Diagnostic chemical shift markers for loop conformation and substrate and cofactor binding in dihydrofolate reductase complexes

Heteronuclear NMR methods have been used to probe the conformation of four complexes of Escherichia coli dihydrofolate reductase (DHFR) in solution. (1)H(N), (15)N, and (13)C(alpha) resonance assignments have been made for the ternary complex with folate and oxidized NADP(+) cofactor and the ternary complex with folate and a reduced cofactor analog, 5,6-dihydroNADPH. The backbone chemical shifts have been compared with those of the binary complex of DHFR with the substrate analog folate and the binary complex with NADPH (the holoenzyme). Analysis of (1)H(N) and (15)N chemical shifts has led to the identification of marker resonances that report on the active site conformation of the enzyme. Other backbone amide resonances report on the presence of ligands in the pterin binding pocket and in the adenosine and nicotinamide-ribose binding sites of the NADPH cofactor. The chemical shift data indicate that the enzyme populates two dominant structural states in solution, with the active site loops in either the closed or occluded conformations defined by X-ray crystallography; there is no evidence that the open conformation observed in some X-ray structures of E. coli DHFR are populated in solution.     

Site-specific mutagenesis of dihydrofolate reductase from Escherichia coli

Two site-specific mutations of dihydrofolate reductase from Escherichia coli based on the x-ray crystallographic structure were constructed. The first mutation (His-45----Gln) is aimed at assessing the interaction between the imidazole moiety and the pyrophosphate backbone of NADPH. The second (Thr-113----Val) is part of a hydrogen bonding network that contacts the dihydrofolate substrate and may be involved in proton delivery to the N5-C6 imine undergoing reduction. The first mutation was shown to alter both the association and dissociation rate constants for the cofactor so that the dissociation constant was increased 6-40-fold. A corresponding but smaller (fourfold) effect was noted in V/K but not in V compared to the wild-type enzyme. The second was demonstrated to increase the dissociation rate constant for methotrexate 20-30-fold, and presumably dihydrofolate also, with a corresponding 20-30-fold increase in the dissociation constant. In this case an identical effect was noted on V/K but not in V relative to the native enzyme. Thus, in both mutant enzymes the decrease in binding has not been translated into a loss of catalytic efficiency.     

Preparation of (-)-5,6,7,8-tetrahydrofolate using immobilized dihydrofolate reductase

Dihydrofolate reductase from methotrexate-resistant Lactobacillus casei was immobilized on carbodiimide-activated CH-Sepharose. The immobilized enzyme was utilized in the synthesis of (-)-5,6,7,8-tetrahydrofolate from dihydrofolate and NADPH in a batchwise reaction system. The products of the reaction, (-)-tetrahydrofolate and NADP+, were separated on a Sephadex G-10 column equilibrated with 50 mM NH4HCO3 containing beta-mercaptoethanol and ethanol. The tetrahydrofolate was then characterized by ultraviolet and circular dichroic spectra and its reactivity as a cofactor in the thymidylate synthetase reaction.     

Crystallographic analysis reveals a novel second binding site for trimethoprim in active site double mutants of human dihydrofolate reductase

In order to produce a more potent replacement for trimethoprim (TMP) used as a therapy for Pneumocystis pneumonia and targets dihydrofolate reductase from Pneumocystis jirovecii (pjDHFR), it is necessary to understand the determinants of potency and selectivity against DHFR from the mammalian host and fungal pathogen cells. To this end, active site residues in human (h) DHFR were replaced with those from pjDHFR. Structural data are reported for two complexes of TMP with the double mutants Gln35Ser/Asn64Phe (Q35S/N64F) and Gln35Lys/Asn64Phe (Q35K/N64F) of hDHFR that unexpectedly show evidence for the binding of two molecules of TMP: one molecule that binds in the normal folate binding site and the second molecule that binds in a novel subpocket site such that the mutated residue Phe64 is involved in van der Waals contacts to the trimethoxyphenyl ring of the second TMP molecule. Kinetic data for the binding of TMP to hDHFR and pjDHFR reveal an 84-fold selectivity of TMP against pjDHFR (K_i 49 nM) compared to hDHFR (K_i 4093 nM). Two mutants that contain one substitution from pj- and one from the closely related Pneumocystis carinii DHFR (pcDHFR) (Q35K/N64F and Q35S/N64F) show K_i values of 593 and 617 nM, respectively; these K_i values are well above both the K_i for pjDHFR and are similar to pcDHFR (Q35K/N64F and Q35S/N64F) (305 nM). These results suggest that active site residues 35 and 64 play key roles in determining selectivity for pneumocystis DHFR, but that other residues contribute to the unique binding of inhibitors to these enzymes.     

