Stopped-flow Kinetic Studies Research Articles

Nobody's Perfect: Choice of the Buffer and the Rate of Cu2+ Ion-Peptide Interaction.

The choice of correct pH buffer is crucial in chemical studies modeling biological processes involving Cu2+ ions. Popular buffers for physiological pH are known to form Cu(II) complexes, but their impact on kinetics of Cu(II) complexation has not been considered. We performed a stopped-flow kinetic study of Cu2+ ion interactions with four popular buffers (phosphate, Tris, HEPES, and MOPS) and two buffers considered as nonbinding (MES and PIPPS). Next, we studied their effects on the rate of Cu2+ reaction with Gly-Gly-His (GGH), a tripeptide modeling physiological Cu(II) sites, which we studied previously at conditions presumably excluding the buffer interference [Kotuniak, R.; Angew. Chem., Int. Ed. 2020, 59, 11234-11239]. We observed that (i) all tested pH 7.4 buffers formed Cu(II) complexes within the stopped-flow instrument dead time; (ii) Cu(II)-peptide complexes were formed via ternary complexes with the buffers; (iii) nevertheless, Good buffers affected the observed rate of Cu(II)-GGH complex formation only slightly; (iv) Tris was a competitive inhibitor of Cu(II)-GGH complexation; while (v) phosphate was a reaction catalyst. This is particularly important as phosphate is a biological buffer.

Oxygen affinities of DosT and DosS sensor kinases with implications for hypoxia adaptation in Mycobacterium tuberculosis

DosT and DosS are heme-based kinases involved in sensing and signaling O2 tension in the microenvironment of Mycobacterium tuberculosis (Mtb). Under conditions of low O2, they activate >50 dormancy-related genes and play a pivotal role in the induction of dormancy and associated drug resistance during tuberculosis infection. In this work, we reexamine the O2 binding affinities of DosT and DosS to show that their equilibrium dissociation constants are 3.3±1.0 μM and 0.46±0.08 μM respectively, which are six to eight-fold stronger than what has been widely referred to in literature. Furthermore, stopped-flow kinetic studies reveal association and dissociation rate constants of 0.84 μM−1 s−1 and 2.8 s−1, respectively for DosT, and 7.2 μM−1 s−1 and 3.3 s−1, respectively for DosS. Remarkably, these tighter O2 binding constants correlate with distinct stages of hypoxia-induced non-replicating persistence in the Wayne model of Mtb. This knowledge opens doors to deconvoluting the intricate interplay between hypoxia adaptation stages and the signal transduction capabilities of these important heme-based O2 sensors.

Regulating the Heme Active Site by Covalent Modifications: Two Case Studies of Myoglobin.

Using myoglobin (Mb) as a model protein, we herein developed a facial approach to modifying the heme active site. A cavity was first generated in the heme distal site by F46 C mutation, and the thiol group of Cys46 was then used for covalently linked to exogenous ligands, 1H-1,2,4-triazole-3-thiol and 1-(4-hydroxyphenyl)-1H-pyrrole-2,5-dione. The engineered proteins, termed F46C-triazole Mb and F46C-phenol Mb, respectively, were characterized by X-ray crystallography, spectroscopic and stopped-flow kinetic studies. The results showed that both the heme coordination state and the protein function such as H2 O2 activation and peroxidase activity could be efficiently regulated, which suggests that this approach might be generally applied to the design of functional heme proteins.

DNA Binding and Cleavage, Stopped-Flow Kinetic, Mechanistic, and Molecular Docking Studies of Cationic Ruthenium(II) Nitrosyl Complexes Containing "NS4" Core.

