Coli Dihydrofolate Reductase Research Articles

Synthesis, Structural Characterization, and Computational Studies of Novel Co(II) and Zn(II) Fluoroquinoline Complexes for Antibacterial and Antioxidant Activities.

Research into heterocyclic ligands has increased in popularity due to their versatile applications in the biomedical field. Quinoline derivatives with their transition metal complexes are popular scaffolding molecules in the ongoing pursuit of newer and more effective bioactive molecules. Subsequently, this work reports on the synthesis and possible biological application of new Zn(II) and Co(II) complexes with a bidentate quinoline derivative ligand (H2 L), [(H2 L):(E)-2-(((6-fluoro-2-((2-hydroxyethyl)amino)quinolin-3-yl)methylene)amino)ethanol]. The ligand and its metal complexes were structurally characterized by spectroscopic methods (1H NMR, 13C NMR, Fourier transform infrared (FTIR), UV-vis, fluorescence, and mass spectroscopy), as well as by thermogravimetric and elemental analysis methods. The spectroscopic findings were further supported by density functional theory (DFT) and time-dependent (TD)-DFT calculations. The biological application was examined by investigating the inhibitory action of the complexes against bacterial strains using diffusion and agar dilution methods, and their profiles against two Gram-positive and Gram-negative bacterial strains were supported by molecular docking analysis. To rationalize the in vitro activity and establish the possible mechanism of action, the interactions and binding affinity of the ligand and complexes were investigated against three different bacterial enzymes (Escherichia coli DNA gyrase (PDB ID 6f86), E. coli dihydrofolate reductase B (PDB ID: 7r6g), and Staphylococcus aureus tyrosyl-tRNA synthetase (PDB ID: 1JIJ)) using AutoDock with the standard protocol. The MIC value of 0.20 μg/mL for zinc complex against E. coli and associated binding affinities -7.2 and -9.9 kcal/mol with DNA gyrase (PDB ID 6f86) and dihydrofolate reductase B (PDB ID: 7r6g), as well as the MIC value of 2.4 μg/mL for cobalt(II) complex against Staphylococcus aureus and the associated binding affinity of -10.5 kcal/mol with tyrosyl-tRNA synthetase (PDB ID: 1JIJ), revealed that the complexes' inhibitory actions were strong and comparable with those of the standard drug in the experiments. In addition, the ability of the new quinoline-based complexes to scavenge 1,1-diphenyl-picrylhydrazyl radicals was investigated; the findings suggested that the complexes exhibit potent antioxidant activities, which may be of therapeutic significance.

Phytochemical Profiling and Pharmacological Evaluation of Leaf Extracts of Ruellia tuberosa L.: An In Vitro and In Silico Approach.

The present study was designed to appraise the photoprotective, antioxidant, and antibacterial bioactivities of Ruellia tuberosa leaves extracts (RtPE, RtChl, RtEA, RtAc, RtMe, and RtHMe). The results showed that, RtHMe extracts of R. tuberosa was rich in total phenolic content, i. e., 1.60 mgGAE/g dry extract, while highest total flavonoid content was found in RtAc extract, i. e., 0.40 mgQE/g. RtMe showed effective antioxidant activity (%RSA: 58.16) at the concentration of 120 μL. RtMe, RtEA and RtHMe exhibited effective in vitro antibacterial activity against Gram-negative bacteria (E. coli). In silico docking studies revealed that paucifloside (-11.743 kcal/mol), indole-3-carboxaldehyde (-7.519 kcal/mol), nuomioside (-7.275 kcal/mol), isocassifolioside (-6.992 kcal/mol) showed best docking score against PDB ID 2EX8 [penicillin binding protein 4 (dacB) from Escherichia coli, complexed with penicillin-G], PDB ID 6CQA (E. coli dihydrofolate reductase protein complexed with inhibitor AMPQD), PDB ID 2Y2I [Penicillin-binding protein 1B in complex with an alkyl boronate (ZA3)] and PDB ID 2OLV (from S. aureus), respectively. Docked phytochemicals also showed good drug likeness properties.

FtsH degrades dihydrofolate reductase by recognizing a partially folded species.

