Structure and dynamics in solution of the complex of lactobacillus casei dihydrofolate reductase with the new lipophilic antifolate drug trimetrexate

  title={Structure and dynamics in solution of the complex of lactobacillus casei dihydrofolate reductase with the new lipophilic antifolate drug trimetrexate},
  author={Vladimir I. Polshakov and Berry Birdsall and Thomas A. Frenkiel and Angelo R. Gargaro and James Feeney},
  journal={Protein Science},
We have determined the three‐dimensional solution structure of the complex of Lactobacillus casei dihydrofolate reductase and the anticancer drug trimetrexate. Two thousand seventy distance, 345 dihedral angle, and 144 hydrogen bond restraints were obtained from analysis of multidimensional NMR spectra recorded for complexes containing 15N‐labeled protein. Simulated annealing calculations produced a family of 22 structures fully consistent with the constraints. Several intermolecular protein… 
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
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.
Letter to the Editor: NMR-based solution structure of the complex of Lactobacillus casei dihydrofolate reductase with trimethoprim and NADPH
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.
Effects of co-operative ligand binding on protein amide NH hydrogen exchange.
The solution structure of Bacillus anthracis dihydrofolate reductase yields insight into the analysis of structure-activity relationships for novel inhibitors.
A three-dimensional solution structure of the ternary complex as determined by NMR reveals a general conservation of the DHFR fold and cofactor interactions as well as differences in the location of an active site helix and specific ligand interactions.
Structural characteristics of antifolate dihydrofolate reductase enzyme interactions
Mechanical questions can now be addressed with the structural data available for atomic resolution enzyme complexes as well as from neutron diffraction data that have recently become available, providing new insight into the design of novel inhibitors that can target specific species with high selectivity of binding.
Backbone resonance assignment and dynamics of 110 kDa hexameric inorganic pyrophosphatase from Mycobacterium tuberculosis.
It was found that the secondary structure of Mt-PPase in solution corresponds well to the crystal structure of this protein, and determined resonance assignments and dynamic properties provide the basis for the subsequent structure-based design of novel inhibitors of Mt -PPase-potential anti-tuberculosis drugs.
NMR resonance assignment and backbone dynamics of a C-terminal domain homolog of orange carotenoid protein.
Results revealed that the structure of AnaCTDH in solution and in the crystal are largely equivalent, and provide the platform for the subsequent analysis of the holo-CTDH structure in solution, for the better understanding of light-triggered protein-protein interactions and the development of antioxidant nanocarriers for biomedical applications in the future.
Structure and dynamics in solution of the stop codon decoding N‐terminal domain of the human polypeptide chain release factor eRF1
The high‐resolution NMR structure of the N‐domain of human eRF1, responsible for stop codon recognition, has been determined in solution and indicates that helices α2 and α3, with the NIKS loop between them, can switch their orientation relative to the β‐core of the protein.
Eukaryotic class 1 translation termination factor eRF1 − the NMR structure and dynamics of the middle domain involved in triggering ribosome‐dependent peptidyl‐tRNA hydrolysis
The protein backbone dynamics, studied using 15N relaxation experiments, showed that the GGQ loop is the most flexible part of the middle domain, which could be a determinant of the functional activity of the eukaryotic class’1 polypeptide chain release factor.


The solution structure of the complex of Lactobacillus casei dihydrofolate reductase with methotrexate.
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 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
NMR solution structure of the antitumor compound PT523 and NADPH in the ternary complex with human dihydrofolate reductase.
NMR data indicate that the binary complex has two distinct conformations in solution which are in slow exchange and that the addition of NADPH stabilizes the ternary complex in a single bound state.
NMR studies of differences in the conformations and dynamics of ligand complexes formed with mutant dihydrofolate reductases.
Two mutants of Lactobacillus casei dihydrofolate reductase, Trp 21----Leu and Asp 26----Glu, have been prepared by using site-directed mutagenesis methods, and their ligand binding and structural
Solution structure of bound trimethoprim in its complex with Lactobacillus casei dihydrofolate reductase.
The protein residues nearest to the bound trimethoprim were found to be very similar in all of the structures and agreed well with corresponding contact residues observed in the X-ray crystal studies on trimethobacillus casei dihydrofolate reductase complexes formed with Escherichia coli and chicken liver DHFRs.
Dihydrofolate reductase: multiple conformations and alternative modes of substrate binding.
The pattern of chemical shift changes in the ligand and the protein indicates that the structural differences are localized within the active site of the enzyme.
13C NMR determination of the tautomeric and ionization states of folate in its complexes with Lactobacillus casei dihydrofolate reductase.
13C NMR spectra of the ternary complexes of the 13C-labeled folic acids with DHFR and NADP+, confirming the previous findings that there are three interconverting conformational forms of bound folate (forms I, IIa, and IIb) in theTernary complex.
A 1H NMR study of the interactions and conformations of rationally designed brodimoprim analogues in complexes with Lactobacillus casei dihydrofolate reductase.
Computer graphic techniques have been used to predict which substituent groups were required at the 3'-O position of brodimoprim (2,4-diamino-5-(3,5-dimethoxy-4-bromobenzyl)pyrimidine) to make additional interactions with the enzyme, and the C4,C6-dicarboxylic acid analogue IX was designed to interact with Arg-57 and His-28 in the enzyme.
Dynamics of the dihydrofolate reductase-folate complex: catalytic sites and regions known to undergo conformational change exhibit diverse dynamical features.
It is concluded that the observed time-dependent structural fluctuations of the binary complex are in fact associated with catalytic properties of the molecule.