Wild-type Dihydrofolate Reductase Research Articles

Time-Resolved Ultraviolet Photodissociation Mass Spectrometry Probes the Mutation-Induced Alterations in Protein Stability and Unfolding Dynamics.

How mutations impact protein stability and structure dynamics is crucial for understanding the pathological process and rational drug design. Herein, we establish a time-resolved native mass spectrometry (TR-nMS) platform via a rapid-mixing capillary apparatus for monitoring the acid-initiated protein unfolding process. The molecular details in protein structure unfolding are further profiled by a 193 nm ultraviolet photodissociation (UVPD) analysis of the structure-informative photofragments. Compared with the wild-type dihydrofolate reductase (WT-DHFR), the M42T/H114R mutant (MT-DHFR) exhibits a significant stability decrease in TR-nMS characterization. UVPD comparisons of the unfolding intermediates and original DHFR forms indicate the special stabilization effect of cofactor NADPH on DHFR structure, and the M42T/H114R mutations lead to a significant decrease in NADPH-DHFR interactions, thus promoting the structure unfolding. Our study paves the way for probing the mutation-induced subtle changes in the stability and structure dynamics of drug targets.

Allosteric Regulatory Control in Dihydrofolate Reductase is Revealed by Dynamic Asymmetry.

We investigated the relationship between mutations and dynamics in Escherichia coli dihydrofolate reductase (DHFR) using computational methods. Our study focused on the M20 and FG loops, which are known to be functionally important and affected by mutations distal to the loops. We used Molecular Dynamics simulations and developed position-specific metrics, including the Dynamic Flexibility Index (DFI) and Dynamic Coupling Index (DCI), to analyze the dynamics of wild-type DHFR and compared our results with existing deep mutational scanning data. Our analysis showed a statistically significant association between DFI and mutational tolerance of the DHFR positions, indicating that DFI can predict functionally beneficial or detrimental substitutions. We also applied an asymmetric version of our DCI metric (DCIasym ) to DHFR and found that certain distal residues control the dynamics of the M20 and FG loops, whereas others are controlled by them. Residues that are suggested to control the M20 and FG loops by our DCIasym metric are evolutionarily non-conserved; mutations at these sites can enhance enzyme activity. On the other hand, residues controlled by the loops are mostly deleterious to function when mutated and are also evolutionary conserved. Our results suggest that dynamics-based metrics can identify residues that explain the relationship between mutation and protein function or can be targeted to rationally engineer enzymes with enhanced activity. This article is protected by copyright. All rights reserved.

Exploring the Effect of Mechanical Anisotropy of Protein Structures in the Unfoldase Mechanism of AAA+ Molecular Machines.

Essential cellular processes of microtubule disassembly and protein degradation, which span lengths from tens of m to nm, are mediated by specialized molecular machines with similar hexameric structure and function. Our molecular simulations at atomistic and coarse-grained scales show that both the microtubule-severing protein spastin and the caseinolytic protease ClpY, accomplish spectacular unfolding of their diverse substrates, a microtubule lattice and dihydrofolate reductase (DHFR), by taking advantage of mechanical anisotropy in these proteins. Unfolding of wild-type DHFR requires disruption of mechanically strong -sheet interfaces near each terminal, which yields branched pathways associated with unzipping along soft directions and shearing along strong directions. By contrast, unfolding of circular permutant DHFR variants involves single pathways due to softer mechanical interfaces near terminals, but translocation hindrance can arise from mechanical resistance of partially unfolded intermediates stabilized by -sheets. For spastin, optimal severing action initiated by pulling on a tubulin subunit is achieved through specific orientation of the machine versus the substrate (microtubule lattice). Moreover, changes in the strength of the interactions between spastin and a microtubule filament, which can be driven by the tubulin code, lead to drastically different outcomes for the integrity of the hexameric structure of the machine.