AAA+ proteolytic machines play essential roles in maintaining and rebalancing the cellular proteome in response to stress, developmental cues, and environmental changes. Of the five AAA+ proteases in Escherichia coli, FtsH is unique in its attachment to the inner membrane and its function in degrading both membrane and cytosolic proteins. E. coli dihydrofolate reductase (DHFR) is a stable and biophysically well‐characterized protein, which a previous study found resisted FtsH degradation despite the presence of an ssrA degron. By contrast, we find that FtsH degrades DHFR fused to a long peptide linker and ssrA tag. Surprisingly, we also find that FtsH degrades DHFR with shorter linkers and ssrA tag, and without any linker or tag. Thus, FtsH must be able to recognize a sequence element or elements within DHFR. We find that FtsH degradation of DHFR is noncanonical in the sense that it does not rely upon recognition of an unstructured polypeptide at or near the N‐terminus or C‐terminus of the substrate. Results using peptide‐array experiments, mutant DHFR proteins, and fusion proteins suggest that FtsH recognizes an internal sequence in a species of DHFR that is partially unfolded. Overall, our findings provide insight into substrate recognition by FtsH and indicate that its degradation capacity is broader than previously reported.

Non-antibiotic Small-Molecule Regulation of DHFR-Based Destabilizing Domains In Vivo

The E. coli dihydrofolate reductase (DHFR) destabilizing domain (DD), which shows promise as a biologic tool and potential gene therapy approach, can be utilized to achieve spatial and temporal control of protein abundance in vivo simply by administration of its stabilizing ligand, the routinely prescribed antibiotic trimethoprim (TMP). However, chronic TMP use drives development of antibiotic resistance (increasing likelihood of subsequent infections) and disrupts the gut microbiota (linked to autoimmune and neurodegenerative diseases), tempering translational excitement of this approach in model systems and for treating human diseases. Herein, we identified a TMP-based, non-antibiotic small molecule, termed 14a (MCC8529), and tested its ability to control multiple DHFR-based reporters and signaling proteins. We found that 14a is non-toxic and can effectively stabilize DHFR DDs expressed in mammalian cells. Furthermore, 14a crosses the blood-retinal barrier and stabilizes DHFR DDs expressed in the mouse eye with kinetics comparable to that of TMP (≤6 h). Surprisingly, 14a stabilized a DHFR DD in the liver significantly better than TMP did, while having no effect on the mouse gut microbiota. Our results suggest that alternative small-molecule DHFR DD stabilizers (such as 14a) may be ideal substitutes for TMP in instances when conditional, non-antibiotic control of protein abundance is desired in the eye and beyond.

Selectable one-step PCR-mediated integration of a degron for rapid depletion of endogenous human proteins.

Manipulation of protein stability with ligand-regulated degron fusions is a powerful method for investigating gene function. We developed a selectable cassette for easy C-terminal tagging of endogenous human proteins with the E. coli dihydrofolate reductase (eDHFR) degron using CRISPR/Cas9 genome editing. This cassette permits high-efficiency recovery of correct integration events using an in-frame self-cleaving 2A peptide and the puromycin resistance gene. PCR amplified donor eDHFR cassette fragments with 100 bases of homology on each end are integrated by homology-directed repair (HDR) of guide RNA (gRNA)-targeted double-stranded DNA breaks at the 3' ends of open reading frames (ORFs). As proof of principle, we generated cell lines in which three endogenous proteins were tagged with the eDHFR degron. When the antibiotic trimethoprim is removed from the media, each of the eDHFR-tagged proteins was depleted by >90% within 2-4 h, and this depletion was reversed by re-addition of trimethoprim. Since puromycin selection permits recovery of in-frame degron fusions with high efficiency using only 100-bp long regions of homology, this method should be applicable on a genome-wide scale for generating libraries of conditional mutant cell lines.

Sequential backbone resonance assignments of the E. coli dihydrofolate reductase Gly67Val mutant: folate complex.

Occasionally, a mutation in an exposed loop region causes a significant change in protein function and/or stability. A single mutation Gly67Val of E. coli dihydrofolate reductase (DHFR) in the exposed CD loop is such an example. We have carried out the chemical shift assignments for H(N), N(H), C(α) and C(β) atoms of the Gly67Val mutant of E. coli DHFR complexed with folate at pH 7.0, 35°C, and then evaluated the H(N), N(H), C(α) and C(β) chemical shift changes caused by the mutation. The result indicates that, while the overall secondary structure remains the same, the single mutation Gly67Val causes site-specific conformational changes of the polypeptide backbone restricted around the adenosine-binding subdomain (residues 38-88) and not in the distant catalytic domain.

Preliminary joint X-ray and neutron protein crystallographic studies of ecDHFR complexed with folate and NADP+.

A crystal of Escherichia coli dihydrofolate reductase (ecDHFR) complexed with folate and NADP+ of 4×1.3×0.7 mm (3.6 mm3) in size was obtained by sequential application of microseeding and macroseeding. A neutron diffraction data set was collected to 2.0 Å resolution using the IMAGINE diffractometer at the High Flux Isotope Reactor within Oak Ridge National Laboratory. A 1.6 Å resolution X-ray data set was also collected from a smaller crystal at room temperature. The neutron and X-ray data were used together for joint refinement of the ecDHFR-folate-NADP+ ternary-complex structure in order to examine the protonation state, protein dynamics and solvent structure of the complex, furthering understanding of the catalytic mechanism.

Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans

With the rapidly growing wealth of genomic data, experimental inquiries on the functional significance of important divergence sites in protein evolution are becoming more accessible. Here we trace the evolution of dihydrofolate reductase (DHFR) and identify multiple key divergence sites among 233 species between humans and bacteria. We connect these sites, experimentally and computationally, to changes in the enzyme's binding properties and catalytic efficiency. One of the identified evolutionarily important sites is the N23PP modification (∼mid-Devonian, 415-385 Mya), which alters the conformational states of the active site loop in Escherichia coli dihydrofolate reductase and negatively impacts catalysis. This enzyme activity was restored with the inclusion of an evolutionarily significant lid domain (G51PEKN in E. coli enzyme; ∼2.4 Gya). Guided by this evolutionary genomic analysis, we generated a human-like E. coli dihydrofolate reductase variant through three simple mutations despite only 26% sequence identity between native human and E. coli DHFRs. Molecular dynamics simulations indicate that the overall conformational motions of the protein within a common scaffold are retained throughout evolution, although subtle changes to the equilibrium conformational sampling altered the free energy barrier of the enzymatic reaction in some cases. The data presented here provide a glimpse into the evolutionary trajectory of functional DHFR through its protein sequence space that lead to the diverged binding and catalytic properties of the E. coli and human enzymes.

A Dynamic Knockout Reveals That Conformational Fluctuations Influence the Chemical Step of Enzyme Catalysis

Conformational dynamics play a key role in enzyme catalysis. Although protein motions have clear implications for ligand flux, a role for dynamics in the chemical step of enzyme catalysis has not been clearly established. We generated a mutant of Escherichia coli dihydrofolate reductase that abrogates millisecond-time-scale fluctuations in the enzyme active site without perturbing its structural and electrostatic preorganization. This dynamic knockout severely impairs hydride transfer. Thus, we have found a link between conformational fluctuations on the millisecond time scale and the chemical step of an enzymatic reaction, with broad implications for our understanding of enzyme mechanisms and for design of novel protein catalysts.

Asparagine repeat function in a Plasmodium falciparum protein assessed via a regulatable fluorescent affinity tag

One in four proteins in Plasmodium falciparum contains asparagine repeats. We probed the function of one such 28-residue asparagine repeat present in the P. falciparum proteasome lid subunit 6, Rpn6. To aid our efforts, we developed a regulatable, fluorescent affinity (RFA) tag that allows cellular localization, manipulation of cellular levels, and affinity isolation of a chosen protein in P. falciparum. The tag comprises a degradation domain derived from Escherichia coli dihydrofolate reductase together with GFP. The expression of RFA-tagged proteins is regulated by the simple folate analog trimethoprim (TMP). Parasite lines were generated in which full-length Rpn6 and an asparagine repeat-deletion mutant of Rpn6 were fused to the RFA tag. The knockdown of Rpn6 upon removal of TMP revealed that this protein is essential for ubiquitinated protein degradation and for parasite survival, but the asparagine repeat is dispensable for protein expression, stability, and function. The data point to a genomic mechanism for repeat perpetuation rather than a positive cellular role. The RFA tag should facilitate study of the role of essential genes in parasite biology.

Time-resolved luminescence resonance energy transfer imaging of protein–protein interactions in living cells

Förster resonance energy transfer (FRET) with fluorescent proteins permits high spatial resolution imaging of protein-protein interactions in living cells. However, substantial non-FRET fluorescence background can obscure small FRET signals, making many potential interactions unobservable by conventional FRET techniques. Here we demonstrate time-resolved microscopy of luminescence resonance energy transfer (LRET) for live-cell imaging of protein-protein interactions. A luminescent terbium complex, TMP-Lumi4, was introduced into cultured cells using two methods: (i) osmotic lysis of pinocytic vesicles; and (ii) reversible membrane permeabilization with streptolysin O. Upon intracellular delivery, the complex was observed to bind specifically and stably to transgenically expressed Escherichia coli dihydrofolate reductase (eDHFR) fusion proteins. LRET between the eDHFR-bound terbium complex and green fluorescent protein (GFP) was detected as long-lifetime, sensitized GFP emission. Background signals from cellular autofluorescence and directly excited GFP fluorescence were effectively eliminated by imposing a time delay (10 micros) between excitation and detection. Background elimination made it possible to detect interactions between the first PDZ domain of ZO-1 (fused to eDHFR) and the C-terminal YV motif of claudin-1 (fused to GFP) in single microscope images at subsecond time scales. We observed a highly significant (P<10(-6)), six-fold difference between the mean, donor-normalized LRET signal from cells expressing interacting fusion proteins and from control cells expressing noninteracting mutants. The results show that time-resolved LRET microscopy with a selectively targeted, luminescent terbium protein label affords improved speed and sensitivity over conventional FRET methods for a variety of live-cell imaging and screening applications.

