10.1021/ja026264y.s001
Jonathan C. T. Carlson
Jonathan
C. T. Carlson
Aaron Kanter
Aaron
Kanter
Guruvasuthevan R. Thuduppathy
Guruvasuthevan R.
Thuduppathy
Vivian Cody
Vivian
Cody
Pamela E. Pineda
Pamela E.
Pineda
R. Scott McIvor
R.
Scott McIvor
Carston R. Wagner
Carston R.
Wagner
Designing Protein Dimerizers: The Importance of Ligand
Conformational Equilibria
American Chemical Society
2003
protein
dimerize Escherichia coli dihydrofolate reductase
coli DHFR
dimerization
MTX
ability
dimerize dihydrofolate reductase
Ligand Conformational Equilibria
conformation
solution
kcal
2003-01-17 00:00:00
Journal contribution
https://acs.figshare.com/articles/journal_contribution/Designing_Protein_Dimerizers_The_Importance_of_Ligand_Conformational_Equilibria/3643368
In an effort to elucidate the role of ligand conformation in induced protein dimerization, we
synthesized a flexible methotrexate (MTX) dimer, demonstrated its ability to selectively dimerize <i>Escherichia
coli</i> dihydrofolate reductase (DHFR), and evaluated the factors regulating its ability to induce cooperative
dimerization. Despite known entropic barriers, bis-MTX proved to possess substantial conformational stability
in aqueous solution (−3.8 kcal/mol ≥ Δ<i>G</i><sub>fold</sub> ≥ −4.9 kcal/mol), exerting a dominant influence on the
thermodynamics of dimerization. To dimerize DHFR, bis-MTX must shift from a folded to an extended
conformation. From this conclusion, the strength of favorable protein−protein interactions in bis-MTX−<i>E.
coli </i>DHFR dimers (−3.1 kcal/mol ≥ Δ<i>G</i><sub>c</sub> ≥ −4.2 kcal/mol), and the selectivity of dimerization for <i>E. coli</i>
DHFR relative to mouse DHFR (>10<sup>7</sup>) could be determined. The crystal structure of bis-MTX in complex
with <i>E. coli</i> DHFR confirms the feasibility of a close-packed dimerization interface and suggests a possible
solution conformation for the induced protein dimers. Consequently, the secondary structure of this minimal
foldamer regulates its ability to dimerize dihydrofolate reductase in solution, providing insight into the complex
energy landscape of induced dimerization.