enzyme was reported before 2010.

In this thesis, we employ state-of-the-art computational tools to study the mechanism of organocatalyzed Diels-Alder in detail, and to redesign existing enzymes into intermolecular Diels-Alder catalysts. Papers I–IV explore the mechanistic variations when employing increasingly activated reactants and the effect of catalysis. In particular, the relation between the traditionally presumed concerted mechanism and a stepwise pathway, forming one bond at a time, is probed. Papers V–X deal with enzyme design and the computational aspects of predicting catalytic activity. Four novel, computationally designed Diels-Alderase candidates are presented in Papers VI–IX. In Paper X, a new parameterization of the Linear Interaction Energy model for predicting protein-ligand affinities is presented.

A general finding in this thesis is that it is difficult to attain large transition state stabilization effects solely by hydrogen bond catalysis. In addition, water (the preferred solvent of enzymes) is well-known for catalyzing Diels- Alder by itself. Therefore, an efficient Diels-Alderase must rely on large binding affinities for the two substrates and preferential binding conformations close to the transition state geometry. In Papers VI–VIII, we co-designed the enzyme active site and substrates in order to achieve the best possible complementarity and maximize binding affinity and pre-organization. Even so, catalysis is limited by the maximum possible stabilization offered by hydrogen bonds, and by the inherently large energy barrier associated with the [4+2] cycloaddition.

The stepwise Diels-Alder pathway, proceeding via a zwitterionic intermediate, may offer a productive alternative for enzyme catalysis, since an enzyme active site may be more differentiated towards stabilizing the high-energy states than for the standard mechanism. In Papers I and III, it is demonstrated that a hydrogen bond donor catalyst provides more stabilization of transition states having pronounced charge-transfer character, which shifts the preference towards a stepwise mechanism.

Another alternative, explored in Paper IX, is to use an α,β -unsaturated ketone as a ’pro-diene’, and let the enzyme generate the diene in situ by general acid/base catalysis. The results show that the potential reduction in the reaction barrier with such a mechanism is much larger than for conventional Diels-Alder. Moreover, an acid/base-mediated pathway is a better mimic of how natural enzymes function, since remarkably few catalyze their reactions solely by non-covalent interactions.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2012. xii, 138 p.
Series
Trita-CHE-Report, ISSN 1654-1081 ; 2012:34
Keyword
Computational chemistry, density functional theory, enzyme design, molecular modeling, organocatalysis, stepwise Diels-Alder, oxyanion hole
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-101706 (URN)978-91-7501-435-7 (ISBN)
Public defence
2012-09-21, K1, Teknikringen 56, KTH, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

QC 20120903

Available from: 2012-09-03 Created: 2012-08-31 Last updated: 2012-09-03Bibliographically approved

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