This work aimed to evaluate in vitro DNA binding mechanistically of cationic nitrosyl ruthenium complex [RuNOTSP]+ and its ligand (TSPH2) in detail, correlate the findings with cleavage activity, and draw conclusions about the impact of the metal center. Theoretical studies were performed for [RuNOTSP]+, TSPH2, and its anion TSP-2 using DFT/B3LYP theory to calculate optimized energy, binding energy, and chemical reactivity. Since nearly all medications function by attaching to a particular protein or DNA, the in vitro calf thymus DNA (ctDNA) binding studies of [RuNOTSP]+ and TSPH2 with ctDNA were examined mechanistically using a variety of biophysical techniques. Fluorescence experiments showed that both compounds effectively bind to ctDNA through intercalative/electrostatic interactions via the DNA helix's phosphate backbone. The intrinsic binding constants (Kb), (2.4 ± 0.2) × 105 M-1 ([RuNOTSP]+) and (1.9 ± 0.3) × 105 M-1 (TSPH2), as well as the enhancement dynamic constants (KD), (3.3 ± 0.3) × 104 M-1 ([RuNOTSP]+) and (2.6 ± 0.2) × 104 M-1 (TSPH2), reveal that [RuNOTSP]+ has a greater binding propensity for DNA compared to TSPH2. Stopped-flow investigations showed that both [RuNOTSP]+ and TSPH2 bind through two reversible steps: a fast second-order binding, followed by a slow first-order isomerization reaction via a static quenching mechanism. For the first and second steps of [RuNOTSP]+ and TSPH2, the detailed binding parameters were established. The total binding constants for [RuNOTSP]+ (Ka = 43.7 M-1, Kd = 2.3 × 10-2 M-1, ΔG0 = -36.6 kJ mol-1) and TSPH2 (Ka = 15.1 M-1, Kd = 66 × 10-2 M, ΔG0 = -19 kJ mol-1) revealed that the relative reactivity is approximately ([RuNOTSP]+)/(TSPH2) = 3/1. The significantly negative ΔG0 values are consistent with a spontaneous binding reaction to both [RuNOTSP]+ and TSPH2, with the former being very favorable. The findings showed that the Ru(II) center had an effect on the reaction rate but not on the mechanism and that the cationic [RuNOTSP]+ was a more highly effective DNA binder than the ligand TSPH2 via strong electrostatic interaction with the phosphate end of DNA. Because of its higher DNA binding affinity, cationic [RuNOTSP]+ demonstrated higher cleavage efficiency towards the minor groove of pBR322 DNA via the hydrolytic pathway than TSPH2, revealing the synergy effect of TSPH2 in the form of the complex. Furthermore, the mode of interaction of both compounds with ctDNA has also been supported by molecular docking.

An NTP-driven mechanism for the nucleotide addition cycle of Escherichia coli RNA polymerase during transcription.

The elementary steps of transcription as catalyzed by E. coli RNA polymerase during one and two rounds of the nucleotide addition cycle (NAC) were resolved in rapid kinetic studies. Modelling of stopped-flow kinetic data of pyrophosphate release in a coupled enzyme assay during one round of the NAC indicates that the rate of pyrophosphate release is significantly less than that for nucleotide incorporation. Upon modelling of the stopped-flow kinetic data for pyrophosphate release during two rounds of the NAC, it was observed that the presence of the next nucleotide for incorporation increases the rate of release of the first pyrophosphate equivalent; incorrect nucleotides for incorporation had no effect on the rate of pyrophosphate release. Although the next nucleotide for incorporation increases the rate of pyrophosphate release, it is still significantly less than the rate of incorporation of the first nucleotide. The results from the stopped-flow kinetic studies were confirmed by using quench-flow followed by thin-layer chromatography (QF-TLC) with only the first nucleotide for incorporation labeled on the gamma phosphate with 32P to monitor pyrophosphate release. Collectively, the results are consistent with an NTP-driven model for the NAC in which the binding of the next cognate nucleotide for incorporation causes a synergistic conformational change in the enzyme that triggers the more rapid release of pyrophosphate, translocation of the enzyme along the DNA template strand and nucleotide incorporation.

Electronic Structure and Reactivity of Dioxygen-Derived Aliphatic Thiolate-Ligated Fe-Peroxo and Fe(IV) Oxo Compounds.

