Product Release Step Research Articles

Synthesis and cavity size effect of Pd-containing macrocycle catalyst for efficient intramolecular hydroamination of allylurethane.

Palladium-containing macrocycle catalysts (PdMCs) with different ring sizes ranging from 24 to 30 members were synthesized. The intramolecular hydroamination of an allylurethane (AU) catalyzed by PdMCs proceeded efficiently to afford the corresponding oxazolidinone (OZ) in 95% isolated yield. The dependence of the hydroamination of AU to OZ on the cavity size indicated that the reaction rate was clearly controlled by both substrate uptake and product release steps.

Mechanism and selectivity of the dinuclear iron benzoyl-coenzyme A epoxidase BoxB.

Benzoyl-CoA epoxidase is a dinuclear iron enzyme that catalyzes the epoxidation reaction of the aromatic ring of benzoyl-CoA with chemo-, regio- and stereo-selectivity. It has been suggested that this enzyme may also catalyze the deoxygenation reaction of epoxide, suggesting a unique bifunctionality among the diiron enzymes. We report a density functional theory study of this enzyme aimed at elucidating its mechanism and the various selectivities. The epoxidation is suggested to start with the binding of the O2 molecule to the diferrous center to generate a diferric peroxide complex, followed by concerted O-O bond cleavage and epoxide formation. Two different pathways have been located, leading to (2S,3R)-epoxy and (2R,3S)-epoxy products, with barriers of 17.6 and 20.4 kcal mol-1, respectively. The barrier difference is 2.8 kcal mol-1, corresponding to a diastereomeric excess of about 99 : 1. Further isomerization from epoxide to phenol is found to have quite a high barrier, which cannot compete with the product release step. After product release into solution, fast epoxide-oxepin isomerization and racemization can take place easily, leading to a racemic mixture of (2S,3R) and (2R,3S) products. The deoxygenation of epoxide to regenerate benzoyl-CoA by a diferrous form of the enzyme proceeds via a stepwise mechanism. The C2-O bond cleavage happens first, coupled with one electron transfer from one iron center to the substrate, to form a radical intermediate, which is followed by the second C3-O bond cleavage. The first step is rate-limiting with a barrier of only 10.8 kcal mol-1. Further experimental studies are encouraged to verify our results.

Converter Mutation Disrupts Lever arm Rotation in Myosin V

Myosins are proposed to utilize a conserved structural mechanism to generate force in which small conformational changes in the active site result in a large swing of the lever arm or light chain binding region. The converter domain is a flexible region that provides a link between the catalytic domain and lever arm and is proposed to play a critical role in the allosteric communication between these two domains. We introduced the R712G mutation in the converter domain and examined the impact of this mutation on the structural and functional properties of myosin V. The mutation resulted in a 16% reduction in the maximum actin-activated ATPase rate and no change in the actin concentration at which the ATPase activity is one-half maximal (KATPase). The sliding velocities examined in the in vitro motility assay were very similar between WT and R712G MV. We have developed a novel FRET system in myosin V (MV) that allows examination of the dynamics of lever arm motion. We labeled MV 11IQ containing an N-terminal (NT) tetracysteine motif with the bisarsenical dye FlAsH (MV.NT.FlAsH). The first IQ motif of MV.NT.FlAsH was exchanged with QSY-9 labeled CaM, a non-fluorescent acceptor. We followed the motion of the lever-arm during the ATP binding (recovery stroke) and actin-activated product release (power stroke) steps using stopped-flow FRET. The R712G mutation reduced the rate of the recovery stroke by 23% while having little impact on the fast power stroke that occurs prior to phosphate release. Thus, a mutation in the converter domain can specifically impact the recovery stroke without altering the power stroke demonstrating different allosteric mechanisms are responsible for these two key structural transitions.

Framework for Managing Mycotoxin Risks in the Food Industry

We propose a methodological framework for managing mycotoxin risks in the food processing industry. Mycotoxin contamination is a well-known threat to public health that has economic significance for the food processing industry; it is imperative to address mycotoxin risks holistically, at all points in the procurement, processing, and distribution pipeline, by tracking the relevant data, adopting best practices, and providing suitable adaptive controls. The proposed framework includes (i) an information and data repository, (ii) a collaborative infrastructure with analysis and simulation tools, (iii) standardized testing and acceptance sampling procedures, and (iv) processes that link the risk assessments and testing results to the sourcing, production, and product release steps. The implementation of suitable acceptance sampling protocols for mycotoxin testing is considered in some detail.

