Predicting enzymatic reactivity: from theory to design

Abstract

Theoretical and computational tools can provide a detailed knowledge of the mode of action of enzymes. This knowledge can be systematized to be used as a guide for the design of new biocatalysts for industrial purposes. In this article, we illustrate the current view about the origin of enzymatic catalysis based on molecular simulations and its use in the design of new enzymes. Transition‐state stabilization in a preorganized active site seems to be the major source of catalysis, although some degree of protein flexibility is needed to reach the maximum catalytic efficiency. Development of a new enzyme must then consider the inclusion of TS stabilizing interactions either in a preexisting enzymatic structure (enzymatic redesign) or in a completely new designed enzyme (de novo design). However, the lack of a detailed understanding of the link between sequence, structure, flexibility, and function still prevents the complete success of these strategies. WIREs Comput Mol Sci 2014, 4:407–421. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Combined QM/MM Methods Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods

Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms

“…Computational methods can be used to overcome some of these limitations, complementing the experimental information and offering a detailed comparative view of different mechanistic proposals, at a structural and energetic level, discarding mechanistic alternatives and proposing new pathways that are consistent with the available experimental data. [8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24] Several computational methods have been used over the last decades, including cluster modeling through first principles quantum mechanics (QM) implemented within a geometry optimization protocol, 18,[25][26][27][28] molecular orbital/density functional theory (DFT) hybrid quantum mechanical/molecular mechanics (QM/MM) implemented either within a geometry optimization or a molecular dynamics (MD) protocol, [15][16][17]19,[29][30][31][32][33] empirical valence bond (EVB), [34][35][36] Car-Parrinello MD (CPMD), [37][38][39][40] among others.…”

Theoretical Study of Primary Reaction of Pseudozyma antarctica Lipase B as the Starting Point To Understand Its Promiscuity

“…In this regard, nowadays the use of computer-based methods, in combination with in vitro directed evolution and labour-intensive screening of microbial cultures for the desired activities appears to be a promising tool. 1 Different goals, apart from increasing or generating activity, have been achieved during the past years in the designing of new biocatalysts, such as altered substrate specificity, improved thermostability, organostability, regioselectivity, enantioselectivity, etc... 2 Among all possible methods, apart from generation of the full protein machinery from scratch, or de novo protein design, that have shown outstanding but limited number of successful challenges, 3,4,5 the re-design of a protein active site is one of the most promising strategies at present. In this technique, the cavity of an existing natural protein is modified by mutating a subset of its side chain amino-acids.…”

Katalyseforschung auf dem Computer

“…Ihre mechanistische Bedeutung wurde in kombinierten experimentellen und theoretischen Untersuchungen erkannt [142] und ist seither sowohl in der homogenen Übergangsmetallkatalyse [61,[142][143][144] als auch in der Biokatalyse mit Metallproteinen [80][81][82] fest etabliert. [138,149] Tunneleffekte werden als Quanteneffekte der Kernbewegung auf Standard-TST-Niveau nicht erfasst; sie sind offenkundig in einigen enzymatischen Reaktionen wichtig (z. [145][146][147][148][149] Bei dieser Thematik gibt es viele Aspekte, die durch Simulationen untersucht werden kçnnen, sobald die postulierten "dynamischen Effekte" sauber definiert sind.…”

“…In der Biokatalyse gibt es zwei rechnergestützte Strategien zum Entwurf neuer Enzyme, nämlich Modifikation des aktiven Zentrums und De-novo-Design. [138] Beispiele für De-novo-Design sind die Entwicklung neuer Enzyme für die Kemp-Eliminierung [139] und die Diels-Alder-Cycloaddition. [140] Derzeit scheint ein solches rechnergestütztes De-novo-Design in der Lage zu sein, neuartige Proteingerüste mit begrenzter enzymatischer Aktivität zu generieren, die anschließend mit den Techniken der gerichteten Evolution weiter optimiert werden kçnnen.…”

“…Simulationen an verschiedenen Enzymen haben jedoch nur recht kleine Abweichungen von 1 ergeben, um Faktoren von 3 oder weniger. [138,149] Tunneleffekte werden als Quanteneffekte der Kernbewegung auf Standard-TST-Niveau nicht erfasst; sie sind offenkundig in einigen enzymatischen Reaktionen wichtig (z. B. bei Protonen-, Wasserstoff-oder Hydridübertragungen), aber nicht wesentlich ausgeprägter als in den entsprechenden Referenzreaktionen in wässriger Lçsung.…”