Herein, we examine the electronic and geometric structural properties of O2-derived aliphatic thiolate-ligated Fe-peroxo, Fe-hydroxo, and Fe(IV) oxo compounds. The latter cleaves strong C-H bonds (96 kcal mol-1) on par with the valine C-H bond cleaved by isopencillin N synthase (IPNS). Stopped-flow kinetics studies indicate that the barrier to O2 binding to [FeII(SMe2N4(tren))]+ (3) is extremely low (Ea = 36(2) kJ mol-1), as theoretically predicted for IPNS. Dioxygen binding to 3 is shown to be reversible, and a superoxo intermediate, [FeIII(SMe2N4(tren))(O2)]+ (6), forms in the first 25 ms of the reaction at -40 °C prior to the rate-determining (Ea = 46(2) kJ mol-1) formation of peroxo-bridged [(SMe2N4(tren))Fe(III)]2(μ-O2)2+ (7). A log(kobs) vs log([Fe]) plot for the formation of 7 is consistent with the second-order dependence on iron, and H2O2 assays are consistent with a 2:1 ratio of Fe/H2O2. Peroxo 7 is shown to convert to ferric-hydroxo [FeIII(SMe2N(tren))(OH)]+ (9, g⊥ = 2.24, g∥ = 1.96), the identity of which was determined via its independent synthesis. Rates of the conversion 7 → 9 are shown to be dependent on the X-H bond strength of the H-atom donor, with a kH/kD = 4 when CD3OD is used in place of CH3OH as a solvent. A crystallographically characterized cis thiolate-ligated high-valent iron oxo, [FeIV(O)(SMe2N4(tren))]+ (11), is shown to form en route to hydroxo 9. Electronic structure calculations were shown to be consistent with 11 being an S = 1 Fe(IV)═O with an unusually high νFe-O stretching frequency at 918 cm-1 in line with the extremely short Fe-O bond (1.603(7) Å).

Structurally Precise Two-Transition-Metal Water Oxidation Catalysts: Quantifying Adjacent 3d Metals by Synchrotron X-Radiation Anomalous Dispersion Scattering.

Mixed 3d metal oxides are some of the most promising water oxidation catalysts (WOCs), but it is very difficult to know the locations and percent occupancies of different 3d metals in these heterogeneous catalysts. Without such information, it is hard to quantify catalysis, stability, and other properties of the WOC as a function of the catalyst active site structure. This study combines the site selective synthesis of a homogeneous WOC with two adjacent 3d metals, [Co2Ni2(PW9O34)2]10- (Co2Ni2P2) as a tractable molecular model for CoNi oxide, with the use of multiwavelength synchrotron X-radiation anomalous dispersion scattering (synchrotron XRAS) that quantifies both the location and percent occupancy of Co (∼97% outer-central-belt positions only) and Ni (∼97% inner-central-belt positions only) in Co2Ni2P2. This mixed-3d-metal complex catalyzes water oxidation an order of magnitude faster than its isostructural analogue, [Co4(PW9O34)2]10- (Co4P2). Four independent and complementary lines of evidence confirm that Co2Ni2P2 and Co4P2 are the principal WOCs and that Co2+(aq) is not. Density functional theory (DFT) studies revealed that Co4P2 and Co2Ni2P2 have similar frontier orbitals, while stopped-flow kinetic studies and DFT calculations indicate that water oxidation by both complexes follows analogous multistep mechanisms, including likely Co-OOH formation, with the energetics of most steps being lower for Co2Ni2P2 than for Co4P2. Synchrotron XRAS should be generally applicable to active-site-structure-reactivity studies of multi-metal heterogeneous and homogeneous catalysts.

Structural and Functional Differences between Homologous Bacterial Ribonucleases.

Small cationic guanyl-preferring ribonucleases (RNases) produced by the Bacillus species share a similar protein tertiary structure with a high degree of amino acid sequence conservation. However, they form dimers that differ in conformation and stability. Here, we have addressed the issues (1) whether the homologous RNases also have distinctions in catalytic activity towards different RNA substrates and interactions with the inhibitor protein barstar, and (2) whether these differences correlate with structural features of the proteins. Circular dichroism and dynamic light scattering assays revealed distinctions in the structures of homologous RNases. The activity levels of the RNases towards natural RNA substrates, as measured spectrometrically by acid-soluble hydrolysis products, were similar and decreased in the row high-polymeric RNA >>> transport RNA > double-stranded RNA. However, stopped flow kinetic studies on model RNA substrates containing the guanosine residue in a hairpin stem or a loop showed that the cleavage rates of these enzymes were different. Moreover, homologous RNases were inhibited by the barstar with diverse efficiency. Therefore, minor changes in structure elements of homologous proteins have a potential to significantly effect molecule stability and functional activities, such as catalysis or ligand binding.