Bioautographic visualization of dihydrofolate reductase in enzyme overproducing BHK mutants

A bioautographic procedure has been developed for the visualization of the isozymes of dihydrofolate reductase (DHFR, E.C. 1.5.1.3). In addition to detecting electrophoretically separated enzymes, bioautography was utilized to visualize DHFR after isoelectric focusing on polyacrylamide gels. Both zone electrophoresis and isoelectric focusing were used to compare wildtype BHK cells to mutants which overproduce dihydrofolate reductase. In agreement with other physical data, the BHK-A5 overproduction mutant appears to produce more dihydrofolate reductase of the same electrophoretic mobility and isoelectric point as wild type cells.This study was supported by Grants GM 21433 and CA 19019 from the National Institutes of Health.     

Large scale production and characterisations of dihydrofolate reductase from a methotrexate-resistant human lymphoid cell line

Dihydrofolate reductase has been purified from a methotrexate-resistant human lymphoid cell line (CCRF/CEM-R3) and up to 1 mg of enzyme has been obtained from 5 litres of culture. The enzyme has a molecular weight of 22000 ±500 as determined by gel filtration. The pH activity profile shows a single optimum at pH 7.7, where marked activation is observed by addition of 0.2 M NaCl. TheK _m for NADPH is 3μM and dihydrofolate 0.7μM. The binding constant for the inhibitor, methotrexate, is 29 pM     

Synthesis and biological evaluation of biguanide and dihydrotriazine derivatives as potential inhibitors of dihydrofolate reductase of opportunistic microorganisms

Twenty-one biguanide and dihydrotriazine derivatives were synthesized and evaluated as inhibitors of dihydrofolate reductase (DHFR) from opportunistic microorganisms: Pneumocystis carinii (pc), Toxoplasma gondii (tg), Mycobacterium avium (ma), and rat liver (rl). The most potent compound in the series was B2-07 with 12?nM activity against tgDHFR. The most striking observation was that B2-07 showed similar potency to trimetrexate, ～233-fold improved potency over trimethoprim and ～7-fold increased selectivity as compared to trimetrexate against tgDHFR. Molecular docking studies in the developed homology model of tgDHFR rationalized the observed potency of B2-07. This molecule can act as a good lead for further design of molecules with better selectivity and improved potency.     

Characterization of thymidylate synthetase and dihydrofolate reductase from Plasmodium berghei

Pattanakitsakul S. and Ruenwongsa P. 1984. Characterization of thymidylate synthetase and dihydrofolate reductase from Plasmodium berghei. International Journal for Parasitology14: 513–520. Thymidylate synthetase (TS) and dihydrofolate reductase (DHFR) from Plasmodium berghei were copurified by Sephacryl S-300 and Sephadex G-200 column chromatography and found to have an apparent mol. wt of 132,000. Electrophoresis of the partially purified enzyme under non-denaturing conditions showed the comigration of TS and DHFR. The mol. wt of TS was estimated to be 65,000 on SDS-gel electrophoresis. Both enzymes exhibit a broad pH optimum in the range of 6.5–8.0. Urea, NaCl and KC1 inhibit TS but activate DHFR. For TS, the apparent K_m for dUMP and methylene-tetrahydrofolate have been found to be 71.4 and 312.5 μM, respectively. For DHFR, the apparent K_m for dihydrofolate and NADPH have been found to be 4.4 and 12.5 μM, respectively. Inhibition of DHFR by pyrimethamine, methotrexate and trimethoprim are competitive with dihydrofolate with K_is of 0.63, 0.5 and 1.88 nM, respectively. FdUMP inhibition of TS is competitive with dUMP with K_is of 0.05 μM, but inhibition by methotrexate is uncompetitive with dUMP and MTHF with K_ii of 103 and 23 μM, respectively.     