Cellular synthesis of protein pretzelanes

Topology has been recognized as a unique dimension in molecular engineering, yet the topological diversity remains largely untapped, especially in macromolecules. Herein, we report the molecular design, cellular synthesis, and detailed characterization of protein pretzelanes with a chemical topology of a bridged Hopf link. The synergy between the intramolecular chain entwining guided by the p53dim (X) domains and the genetically encoded side-chain coupling by SpyTag(A)-SpyCatcher(B) reaction facilitates the direct synthesis of the model protein pretzelane BXA-BXA in Escherichia coli. The approach tolerates the insertion of various proteins-of-interest, such as elastin-like protein (ELP), superfolder green fluorescent protein (GFP) and dihydrofolate reductase (DHFR), at the bridge region between two rings, giving rise to three protein pretzelanes BXA-ELP-BXA, BXA-GFP-BXA, and BXA-DHFR-BXA. Their topology has been verified by combined techniques of MALDI-TOF mass spectrometry, ion mobility-mass spectrometry, site-specific mutation, and orthogonal proteolytic digestion experiments. Not only are the fluorescent properties of GFP and the catalytic properties of DHFR fully retained, the pretzelane topology also renders BXA-DHFR-BXA more thermally resilient than the wild-type DHFR. These results expand the topological diversity of proteins and demonstrate protein stabilization as a potential functional benefit for the pretzelane topology.

Site-Specific Tryptophan Labels Reveal Local Microsecond-Millisecond Motions of Dihydrofolate Reductase.

Many enzymes are known to change conformations during their catalytic cycle, but the role of these protein motions is not well understood. Escherichia coli dihydrofolate reductase (DHFR) is a small, flexible enzyme that is often used as a model system for understanding enzyme dynamics. Recently, native tryptophan fluorescence was used as a probe to study micro- to millisecond dynamics of DHFR. Yet, because DHFR has five native tryptophans, the origin of the observed conformational changes could not be assigned to a specific region within the enzyme. Here, we use DHFR mutants, each with a single tryptophan as a probe for temperature jump fluorescence spectroscopy, to further inform our understanding of DHFR dynamics. The equilibrium tryptophan fluorescence of the mutants shows that each tryptophan is in a different environment and that wild-type DHFR fluorescence is not a simple summation of all the individual tryptophan fluorescence signatures due to tryptophan–tryptophan interactions. Additionally, each mutant exhibits a two-phase relaxation profile corresponding to ligand association/dissociation convolved with associated conformational changes and a slow conformational change that is independent of ligand association and dissociation, similar to the wild-type enzyme. However, the relaxation rate of the slow phase depends on the location of the tryptophan within the enzyme, supporting the conclusion that the individual tryptophan fluorescence dynamics do not originate from a single collective motion, but instead report on local motions throughout the enzyme.

Asymptomatic Natural Human Infections With the Simian Malaria Parasites Plasmodium cynomolgi and Plasmodium knowlesi.

BackgroundIn Southeast Asia, Plasmodium knowlesi, a parasite of long-tailed macaques (Macaca fascicularis), is an important cause of human malaria. Plasmodium cynomolgi also commonly infects these monkeys, but only one naturally acquired symptomatic human case has been reported previously.MethodsMalariometric studies involving 5422 subjects (aged 6 months to 65 years) were conducted in 23 villages in Pailin and Battambang, western Cambodia. Parasite detection and genotyping was conducted on blood samples, using high-volume quantitative PCR (uPCR).ResultsAsymptomatic malaria parasite infections were detected in 1361 of 14732 samples (9.2%). Asymptomatic infections with nonhuman primate malaria parasites were found in 21 individuals living close to forested areas; P. cynomolgi was found in 11, P. knowlesi was found in 8, and P. vivax and P. cynomolgi were both found in 2. Only 2 subjects were female, and 14 were men aged 20–40 years. Geometric mean parasite densities were 3604 parasites/mL in P. cynomolgi infections and 52488 parasites/mL in P. knowlesi infections. All P. cynomolgi isolates had wild-type dihydrofolate reductase genes, in contrast to the very high prevalence of mutations in the human malaria parasites. Asymptomatic reappearance of P. cynomolgi occurred in 2 subjects 3 months after the first infection.ConclusionsAsymptomatic naturally acquired P. cynomolgi and P. knowlesi infections can both occur in humans.Clinical Trials RegistrationNCT01872702.

Protein Catenation Enhances Both the Stability and Activity of Folded Structural Domains.

Catenanes are intriguing molecular architectures with unique properties. Herein, we report the cellular synthesis of protein catenanes containing folded structural domains, aided by synergy between p53 dimerization and SpyTag/SpyCatcher chemistry. Concatenation of green fluorescent protein (GFP) was shown to increase chemical stability without disrupting the fluorescence properties, and concatenated dihydrofolate reductase (DHFR) exhibited a melting temperature around 4 °C higher and catalytic activity around 27 % higher than the wild-type DHFR and the cyclic/linear controls. Catenation also confers considerable proteolytic resistance on DHFR. The results suggest that catenation could enhance both the stability and activity of folded proteins, thus making topology engineering an attractive approach for tailoring protein properties without varying their native sequences.