Phosphorylation of eukaryotic initiation factor eIFiso4E enhances the binding rates to VPg of turnip mosaic virus.

Binding of phosphorylated eIFiso4E with viral genome-linked protein (VPg) of turnip mosaic virus was examined by stopped-flow, fluorescence, circular dichroism (CD) spectroscopy, and molecular docking analysis. Phosphorylation of eIFiso4E increased (4-fold) the binding rates as compared to unphosphorylated eIFiso4E with VPg. Stopped-flow kinetic studies of phosphorylated eIFiso4E with VPg showed a concentration-independent conformational change. The dissociation rate was about 3-fold slower for eIFiso4E∙VPg complex upon phosphorylation. Phosphorylation enhanced the association rates and lowered the dissociation rates for the eIFiso4E∙VPg binding, with having higher preferential binding to eIFiso4Ep. Binding rates for the interaction of eIFiso4Ep with VPg increased (6-fold) with an increase in temperature, 278 K to 298 K. The activation energies for binding of eIFiso4Ep and eIFiso4E with VPg were 37.2 ± 2.8 and 52.6 ± 3.6 kJ/mol, respectively. Phosphorylation decreased the activation energy for the binding of eIFiso4E to VPg. The reduced energy barrier suggests more stable platform for eIFiso4Ep∙VPg initiation complex formation, which was further supported by molecular docking analysis. Moreover, far-UV CD studies revealed that VPg formed complex with eIFiso4Ep with substantial change in the secondary structure. These results suggested that phosphorylation, not only reduced the energy barrier and dissociation rate but also enhanced binding rate, and an overall conformational change, which provides a more stable platform for efficient viral translation.

Human POT1 unfolds G-quadruplexes by conformational selection

The reaction mechanism by which the shelterin protein POT1 (Protection of Telomeres 1) unfolds human telomeric G-quadruplex structures is not fully understood. We report here kinetic, thermodynamic, hydrodynamic and computational studies that show that a conformational selection mechanism, in which POT1 binding is coupled to an obligatory unfolding reaction, is the most plausible mechanism. Stopped-flow kinetic and spectroscopic titration studies, along with isothermal calorimetry, were used to show that binding of the single-strand oligonucleotide d[TTAGGGTTAG] to POT1 is both fast (80 ms) and strong (−10.1 ± 0.3 kcal mol−1). In sharp contrast, kinetic studies showed the binding of POT1 to an initially folded 24 nt G-quadruplex structure is four orders of magnitude slower. Fluorescence, circular dichroism and analytical ultracentrifugation studies showed that POT1 binding is coupled to quadruplex unfolding, with a final complex with a stoichiometry of 2 POT1 per 24 nt DNA. The binding isotherm for the POT1-quadruplex interaction was sigmoidal, indicative of a complex reaction. A conformational selection model that includes equilibrium constants for both G-quadruplex unfolding and POT1 binding to the resultant single-strand provided an excellent quantitative fit to the experimental binding data. POT1 unfolded and bound to any conformational form of human telomeric G-quadruplex (antiparallel, hybrid, parallel monomers or a 48 nt sequence with two contiguous quadruplexes), but did not avidly interact with duplex DNA or with other G-quadruplex structures. Finally, molecular dynamics simulations provided a detailed structural model of a 2:1 POT1:DNA complex that is fully consistent with experimental biophysical results.

Kinetics of competitive Cd2+ binding pathways: the realistic structure of intrinsically disordered, partially metallated metallothioneins.