A sensitive high-performance liquid chromatographic-fluoromotric assay for dihydrofolate reductase in adult rat brain, using 7,8-dihydrobiopterin as substrate

A liquid chromatographic-fluorometric assay has been developed to study the role of dihydrofolate reductase in adult rat brain since low levels of the enzyme preclude measurement by current spectrophotometric procedures. This method involves in vitro incubation of desalted, cell-free brain extracts with 7,8-dihydrobiopterin, NADPH, and an NADPH-regenerating system. The tetrahydrobiopterin formed is quantitatively converted to pterin using alkaline iodine oxidation, and the pterin formed is separated by liquid chromatography and detected fluorometrically. The method is linear from 100 fmol to ≥ 1 nmol of product, and the sensitivity is at least 100 times greater than that of existing spectrophotometric assays. Enzyme activity of desalted brain extracts is linear with both time (to 100 min) and protein (from 50 to 620 μg). The enzyme shows an absolute requirement for NADPH, does not use NADH, and is completely inhibited by 10 n methotrexate. The K_m of the enzyme for NADPH was found to be 7.5 μ , while the K_m for 7,8-dihydrobiopterin was 88 μ . Since brain dihydrobiopterin reductase has the same properties as dihydrofolate reductase, this fluorometric procedure can serve as a sensitive assay for dihydrofolate reductase.     

A sensitive high-performance liquid chromatographic-fluorometric assay for dihydrofolate reductase in adult rat brain, using 7,8-dihydrobiopterin as substrate

A liquid chromatographic-fluorometric assay has been developed to study the role of dihydrofolate reductase in adult rat brain since low levels of the enzyme preclude measurement by current spectrophotometric procedures. This method involves in vitro incubation of desalted, cell-free brain extracts with 7,8-dihydrobiopterin, NADPH, and an NADPH-regenerating system. The tetrahydrobiopterin formed is quantitatively converted to pterin using alkaline iodine oxidation, and the pterin formed is separated by liquid chromatography and detected fluorometrically. The method is linear from 100 fmol to greater than or equal to 1 nmol of product, and the sensitivity is at least 100 times greater than that of existing spectrophotometric assays. Enzyme activity of desalted brain extracts is linear with both time (to 100 min) and protein (from 50 to 620 micrograms). The enzyme shows an absolute requirement for NADPH, does not use NADH, and is completely inhibited by 10 nM methotrexate. The Km of the enzyme for NADPH was found to be 7.5 microM, while the Km for 7,8-dihydrobiopterin was 88 microM. Since brain dihydrobiopterin reductase has the same properties as dihydrofolate reductase, this fluorometric procedure can serve as a sensitive assay for dihydrofolate reductase.     

磁珠固定化结核分枝杆菌二氢叶酸还原酶及其表征

比较Ni~(2+)-NTA磁珠和羧基磁珠固定结核分枝杆菌二氢叶酸还原酶(Mycobacteriumtuberculosis dihydrofolate reductase,Mt DHFR),探索适合小分子配体混合物库筛选的Mt DHFR固定化方法。重组表达带6×His标签Mt DHFR,纯化后表征酶学性质,比较用Ni~(2+)-NTA磁珠和羧基磁珠固定化时相应固定化容量、保留活性、稳定性及对抑制剂响应。结果表明,Ni~(2+)-NTA磁珠对Mt DHFR固定化容量为(93±12)mg/g磁珠(n=3),但酶比活保留不超过32%,Ni~(2+)明显抑制酶活性,EDTA与Ni~(2+)呈协同抑制效应,Fe~(3+)无显著干扰。羧基磁珠活化固定Mt DHFR的容量(8.6±0.6) mg/g磁珠(n=3),固定化酶比活保留(87±4)%(n=3)。在含50 mmol/L KCl的100 mmol/L HEPES (pH 7.0)中,游离和固定化Mt DHFR在0℃保存16 h活性都无显著改变,但在25℃保存16 h,游离酶活性下降近60%而羧基磁珠固定化Mt DHFR活性下降仅35%。甲氨喋呤对游离Mt DHFR和固定化Mt DHFR的IC50无显著差异(P0.05)。综上,Ni~(2+)-NTA磁珠不适合固定化Mt DHFR;羧基磁珠固定化Mt DHFR能保留活性、热稳定性及对抑制剂的响应,该固定化方法有望用于快速筛选其配体混合物库。     

