Solution structure of bound trimethoprim in its complex with Lactobacillus casei dihydrofolate reductase.

@article{Martorell1994SolutionSO,
  title={Solution structure of bound trimethoprim in its complex with Lactobacillus casei dihydrofolate reductase.},
  author={Gabriel Martorell and Michael J. Gradwell and Berry Birdsall and Christopher J. Bauer and Thomas A. Frenkiel and H. T. Andrew Cheung and Vladimir I. Polshakov and Lee F. Kuyper and James Feeney},
  journal={Biochemistry},
  year={1994},
  volume={33 41},
  pages={
          12416-26
        }
}
Two- and three-dimensional (2D and 3D) NMR techniques have been used to assign the signals from nearly all of the protons in Lactobacillus casei dihydrofolate reductase (DHFR) (M(r) 18,300) in its 1:1 complex with the antibacterial drug trimethoprim. A sample of uniformly 15N-labeled protein was examined using 3D 15N/1H experiments [nuclear Overhauser, heteronuclear multiple quantum coherence (NOESY-HMQC) and total correlation, heteronuclear multiple quantum coherence (TOCSY-HMQC) experiments… 

Figures and Tables from this paper

Solution structure of a brodimoprim analogue in its complex with Lactobacillus casei dihydrofolate reductase.
TLDR
Inclusion of the electrostatic interactions into the energy minimizations indicated that structures in which the 4,6-dicarboxylate group of the ligand interacts with the side chains of Arg 57 and His 28 are of low energy.
Structure and dynamics in solution of the complex of lactobacillus casei dihydrofolate reductase with the new lipophilic antifolate drug trimetrexate
TLDR
The binding site for trimetrexate is well defined and this was compared with the binding sites in related complexes formed with methotrexate and trimethoprim, and no major conformational differences were detected between the different complexes.
NMR detection of arginine-ligand interactions in complexes of Lactobacillus casei dihydrofolate reductase.
1H-NMR and 15N-NMR signal assignments have been made for the eight arginine residues in Lactobacillus casei dihydrofolate reductase in its binary complex with methotrexate and in its ternary complex
Letter to the Editor: NMR-based solution structure of the complex of Lactobacillus casei dihydrofolate reductase with trimethoprim and NADPH
TLDR
A comparison of the so-lution structures of binary and ternary complexes of DHFR formed with TMP and NADPH in order to re-veal differences which might be responsible for the decrease in binding to the human en-zyme.
The solution structure of the complex of Lactobacillus casei dihydrofolate reductase with methotrexate.
TLDR
The three-dimensional solution structure of the complex of Lactobacillus casei dihydrofolate reductase formed with the anticancer drug methotrexate is determined using 2531 distance, 361 dihedral angle and 48 hydrogen bond restraints obtained from analysis of multidimensional NMR spectra.
NMR Structures of Apo L. casei Dihydrofolate Reductase and Its Complexes with Trimethoprim and NADPH: Contributions to Positive Cooperative Binding from Ligand-Induced Refolding, Conformational Changes, and Interligand Hydrophobic Interactions
TLDR
Thermodynamic and NMR measurements suggested that a significant contribution to the cooperativity comes from refolding of apo DHFR on binding the first ligand, and that the binary structures are approaching that of the ternary complex as would be expected for positive cooperativity.
Supporting Material
Table S2. The H and N chemical shifts at 15C of L. casei apo DHFR and its binary and ternary complexes with trimethoprim (TMP), NADPH and folinic acid. The DHFR has an N-terminal Met residue. Red
New insights into DHFR interactions: Analysis of Pneumocystis carinii and mouse DHFR complexes with NADPH and two highly potent 5‐(ω‐carboxy(alkyloxy) trimethoprim derivatives reveals conformational correlations with activity and novel parallel ring stacking interactions
TLDR
The data suggest that the enhanced inhibitory activity of PY1011 compared with PY957 is, in part, due to the favorable contacts with Phe69 of pcDHFR by the methylene carbons of the inhibitor side chain that are oriented by the triple bond of the 1‐pentynyl side chain.
Effects of co-operative ligand binding on protein amide NH hydrogen exchange.
...
...

References

SHOWING 1-10 OF 51 REFERENCES
Dihydrofolate reductase: sequential resonance assignments using 2D and 3D NMR and secondary structure determination in solution.
Three-dimensional (3D) heteronuclear NMR techniques have been used to make sequential 1H and 15N resonance assignments for most of the residues of Lactobacillus casei dihydrofolate reductase (DHFR),
Trimethoprim binding to bacterial and mammalian dihydrofolate reductase: a comparison by proton and carbon-13 nuclear magnetic resonance.
TLDR
The binding of trimethoprim to dihydrofolate reductase from L1210 mouse lymphoma cells has been studied by measuring the changes in chemical shift of nuclei of the ligand that accompanying binding, and it is shown that this difference arises largely from the fact that trimethobacillus casei and Escherichia coli reductases adopts different conformations when bound to mammalian and to bacteria.
Multinuclear NMR characterization of two coexisting conformational states of the Lactobacillus casei dihydrofolate reductase-trimethoprim-NADP+ complex.
TLDR
The complex of Lactobacillus casei dihydrofolate reductase with trimethoprim and NADP+ exists in solution as a mixture of approximately equal amounts of two slowly interconverting conformational states, and a partial structural model has been proposed.
Sequence-specific 1H and 15N resonance assignments for human dihydrofolate reductase in solution.
TLDR
Heteronuclear three-dimensional NMR spectroscopy has been used to make sequential resonance assignments for more than 90% of the residues in human dihydrofolate reductase complexed with methotrexate.
Crystal structure of human dihydrofolate reductase complexed with folate.
The crystal structure of recombinant human dihydrofolate reductase with folate bound in the active site has been determined and the structural model refined at 0.2-nm resolution. Preliminary studies
Refined crystal structures of Escherichia coli and chicken liver dihydrofolate reductase containing bound trimethoprim.
TLDR
Structural comparison of these two complexes reveals major geometrical differences in TMP binding that may be important in understanding the stereo-chemical basis of this inhibitor's selectivity for bacterial dihydrofolate reductases.
The 1H-NMR assignments of the aromatic resonances in complexes of Lactobacillus casei dihydrofolate reductase and the origins of their chemical shifts.
TLDR
All the aromatic proton resonances in the 500-MHz NMR spectra of Lactobacillus casei dihydrofolate reductase have been assigned for several of its complexes with inhibitors by using a combination of NMR techniques in conjunction with a selectively deuterated protein designed to simplify the spectra such that nuclear Overhauser effect connections could be detected with greater ease and certainty.
3D 13C/1H NMR-based assignments for side-chain resonances of Lactobacillus casei dihydrofolate reductase. Evidence for similarities between the solution and crystal structures of the enzyme
TLDR
13C-based three-dimensional 1H−1H correlation experiments have been used to determine essentially complete 13C and 1H resonance assignments for the amino acid side chains of uniformly 13C/15N labelled L. casei dihydrofolate reductase in a complex with the drug methotrexate, indicating that the tertiary structure of the enzyme is similar in solution and in the crystal state.
Carbon-13 nuclear magnetic resonance study of protonation of methotrexate and aminopterin bound to dihydrofolate reductase.
TLDR
The data indicate that the association constant for binding of methotrexate is increased enough when protonation of N-1 occurs to account for the enhanced binding of meethotrexates as compared with folate.
...
...