Evolution Conserves the Network of Coupled Residues in Dihydrofolate Reductase

Jiayue Li; Gabriel Fortunato; Jennifer Lin; Pratul K Agarwal; Amnon Kohen; Priyanka Singh; Christopher M Cheatum

doi:10.1021/acs.biochem.9b00460

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Evolution Conserves the Network of Coupled Residues in Dihydrofolate Reductase

Journal article

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Evolution Conserves the Network of Coupled Residues in Dihydrofolate Reductase

Jiayue Li, Gabriel Fortunato, Jennifer Lin, Pratul K Agarwal, Amnon Kohen, Priyanka Singh and Christopher M Cheatum

Biochemistry (Easton), Vol.58(37), pp.3861-3868

09/17/2019

DOI: 10.1021/acs.biochem.9b00460

PMCID: PMC7296831

PMID: 31423766

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https://www.ncbi.nlm.nih.gov/pmc/articles/7296831View

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Abstract

Understanding protein motions and their role in enzymatic reactions is an important and timely topic in enzymology. Protein motions that are involved in the chemical step of catalysis are particularly intriguing but difficult to identify. A global network of coupled residues in dihydrofolate reductase ( DHFR), which assists in catalyzing the chemical step, has previously been demonstrated through quantum mechanical/molecular mechanical and molecular dynamics simulations as well as bioinformatic analyses. A few specific residues (M42, G121, F125, and I14) were shown to function synergistically with measurements of single-turnover rates and the temperature dependence of intrinsic kinetic isotope effects (KIEs ) of site-directed mutants. This study hypothesizes that the global network of residues involved in the chemical step is evolutionarily conserved and probes homologous residues of the potential global network in human DHFR through measurements of the temperature dependence of KIEs and computer simulations based on the empirical valence bond method. We study mutants M53W and S145V. Both of these remote residues are homologous to network residues in DHFR. Non-additive isotope effects on activation energy are observed between M53 and S145, indicating their synergistic effect on the chemical step in human DHFR, which suggests that both of these residues are part of a network affecting the chemical step in enzyme catalysis. This finding supports the hypothesis that human and DHFR share similar networks, consistent with evolutionary preservation of such networks.

Details

Title: Subtitle: Evolution Conserves the Network of Coupled Residues in Dihydrofolate Reductase
Creators: Jiayue Li - Department of Chemistry , The University of Iowa , Iowa City , Iowa 52242 , United States
Gabriel Fortunato - Department of Chemistry , The University of Iowa , Iowa City , Iowa 52242 , United States
Jennifer Lin - Department of Chemistry , The University of Iowa , Iowa City , Iowa 52242 , United States
Pratul K Agarwal - Department of Biochemistry & Cellular and Molecular Biology , The University of Tennessee, Knoxville , Knoxville , Tennessee 37996 , United States
Amnon Kohen - Department of Chemistry , The University of Iowa , Iowa City , Iowa 52242 , United States
Priyanka Singh - Department of Chemistry , The University of Iowa , Iowa City , Iowa 52242 , United States
Christopher M Cheatum - Department of Chemistry , The University of Iowa , Iowa City , Iowa 52242 , United States
Resource Type: Journal article
Publication Details: Biochemistry (Easton), Vol.58(37), pp.3861-3868
DOI: 10.1021/acs.biochem.9b00460
PMID: 31423766
PMCID: PMC7296831
NLM abbreviation: Biochemistry
ISSN: 0006-2960
eISSN: 1520-4995
Grant note: R01 GM105978 / NIGMS NIH HHS
Language: English
Date published: 09/17/2019
Academic Unit: Liberal Arts and Science Admin; Chemistry
Record Identifier: 9984216674002771

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