Probing the Suitability of Different Ca2+ Parameters for Long Simulations of Diisopropyl Fluorophosphatase

Zlobin, Alexander; Diankin, Igor D.; Pushkarev, Sergey V.; Golovin, Andrey V.

doi:10.3390/molecules26195839

Cited by 7 publications

(10 citation statements)

References 74 publications

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“…66 No unrestrained dynamics was performed to ensure the substrate peptide would not dissociate and calcium-binding sites would not break. 67 All QM/MM systems were built from this last equilibration run. DFTB3 with 3ob-3-1 parameter set and d4 dispersion correction, and GFN2-XTB were used to treat the QM region.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

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Challenges in Protein QM/MM Simulations with Intra-Backbone Link Atoms

Zlobin

Belyaeva

Golovin

2023

J. Chem. Inf. Model.

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Hybrid quantum mechanical/molecular mechanical (QM/MM) simulations fuel discoveries in many fields of science including computational biochemistry and enzymology. Development of more convenient tools leads to an increase in the number of works in which mechanical insights into enzymes’ mode of operation are obtained. Most commonly, these tools feature hydrogen-capping (link atom) approach to provide coupling between QM and MM subsystems across a covalent bond. Extensive studies were conducted to provide a solid foundation for the correctness of such an approach when a bond to a nonpolar MM atom is considered. However, not every task may be accomplished this way. Certain scenarios of using QM/MM in computational enzymology encourage or even necessitate the incorporation of backbone atoms into the QM region. Two out of three backbone atoms are polar, and in QM/MM with electrostatic embedding, a neighboring link atom will be hyperpolarized. Several schemes to mitigate this effect were previously proposed alongside a rigorous assessment of quantitative effects on model systems. However, it was not clear whether they may translate into qualitatively different results and how link atom hyperpolarization may manifest itself in a real-life enzymological scenario. Here, we show that the consequences of such an artifact may be severe and may completely overturn the conclusions drawn from the simulations. Our case advocates for the use of charge redistribution schemes whenever intra-backbone QM/MM boundaries are considered. Moreover, we addressed how different boundary types and charge redistribution schemes influence backbone dynamics. We showed that the results are heavily dependent on which boundary MM terms are retained, with charge alteration being of secondary importance. In the worst case, only three intra-backbone boundaries may be used with relative confidence in the adequacy of resulting simulations, irrespective of the hyperpolarization mitigation scheme. Thus, advances in the field are certainly needed to fuel new discoveries. As of now, we believe that issues raised in this work might encourage authors in the field to report what boundaries, boundary MM terms, and charge redistribution schemes they are using, so their results may be correctly interpreted.

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Section: ■ Materials and Methodsmentioning

confidence: 99%

“…Stochastic cell-rescale barostat was used for pressure control . No unrestrained dynamics was performed to ensure the substrate peptide would not dissociate and calcium-binding sites would not break . All QM/MM systems were built from this last equilibration run.…”

Section: Methodsmentioning

confidence: 99%

Challenges in Protein QM/MM Simulations with Intra-Backbone Link Atoms

Zlobin

Belyaeva

Golovin

2023

J. Chem. Inf. Model.

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“…All previously listed models were parameterized in the Amber19 force field ported from Amber to Gromacs notation in-house . Each system was placed in a cubic box with periodic boundary conditions and solvated with tip3p-FB .…”

Section: Methodsmentioning

confidence: 99%

“…All previously listed models were parameterized in the Amber19 force field 49 ported from Amber to Gromacs notation in-house. 50 Each system was placed in a cubic box with periodic boundary conditions and solvated with tip3p-FB. 51 All crystallographic water molecules were retained, while all added were manually filtered in case of incorrect solvation.…”

Section: Methodsmentioning

confidence: 99%

Between Protein Fold and Nucleophile Identity: Multiscale Modeling of the TEV Protease Enzyme–Substrate Complex

Zlobin

Golovin

2022

ACS Omega

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The cysteine protease from the tobacco etch virus (TEVp) is a well-known and widely utilized enzyme. TEVp's chymotrypsin-like fold is generally associated with serine catalytic triads that differ in terms of a reaction mechanism from the most well-studied papain-like cysteine proteases. The question of what dominates the TEVp mechanism, nucleophile identity, or structural composition has never been previously addressed. Here, we use enhanced sampling multiscale modeling to uncover that TEVp combines the features of two worlds in such a way that potentially hampers its activity. We show that TEVp cysteine is strictly in the anionic form in a free enzyme similar to papain. Peptide binding shifts the equilibrium toward the nucleophile′s protonated form, characteristic of chymotrypsin-like proteases, although the cysteinyl anion form is still present and interconversion is rapid. This way cysteine protonation generates enzyme states that are a diversion from the most effective course of action, with only 13.2% of Michaelis complex sub-states able to initiate the reaction. As a result, we propose an updated view on the reaction mechanism catalyzed by TEVp. We also demonstrate that AlphaFold is able to construct protease−substrate complexes with high accuracy. We propose that our findings open a way for its industrious use in enzymological tasks. Unique features of TEVp discovered in this work open a discussion on the evolutionary history and trade-offs of optimizing serine triad-associated folds to cysteine as a nucleophile.

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“…In particular, classical MD empowers the advances in enzymology. It allows to track down the conformational changes associated with the regulation of enzymatic activity, 12,13 the process of the substrate binding and accommodation within the binding pocket, [14][15][16][17] to explain or even predict the outcomes of substitutions. 18,19 Among various enzymatic classes, several are particularly interesting for industrial or clinical use.…”

Section: Introductionmentioning

confidence: 99%