Sequential conformation change and activation of chicken liver dihydrofolate reductase in low concentration of guanidine hydrochloride

The conformation changes of dihydrofolate reductase (DHFR) from chicken liver in guanidine hy-drochloride were monitored by protein intrinsic fluorescence, hydrophobic fluorescence probe TNS and limited proteol-ysis by proteinase K. The kinetics of the enzyme denaturation were also studied and compared with its activity changes. It was indicated by the enhanced fluorescence of 2-p-toluidinylnaphthalene (TNS) that a subtle conforma-tional change of the enzyme in dilute GuHCl parallels GuHCl-induced activation. At GuHCl concentration higher than 0.75 mol/L, the conformational change can be detected by increased susceptibility of the enzyme to proteinase K, but no significant gross conformational change of the enzyme molecule is observed by intrinsic fluorescence up to a GuHCl concentration of 1.2 mol/L. The results suggest that the denaturation of DHFR by GuHCl does not follow strictly the two-state model. The enzyme seems to open up sequentially with increasing concentrations of denaturants, mainly at th     

大肠杆菌二氢叶酸还原酶基因folA的克隆、表达纯化及分子间交联

利用PCR技术从大肠杆菌DH5α中获取二氢叶酸还原酶(DHFR)基因folA。用限制性内切酶BamHI与PstI将该片段插入到克隆载体pUC18上,DNA测序鉴定目的基因。而后再将该基因亚克隆到表达载体pTrcHisC上,IPTG诱导表达重组蛋白。在非变性条件下,用TALON金属亲和层析树脂纯化含组氨酸标记的重组DHFR。纯化产物在热诱导条件下行SDSPAGE分析,除23000大小的单体外,还出现了交联的二聚体和多聚体;而当反应体系中含有还原剂β-巯基乙醇时,二聚体和多聚体都被减弱。推断蛋白质在热诱导条件下二级结构发生改变而产生交联,并且有二硫键的参与。     

Testing the relationship between foldability and the early folding events of dihydrofolate reductase from Escherichia coli

A "folding element" is a contiguous peptide segment crucial for a protein to be foldable and is a new concept that could assist in our understanding of the protein-folding problem. It is known that the presence of the complete set of folding elements of dihydrofolate reductase (DHFR) from Escherichia coli is essential for the protein to be foldable. Since almost all of the amino acid residues known to be involved in the early folding events of DHFR are located within the folding elements, a close relationship between the folding elements and early folding events is hypothesized. In order to test this hypothesis, we have investigated whether or not the early folding events are preserved in circular permutants and topological mutants of DHFR, in which the order of the folding elements is changed but the complete set of folding elements is present. The stopped-flow circular dichroism (CD) measurements show that the CD spectra at the early stages of folding are similar among the mutants and the wild-type DHFR, indicating that the presence of the complete set of folding elements is sufficient to preserve the early folding events. We have further examined whether or not sequence perturbation on the folding elements by a single amino acid substitution affects the early folding events of DHFR. The results show that the amino acid substitutions inside of the folding elements can affect the burst-phase CD spectra, whereas the substitutions outside do not. Taken together, these results indicate that the above hypothesis is true, suggesting a close relationship between the foldability of a protein and the early folding events. We propose that the folding elements interact with each other and coalesce to form a productive intermediate(s) early in the folding, and these early folding events are important for a protein to be foldable.     