General Methods to Conditionally Regulate Protein Function

Advances in our understanding of complex, sometimes interconnected, signaling networks will likely require the implementation of tunable perturbation techniques that enable sensitivity analyses of these circuits. We have developed a general experimental technique in which the stability of a specific protein is regulated by a synthetic small molecule. Mutants of the E. coli dihydrofolate reductase (ecDHFR) protein were engineered to be degraded when expressed in mammalian cells. Trimethoprim (TMP) is a high‐affinity ligand for ecDHFR that stabilizes fusion proteins in a predictable, dose‐dependent manner, allowing investigators to tunably regulate genetically engineered alleles of any protein of interest. DD‐regulated proteins are degraded very rapidly upon withdrawal of TMP, and protein levels in the absence of TMP are barely detectable. The ability of TMP to cross the blood‐brain barrier enables the tunable regulation of proteins expressed in cells found within the mammalian central nervous system.

Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands

Enzyme catalysis can be described as progress over a multi-dimensional energy landscape where ensembles of interconverting conformational substates channel the enzyme through its catalytic cycle. We applied NMR relaxation dispersion to investigate the role of bound ligands in modulating the dynamics and energy landscape of Escherichia coli dihydrofolate reductase to obtain insights into the mechanism by which the enzyme efficiently samples functional conformations as it traverses its reaction pathway. Although the structural differences between the occluded substrate binary complexes and product ternary complexes are very small, there are substantial differences in protein dynamics. Backbone fluctuations on the micros-ms timescale in the cofactor binding cleft are similar for the substrate and product binary complexes, but fluctuations on this timescale in the active site loops are observed only for complexes with substrate or substrate analog and are not observed for the binary product complex. The dynamics in the substrate and product binary complexes are governed by quite different kinetic and thermodynamic parameters. Analogous dynamic differences in the E:THF:NADPH and E:THF:NADP(+) product ternary complexes are difficult to rationalize from ground-state structures. For both of these complexes, the nicotinamide ring resides outside the active site pocket in the ground state. However, they differ in the structure, energetics, and dynamics of accessible higher energy substates where the nicotinamide ring transiently occupies the active site. Overall, our results suggest that dynamics in dihydrofolate reductase are exquisitely "tuned" for every intermediate in the catalytic cycle; structural fluctuations efficiently channel the enzyme through functionally relevant conformational space.

NMR study of the role of M42 in the solution dynamics of E. COLI dihydrofolate reductase

NMR study of the role of M42 in the solution dynamics of E. COLI dihydrofolate reductase

Sequence Perturbation Analysis: Addressing Amino Acid Indices to Elucidate the C-Terminal Role of Escherichia Coli Dihydrofolate Reductase

Because amino acid residues intrinsically possess many factors participating in protein structures and functions, to determine main (or unique) factors at a specific site in a protein sequence should be of great help for understanding how a protein obtains its structure and function. In this study, we proposed a means of sequence perturbation analysis to address the above concerns involving comprehensive AA indices. We constructed all 19 possible single mutant proteins as to the three sites in the C-terminal of Escherichia coli dihydrofolate reductase (DHFR), and measured the activity and thermal stability of each of all the single mutant proteins. The significantly perturbed properties with each systematic single mutation at each mutational site were examined in terms of the linear correlation with each AA index. As a result, at each of Arg158 and Arg159 of DHFR, the AA index for the isoelectric points of amino acids showed strong correlation with the transition temperature of thermal denatuation, suggesting that the electrostatic interaction is the main factor influencing the C-terminal role of the DHFR. The feasibility and general versatility of our sequence perturbation analysis were also examined by application to other sites of DHFR.