Structure-based analysis of Bacilli and plasmid dihydrofolate reductase evolution

Dihydrofolate reductase (DHFR), a key enzyme in tetrahydrofolate-mediated biosynthetic pathways, has a structural motif known to be highly conserved over a wide range of organisms. Given its critical role in purine and amino acid synthesis, DHFR is a well established therapeutic target for treating a wide range of prokaryotic and eukaryotic infections as well as certain types of cancer. Here we present a structural-based computer analysis of bacterial (Bacilli) and plasmid DHFR evolution. We generated a structure-based sequence alignment using 7 wild-type DHFR x-ray crystal structures obtained from the RCSB Protein Data Bank and 350 chromosomal and plasmid homology models we generated from sequences obtained from the NCBI Protein Database. We used these alignments to compare active site and non-active site conservation in terms of amino acid residues, secondary structure and amino acid residue class. With respect to amino acid sequences and residue classes, active-site positions in both plasmid and chromosomal DHFR are significantly more conserved than non-active site positions. Secondary structure conservation was similar for active site and non-active site positions. Plasmid-encoded DHFR proteins have greater degree of sequence and residue class conservation, particularly in sequence positions associated with a network of concerted protein motions, than chromosomal-encoded DHFR proteins. These structure-based were used to build DHFR specific phylogenetic trees from which evidence for horizontal gene transfer was identified.

Effect of circular permutations on transient partial unfolding in proteins.

Under native conditions, proteins can undergo transient partial unfolding, which may cause proteins to misfold or aggregate. A change in sequence connectivity by circular permutation may affect the energetics of transient partial unfolding in proteins without altering the three-dimensional structures. Using Escherichia coli dihydrofolate reductase (DHFR) as a model system, we investigated how circular permutation affects transient partial unfolding in proteins. We constructed three circular permutants, CP18, CP37, and CP87, with the new N-termini at residue 18, 37, and 87, respectively, and probed transient partial unfolding by native-state proteolysis. The new termini in CP18, CP37, and CP87 are within, near, and distal to the Met20 loop, which is known to be dynamic and also part of the region that undergoes transient unfolding in wild-type DHFR. The stabilities of both native and partially unfolded forms of CP18 are similar to those of wild-type DHFR, suggesting that the influence of introducing new termini in a dynamic region to the protein is minimal. CP37 has a significantly more accessible partially unfolded form than wild-type DHFR, demonstrating that introducing new termini near a dynamic region may promote transient partial unfolding. CP87 has significantly destabilized native and partially unfolded forms, confirming that modification of the folded region in a partially unfolded form destabilizes the partially unfolded form similar to the native form. Our findings provide valuable guidelines to control transient partial unfolding in designing circular permutants in proteins.

Crystal Structures of Trimethoprim-Resistant DfrA1 Rationalize Potent Inhibition by Propargyl-Linked Antifolates.

Multidrug-resistant Enterobacteriaceae, notably Escherichia coli and Klebsiella pneumoniae, have become major health concerns worldwide. Resistance to effective therapeutics is often carried by class I and II integrons that can confer insensitivity to carbapenems, extended spectrum β-lactamases, the antifolate trimethoprim, fluoroquinolones, and aminoglycosides. Specifically of interest to the study here, a prevalent gene (dfrA1) coding for an insensitive dihydrofolate reductase (DHFR) confers 190- or 1000-fold resistance to trimethoprim for K. pneumoniae and E. coli, respectively. Attaining inhibition of both the wild-type and resistant forms of the enzyme is critical for new antifolates. For several years, we have been developing the propargyl-linked antifolates (PLAs) as effective inhibitors against trimethoprim-resistant DHFR enzymes. Here, we show that the PLAs are active against both the wild-type and DfrA1 DHFR proteins. We report two high-resolution crystal structures of DfrA1 bound to potent PLAs. The structure-activity relationships and crystal structures will be critical in driving the design of broadly active inhibitors against wild-type and resistant DHFR.

