Slow Conformational Change Research Articles

Kinetic Mechanism of DNA Polymerization Catalyzed by Human DNA Polymerase ε

Eukaryotes require highly accurate and processive DNA polymerases to ensure faithful and efficient replication of their genomes. DNA polymerase ε (Polε) has been shown to catalyze leading-strand DNA synthesis during replication in vivo, but little is known about the kinetic mechanism of polymerization catalyzed by this replicative enzyme. To elucidate this mechanism, we have generated a truncated, exonuclease-deficient mutant of the catalytic subunit of human Polε (Polε exo-) and carried out pre-steady-state kinetic analysis of this enzyme. Our results show that Polε exo-, as other DNA polymerases, follows an induced-fit mechanism when catalyzing correct nucleotide incorporation. Polε exo- binds DNA with a Kd(DNA) of 79 nM and dissociates from the E·DNA binary complex with a rate constant of 0.021 s(-1). Although Polε exo- binds a correct incoming nucleotide weakly with a Kd(dTTP) of 31 μM, it catalyzes correct nucleotide incorporation at a fast rate constant of 248 s(-1) at 20 °C. Both a large reaction amplitude difference (42%) between pulse-chase and pulse-quench assays and a small elemental effect (0.9) for correct dTTP incorporation suggest that a slow conformational change preceding the chemistry step limits the rate of correct nucleotide incorporation. In addition, our kinetic analysis shows that Polε exo- exhibits low processivity during polymerization. To catalyze leading-strand synthesis in vivo, Polε likely interacts with its three smaller subunits and additional replication factors in order to assemble a replication complex and significantly enhance its polymerization processivity.

Slow Conformational Changes in MutS and DNA Direct Ordered Transitions between Mismatch Search, Recognition and Signaling of DNA Repair

MutS functions in mismatch repair (MMR) to scan DNA for errors, identify a target site and trigger subsequent events in the pathway leading to error removal and DNA re-synthesis. These actions, enabled by the ATPase activity of MutS, are now beginning to be analyzed from the perspective of the protein itself. This study provides the first ensemble transient kinetic data on MutS conformational dynamics as it works with DNA and ATP in MMR. Using a combination of fluorescence probes (on Thermus aquaticus MutS and DNA) and signals (intensity, anisotropy and resonance energy transfer), we have monitored the timing of key conformational changes in MutS that are coupled to mismatch binding and recognition, ATP binding and hydrolysis, as well as sliding clamp formation and signaling of repair. Significant findings include (a) a slow step that follows weak initial interaction between MutS and DNA, in which concerted conformational changes in both macromolecules control mismatch recognition, and (b) rapid, binary switching of MutS conformations that is concerted with ATP binding and hydrolysis and (c) is stalled after mismatch recognition to control formation of the ATP-bound MutS sliding clamp. These rate-limiting pre- and post-mismatch recognition events outline the mechanism of action of MutS on DNA during initiation of MMR.

Transient kinetic studies reveal isomerization steps along the kinetic pathway of Thermus thermophilus 3‐isopropylmalate dehydrogenase

To identify the rate-limiting step(s) of the 3-isopropylmalate dehydrogenase-catalysed reaction, time courses of NADH production were followed by stopped flow (SF) and quenched flow (QF). The steady state kcat and Km values did not vary between enzyme concentrations of 0.1 and 20 μm. A burst phase of NADH formation was shown by QF, indicating that the rate-limiting step occurs after the redox step. The kinetics of protein conformational change(s) induced by the complex of 3-isopropylmalate with Mg(2+) were followed by using the fluorescence resonance energy transfer signal between protein tryptophan(s) and the bound NADH. A reaction scheme was proposed by incorporating the rate constant of a fast protein conformational change (possibly domain closure) derived from the separately recorded time-dependent formation of the fluorescence resonance energy transfer signal. The rate-limiting step seems to be another slower conformational change (domain opening) that allows product release.

