Novel Approach for Identifying Key Residues in Enzymatic Reactions: Proton Abstraction in Ketosteroid Isomerase

Ito, Mika; Brinck, Tore

doi:10.1021/jp508423s

Cited by 16 publications

(22 citation statements)

References 60 publications

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“…PIEs can be used to identify the residue fragments, which are important factors in the catalytic activity. [71][72][73] It should be noted that here, as in other FMO publications, fragments are defined by detaching Cα-C bonds at Cα, so that fragment residues in FMO are shifted compared to conventional residues by a carboxyl group.…”

Section: An Application Of Fmo/fdd To An Enzymatic Reactionmentioning

confidence: 99%

“…69,70 FMO has also been used to refine enzymatic reaction energetics for structures obtained with other methods. [71][72][73] In this work, previously 65 neglected terms in the analytic gradient are derived and implemented for the frozen domain with dimers (FDD) formulation of FMO (FMO/FDD), achieving fully analytic gradient. Secondly, analytic second derivatives are developed for FMO/FDD.…”

Section: Introductionmentioning

confidence: 99%

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Simulations of Chemical Reactions with the Frozen Domain Formulation of the Fragment Molecular Orbital Method

Nakata

Fedorov

Nagata

et al. 2015

J. Chem. Theory Comput.

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The fully analytic first and second derivatives of the energy in the frozen domain formulation of the fragment molecular orbital (FMO) were developed and applied to locate transition states and determine vibrational contributions to free energies. The development is focused on the frozen domain with dimers (FDD) model. The intrinsic reaction coordinate method was interfaced with FMO. Simulations of IR and Raman spectra were enabled using FMO/FDD by developing the calculation of intensities. The accuracy is evaluated for S(N)2 reactions in explicit solvent, and for the free binding energies of a protein-ligand complex of the Trp cage protein (PDB: 1L2Y ). FMO/FDD is applied to study the keto-enol tautomeric reaction of phosphoglycolohydroxamic acid and the triosephosphate isomerase (PDB: 7TIM ), and the role of amino acid residue fragments in the reaction is discussed.

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Section: An Application Of Fmo/fdd To An Enzymatic Reactionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Simulations of Chemical Reactions with the Frozen Domain Formulation of the Fragment Molecular Orbital Method

Nakata

Fedorov

Nagata

et al. 2015

J. Chem. Theory Comput.

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“…These fast electronic calculations, united with algorithms for large scale systems such as FMO [174,188] or the much faster Effective Fragment Molecular Orbital (EFMO) [189], make "ab initio biochemistry" [190] closer, albeit still far away for design purposes.…”