ChemInform Abstract: Incorporating Dynamics in E. coli Dihydrofolate Reductase Enhances Structure‐Based Drug Discovery.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

An orthogonal dexamethasone–trimethoprim yeast three-hybrid system

The yeast three-hybrid assay is an important tool for the detection of protein-ligand interactions in vivo and has recently been used successfully for the discovery of novel drug targets and the directed evolution of enzymes[1–6]. Schreiber and co-workers developed the first chemical inducer of dimerization (CID)3, a dimer of the immunosuppressant FK506[7]. Building from this work, a number of yeast three-hybrid systems based on different CIDs have been reported[2, 8]. We previously developed and optimized a three-hybrid system built around the small molecule CID dexamethasone-methotrexate (Dex-Mtx)[9–11]. The Dex and Mtx ligands were chosen because of their high affinities for their respective protein receptors, the rat glucocorticoid receptor and Escherichia coli dihydrofolate reductase, respectively[12, 13]. However, we hypothesized that the cross-reactivity of Mtx with endogenous DHFR in the yeast cells could impair transcription activation by Dex-Mtx in the yeast three-hybrid assay. In order to overcome this partial limitation we set out to design a CID that would selectively bind to E. coli DHFR and not to endogenous yeast DHFR. As an alternative to Mtx, we chose the DHFR inhibitor trimethoprim (TMP), which is known for its selectivity for bacterial forms of DHFR[14]. Studies have confirmed that while Mtx inhibits growth of wild type Saccrharomyces cerevisiae, TMP does not[15], suggesting that TMP could be a superior CID in yeast. Here we report the design, synthesis, and in vivo activity of Dex-TMP in the yeast three-hybrid assay. By analogy to our dexamethasone-methotrexate system, we chose to build a heterodimeric CID using the ligand-receptor pairs dexamethasone (Dex)-rat glucocorticoid receptor (GR) and trimethoprim (TMP)-E. coli dihydrofolate reductase (DHFR). Both Dex and TMP can be modified without disrupting receptor binding, making them suitable CIDs[16–18]. Both ligands are cell-permeable and commercially available. The ligand-receptor pair Dex-GR has a KD of 5 nM and has been used successfully in yeast three-hybrid systems[9]. E. coli dihydrofolate reductase (DHFR) has a KI of 1.3 nM for inhibition by TMP[14]. We anticipated that the two interactions would be sufficiently strong to induce protein dimerization and transcription activation in the yeast three-hybrid assay.

Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate

Hydrogen atoms play a central role in many biochemical processes yet are difficult to visualize by x-ray crystallography. Spallation neutron sources provide a new arena for protein crystallography with TOF measurements enhancing data collection efficiency and allowing hydrogen atoms to be located in smaller crystals of larger biological macromolecules. Here we report a 2.2-A resolution neutron structure of Escherichia coli dihydrofolate reductase (DHFR) in complex with methotrexate (MTX). Neutron data were collected on a 0.3-mm(3) D(2)O-soaked crystal at the Los Alamos Neutron Scattering Center. This study provides an example of using spallation neutrons to study protein dynamics, to identify protonation states directly from nuclear density maps, and to analyze solvent structure. Our structure reveals that the occluded loop conformation [monomer (mon.) A] of the DHFR.MTX complex undergoes greater H/D exchange compared with the closed-loop conformer (mon. B), partly because the Met-20 and beta(F-G) loops readily exchange in mon. A. The eight-stranded beta sheet of both DHFR molecules resists H/D exchange more than the helices and loops. However, the C-terminal strand, betaH, in mon. A is almost fully exchanged. Several D(2)Os form hydrogen bonds with exchanged amides. At the active site, the N1 atom of MTX is protonated and thus charged when bound to DHFR. Several D(2)Os are observed at hydrophobic surfaces, including two pockets near the MTX-binding site. A previously unidentified D(2)O hydrogen bonds with the catalytic D27 in mon. B, stabilizing its negative charge.

The Dynamic Energy Landscape of Dihydrofolate Reductase Catalysis

We used nuclear magnetic resonance relaxation dispersion to characterize higher energy conformational substates of Escherichia coli dihydrofolate reductase. Each intermediate in the catalytic cycle samples low-lying excited states whose conformations resemble the ground-state structures of preceding and following intermediates. Substrate and cofactor exchange occurs through these excited substates. The maximum hydride transfer and steady-state turnover rates are governed by the dynamics of transitions between ground and excited states of the intermediates. Thus, the modulation of the energy landscape by the bound ligands funnels the enzyme through its reaction cycle along a preferred kinetic path.

1P085 Exploring the Complete Sequence Space at a Hamming Distance One around E. coli Dihydrofolate Reductase : Stability and Activity(2. Protein function (I),Poster Session,Abstract,Meeting Program of EABS &amp; BSJ 2006)

1P085 Exploring the Complete Sequence Space at a Hamming Distance One around E. coli Dihydrofolate Reductase : Stability and Activity(2. Protein function (I),Poster Session,Abstract,Meeting Program of EABS &amp; BSJ 2006)