The Parkinson Disease-linked LRRK2 Protein Mutation I2020T Stabilizes an Active State Conformation Leading to Increased Kinase Activity

The effect of leucine-rich repeat kinase 2 (LRRK2) mutation I2020T on its kinase activity has been controversial, with both increased and decreased effects being reported. We conducted steady-state and pre-steady-state kinetic studies on LRRKtide and its analog LRRKtide(S). Their phosphorylation differs by the rate-limiting steps: product release is rate-limiting for LRRKtide and phosphoryl transfer is rate-limiting for LRRKtide(S). As a result, we observed that the I2020T mutant is more active than wild type (WT) LRRK2 for LRRKtide(S) phosphorylation, whereas it is less active than WT for LRRKtide phosphorylation. Our pre-steady-state kinetic data suggest that (i) the I2020T mutant accelerates the rates of phosphoryl transfer of both reactions by 3-7-fold; (ii) this increase is masked by a rate-limiting product release step for LRRKtide phosphorylation; and (iii) the observed lower activity of the mutant for LRRKtide phosphorylation is a consequence of its instability: the concentration of the active form of the mutant is 3-fold lower than WT. The I2020T mutant has a dramatically low KATP and therefore leads to resistance to ATP competitive inhibitors. Two well known DFG-out or type II inhibitors are also weaker toward the mutant because they inhibit the mutant in an unexpected ATP competitive mechanism. The I2020 residue lies next to the DYG motif of the activation loop of the LRRK2 kinase domain. Our modeling and metadynamic simulations suggest that the I2020T mutant stabilizes the DYG-in active conformation and creates an unusual allosteric pocket that can bind type II inhibitors but in an ATP competitive fashion.

Dependence of the Rate of Phosphate Dissociation from Actomyosin-ADP-Pi Upon the Alkali Light Chains in Skeletal Muscle Myosin

The A1 light chain of rabbit skeletal myosin possesses a unique N-terminal extension of ∼40 amino acids which is lacking in A2. A C-terminal block of ∼140 amino acids is identical to both. The primary structures are completed by a small, non-identical peptide which is sandwiched between the above two sections of A1 and which is N-terminal in A2. The effect which A1 and A2 have on the product release step has been investigated by double-mixing stopped-flow in conjunction with a fluorescent phosphate binding protein (Buffer, 5mM MOPS, 2mM Mg acetate, pH 7). Rabbit skeletal myosin-S1 was chromatographically separated into A1 and A2 containing fractions. A slight excess of myosin-S1 over nucleotide was used in the first mix to ensure complete binding of the latter as well as a single turnover. After a 2 s delay to assure that ATP binding was complete, thin filaments (+Ca) were combined with the myosin-nucleotide mixture (M-ATP U M-ADP-Pi) in the second mix. The dominant component of the observed biphasic increase in fluorescence corresponds to Pi release from AM-ADP-Pi. Hyperbolic fits of the dependence of the rate upon the thin filament give maximum rates of: 80 s-1 (S1A1) and 139 s-1 (S1A2) and apparent binding constants of 10 μM (S1A1) and 72 μM (S1A2). The rates of phosphate dissociation are 4-5 more rapid than the steady state measurements of 20 s-1 (A1) and 36 s-1 (A2) and therefore cannot limit the rate of ATP hydrolysis. It is also evident that the N-terminal extension strengthens light chain affinity.

Spectroscopic System for Characterization of Human β-Cardiac Myosin

We designed a system to examine the structural properties of human β-cardiac myosin using fluorescence spectroscopy. Expression of human β-cardiac myosin subfragment 1 (M2B-S1) was achieved through the generation of recombinant adenovirus with subsequent infection in the C2C12 embryonic muscle cell line. A tetracysteine site, which enables site-specific labeling of the fluorescein biarscenical hairpin-binding dye (FlAsH), was introduced in the upper 50 kDa (U50) region (residues 316-321) corresponding to the previously utilized site in myosin V. Key conformational changes in the myosin motor, including those associated with nucleotide and actin binding, can be examined by fluorescence resonance energy transfer (FRET) using M2B-S1 FlAsH and fluorescent nucleotides or IAEDANs-labeled actin. We demonstrate the enzymatic properties of M2B-S1 FlAsH are similar to unlabeled M2B-S1, and both are capable of moving actin filaments in the in vitro motility assay. We utilized FRET between M2B-S1 FlAsH and Cy3ATP to examine structural changes in the U50 domain. The kinetics of structural changes were examined during the ATP-binding and actin-activated product release steps. We also designed a system to study structural changes in the force-generating lever arm using FlAsH labeling at the N-terminus of a human β-cardiac myosin construct containing a C-terminal GFP (M2B-GFP). The spectroscopic approach can be used as a tool to study the effects of hypertrophic cardiomyopathy (HCM) mutations on myosin structure or to study the impact of drugs that alter myosin motor activity.

