TY - JOUR
T1 - Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR
AU - Cetin, Ebru
AU - Guclu, Tandac F.
AU - Kantarcioglu, Isik
AU - Gaszek, Ilona K.
AU - Toprak, Erdal
AU - Atilgan, Ali Rana
AU - Dedeoglu, Burcu
AU - Atilgan, Canan
N1 - Funding Information:
The numerical calculations reported in this paper were partially performed at TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA resources). We thank TUBITAK project no. 121Z329 for partial support. This work was partially supported by National Institutes of Health grant R01GM125748 (E.T.) and Welch Foundation I-2082-20210327 (E.T.). B.D. thanks TUBITAK project no. 118C487 for the support. I.K. was partially supported by TUBITAK 2214-A visiting research fellowship (Application Number: 1059B142100453).
Publisher Copyright:
© 2023 The Authors. Published by American Chemical Society.
PY - 2023/8/14
Y1 - 2023/8/14
N2 - Dihydrofolate reductase (DHFR) is an important drug target and a highly studied model protein for understanding enzyme dynamics. DHFR’s crucial role in folate synthesis renders it an ideal candidate to understand protein function and protein evolution mechanisms. In this study, to understand how a newly proposed DHFR inhibitor, 4′-deoxy methyl trimethoprim (4′-DTMP), alters evolutionary trajectories, we studied interactions that lead to its superior performance over that of trimethoprim (TMP). To elucidate the inhibition mechanism of 4′-DTMP, we first confirmed, both computationally and experimentally, that the relative binding free energy cost for the mutation of TMP and 4′-DTMP is the same, pointing the origin of the characteristic differences to be kinetic rather than thermodynamic. We then employed an interaction-based analysis by focusing first on the active site and then on the whole enzyme. We confirmed that the polar modification in 4′-DTMP induces additional local interactions with the enzyme, particularly, the M20 loop. These changes are propagated to the whole enzyme as shifts in the hydrogen bond networks. To shed light on the allosteric interactions, we support our analysis with network-based community analysis and show that segmentation of the loop domain of inhibitor-bound DHFR must be avoided by a successful inhibitor.
AB - Dihydrofolate reductase (DHFR) is an important drug target and a highly studied model protein for understanding enzyme dynamics. DHFR’s crucial role in folate synthesis renders it an ideal candidate to understand protein function and protein evolution mechanisms. In this study, to understand how a newly proposed DHFR inhibitor, 4′-deoxy methyl trimethoprim (4′-DTMP), alters evolutionary trajectories, we studied interactions that lead to its superior performance over that of trimethoprim (TMP). To elucidate the inhibition mechanism of 4′-DTMP, we first confirmed, both computationally and experimentally, that the relative binding free energy cost for the mutation of TMP and 4′-DTMP is the same, pointing the origin of the characteristic differences to be kinetic rather than thermodynamic. We then employed an interaction-based analysis by focusing first on the active site and then on the whole enzyme. We confirmed that the polar modification in 4′-DTMP induces additional local interactions with the enzyme, particularly, the M20 loop. These changes are propagated to the whole enzyme as shifts in the hydrogen bond networks. To shed light on the allosteric interactions, we support our analysis with network-based community analysis and show that segmentation of the loop domain of inhibitor-bound DHFR must be avoided by a successful inhibitor.
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U2 - 10.1021/acs.jcim.3c00818
DO - 10.1021/acs.jcim.3c00818
M3 - Article
C2 - 37491825
AN - SCOPUS:85167784427
SN - 1549-9596
VL - 63
SP - 4839
EP - 4849
JO - Journal of Chemical Information and Modeling
JF - Journal of Chemical Information and Modeling
IS - 15
ER -