The 20-cysteine mammalian metallothioneins are considered to be central to the homeostatic control of the essential metals Zn(ii) and Cu(i) and, as part of their metal-loaded status, play a role in reversing oxidative stress. Native apo-MT does not adopt a well-known structural motif, being described as a random-coil or intrinsically-disordered. Conclusions reached from a combination of ESI-mass spectral charge states, As(iii) metallation of apo-MT at low pH, from molecular dynamic calculations and from metallation of the α-domain fragment, suggest that in fact the native apo-MT adopts a structure that is highly efficient towards metallation at physiological pH. The results in this paper show that the initial (M < 5) Cd(ii) metallation at physiological pH takes place to form structures based on isolated Cd(SCYS)4 units, beads. At pH 5, cysteine bridged Cd4(SCYS)11 clusters form. ESI-mass spectral profile of cysteine modification of apo-MT at physiological pH shows that it is folded, whereas in the presence of 3 M guandinium hydrochloride the apo-MT is unfolded. Stopped flow kinetic studies of the Cd(ii) metallation shows that the reaction is much slower for the unfolded vs. the folded apo-MT for formation of either beads or clusters. Metallation is also much slower for the formation of clusters than the formation of beads. These results are first to quantify the presence of structure in native apo-MT in terms of the critical metallation properties. The implications of this study suggest that oxidation of apo-MT due to ageing or other agent will negatively impact the metallation process for essential metals.

Colloidal FeIII , MnIII , CoIII , and CuII Hydroxides Stabilized by Starch as Catalysts of Water Oxidation Reaction with One Electron Oxidant Ru(bpy)33.

Colloidal catalysts for oxidation of water to dioxygen, which are stable on storage and under the reaction conditions, are synthesized based on CoIII , MnIII , FeIII and CuII hydroxides. Stabilization of the colloids with dextrated starch allows the process of hydroxide ageing to be stopped at the stage of the formation of primary nuclei (ca. 2-3 nm from transmission electron microscopy data). Molecular mechanics and dynamic light scattering studies indicate a core-shell type structure of the catalysts, where the hydroxide core is stabilized by the molecular starch network (ca. 5-7 nm). The colloidal catalysts are highly efficient in oxidizing water with one electron oxidant Ru(bpy)33+ at pH 7 to 10. The influence of pH, catalyst concentration, and buffer nature on the oxygen yield is studied. The maximal yields are 72, 53, and 78 % over Fe-, Mn- and Co-containing catalysts, respectively, and turnover numbers are 7.8; 54 and 360, respectively. The Cu-containing catalyst is poorly effective to the water oxidation (the maximal yield is 28 % O2 ). The synthesized catalysts are of interest for stopped-flow kinetic studies of the mechanism of the water oxidation and as precursors for anchoring nanosized hydroxides onto various supports in order to develop biomimetic systems for artificial photosynthesis.

Superoxide dismutase activity enabled by a redox-active ligand rather than metal.

Reactive oxygen species are integral to many physiological processes. Although their roles are still being elucidated, they seem to be linked to a variety of disorders and may represent promising drug targets. Mimics of superoxide dismutases, which catalyse the decomposition of O2•- to H2O2 and O2, have traditionally used redox-active metals, which are toxic outside of a tightly coordinating ligand. Purely organic antioxidants have also been investigated but generally require stoichiometric, rather than catalytic, doses. Here, we show that a complex of the redox-inactive metal zinc(II) with a hexadentate ligand containing a redox-active quinol can catalytically degrade superoxide, as demonstrated by both reactivity assays and stopped-flow kinetics studies of direct reactions with O2•- and the zinc(II) complex. The observed superoxide dismutase catalysis has an important advantage over previously reported work in that it is hastened, rather than impeded, by the presence of phosphate, the concentration of which is high under physiological conditions.

Kinetics and mechanism for reduction of Pt(IV) anticancer model compounds by Se-methyl L-selenocysteine. Comparison with L-selenomethionine