Dynamics of the Lever-Arm Swing in Myosin V

Myosins utilize a conserved structural mechanism to convert the energy from ATP hydrolysis to a large swing in the force generating lever-arm. However, there remains an ongoing controversy about the kinetics of lever-arm swing in relation to the steps in the ATPase cycle. To address this question we have developed a novel FRET system in myosin V (MV) that utilizes several donor-acceptor pairs to examine the dynamics of lever arm motion. MV containing a single IQ motif and an N-terminal (NT) tetracysteine site was labeled with the bisarsenical dye FlAsH (MV.NT.FlAsH). The first IQ motif of MV.NT.FlAsH was exchanged either with IAANS labeled CaM, a donor, or QSY-9 labeled CaM, a non-fluorescent acceptor. Steady-state and transient kinetic experiments reveal a decrease in FRET upon ATP binding (recovery stroke) in both donor-acceptor pairs. We utilized transient kinetic experiments to demonstrate that upon mixing the MV.ADP.Pi complex with actin there was a FRET increase that occurred in two phases, and the fast and slow phases correlated well with the release rates of Pi and ADP, respectively. We also labeled the upper-50kDa tetracysteine site with FlAsH (MV.U50.FlAsH) and exchanged the QSY labeled CaM on to the first IQ motif. We observed structural changes during ATP binding that were very similar to the MV.NT.FlAsH results. During actin-activated product release we observed two-phases, a rapid increase in FRET followed by a slower decrease in FRET, which correlated well with ADP release. We find that the force generating motion of the lever arm occurs in two steps which are closely coupled to the product release steps. Our results also indicate that the conformational changes in the lever arm associated with the power stroke may follow a unique pathway that is not simply the reversal of the recovery stroke.

DNA Damage Processing by Human 8-Oxoguanine-DNA Glycosylase Mutants with the Occluded Active Site

8-Oxoguanine-DNA glycosylase (OGG1) removes premutagenic lesion 8-oxoguanine (8-oxo-G) from DNA and then nicks the nascent abasic (apurinic/apyrimidinic) site by β-elimination. Although the structure of OGG1 bound to damaged DNA is known, the dynamic aspects of 8-oxo-G recognition are not well understood. To comprehend the mechanisms of substrate recognition and processing, we have constructed OGG1 mutants with the active site occluded by replacement of Cys-253, which forms a wall of the base-binding pocket, with bulky leucine or isoleucine. The conformational dynamics of OGG1 mutants were characterized by single-turnover kinetics and stopped-flow kinetics with fluorescent detection. Additionally, the conformational mobility of wild type and the mutant OGG1 substrate complex was assessed using molecular dynamics simulations. Although pocket occlusion distorted the active site and greatly decreased the catalytic activity of OGG1, it did not fully prevent processing of 8-oxo-G and apurinic/apyrimidinic sites. Both mutants were notably stimulated in the presence of free 8-bromoguanine, indicating that this base can bind to the distorted OGG1 and facilitate β-elimination. The results agree with the concept of enzyme plasticity, suggesting that the active site of OGG1 is flexible enough to compensate partially for distortions caused by mutation.

