Computational Enzyme Design

Kiss, Gert; Çelebi‐Ölçüm, Nihan; Moretti, Rocco; Baker, David; Houk, K. N.

doi:10.1002/anie.201204077

Cited by 441 publications

(422 citation statements)

References 217 publications

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“…The present analysis shows that computational studies of enzymatic promiscuity may provide us guiding principles for the design of new functions into existing enzymes or for the de novo design of new activities in protein scaffolds. 6 Figure S1 shows the interactions of OSB substrate in the 1SJB structure. A representation of the simulated system is provided as Supporting Information in Figure S2.…”

Section: Discussionmentioning

confidence: 99%

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Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods

et al. 2015

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The promiscuous activity of the enzyme o-Succinylbenzoate Synthase (OSBS) from the actinobacteria Amycolatopsis is investigated by means of QM/MM methods, using both Density Functional Theory and Semiempirical Hamiltonians. This enzyme catalyzes not only the dehydration of 2-succinyl-6R-hydroxy-2,4-cyclohexadiene-1R-carboxylate but also catalyzes racemization of different acylaminoacids, being N-succinyl-Rphenylglycine the best substrate. We investigated the molecular mechanisms for both reactions exploring the Potential Energy Surface. Then, Molecular Dynamics simulations were performed to obtain the free energy profiles and the averaged interaction energies of enzymatic residues with the reacting system. Our results confirm the plausibility of the reaction mechanisms proposed in the literature, with a good agreement between theoretical and experimentally-derived activation free energies. Our simulations unravel the role played by the different residues in each of the two possible reactions. The presence of flexible loops in the active site and the selection of structural modifications in the substrate seem to be key elements to promote the promiscuity of this enzyme.

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Section: Discussionmentioning

confidence: 99%

“…6,7 Scientists began to use evolutionary strategies (Directed Evolution) 8 to tailor the properties of individual molecules. Random mutations or recombination can, in many cases, be done efficiently, leading in this way to molecular evolution in the laboratory.…”

Section: Introductionmentioning

confidence: 99%

Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods

et al. 2015

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“…5,6 Arguably the most successful of these use theoretical enzyme substructures ("theozymes") that can be incorporated into such proteins for experimental validation. The designs are selected through computational modeling of transition-state analogues within side-chain constellations.…”

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confidence: 99%

Installing hydrolytic activity into a completely de novo protein framework

et al. 2016

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Designing enzyme-like catalysts tests our understanding of sequence-tostructure/function relationships in proteins. Here, we install hydrolytic activity predictably into a completely de novo and thermo-stable -helical barrel, which comprises 7 helices arranged around an accessible channel. We show that the lumen of the barrel accepts 21 mutations to functional polar residues. The resulting variant, which has cysteine-histidine-glutamic acid triads on each helix, hydrolyses pnitrophenyl acetate with catalytic efficiencies matching the most-efficient redesigned hydrolases based on natural protein scaffolds. This is the first report of a functional catalytic triad engineered into a de novo protein framework. The flexibility of our system also allows the facile incorporation of unnatural side chains to improve activity and probe the catalytic mechanism. Such predictable and robust construction of truly de novo biocatalysts holds promise for applications in chemical and biochemical synthesis.(134 words)

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“…In nearly all projects, the central objective is optimizing the thermodynamic stability of a unique folded state that is able to perform the desired function. Thermodynamic stability is computed using chemical models of various degrees of resolution from heuristic sequence-based scoring functions (Nautiyal et al 1995;Summa et al 2002) to high-accuracy but computationally expensive quantum mechanics calculations of energetics (Kiss et al 2013). The majority of computational protein design platforms calculate energetics of interactions at the atomic level, emphasizing non-bonding interactions, i.e., van der Waals packing, hydrogen bonding, and electrostatics (Kuhlman et al 2003).…”

Section: Introductionmentioning

confidence: 99%

Searching for the Pareto frontier in multi-objective protein design

2017

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The goal of protein engineering and design is to identify sequences that adopt three-dimensional structures of desired function. Often, this is treated as a single-objective optimization problem, identifying the sequence-structure solution with the lowest computed free energy of folding. However, many design problems are multi-state, multi-specificity, or otherwise require concurrent optimization of multiple objectives. There may be tradeoffs among objectives, where improving one feature requires compromising another. The challenge lies in determining solutions that are part of the Pareto optimal set-designs where no further improvement can be achieved in any of the objectives without degrading one of the others. Pareto optimality problems are found in all areas of study, from economics to engineering to biology, and computational methods have been developed specifically to identify the Pareto frontier. We review progress in multiobjective protein design, the development of Pareto optimization methods, and present a specific case study using multiobjective optimization methods to model the tradeoff between three parameters, stability, specificity, and complexity, of a set of interacting synthetic collagen peptides.

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Computational Enzyme Design

Cited by 441 publications

References 217 publications

Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods

Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods

Installing hydrolytic activity into a completely de novo protein framework

Searching for the Pareto frontier in multi-objective protein design

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