Precise Monitoring of Chemical Changes through Localization Analysis of Dynamic Spectra (LADS)

We present a method for monitoring subtle (sub-wavenumber) dynamics within time-varying spectra. Peak fitting is performed for large numbers of spectra in a series, allowing for monitoring time evolutions of peak positions with high precision and confidence. Sub-wavenumber peak shifts due to physical or chemical changes in the sample can be monitored and their temporal evolution characterized. In surface-enhanced Raman scattering experiments, we were able to distinguish between slow photo-damage and fast conformational change dynamics. Fluctuations in peak positions of Raman spectra recorded from a single yeast cell indicated that no significant irreversible photo-damage occurred, but these fluctuations suggest changes in the trapping conditions or biochemical changes associated with the cellular machinery in the cell. The technique is particularly suitable for applications where dynamics of spectra are of interest.

Modulation of cell adhesion and detachment on thermo-responsive polymeric surfaces through the observation of surface dynamics

Various thermo-responsive polymeric surfaces were evaluated in terms of cell adhesion/detachment and surface analysis. Three kinds of thermo-responsive poly(N-isopropylacrylamide) (PIPAAm) surfaces were prepared by an electron beam irradiation (PIPAAm-EB), a reversible addition fragmentation polymerization (PIPAAm-RAFT), and a redox polymerization (PIPAAm-Redox). Although cell adhesion and detachment on surfaces of PIPAAm-EB and PIPAAm-RAFT were able to be modulated by altering their surface characters with changing the amounts of polymers, the adhesion and detachment were hardly controlled on PIPAAm-Redox surfaces, even though the amounts of polymers on the surface were able to be modulated. Atomic force microscopy (AFM) probed the interactions between AFM tip and the polymeric surface for further investigating a different conformation of polymeric surface. The modification of AFM tip surface coated with octadecyltrichlorosilane was found to change the interaction between the thermo-responsive surface and the tip. Adhesion force analysis clearly showed changes in the hydrophilic/hydrophobic characters of three kinds of thermo-responsive surfaces immediately after a change in temperature. From the kinetics study of AFM, PIPAAm-EB and PIPAAm-RAFT surfaces became hydrophilic less than 30min after temperature decrease, but PIPAAm-Redox surfaces required 120min to become hydrophilic after temperature reduction. These results indicated that a faster conformational change triggered cell detachment and a slow conformation change hardly affected cell detachment. Therefore, polymeric conformation on solid substrate was an important factor for modulating cell adhesion and detachment.

Heat Transfer Pathways in Proteins

Proteins propagate excess thermal energy surprisingly fast and efficient. The theoretical description of thermal transport dynamics in proteins is challenging as it involves both fast quantum vibrations as well as more classical slow conformational changes. Existing protein Molecular Dynamics methods describe these conformational changes well but perform poorly for fast quantum degrees of freedom. Dye labeled Azido-PEG oligomers are experimentally well studied model systems for excess energy transport. Relaxation-assisted two-dimensional infrared (RA 2DIR) spectroscopy has been applied 1) 2) to measure the time-dependent correlation of frequencies belonging to the dye and the Azido group.Thermal energy is generated at the dye and propagates through the flexible oligomer chain (intramolecular) as well as into the solvent (intermolecular). The oligomer chain undergoes conformational changes on the ps time scales of the transfer process. These slow changes were sampled using Molecular Dynamics trajectories. The resulting structural ensemble was used to map the mode coupling pathways for the fast quantum degrees of freedom. All pairwise mode-mode coupling potentials along pairs of dynamic normal mode vectors were calculated. A molecular heat map was generated using the spatial delocalization of the modes and the inter mode coupling strengths. Molecular heat maps have the potential to extend the theoretical understanding of intramolecular heat transduction pathways in proteins.1) Lin, Z., Rubtsov, I.V., PNAS, 2012, 105, 5, 1413-14182) Lin, Z., Rubtsov, I.V., et al., Phys. Chem. Chem. Phys., 2012, 14, 10445-10454

Ultrafast Red Light Activation of Synechocystis Phytochrome Cph1 Triggers Major Structural Change to Form the Pfr Signalling-Competent State

