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Open AccessArticle
Computational Modeling Study of the Molecular Basis of dNTP Selectivity in Human Terminal Deoxynucleotidyltransferase
by
Egor O. Ukladov
Egor O. Ukladov 1,2,†,
Timofey E. Tyugashev
Timofey E. Tyugashev 1,†
and
Nikita A. Kuznetsov
Nikita A. Kuznetsov 1,2,*
1
Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
2
Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Biomolecules 2024, 14(8), 961; https://doi.org/10.3390/biom14080961 (registering DOI)
Submission received: 22 July 2024
/
Revised: 3 August 2024
/
Accepted: 5 August 2024
/
Published: 7 August 2024
Abstract
Human terminal deoxynucleotidyl transferase (TdT) can catalyze template-independent DNA synthesis during the V(D)J recombination and DNA repair through nonhomologous end joining. The capacity for template-independent random addition of nucleotides to single-stranded DNA makes this polymerase useful in various molecular biological applications involving sequential stepwise synthesis of oligonucleotides using modified dNTP. Nonetheless, a serious limitation to the applications of this enzyme is strong selectivity of human TdT toward dNTPs in the order dGTP > dTTP ≈ dATP > dCTP. This study involved molecular dynamics to simulate a potential impact of amino acid substitutions on the enzyme’s selectivity toward dNTPs. It was found that the formation of stable hydrogen bonds between a nitrogenous base and amino acid residues at positions 395 and 456 is crucial for the preferences for dNTPs. A set of single-substitution and double-substitution mutants at these positions was analyzed by molecular dynamics simulations. The data revealed two TdT mutants—containing either substitution D395N or substitutions D395N+E456N—that possess substantially equalized selectivity toward various dNTPs as compared to the wild-type enzyme. These results will enable rational design of TdT-like enzymes with equalized dNTP selectivity for biotechnological applications.
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MDPI and ACS Style
Ukladov, E.O.; Tyugashev, T.E.; Kuznetsov, N.A.
Computational Modeling Study of the Molecular Basis of dNTP Selectivity in Human Terminal Deoxynucleotidyltransferase. Biomolecules 2024, 14, 961.
https://doi.org/10.3390/biom14080961
AMA Style
Ukladov EO, Tyugashev TE, Kuznetsov NA.
Computational Modeling Study of the Molecular Basis of dNTP Selectivity in Human Terminal Deoxynucleotidyltransferase. Biomolecules. 2024; 14(8):961.
https://doi.org/10.3390/biom14080961
Chicago/Turabian Style
Ukladov, Egor O., Timofey E. Tyugashev, and Nikita A. Kuznetsov.
2024. "Computational Modeling Study of the Molecular Basis of dNTP Selectivity in Human Terminal Deoxynucleotidyltransferase" Biomolecules 14, no. 8: 961.
https://doi.org/10.3390/biom14080961
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