The key role of a non-active-site residue Met148 on the catalytic efficiency of meta-cleavage product hydrolase BphD

meta-Cleavage product (MCP) hydrolases (EC 3.7.1.9) can catalyze a specific C-C bond fission during the microbial aerobic degradation of aromatics. The previous studies on structure-function relationship of MCP hydrolases mainly focus on the active site residues by site-directed mutagenesis. However, the information about the role of the non-active-site residues is still unclear. In this study, a non-active-site residue Met148 of MCP hydrolase BphD was selected as the mutagenesis site according to the sequence alignments, structure superimpose and the tunnel analysis, which underwent the saturation mutagenesis resulting 19 mutants. The catalytic efficiencies of the mutants on 6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) were all decreased compared with the wild-type one except for the M148D mutant. Especially, the M148P mutant exhibited 290-fold lower k cat/K m than that of the wild-type BphD. Transient kinetic analyses of M148P showed the reciprocal relaxation time corresponded to C-C bond cleavage and product release steps (9.6 s(-1)) was 4.08-fold lower than BphD WT (39.2 s(-1)). Tunnel cluster analysis of BphD WT, M148P and M148W demonstrated that only the bulky Trp148 could block tunnel T2 in the BphD WT, but it exhibited slight effects on the catalytic efficiency (0.94-fold of BphD WT). Therefore, product release was not the main reason for the efficiency decrease of M148P. On the other hand, molecular dynamics simulations on the BphD WT and BphD M148P in complex with HOPDA indicated that the dramatic decrease of the catalytic efficiencies of BphD M148P should be due to the unproductive binding of HOPDA. The study demonstrated the catalytic efficiency of MCP hydrolase can be engineered by modification of non-active site residue.

Dynamics of the N-Terminal Domain of Myosin V Monitored by FRET

The N-terminus is a highly variable region among the myosin superfamily and has been associated with alterations in rotation of the lever arm and step size. We examined the structural dynamics of the N-terminal region of myosin V using steady-state and stopped-flow FRET. We introduced a tetra-cysteine site at the extreme N-terminus of a Myosin V 1IQ construct and labeled it with a bisarsenical fluorescin derivative (FlAsH) (MV NT-FLAsH). Energy transfer between FlAsH and mant or deac labeled nucleotides (dmantATP, dmantADP and deacATP) was monitored. Steady-state FRET experiments with the mant-FlAsH pair demonstrated a high FRET state in the presence of dmantATP and a low FRET state in the presence of dmantADP. Sequential-mix, in which MV NT-FLAsH is first mixed with dmantATP, aged to allow formation of the M.ADP.Pi state, and then mixed with saturating actin allowed us to explore the actin-acitvated product release steps. Biphasic transients with rates corresponding to the fast and slow rate of dmantADP release were observed. The sequential mix experiments with deacATP yielded three phases; a fast, actin dependent, phosphate release phase followed by the two phases of ADP release. Our results suggest the FRET signal monitors a structural change in the N-terminus associated with the sequential release of products. A high FRET state upon binding of ATP is associated with formation of the pre-powerstroke state of the lever arm and a low or no FRET state in the presence of ADP suggests formation of the post-powerstroke state. Our results allow us to hypothesize that movement of the N-terminal domain follows the movement of the converter/lever arm. Further experiments will explore the dynamics of the N-terminal domain and examine how its motion correlates with the conformation of the nucleotide binding pocket and lever arm.

Colon Cancer-associated DNA Polymerase β Variant Induces Genomic Instability and Cellular Transformation

Rapidly advancing technology has resulted in the generation of the genomic sequences of several human tumors. We have identified several mutations of the DNA polymerase β (pol β) gene in human colorectal cancer. We have demonstrated that the expression of the pol β G231D variant increased chromosomal aberrations and induced cellular transformation. The transformed phenotype persisted in the cells even once the expression of G231D was extinguished, suggesting that it resulted as a consequence of genomic instability. Biochemical analysis revealed that its catalytic rate was 140-fold slower than WT pol β, and this was a result of the decreased binding affinity of nucleotides by G231D. Residue 231 of pol β lies in close proximity to the template strand of the DNA. Molecular modeling demonstrated that the change from a small and nonpolar glycine to a negatively charged aspartate resulted in a repulsion between the template and residue 231 leading to the distortion of the dNTP binding pocket. In addition, expression of G231D was insufficient to rescue pol β-deficient cells treated with chemotherapeutic agents suggesting that these agents may be effectively used to treat tumors harboring this mutation. More importantly, this suggests that the G231D variant has impaired base excision repair. Together, these data indicate that the G231D variant plays a role in driving cancer.