Dihydrofolate Reductase as a Model for Enzyme Catalysis

Dihydrofolate reductase (DHFR) has emerged as a model enzyme to investigate the role of dynamics in catalysis. This review begins with a description of the timing of the protonation of the dihydrofolate substrate and the subsequent hydride transfer reaction. This is followed by a summary of the results obtained from bioinformatics, theoretical and experimental studies of coevolving DHFR residues. Some of these residues appear to be dynamically coupled to each other and to the reaction coordinate. Importantly, the coupling appears to expand across the entire enzyme as many of the coevolved amino acids are remote from the active site. The importance of introducing mutations during evolution in the correct evolutionary order is also discussed. These studies involved a combination of steady state and pre-steady state rate measurements, kinetic isotope effects, NMR spectroscopy and computational investigations of the wild type DHFR from E. coli and several mutants. The cumulative results implicate a role of motions across the entire protein in DHFR catalysis, which may serve as a guide in studies of other enzymatic systems. Keywords: Dihydrofolate reductase, enzyme dynamics, enzyme evolution, global network, hydride transfer, kinetic isotope effect.

Nonracemic Antifolates Stereoselectively Recruit Alternate Cofactors and Overcome Resistance in S. aureus.

While antifolates such as Bactrim (trimethoprim-sulfamethoxazole; TMP-SMX) continue to play an important role in treating community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA), resistance-conferring mutations, specifically F98Y of dihydrofolate reductase (DHFR), have arisen and compromise continued use. In an attempt to extend the lifetime of this important class, we have developed a class of propargyl-linked antifolates (PLAs) that exhibit potent inhibition of the enzyme and bacterial strains. Probing the role of the configuration at the single propargylic stereocenter in these inhibitors required us to develop a new approach to nonracemic 3-aryl-1-butyne building blocks by the pairwise use of asymmetric conjugate addition and aldehyde dehydration protocols. Using this new route, a series of nonracemic PLA inhibitors was prepared and shown to possess potent enzyme inhibition (IC50 values <50 nM), antibacterial effects (several with MIC values <1 μg/mL) and to form stable ternary complexes with both wild-type and resistant mutants. Unexpectedly, crystal structures of a pair of individual enantiomers in the wild-type DHFR revealed that the single change in configuration of the stereocenter drove the selection of an alternative NADPH cofactor, with the minor α-anomer appearing with R-27. Remarkably, this cofactor switching becomes much more prevalent when the F98Y mutation is present. The observation of cofactor site plasticity leads to a postulate for the structural basis of TMP resistance in DHFR and also suggests design strategies that can be used to target these resistant enzymes.

Folding pathway of a multidomain protein depends on its topology of domain connectivity

How do the folding mechanisms of multidomain proteins depend on protein topology? We addressed this question by developing an Ising-like structure-based model and applying it for the analysis of free-energy landscapes and folding kinetics of an example protein, Escherichia coli dihydrofolate reductase (DHFR). DHFR has two domains, one comprising discontinuous N- and C-terminal parts and the other comprising a continuous middle part of the chain. The simulated folding pathway of DHFR is a sequential process during which the continuous domain folds first, followed by the discontinuous domain, thereby avoiding the rapid decrease in conformation entropy caused by the association of the N- and C-terminal parts during the early phase of folding. Our simulated results consistently explain the observed experimental data on folding kinetics and predict an off-pathway structural fluctuation at equilibrium. For a circular permutant for which the topological complexity of wild-type DHFR is resolved, the balance between energy and entropy is modulated, resulting in the coexistence of the two folding pathways. This coexistence of pathways should account for the experimentally observed complex folding behavior of the circular permutant.

Role of E2F transcriptional factor family in hydrogen peroxide regulation of dihydrofolate reductase in endothelial cells (855.5)

Endothelial nitric oxide synthase (eNOS) uncoupling consequent to a deficiency in eNOS cofactor tetrahydrobiopterin (H4B) is an important mechanism of vascular dysfunction. Our previous work has shown that endothelial hydrogen peroxide (H2O2) overproduction specifically downregulates H4B salvage enzyme dihydrofolate reductase (DHFR), which mediates persistent H4B deficiency, eNOS uncoupling and elevated blood pressure in Angiotensin II‐infused mice. However, detailed molecular mechanisms underlying H2O2 regulation of DHFR in endothelial cells remain unclear. In this study, we found that hydrogen peroxide dose and time dependently downregulated DHFR protein expression and its enzyme activity in bovine aortic endothelial cells (BAECs). The DHFR mRNA levels were also decreased by H2O2, implicating transcriptional regulation. Based on the fact that DHFR promoter contains cis‐acting elements for Sp1 and E2F, we constructed wildtype DHFR promoter reporter construct (WT‐DHFR), and mutant DHFR promoter constructs that were deleted of either Sp1 or E2F binding sites. The dual‐luciferase reporter assay showed that while the promoter activities of both WT‐DHFR and Sp1 deletion mutant remained inhibited by H2O2, deletion of the E2F binding sites completely abolished H2O2 attenuation of DHFR promoter activity. RT‐PCR analyses indicated that H2O2 treatment resulted in marked downregulation of E2F1, E2F7 and E2F8 by 38%, 43% and 82% respectively. Intriguingly, overexpression of E2F1, E2F7 or E2F8 restored DHFR expression in response to H2O2, and cotransfection with E2F1 also significantly increased DHFR promoter activity. In conclusion, these results suggest that DHFR is downregulated by H2O2 in endothelial cells transcriptionally via a E2F‐dependent manner, and that restoration of E2F family‐transcription factor activity is effective in preserving DHFR function under oxidative stress.Grant Funding Source: Supported by NHLBI awards HL077440 (HC), HL088975 (HC) and an AHA EI award 12EIA8990025 (HC)