Phytochromes are dimeric photoreceptors that regulate a range of responses in plants and microorganisms through interconversion of red light-absorbing (Pr) and far-red light-absorbing (Pfr) states. Photoconversion between these states is initiated by light-driven isomerization of a bilin cofactor, which triggers protein structural change. The extent of this change, and how light-driven structural changes in the N-terminal photosensory region are transmitted to the C-terminal regulatory domain to initiate the signalling cascade, is unknown. We have used pulsed electron-electron double resonance (PELDOR) spectroscopy to identify multiple structural transitions in a phytochrome from Synechocystis sp. PCC6803 (Cph1) by measuring distances between nitroxide labels introduced into the protein. We show that monomers in the Cph1 dimer are aligned in a parallel ‘head-to-head’ arrangement and that photoconversion between the Pr and Pfr forms involves conformational change in both the N- and C-terminal domains of the protein. Cryo-trapping and kinetic measurements were used to probe the extent and temporal properties of protein motions for individual steps during photoconversion of Cph1. Formation of the primary photoproduct Lumi-R is not affected by changes in solvent viscosity and dielectric constant. Lumi-R formation occurs at cryogenic temperatures, consistent with their being no major structural reorganization of Cph1 during primary photoproduct formation. All remaining steps in the formation of the Pfr state are affected by solvent viscosity and dielectric constant and occur only at elevated temperatures, implying involvement of a series of long-range solvent-coupled conformational changes in Cph1. We show that signalling is achieved through ultrafast photoisomerization where localized structural change in the GAF domain is transmitted and amplified to cause larger-scale and slower conformational change in the PHY and histidine kinase domains. This hierarchy of timescales and extent of structural change orientates the histidine kinase domain to elicit the desired light-activated biological response.

The value of numerical modeling of aquifers in data-poor regions

The adsorption and desorption of plasma proteins—albumin, γ-globulin, and fibrinogen—on copolypeptide and silicone surfaces have been studied. The process is characterized by three stages; an initial brief period where adsorption is reversible; a second phase where the adsorbed proteins undergo a slow conformation change based on the period of adsorption and where protein is essentially irreversibly adsorbed; in the final stage, denatured material is slowly desorbed. In the second stage the process is essentially irreversible, desorption being very slow; the third stage is essentially irreversible, adsorption of denatured material being improbable. The adsorption process may be represented by a two-state Oreskes/Singer plot, there being an apparent surface phase change at 50–60% surface coverage. Albumin and fibrinogen molecules are adsorbed side-on; γ-globulin is adsorbed in an end-on configuration. Surface denaturation seems to be driven by a need to increase hydrophobic bonding with the surface and adsorption is heavily entropic in nature. In the desorbed material, albumin and fibrinogen sustain a marked decrease in α-helical content; γ-globulin loses most of its β-sheet structure.

Thermodynamic versus Conformational Metastability in Fibril-Forming Lysozyme Solutions

The role of intermolecular interaction in fibril-forming protein solutions and its relation with molecular conformation is a crucial aspect for the control and inhibition of amyloid structures. Here, we study the fibril formation and the protein-protein interactions of lysozyme at acidic pH and low ionic strength. The amyloid formation occurs after a long lag time and is preceded by the formation of oligomers, which seems to be off-pathway with respect to fibrillation. By measuring the osmotic isothermal compressibility and the collective diffusion coefficient of lysozyme in solution, we observe that the monomeric solution is kept in a thermodynamically metastable state by strong electrostatic repulsion, even in denaturing conditions. The measured repulsive interaction between monomers is satisfactorily accounted for by classical polyelectrolyte theory. Further, we observe a slow conformational change involving both secondary and tertiary structure, which drives the proteins toward a more hydrophobic conformation. Denatured proteins are driven out of metastability through conformational substates, which are kinetically populated and experience a lower activation energy for fibril formation. Thus, our results highlight the role of electrostatic repulsion, which hinders the aggregation of partially denatured proteins and operates as a gatekeeper favoring the association of those monomers whose conformation is capable of forming amyloid structure.