Many of the functional differences between acetohydroxyacid synthase (AHAS) isozyme I and other AHASs are a result of the rapid formation and breakdown of the covalent acetolactate–thiamin diphosphate adduct in AHAS I

Acetohydroxy acid synthase (AHAS; EC 2.2.1.6) is a thiamin diphosphate (ThDP)-dependent decarboxylase-ligase that catalyzes the first common step in the biosynthesis of branched-chain amino acids. In the first stage of the reaction, pyruvate is decarboxylated and the reactive intermediate hydroxyethyl-ThDP carbanion/enamine is formed. In the second stage, the intermediate is ligated to another 2-ketoacid to form either acetolactate or acetohydroxybutyrate. AHAS isozyme I from Escherichia coli is unique among the AHAS isozymes in that it is not specific for 2-ketobutyrate (2-KB) over pyruvate as an acceptor substrate. It also appears to have a different mechanism for inhibition by valine than does AHAS III from E. coli. An investigation of this enzyme by directed mutagenesis and knowledge of detailed kinetics using the rapid mixing-quench NMR method or stopped-flow spectroscopy, as well as the use of alternative substrates, suggests that two residues determine most of the unique properties of AHAS I. Gln480 and Met476 in AHAS I replace the Trp and Leu residues conserved in other AHASs and lead to accelerated ligation and product release steps. This difference in kinetics accounts for the unique specificity, reversibility and allosteric response of AHAS I. The rate of decarboxylation of the initially formed 2-lactyl-ThDP intermediate is, in some AHAS I mutants, different for the alternative acceptors pyruvate and 2-KB, putting into question whether AHAS operates via a pure ping-pong mechanism. This finding might be compatible with a concerted mechanism (i.e. the formation of a ternary donor-acceptor:enzyme complex followed by covalent, ThDP-promoted catalysis with concerted decarboxylation-carboligation). It might alternatively be explained by an allosteric interaction between the multiple catalytic sites in AHAS.

Differential Impact of Temperature and Magnesium on Myosin V and Myosin II

We examined the impact of temperature and free magnesium concentration on monomeric FlAsH labeled myosin V (MV FlAsH), dimeric myosin V (MV HMM), and dimeric fast skeletal muscle myosin II (SK HMM) using ATPase and motility assays. Our results indicate that MV HMM and SK HMM both have a linear dependence on temperature that is similar in both ATPase and motility assays. However, MV FlAsH contains a different temperature dependence in ATPase and motility assays suggesting its short lever arm may impart a high strain dependence in the motility assay. MV HMM and MV FlAsH are inhibited by high concentrations of magnesium in both ATPase and motility assays. The rate-limiting step in myosin V is known to be ADP release, which we demonstrate correlates well with the magnesium and temperature dependence of ATPase and motility assays. Interestingly, SK HMM exhibits magnesium inhibition in ATPase assays, but only a slight decrease is observed in the motility assay. In SK HMM the rate-limiting step in ATPase assays is thought to be attachment to actin or phosphate release, while in motility assays it is controversial. Our results indicate that SK HMM is better described by an attachment limited model in the motility assay. Magnesium may reduce the duty ratio of SK HMM which alters ATPase activity but not velocity in the motility assay. Future experiments will determine if magnesium alters the actin binding and/or the product release steps in myosin V and skeletal muscle myosin. Myosin V contains a tyrosine (residue 439) in the switch II region, which is an alanine at the corresponding position in myosin II, suggesting this residue may play a key role in differentially altering magnesium coordination in the active site of myosins.

Enzymes of mannitol metabolism in the human pathogenic fungus Aspergillus fumigatus – kinetic properties of mannitol‐1‐phosphate 5‐dehydrogenase and mannitol 2‐dehydrogenase, and their physiological implications