Solvent environments significantly affect the enzymatic function of Escherichia coli dihydrofolate reductase: Comparison of wild-type protein and active-site mutant D27E

To investigate the contribution of solvent environments to the enzymatic function of Escherichia coli dihydrofolate reductase (DHFR), the salt-, pH-, and pressure-dependence of the enzymatic function of the wild-type protein were compared with those of the active-site mutant D27E in relation to their structure and stability. The salt concentration-dependence of enzymatic activity indicated that inorganic cations bound to and inhibited the activity of wild-type DHFR at neutral pH. The BaCl2 concentration-dependence of the 1H–15N HSQC spectra of the wild-type DHFR–folate binary complex showed that the cation-binding site was located adjacent to the Met20 loop. The insensitivity of the D27E mutant to univalent cations, the decreased optimal pH for its enzymatic activity, and the increased Km and Kd values for its substrate dihydrofolate suggested that the substrate-binding cleft of the mutant was slightly opened to expose the active-site side chain to the solvent. The marginally increased fluorescence intensity and decreased volume change due to unfolding of the mutant also supported this structural change or the modified cavity and hydration. Surprisingly, the enzymatic activity of the mutant increased with pressurization up to 250MPa together with negative activation volumes of −4.0 or −4.8mL/mol, depending on the solvent system, while that of the wild-type was decreased and had positive activation volumes of 6.1 or 7.7mL/mol. These results clearly indicate that the insertion of a single methylene at the active site could substantially change the enzymatic reaction mechanism of DHFR, and solvent environments play important roles in the function of this enzyme.

Determination of Allosteric Residues Involved in Ligand Selectivity in the Dihydrofolate Reductase Family

Dihydrofolate Reductase (DHFR) is an essential enzyme for most organisms, ranging from bacteria to humans. It has essential functions in DNA biosynthesis and cell replication and cell growth can be diminished by inhibition of DHFR. It is critical to understand inhibitor specificity of DHFR homologs from different organisms. To design compounds that inhibit DHFR from infectious organisms while leaving human DHFR alone. A computational analysis was previously developed to predict residues away from the active site that are significant in ligand specificity in the DHFR enzyme family. Allosteric residues H38, A39, I86, W85, Q84, T125, F126, and Y127 (human DHFR numbering) were predicted to be key residues in ligand specificity in the DHFR enzyme family. To validate these predictions, mutations (H38N, A39Y, I86A, T125A, F126L, and Y127A) have been introduced into the B. Strearothermophilus DHFR gene and the mutants have been expressed and purified. We have measured the binding constants to select ligands (Trimethoprim, Raltitrexed, and Pyrimethamine) by equilibrium binding titrations using Fluoromax‐4. Comparisons on the ligand binding profiles of the mutants to those of the wild type enzyme have revealed that some of the mutated amino acid positions do have an effect on ligand selectivity and this work is still going on. Turnover (kcat) values have also been determined for the mutants and wildtype DHFR and showed that mutations do not affect catalytic activity, with the exception of the I86A mutant. Further comparison of the ligand specificity of double mutants with two mutated positions is currently in progress to investigate synergy between different positions in ligand binding specificity in this enzyme family.