Functional Roles of Slow Enzyme Conformational Changes in Network Dynamics

Extensive studies from different fields reveal that many macromolecules, especially enzymes, show slow transitions among different conformations. This phenomenon is named such things as dynamic disorder, heterogeneity, hysteretic or mnemonic enzymes across these different fields, and has been directly demonstrated by single molecule enzymology and NMR studies recently. We analyzed enzyme slow conformational changes in the context of regulatory networks. A single enzymatic reaction with slow conformational changes can filter upstream network noises, and can either resonantly respond to the system stimulus at certain frequencies or respond adaptively for sustained input signals of the network fluctuations. It thus can serve as a basic functional motif with properties that are normally for larger intermolecular networks in the field of systems biology. We further analyzed examples including enzymes functioning against pH fluctuations, metabolic state change of Artemia embryos, and kinetic insulation of fluctuations in metabolic networks. The study also suggests that hysteretic enzymes may be building blocks of synthetic networks with various properties such as narrow-banded filtering. The work fills the missing gap between studies on enzyme biophysics and network level dynamics, and reveals that the coupling between the two is functionally important; it also suggests that the conformational dynamics of some enzymes may be evolutionally selected.

Kinetic Mechanism of Ca2+-controlled Changes of Skeletal Troponin I in Psoas Myofibrils

Conformational changes in the skeletal troponin complex (sTn) induced by rapidly increasing or decreasing the [Ca2+] were probed by 5-iodoacetamidofluorescein covalently bound to Cys-133 of skeletal troponin I (sTnI). Kinetics of conformational changes was determined for the isolated complex and after incorporating the complex into rabbit psoas myofibrils. Isolated and incorporated sTn exhibited biphasic Ca2+-activation kinetics. Whereas the fast phase (kobs∼1000 s−1) is only observed in this study, where kinetics were induced by Ca2+, the slower phase resembles the monophasic kinetics of sTnI switching observed in another study (Brenner and Chalovich. 1999. Biophys. J. 77:2692–2708) that investigated the sTnI switching induced by releasing the feedback of force-generating cross-bridges on thin filament activation. Therefore, the slower conformational change likely reflects the sTnI switch that regulates force development. Modeling reveals that the fast conformational change can occur after the first Ca2+ ion binds to skeletal troponin C (sTnC), whereas the slower change requires Ca2+ binding to both regulatory sites of sTnC. Incorporating sTn into myofibrils increased the off-rate and lowered the Ca2+ sensitivity of sTnI switching. Comparison of switch-off kinetics with myofibril force relaxation kinetics measured in a mechanical setup indicates that sTnI switching might limit the rate of fast skeletal muscle relaxation.

Quantifying Protein Adsorption and Function at Nanostructured Materials: Enzymatic Activity of Glucose Oxidase at GLAD Structured Electrodes

Nanostructured materials strongly modulate the behavior of adsorbed proteins; however, the characterization of such interactions is challenging. Here we present a novel method combining protein adsorption studies at nanostructured quartz crystal microbalance sensor surfaces (QCM-D) with optical (surface plasmon resonance SPR) and electrochemical methods (cyclic voltammetry CV) allowing quantification of both bound protein amount and activity. The redox enzyme glucose oxidase is studied as a model system to explore alterations in protein functional behavior caused by adsorption onto flat and nanostructured surfaces. This enzyme and such materials interactions are relevant for biosensor applications. Novel nanostructured gold electrode surfaces with controlled curvature were fabricated using colloidal lithography and glancing angle deposition (GLAD). The adsorption of enzyme to nanostructured interfaces was found to be significantly larger compared to flat interfaces even after normalization for the increased surface area, and no substantial desorption was observed within 24 h. A decreased enzymatic activity was observed over the same period of time, which indicates a slow conformational change of the adsorbed enzyme induced by the materials interface. Additionally, we make use of inherent localized surface plasmon resonances in these nanostructured materials to directly quantify the protein binding. We hereby demonstrate a QCM-D-based methodology to quantify protein binding at complex nanostructured materials. Our approach allows label free quantification of protein binding at nanostructured interfaces.