The human pathogenic fungus Aspergillus fumigatus accumulates large amounts of intracellular mannitol to enhance its resistance against defense strategies of the infected host. To explore their currently unknown roles in mannitol metabolism, we studied A. fumigatus mannitol-1-phosphate 5-dehydrogenase (AfM1PDH) and mannitol 2-dehydrogenase (AfM2DH), each recombinantly produced in Escherichia coli, and performed a detailed steady-state kinetic characterization of the two enzymes at 25 °C and pH 7.1. Primary kinetic isotope effects resulting from deuteration of alcohol substrate or NADH showed that, for AfM1PDH, binding of D-mannitol 1-phosphate and NAD(+) is random, whereas D-fructose 6-phosphate binds only after NADH has bound to the enzyme. Binding of substrate and NAD(H) by AfM2DH is random for both D-mannitol oxidation and D-fructose reduction. Hydride transfer is rate-determining for D-mannitol 1-phosphate oxidation by AfM1PDH (k(cat) = 10.6 s(-1)) as well as D-fructose reduction by AfM2DH (k(cat) = 94 s(-1)). Product release steps control the maximum rates in the other direction of the two enzymatic reactions. Free energy profiles for the enzymatic reaction under physiological boundary conditions suggest that AfM1PDH primarily functions as a D-fructose-6-phosphate reductase, whereas AfM2DH acts in D-mannitol oxidation, thus establishing distinct routes for production and mobilization of mannitol in A. fumigatus. ATP, ADP and AMP do not affect the activity of AfM1PDH, suggesting the absence of flux control by cellular energy charge at the level of D-fructose 6-phosphate reduction. AfM1PDH is remarkably resistant to inactivation by heat (half-life at 40 °C of 20 h), consistent with the idea that formation of mannitol is an essential component of the temperature stress response of A. fumigatus. Inhibition of AfM1PDH might be a useful target for therapy of A. fumigatus infections.

The intriguing modeling of cis–trans selectivity in ruthenium-catalyzed olefin metathesis

In this study we have investigated computationally the origin of the cis–trans selectivity in the Ru-catalyzed cross metathesis (CM) of a prototype monosubstituted olefin, i.e., propene. Our calculations suggest that the origin of the preferential formation of trans-olefins is in the product release step, which prevents the initially formed cis-olefin from escaping the metal, and returns it to the reaction pool until the trans-olefin is formed.

Improving a Natural Enzyme Activity through Incorporation of Unnatural Amino Acids

The bacterial phosphotriesterases catalyze hydrolysis of the pesticide paraoxon with very fast turnover rates and are thought to be near to their evolutionary limit for this activity. To test whether the naturally evolved turnover rate could be improved through the incorporation of unnatural amino acids and to probe the role of peripheral active site residues in nonchemical steps of the catalytic cycle (substrate binding and product release), we replaced the naturally occurring tyrosine amino acid at position 309 with unnatural L-(7-hydroxycoumarin-4-yl)ethylglycine (Hco) and L-(7-methylcoumarin-4-yl)ethylglycine amino acids, as well as leucine, phenylalanine, and tryptophan. Kinetic analysis suggests that the 7-hydroxyl group of Hco, particularly in its deprotonated state, contributes to an increase in the rate-limiting product release step of substrate turnover as a result of its electrostatic repulsion of the negatively charged 4-nitrophenolate product of paraoxon hydrolysis. The 8-11-fold improvement of this already highly efficient catalyst through a single rationally designed mutation using an unnatural amino acid stands in contrast to the difficulty in improving this native activity through screening hundreds of thousands of mutants with natural amino acids. These results demonstrate that designer amino acids provide easy access to new and valuable sequence and functional space for the engineering and evolution of existing enzyme functions.

Kinetics of oxidative phosphorylation catalyzed by inside-out plasma membrane vesicles of Paracoccus denitrificans

Coupled inside-out plasma membrane vesicles of Paracoccus denitrificans are capable of proton-motive force (pmf)-required, pmf-generating ATP hydrolysis [1]. The steady-state ATP hydrolysis, catalyzed by P. denitrificans FO·F1 (PFO·F1) proceeds via compulsory sequential mechanism where ADP leaves the enzyme–products (ADP and Pi) complex first followed by irreversible release of Pi [2]. Inasmuch operation of PFO·F1 ATPase (synthase) is macroscopically reversible it seems imperative to reconcile the steady-state kinetics of pmf-generating ATP hydrolysis with that of pmf-utilising ATP synthesis. To reach this goal the dependencies of the initial steadystate rates of oxidative phosphorylation on ADP and Pi concentrations and on pmf were measured. ATP synthesis rate showed simple hyperbolic dependence on either substrate (within the concentration ranges of 1.5–50 μM for ADP and 10–500 μM for Pi) with no mutual dependence of apparent Km values thus suggesting random formation of the enzyme–ADP·Pi complex. When the ‘third substrate’, pmf was varied by limitation of succinate or NADH oxidation rates an apparent ‘ping-pong’ mechanism was evident: a decrease of the maximal rates caused by a decrease of pmf resulted in proportional decrease of apparent Km values for either Pi or ADP. This pattern suggests that an irreversible step, presumably ATP formation at the enzyme active site, precedes the involvement of pmf in the overall reaction (likely at the product release step). Comparison of the steady-state kinetics of ATP hydrolysis [2] and synthesis shows that macroscopic reversibility of the PFO·F1 ATPase (synthase) reaction cannot be ascribed to operation of single microscopically reversible enzyme species. We propose that apparent equilibrium between any given pmf and intracellular (intramitochondrial) phosphoryl potential ([ATP]/[ADP]·[Pi]) is maintained by ‘futile cycle’ of ATP synthesis and hydrolysis catalyzed by kinetically (and structurally) distinct FO·F1 species. Supported by the Russian Foundation for Fundamental Research grant 08-04-00594.

