Electrostatics as a Guiding Principle in Understanding and Designing Enzymes

Ruiz-Pernía, J. Javier; Świderek, Katarzyna; Bertran, Joan; Moliner, Vicent; Tuñón, Iñaki

doi:10.1021/acs.jctc.3c01395

Cited by 3 publications

(1 citation statement)

References 70 publications

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“…For the peptide bond formation catalyzed by the ribosome, in addition to the catalytic effect arising from an entropic factor, , a particular attention has focused on a possible proton shuttle between the nucleophile proton donor and the leaving group proton acceptor, mediated by bases and water molecules, rather than the general base catalysis mechanism. ,− Our results are consistent with the key role played by the A76 O 2 ’H hydrogen-bond donor group identified in the ribosome. ,,, Our mechanism 2 involving the P ± transition state shows why stabilizing the negative charge on the leaving group oxygen can lower the reaction barrier. More generally, the P ± transition state of this mechanism has a strong ion pair character that can be stabilized by electric fields created in the active site of ribosome. , In solution, the KIE for the reaction of ribosomal substrates are similar to these of the amide bond discussed here, suggesting that they react via the same mechanism 2 in which no proton transfer occurs before the transition state is reached. In the ribosome, our results therefore suggest that in addition to proton relay considerations, the electrostatic stabilization of the leaving group negative charge should also play an important role.…”

Section: Resultsmentioning

confidence: 55%

Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling

David,

Tuñón,

Laage

2024

J. Am. Chem. Soc.

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The formation of an amide bond is an essential step in the synthesis of materials and drugs, and in the assembly of amino acids to form peptides. The mechanism of this reaction has been studied extensively, in particular to understand how it can be catalyzed, but a representation capable of explaining all the experimental data is still lacking. Numerical simulation should provide the necessary molecular description, but the solvent involvement poses a number of challenges. Here, we combine the efficiency and accuracy of neural network potential-based reactive molecular dynamics with the extensive and unbiased exploration of reaction pathways provided by transition path sampling. Using microsecond-scale simulations at the density functional theory level, we show that this method reveals the presence of two competing distinct mechanisms for peptide bond formation between alanine esters in aqueous solution. We describe how both reaction pathways, via a general base catalysis mechanism and via direct cleavage of the tetrahedral intermediate respectively, change with pH. This result contrasts with the conventional mechanism involving a single pathway in which only the barrier heights are affected by pH. We show that this new proposal involving two competing mechanisms is consistent with the experimental data, and we discuss the implications for peptide bond formation under prebiotic conditions and in the ribosome. Our work shows that integrating deep potential molecular dynamics with path sampling provides a powerful approach for exploring complex chemical mechanisms.

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Section: Resultsmentioning

confidence: 55%

Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling

David,

Tuñón,

Laage

2024

J. Am. Chem. Soc.

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Enhancing the specific activity of 3α-hydroxysteroid dehydrogenase through cross-regional combinatorial mutagenesis

Ma,

Li,

Yan

et al. 2024

International Journal of Biological Macromolecules

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Electrostatic Preorganization in Three Distinct Heterogeneous Proteasome β-Subunits

Ferrer,

Moliner,

Świderek

2024

ACS Catal.

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The origin of the enzyme's powerful role in accelerating chemical reactions is one of the most critical and still widely discussed questions. It is already accepted that enzymes impose an electrostatic field onto their substrates by adopting complex three-dimensional structures; therefore, the preorganization of electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanisms and rate constant enhancement. In this work, we focus on three catalytically active βsubunits of 20S proteasomes with low sequence identity (∼30%) whose active sites, although situated in an electrostatically miscellaneous environment, catalyze the same chemical reaction with similar catalytic efficiency. Our in silico experiments reproduce the experimentally observed equivalent reactivity of the three sites and show that obliteration of the electrostatic potential in all active sites would deprive the enzymes of their catalytic power by slowing down the chemical process by a factor of 10 35 . To regain enzymatic efficiency, besides catalytic Thr1 and Lys33 residues, the presence of aspartic acid in position 17 and an aqueous solvent is required, proving that the electrostatic potential generated by the remaining residues is insignificant for catalysis. Moreover, it was found that the gradual decay of atomic charges on Asp17 strongly correlates with the enzyme's catalytic rate deterioration as well as with a change in the charge distributions due to introduced mutations. The computational procedure used and described here may help identify key residues for catalysis in other biomolecular systems and consequently may contribute to the process of designing enzyme-like synthetic catalysts.

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Electrostatics as a Guiding Principle in Understanding and Designing Enzymes

Cited by 3 publications

References 70 publications

Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling

Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling

Enhancing the specific activity of 3α-hydroxysteroid dehydrogenase through cross-regional combinatorial mutagenesis

Electrostatic Preorganization in Three Distinct Heterogeneous Proteasome β-Subunits

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