Neuromodulatory changes in short-term synaptic dynamics may be mediated by two distinct mechanisms of presynaptic calcium entry

Although synaptic output is known to be modulated by changes in presynaptic calcium channels, additional pathways for calcium entry into the presynaptic terminal, such as non-selective channels, could contribute to modulation of short term synaptic dynamics. We address this issue using computational modeling. The neuropeptide proctolin modulates the inhibitory synapse from the lateral pyloric (LP) to the pyloric dilator (PD) neuron, two slow-wave bursting neurons in the pyloric network of the crab Cancer borealis. Proctolin enhances the strength of this synapse and also changes its dynamics. Whereas in control saline the synapse shows depression independent of the amplitude of the presynaptic LP signal, in proctolin, with high-amplitude presynaptic LP stimulation the synapse remains depressing while low-amplitude stimulation causes facilitation. We use simple calcium-dependent release models to explore two alternative mechanisms underlying these modulatory effects. In the first model, proctolin directly targets calcium channels by changing their activation kinetics which results in gradual accumulation of calcium with low-amplitude presynaptic stimulation, leading to facilitation. The second model uses the fact that proctolin is known to activate a non-specific cation current I ( MI ). In this model, we assume that the MI channels have some permeability to calcium, modeled to be a result of slow conformation change after binding calcium. This generates a gradual increase in calcium influx into the presynaptic terminals through the modulatory channel similar to that described in the first model. Each of these models can explain the modulation of the synapse by proctolin but with different consequences for network activity.

Internal Motions and Exchange Processes in Human Ileal Bile Acid Binding Protein As Studied by Backbone 15N Nuclear Magnetic Resonance Spectroscopy

Human ileal bile acid binding protein (I-BABP), a member of the family of intracellular lipid binding proteins, is thought to play a role in the enterohepatic circulation of bile salts. Previously, we have shown by stopped-flow fluorescence analysis that positive binding cooperativity exhibited by I-BABP in its interactions with glycocholate (GCA) and glycochenodeoxycholate (GCDA), the two primary bile salts in humans, is related to a slow conformational change in the protein. In this study, we used backbone (15)N relaxation nuclear magnetic resonance (NMR) techniques to obtain residue-specific information about the internal dynamics of apo I-BABP and the doubly ligated I-BABP:GCA:GCDA complex on various time scales. According to our NMR data, bile salt binding is accompanied by a slight rigidification of the (15)N-(1)H bond vectors on the picosecond to nanosecond time scale, with most pronounced changes occurring in the C-D region. In contrast to the minor effects of ligation on fast motions, relaxation dispersion NMR experiments indicate a marked difference between the two protein states on the microsecond to millisecond time scale. In the apo form, an extensive network of conformational fluctuations is detected throughout segments of the EFGHIJ β-strands and the C-D loop, which cease upon complexation. Our NMR data are in agreement with a conformational selection model we proposed earlier for I-BABP and support the hypothesis of an allosteric mechanism of ligand binding. According to the NMR measurements, the helical cap region may have a less crucial role in mediating ligand entry and release than what has been indicated for fatty acid binding proteins.

Allosterically Gated Enzyme Dynamics in the Cysteine Synthase Complex Regulate Cysteine Biosynthesis in Arabidopsis thaliana

Plants and bacteria assimilate sulfur into cysteine. Cysteine biosynthesis involves a bienzyme complex, the cysteine synthase complex (CSC), which consists of serine-acetyl-transferase (SAT) and O-acetyl-serine-(thiol)-lyase (OAS-TL) enzymes. The activity of OAS-TL is reduced by formation of the CSC. Although this reduction is an inherent part of the self-regulation cycle of cysteine biosynthesis, there has until now been no explanation as to how OAS-TL loses activity in plants. Complexation of SAT and OAS-TL involves binding of the C-terminal tail of SAT in one of the active sites of the homodimeric OAS-TL. We here explore the flexibility of the unoccupied active site in Arabidopsis thaliana cytosolic and mitochondrial OAS-TLs. Our results reveal two gates in the OAS-TL active site that define its accessibility. The observed dynamics of the gates show allosteric closure of the unoccupied active site of OAS-TL in the CSC, which can hinder substrate binding, abolishing its turnover to cysteine.