Section: Catalytic Rate Constant Enhancementmentioning

confidence: 99%

Molecular Modeling in Enzyme Design, Toward In Silico Guided Directed Evolution

Monza

Acebes

Lucas

et al. 2017

Directed Enzyme Evolution: Advances and Applications

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Directed evolution creates diversity in subsequent rounds of mutagenesis in the quest of increased protein stability, substrate binding and catalysis. Although this technique does not require any structural/mechanistic knowledge of the system, the frequency of improved mutations is usually low. For this reason, computational tools are increasingly used to focus the search in sequence space, enhancing the efficiency of laboratory evolution. In particular, molecular modeling methods provide a unique tool to grasp the sequence/structure/function relationship The final publication is available at Springer via https://link.springer.com/chapter/10.1007/978-3-319-50413-1_10/fulltext.html of the protein to evolve, with the only condition that a structural model is provided. With this book chapter, we tried to guide the reader through the state of art of molecular modeling, discussing their strengths, limitations and directions. In addition, we suggest a possible future template for in silico directed evolution where we underline two main points: a hierarchical computational protocol combining several different techniques, and a synergic effort between simulations and experimental validation. IntroductionBiotechnology needs catalysts that can work under harsh conditions, catalyze a broad range of substrates, generate maximum amount of product, and tolerate changes in the environment. Enzymes, which are biodegradable and reusable catalysts [1], in addition to remarkable reaction rates, can work in environmentally friendly pH and temperature ranges, and display control over stereochemistry and regioselectivity which makes them ideal for many applications [2,3]. When thinking about enzymes, people normally associate them to expressions such as "perfect catalysts" or "outstanding reaction rate". In fact, there are examples of enzymes that catalyze reactions at extremely high rates such as triose phosphate isomerase, superoxide dismutase or carbonic anhydrase [4]. These are often limited only by the rate of ligand diffusion into the active site (diffusion-controlled rate). Nevertheless, an extensive analysis by Bar-Even et al., of nearly 2000 enzymes, showed that the median maximal turnover rate value over all measured enzymes is about 10 s −1 nowhere close to the values of 10 5 or 10 6 normally associated with catalysts [5,6].So, it would appear that natural enzymes are "just good enough" for the function they must perform in a given organism [7]. One might conclude that if they had evolved to their optimum performance then trying to improve them (from a kinetic point of view) would be attempting the impossible. On the contrary, as seen by the distribution of reaction rates, k cat , most enzymes function at a lower rate than the diffusion-limit and thus, there is space to further increase their kinetic properties to meet industrial needs. Additionally, we need enzymes capable of catalyzing reactions for which no known enzymes exist, to work with different substrates and for particular conditions that are industrially...

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“…The fragment molecular orbital (FMO) method 4 is a considerably faster alternative to full ab initio methods and has previously been applied in studies of enzyme catalysis. [5][6][7][8] In the FMO approach the molecule or molecular system is divided into smaller fragments and each fragment is computed fully ab initio in the Coulomb field from the entire molecular system. All interactions between any two fragments (dimers) are considered quantum mechanically as well but only up to a certain cutoff outside of which the fragments are represented by point charges.…”

Section: Introductionmentioning

confidence: 99%

“…In a recent study by Ito and Brinck, 8 the contribution of different residues to ketosteroid isomerase catalyzed proton abstraction was investigated using FMO. In addition to considering inter-fragment interaction energies to evaluate the importance of key residues to the activity, the effect on the activation energy of the enzyme-catalyzed reaction by virtually deleting a residue (relative deletion energy) was studied.…”

Section: Introductionmentioning

confidence: 99%

Fragment molecular orbital study of the cAMP-dependent protein kinase catalyzed phosphoryl transfer: a comparison with the differential transition state stabilization method

Öberg

Brinck

2016

Phys. Chem. Chem. Phys.

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The importance of key residues to the activity of the cAMP-dependent protein kinase catalyzed phosphoryl transfer and to the stabilization of the transition state of the reaction has been investigated by means of the fragment molecular orbital (FMO) method. To evaluate the accuracy of the method and its capability of fragmenting covalent bonds, we have compared stabilization energies due to the interactions between individual residues and the reaction center to results obtained with the differential transition state stabilization method (Szarek, et al., J. Phys. Chem. B, 2008, 112, 11819-11826) and observe, despite a size difference in the fragment describing the reaction center, near-quantitative agreement. We have also computed deletion energies to investigate the effect of virtual deletion of key residues on the activation energy. These results are consistent with the stabilization energies and yield additional information as they clearly capture the effect of secondary interactions, i.e. interactions in the second coordination layer of the reaction center. We find that using FMO to calculate deletion energies is a powerful and time efficient approach to analyze the importance of key residues to the activity of an enzyme catalyzed reaction.

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Novel Approach for Identifying Key Residues in Enzymatic Reactions: Proton Abstraction in Ketosteroid Isomerase

Cited by 16 publications

References 60 publications

Simulations of Chemical Reactions with the Frozen Domain Formulation of the Fragment Molecular Orbital Method

Simulations of Chemical Reactions with the Frozen Domain Formulation of the Fragment Molecular Orbital Method

Molecular Modeling in Enzyme Design, Toward In Silico Guided Directed Evolution

Fragment molecular orbital study of the cAMP-dependent protein kinase catalyzed phosphoryl transfer: a comparison with the differential transition state stabilization method

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