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Establishing a substrate-assisted mechanism for the pre-transfer editing in SerRS and IleRS: a QM/QM investigation

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Abstract

Aminoacyl-tRNA synthetases (aaRS) are key enzymes in protein biosynthesis that employ various editing mechanisms to ensure faithful translation of genetic information. Seryl-tRNA synthetase (SerRS) and isoleucine-tRNA synthetase (IleRS) utilize pre-transfer editing mechanisms to prevent the incorporation of the undesired misactivated amino acids. In this study, molecular dynamics (MD) and quantum mechanics/QM (QM/semiempirical) were used to provide atomistic details regarding the pre-transfer editing against the non-cognates homocysteine (Hcy) by IleRS as well as cysteine (Cys) and threonine (Thr) by SerRS. Notably, in both enzymes, the mechanism is found to follow a stepwise self-cyclization substrate-assisted mechanism. Initially, dihedral scan around the substrate’s Cβ__Cγ bond takes place followed by a concerted step of R-S(O)H deprotonation concomitant with a nucleophilic attack. The rate limiting step to edit against Hcy by IleRS is the dihedral scan step and require 24.3 kcal/mol to proceed. Meanwhile, the rate-limiting step for editing against both Cys and Thr by SerRS is found to be the second step with Gibbs energy barriers of 20.4 and 26.6 kcal/mol, respectively. Interestingly, following the same pre-transfer editing pathway against the cognate Ser by SerRS results in a significantly higher energy barrier of 31.4 kcal/mol and energetically less favoured product complex lies at 17.7 kcal/mol. This finding clearly indicates an enzymatically infeasible process against Ser-AMP from kinetic and thermodynamic perspectives. The provided mechanistic insights should provide novel foundation required for the development of effective therapeutic agents for the treatment of the many disease states associated with these enzymes.

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Coordinates for the optimized structures have been provided with the manuscript and more date can be provided once requested.

Abbreviations

aaRS:

Aminoacyl-tRNA Synthetases

SerRS:

Seryl-tRNA synthetases

IleRS:

Isoleucine-tRNA synthetase

Ser:

Serine

Thr:

Threonine

Hcy:

Homocysteine

RC:

Reactive complex

TS:

Transition state

IC:

Intermediate complex

PC:

Product complex

Op:

Non-bridged phosphate oxygen

H-bond:

Hydrogen bond

ATP:

Adenosine triphosphate

AMP:

Adenosine monophosphate

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Funding

Funding

We acknowledge the Natural Science and Engineering Research Council of Canada (NSERC) for financial support and Compute Canada for an award allocation of computational resources.

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Authors and Affiliations

  1. Department of Chemistry, Faculty of Science, Damietta University, New Damietta, 35411, Egypt

    Mohamed M. Aboelnga

  2. Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, N9B 3P4, Canada

    James W. Gauld

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  1. Mohamed M. Aboelnga
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  2. James W. Gauld
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Author contribution

M. M. Aboelnga: investigation, methodology, formal analysis, project administration, validation, visualization, and writing—original draft. J. W. Gauld: conceptualization, methodology, project administration, supervision, resources, funding acquisition, and writing.

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Correspondence to Mohamed M. Aboelnga or James W. Gauld.

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Aboelnga, M.M., Gauld, J.W. Establishing a substrate-assisted mechanism for the pre-transfer editing in SerRS and IleRS: a QM/QM investigation. Struct Chem 35, 519–530 (2024). https://doi.org/10.1007/s11224-023-02204-1

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