Extraction of Am(iii) using novel solvent systems containing a tripodal diglycolamide ligand in room temperature ionic liquids: a ‘green’ approach for radioactive waste processing

Extraction of Am3+ from acidic feed solutions was investigated using novel solvent systems containing a tripodal diglycolamide (T-DGA) in three room temperature ionic liquids (RTIL), viz. [C4mim][NTf2], [C6mim][NTf2] and [C8mim][NTf2]. Compared to the results obtained with N,N,N′,N′-tetra-n-octyl diglycolamide (TODGA), T-DGA gave significantly higher distribution coefficients in these RTILs. The DAm values decreased with increasing carbon chain length in the RTILs, which was related to the solubility of the RTIL in the aqueous phase. The distribution studies included the effect of equilibration time, aqueous phase acid concentration variation and T-DGA concentration variation. In general, significantly higher equilibration times were observed for the extraction systems, which was partly due to the viscous RTIL phase and partly due to the slow conformational changes of the T-DGA ligand during complexation. Apart from Am3+, extraction of Pu4+, UO22+, Eu3+, Sr2+ and Cs+ was also investigated, since they have significant implications in radioactive waste processing. Stripping studies indicated >99% stripping in three stages using 0.5 M EDTA or DTPA in 1 M guanidine carbonate. Slope analysis indicated the extraction of 1 : 1 complexed species of Am(III) with T-DGA. Time resolved laser fluorescence spectroscopy (TRLFS) studies showed a strong complexation with no inner-sphere water molecules in the Eu(III)–T-DGA complexes for [C4mim][NTf2] as the diluent. Radiolytic degradation studies of the solvent systems containing T-DGA in the three RTILs were also carried out and while the DAm values decreased marginally when the solvents were exposed to 500 kGy absorbed dose, a relatively sharp decrease (60%) was seen when the solvents were exposed further to 1000 kGy absorbed dose, suggesting the possibility of recycling. Extraction studies were also carried out at varying temperatures and the thermodynamic parameters were calculated.

Effects of Extracellular DNA on Plasminogen Activation and Fibrinolysis

The increased levels of extracellular DNA found in a number of disorders involving dysregulation of the fibrinolytic system may affect interactions between fibrinolytic enzymes and inhibitors. Double-stranded (ds) DNA and oligonucleotides bind tissue-(tPA) and urokinase (uPA)-type plasminogen activators, plasmin, and plasminogen with submicromolar affinity. The binding of enzymes to DNA was detected by EMSA, steady-state, and stopped-flow fluorimetry. The interaction of dsDNA/oligonucleotides with tPA and uPA includes a fast bimolecular step, followed by two monomolecular steps, likely indicating slow conformational changes in the enzyme. DNA (0.1-5.0 μg/ml), but not RNA, potentiates the activation of Glu- and Lys-plasminogen by tPA and uPA by 480- and 70-fold and 10.7- and 17-fold, respectively, via a template mechanism similar to that known for fibrin. However, unlike fibrin, dsDNA/oligonucleotides moderately affect the reaction between plasmin and α(2)-antiplasmin and accelerate the inactivation of tPA and two chain uPA by plasminogen activator inhibitor-1 (PAI-1), which is potentiated by vitronectin. dsDNA (0.1-1.0 μg/ml) does not affect the rate of fibrinolysis by plasmin but increases by 4-5-fold the rate of fibrinolysis by Glu-plasminogen/plasminogen activator. The presence of α(2)-antiplasmin abolishes the potentiation of fibrinolysis by dsDNA. At higher concentrations (1.0-20 μg/ml), dsDNA competes for plasmin with fibrin and decreases the rate of fibrinolysis. dsDNA/oligonucleotides incorporated into a fibrin film also inhibit fibrinolysis. Thus, extracellular DNA at physiological concentrations may potentiate fibrinolysis by stimulating fibrin-independent plasminogen activation. Conversely, DNA could inhibit fibrinolysis by increasing the susceptibility of fibrinolytic enzymes to serpins.