Structures of Leishmania major pteridine reductase complexes reveal the active site features important for ligand binding and to guide inhibitor design

Pteridine reductase (PTR1) is an NADPH-dependent short-chain reductase found in parasitic trypanosomatid protozoans. The enzyme participates in the salvage of pterins and represents a target for the development of improved therapies for infections caused by these parasites. A series of crystallographic analyses of Leishmania major PTR1 are reported. Structures of the enzyme in a binary complex with the cofactor NADPH, and ternary complexes with cofactor and biopterin, 5,6-dihydrobiopterin, and 5,6,7,8-tetrahydrobiopterin reveal that PTR1 does not undergo any major conformational changes to accomplish binding and processing of substrates, and confirm that these molecules bind in a single orientation at the catalytic center suitable for two distinct reductions. Ternary complexes with cofactor and CB3717 and trimethoprim (TOP), potent inhibitors of thymidylate synthase and dihydrofolate reductase, respectively, have been characterized. The structure with CB3717 reveals that the quinazoline moiety binds in similar fashion to the pterin substrates/products and dominates interactions with the enzyme. In the complex with TOP, steric restrictions enforced on the trimethoxyphenyl substituent prevent the 2,4-diaminopyrimidine moiety from adopting the pterin mode of binding observed in dihydrofolate reductase, and explain the inhibition properties of a range of pyrimidine derivates. The molecular detail provided by these complex structures identifies the important interactions necessary to assist the structure-based development of novel enzyme inhibitors of potential therapeutic value.     

Effects of the difference in the unfolded-state ensemble on the folding of Escherichia coli dihydrofolate reductase

The unfolded state of a protein is an ensemble of a large number of conformations ranging from fully extended to compact structures. To investigate the effects of the difference in the unfolded-state ensemble on protein folding, we have studied the structure, stability, and folding of "circular" dihydrofolate reductase (DHFR) from Escherichia coli in which the N and C-terminal regions are cross-linked by a disulfide bond, and compared the results with those of disulfide-reduced "linear" DHFR. Equilibrium studies by circular dichroism, difference absorption spectra, solution X-ray scattering, and size-exclusion chromatography show that whereas the native structures of both proteins are essentially the same, the unfolded state of circular DHFR adopts more compact conformations than the unfolded state of the linear form, even with the absence of secondary structure. Circular DHFR is more stable than linear DHFR, which may be due to the decrease in the conformational entropy of the unfolded state as a result of circularization. Kinetic refolding measurements by stopped-flow circular dichroism and fluorescence show that under the native conditions both proteins accumulate a burst-phase intermediate having the same structures and both fold by the same complex folding mechanism with the same folding rates. Thus, the effects of the difference in the unfolded state of circular and linear DHFRs on the refolding reaction are not observed after the formation of the intermediate. This suggests that for the proteins with close termini in the native structure, early compaction of a protein molecule to form a specific folding intermediate with the N and C-terminal regions in close proximity is a crucial event in folding. If there is an enhancement in the folding reflecting the reduction in the breadth of the unfolded-state ensemble for circular DHFR, this acceleration must occur in the sub-millisecond time-range.     

Conformational selection and induced changes along the catalytic cycle of Escherichia coli dihydrofolate reductase

Protein function often involves changes between different conformations. Central questions are how these conformational changes are coupled to the binding or catalytic processes during which they occur, and how they affect the catalytic rates of enzymes. An important model system is the enzyme dihydrofolate reductase (DHFR) from Escherichia coli, which exhibits characteristic conformational changes of the active‐site loop during the catalytic step and during unbinding of the product. In this article, we present a general kinetic framework that can be used (1) to identify the ordering of events in the coupling of conformational changes, binding, and catalysis and (2) to determine the rates of the substeps of coupled processes from a combined analysis of nuclear magnetic resonance R₂ relaxation dispersion experiments and traditional enzyme kinetics measurements. We apply this framework to E. coli DHFR and find that the conformational change during product unbinding follows a conformational‐selection mechanism, that is, the conformational change occurs predominantly prior to unbinding. The conformational change during the catalytic step, in contrast, is an induced change, that is, the change occurs after the chemical reaction. We propose that the reason for these conformational changes, which are absent in human and other vertebrate DHFRs, is robustness of the catalytic rate against large pH variations and changes to substrate/product concentrations in E. coli. Proteins 2012;. © 2012 Wiley Periodicals, Inc.