Phosphorylation of the Transcription Factor Ets-1 by ERK2: Rapid Dissociation of ADP and Phospho-Ets-1

ERK2, a major effector of the BRAF oncogene, is a promiscuous protein kinase that has a strong preference for phosphorylating substrates on Ser-Pro or Thr-Pro motifs. As part of a program to understand the fundamental basis for ERK2 substrate recognition and catalysis, we have studied the mechanism by which ERK2 phosphorylates the transcription factor Ets-1 at Thr-38. A feature of the mechanism in the forward direction is a partially rate-limiting product release step (koff = 59 +/- 6 s(-1)), which is significant because to approach maximum efficiency substrates for ERK2 may evolve to ensure that ADP dissociation is rate-limiting. To improve our understanding of the mechanism of product release, the binding of the products to ERK2 was assessed and the reaction was examined in the reverse direction. These studies demonstrated that phospho-Ets-1 (p-Ets) binds >20-fold more tightly to ERK2 than ADP (Kd = 7.3 and 165 microM, respectively) and revealed that the products exhibit little interaction energetically while bound to ERK2 and that they can dissociate ERK2 in a random order. The overall equilibrium for the reaction in solution (Keq = 250 M(-1)) was found to be similar to that with the substrate bound to the enzyme (Kint = 525 M(-1)). To determine what limits koff, several pre-steady-state experiments were performed. A catalytic trapping approach furnished a rate constant (k-ADPa) of 61 +/- 12 s(-1) for the dissociation of ADP from the abortive ternary complex, ERK2.Ets.ADP. To examine p-Ets dissociation, the binding of a fluorescent derivative (p-Ets-F), which binds ERK2 with an affinity similar to that of p-Ets, was examined by stopped-flow kinetics. Using this approach, p-Ets-F was found to bind through a single-step mechanism, with the following parameters: k-p-Ets-F = 121 +/- 3.8 s(-1), and kp-Ets-F = (9.4 +/- 0.3) X 10(6) M(-1) s(-1). Similar results were found in the presence of a saturating ADP concentration. These data suggest that koff may be limited by the dissociation of both products and are consistent with the notion that Ets-1 has evolved to be an efficient substrate for ERK2, where ADP release is, at least, partially rate-limiting. A molecular mechanics model of the complex formed between ERK2 and residues 28-138 of Ets-1 provides insight into the role of substrate docking interactions.

Myosin VI undergoes a 180° power stroke implying an uncoupling of the front lever arm

We simultaneously measure both the step size, via FIONA, and the 3-D orientation, via DOPI, of the light-chain domain of individual dimeric myosin VIs. This allows for the correlation of the change in orientation of the light chain domain to the stepping of the motor. Three different pairs of positions were tested using a rigid bifunctional rhodamine on the calmodulin of the IQ domain. The data for all three labeling positions support the model that the light chain domain undergoes a significant rotation of approximately 180 degrees . Contrary to an earlier study [Sun, Y. et al. (2007) Mol Cell 28, 954-964], our data does not support a model of multiple angles of the lever arm of the lead head, nor "wiggly" walking on actin. Instead, we propose that for the two heads of myosin VI to coordinate their processive movement, the lever arm of the lead head must be uncoupled from the converter until the rear head detaches. More specifically, intramolecular strain causes the myosin VI lever arm of the lead head to uncouple from the motor domain, allowing the motor domain to go through its product-release (phosphate and ADP) steps at an unstrained rate. The lever arm of the lead head rebinds to the motor and attains a rigor conformation when the rear head detaches. By coupling the orientation and position information with previously described kinetics, this allows us to explain how myosin VI coordinates its heads processively while maintaining the ability to move under load with a (semi-) rigid lever arm.