Intraprotein electron transfer between the FMN and heme domains in endothelial nitric oxide synthase holoenzyme

Intraprotein electron transfer (IET) from flavin mononucleotide (FMN) to heme is an essential step in nitric oxide (NO) synthesis by NO synthase (NOS). The IET kinetics in neuronal and inducible NOS (nNOS and iNOS) holoenzymes have been previously determined in our laboratories by laser flash photolysis [reviewed in: C.J. Feng, G. Tollin, Dalton Trans., (2009) 6692–6700]. Here we report the kinetics of the IET in a bovine endothelial NOS (eNOS) holoenzyme in the presence and absence of added calmodulin (CaM). The IET rate constant in the presence of CaM is estimated to be ~4.3s−1. No IET was observed in the absence of CaM, indicating that CaM is the primary factor in controlling the FMN−heme IET in the eNOS enzyme. The IET rate constant value for the eNOS holoenzyme is approximately 10 times smaller than those obtained for the iNOS and CaM-bound nNOS holoenzymes. Possible mechanisms underlying the difference in IET kinetics among the NOS isoforms are discussed. Because the rate-limiting step in the IET process in these enzymes is the conformational change from input state to output state, a slower conformational change (than in the other isoforms) is most likely to cause the slower IET in eNOS.

Kinetic and Chemical Mechanisms of Homocitrate Synthase from Thermus thermophilus

The homocitrate synthase from Thermus thermophilus (TtHCS) is a metal-activated enzyme with either Mg(2+) or Mn(2+) capable of serving as the divalent cation. The enzyme exhibits a sequential kinetic mechanism. The mechanism is steady state ordered with α-ketoglutarate (α-Kg) binding prior to acetyl-CoA (AcCoA) with Mn(2+), whereas it is steady state random with Mg(2+), suggesting a difference in the competence of the E·Mn·α-Kg·AcCoA and E·Mg·α-Kg·AcCoA complexes. The mechanism is supported by product and dead-end inhibition studies. The primary isotope effect obtained with deuterioacetylCoA (AcCoA-d(3)) in the presence of Mg(2+) is unity (value 1.0) at low concentrations of AcCoA, whereas it is 2 at high concentrations of AcCoA. Data suggest the presence of a slow conformational change induced by binding of AcCoA that accompanies deprotonation of the methyl group of AcCoA. The solvent kinetic deuterium isotope effect is also unity at low AcCoA, but is 1.7 at high AcCoA, consistent with the proposed slow conformational change. The maximum rate is pH independent with either Mg(2+) or Mn(2+) as the divalent metal ion, whereas V/K(α-Kg) (with Mn(2+)) decreases at low and high pH giving pK values of about 6.5 and 8.0. Lysine is a competitive inhibitor that binds to the active site of TtHCS, and shares some of the same binding determinants as α-Kg. Lysine binding exhibits negative cooperativity, indicating cross-talk between the two monomers of the TtHCS dimer. Data are discussed in terms of the overall mechanism of TtHCS.

Charge Recombination Time Distributions in Photosynthetic Reaction Centers Exposed to Alternating Intervals of Photoexcitation and Dark Relaxation

The charge recombination lifetime of photosynthetic reaction centers (RCs) increases significantly upon lengthy illumination, revealing nonequilibrium structural transitions in the protein-cofactor system. This paper analyzes the charge recombination kinetics measured in isolated RCs following a systematic variation of actinic illumination times (pulses) from 0.1 s to hundreds of seconds. The maximum entropy method (MEM) was utilized for optimizing the fitting procedure to retrieve the relaxation spectrum from the experimental recombination kinetics curves. The MEM-assisted analysis reveals that each relaxation curve contains at least three peaks in the relaxation time-distribution domain. Two peaks are always observed, one near 0.1 s and the other near 1 s recombination times. A third peak appears after prolonged photoexcitation with a relaxation time significantly greater than 1 s, and the time of this peak increases further in recombination time as the photoexcitation pulse duration is increased. In addition to the shifts of the time constant distributions, the amplitudes of the distributions in the time domain spectrum demonstrate a variation in the quinone occupancy of the RCs. The results reported here support our previous claim that accumulation of slow conformational changes, triggered by charge separation events in the RCs, controls system dynamics and favors stabilization of more efficient functioning regimes of the RCs.