Connecting Protein Conformational Dynamics with Catalytic Function As Illustrated in Dihydrofolate Reductase

Combined quantum mechanics/molecular mechanics molecular dynamics simulations reveal that the M20 loop conformational dynamics of dihydrofolate reductase (DHFR) is severely restricted at the transition state of the hydride transfer as a result of the M42W/G121V double mutation. Consequently, the double-mutant enzyme has a reduced entropy of activation, i.e., increased entropic barrier, and altered temperature dependence of kinetic isotope effects in comparison with those of wild-type DHFR. Interestingly, in both wild-type DHFR and the double mutant, the average donor-acceptor distances are essentially the same in the Michaelis complex state (~3.5 Å) and the transition state (2.7 Å). It was found that an additional hydrogen bond is formed to stabilize the M20 loop in the closed conformation in the M42W/G121V double mutant. The computational results reflect a similar aim designed to knock out precisely the dynamic flexibility of the M20 loop in a different double mutant, N23PP/S148A.

Teaching biochemistry and molecular biology using dihydrofolate reductase as an expression system

The enzyme dihydrofolate reductase (DHFR) converts dihydrofolic acid to tetrahydrofolic acid, thereby regulating the synthesis of purine and certain amino acids. Since DHFR plays such an important role in cell proliferation and growth, it was the first enzyme targeted for chemotherapy. The objective of this project is to teach molecular and biochemical techniques by having students induce gene expression, purify and enzymatically assay for DHFR activity. During this semester‐long project, students induce expression in recombinant bacteria and purify the DHFR protein using IMAC (immobilized metal affinity chromatography) resin. Students check purity via SDS‐PAGE electrophoresis and identify the fraction (insoluble vs. soluble) containing DHFR. Additionally, they design PCR primers for site‐directed mutagenesis, verify PCR success via restriction enzyme digestion and agarose gel electrophoresis, transform into expression competent cells, and confirm the amino acid mutation by DNA sequencing. Students then examine specific activity of the wildtype DHFR protein and compare it with the mutant DHFR protein. They also determine protein concentrations using the Bradford assay and perform Western blot analysis to detect glutathione S‐transferase (GST) and histidine (His) tags. All student groups successfully purified DHFR and detected both GST and His tags by Western blot analysis. Site‐directed mutagenesis showed a decrease in specific activity ranging from 32–122% compared to the wild‐type protein. This project provides students with the opportunity to gain hands‐on experience with a multitude of laboratory techniques as well as the opportunity to design and implement cutting edge research approaches.

Two Parallel Pathways in the Kinetic Sequence of the Dihydrofolate Reductase from Mycobacterium tuberculosis

Dihydrofolate reductase from Mycobacterium tuberculosis (MtDHFR) catalyzes the NAD(P)H-dependent reduction of dihydrofolate, yielding NAD(P)(+) and tetrahydrofolate, the primary one-carbon unit carrier in biology. Tetrahydrofolate needs to be recycled so that reactions involved in dTMP synthesis and purine metabolism can be maintained. Previously, steady-state studies revealed that the chemical step significantly contributes to the steady-state turnover number, but that a step after the chemical step was likely limiting the reaction rate. Here, we report the first pre-steady-state investigation of the kinetic sequence of the MtDHFR aiming to identify kinetic intermediates, and the identity of the rate-limiting steps. This kinetic analysis suggests a kinetic sequence comprising two parallel pathways with a rate-determining product release. Although product release is likely occurring in a random fashion, there is a slight preference for the release of THF first, a kinetic sequence never observed for a wild-type dihydrofolate reductase of any organism studied to date. Temperature studies were conducted to determine the magnitude of the energetic barrier posed by the chemical step, and the pH dependence of the chemical step was studied, demonstrating an acidic shift from the pK(a) observed at the steady state. The rate constants obtained here were combined with the activation energy for the chemical step to compare energy profiles for each kinetic sequence. The two parallel pathways are discussed, as well as their implications for the catalytic cycle of this enzyme.

Structural-based analysis of dihydrofolate reductase evolution

The evolution of dihydrofolate reductase (DHFR) was studied through a comprehensive structural-based analysis. An amino acid sequence alignment was generated from a superposition of experimentally determined X-ray crystal structures of wild-type (wt) DHFR from the Protein Data Bank (PDB). Using this structure-based alignment of DHFR, a metric was generated for the degree of conservation at each alignment site – not only in terms of amino acid residue, but also secondary structure, and residue class. A phylogenetic tree was generated using the alignment that compared favorably with the canonical phylogeny. This structure-based alignment was used to confirm that the degree of conservation of active-site residues in terms of both sequence as well as structure was significantly greater than non-active site residues. These results can be used in helping to understand the likely future evolution of DHFR in response to novel therapies.