Se-methyl L-selenocysteine (MeSeCys) is one of the major organic selenium compounds acquired from the diet by human beings. It has been shown to have anticancer activity and cancer prevention functions. However, its antioxidant activity, largely related to its biological function, has not been well characterized so far. We here report a stopped-flow kinetic study of the reduction of the Pt(IV) anticancer model compounds trans-[PtX2(CN)4]2− (X = Cl; Br) by MeSeCys in a wide pH range. Overall second-order kinetics is established for the redox reactions, and spectrophotometric titrations indicate a 1:1 reaction stoichiometry. The MeSeCys is oxidized to its selenoxide form, as identified by high-resolution mass spectra. The proposed reaction mechanism involves parallel attack on one of the trans-coordinated halides of the Pt(IV) complexes by the selenium atom of the various MeSeCys protolytic species. Rate constants for the rate determining steps as well as the pKa values of the various protolytic species of MeSeCys have been determined at 25.0 °C and 1.0 M ionic strength. A bridged two-electron transfer mechanism for the rate-determining steps is supported by rapid-scan spectra, activation parameters, and by the much larger reaction rate of [PtBr2(CN)4]2− compared to [PtCl2(CN)4]2−. The experiments indicate that the reduction of [PtX2(CN)4]2− by MeSeCys proceeds via a similar reaction mechanism as L-selenomethionine (SeMet) studied previously. However, there is a large reactivity difference between these two selenium compounds, as a matter of fact the largest one observed so far when compared to other redox systems. It differs between the various protolytic species of MeSeCys and SeMet. The different reactivity of MeSeCys and SeMet in the reduction of various biologically relevant oxidants might account for their disparate efficacies as anticancer agents.

Stereochemistry and amyloid inhibition: Asymmetric triplex metallohelices enantioselectively bind to Aβ peptide.

Stereochemistry is vital for pharmaceutical development and can determine drug efficacy. Herein, 10 pairs of asymmetric triplex metallohelix enantiomers as a library were used to screen inhibitors of amyloid β (Aβ) aggregation via a fluorescent cell-based high-throughput method. Intriguingly, Λ enantiomers show a stronger inhibition effect than Δ enantiomers. In addition, the metallohelices with aromatic substituents are more effective than those without, revealing that these groups play a key role in the Aβ interaction. Fluorescence stopped-flow kinetic studies indicate that binding of the Λ enantiomer to Aβ is much faster than that of the Δ enantiomer. Furthermore, studies in enzyme digestion, isothermal titration calorimetry, nuclear magnetic resonance, and computational docking demonstrate that the enantiomers bind to the central hydrophobic α-helical region of Aβ13-23, although with different modes for the Λ and Δ enantiomers. Finally, an in vivo study showed that these metallohelices extend the life span of the Caenorhabditis elegans CL2006 strain by attenuating Aβ-induced toxicity. Our work will shed light on the design and screening of a metal complex as an amyloid inhibitor against Alzheimer's disease.

The G41S Variant of Human Cytochrome C Enhances Apoptosis via Increased Dynamics

In addition to its well-known role as a component of the electron transport chain, mitochondrial cytochrome c can also act as a peroxidase in the early stages of the intrinsic apoptosis pathway. Ferricytochrome c contains a hexacoordinated heme iron, for which H18 and M80 are the axial ligands. Residual peroxidase activity under native conditions arises from a minor populated pentacoordinated form, in which M80 is not coordinated to the heme iron. At the onset of apoptosis, binding to cardiolipin increases the proportion of the pentacoordinated form, increasing peroxidase activity which eventually leads to apoptosis. Mutations in the human gene for cytochrome c, which result in enhanced mitochondrial apoptotic activity, cause thrombocytopenia 4, an inherited autosomal dominant thrombocytopenia, characterised by a deficiency in the number of platelets in the blood and leading to abnormal bleeding. The first such mutation to be reported was G41S. Here we use stopped-flow kinetic studies of azide binding to human ferricytochrome c, backbone amide H/D exchange and 15N-relaxation dynamics measured by NMR spectroscopy to compare the wild type and G41S forms of human cytochrome c. We show that alternative conformations are kinetically and thermodynamically more readily accessible for the G41S variant than for the wild-type protein. Residue 41 is located in the 40-57 Ω-loop, and the increased loop dynamics in the G41S variant promote the dissociation from the heme iron of the M80 ligand, revealing a direct conformational link between the loop and the axial ligand to the heme iron. Increased dissociation of M80 increases the population of a peroxidase active state, which is a key non-native conformational state in apoptosis.

Stopped-Flow Kinetic Study of Reduction of Ferric Maltol Complex by Ascorbate

Stopped-flow kinetic investigation of reduction of Fe(III)-maltol complex is reported. The rates are dependent on pH in a complex way. On one hand at low pH there is a predominance of Fe(III)(maltol)2 which is easier to reduce compared to Fe(III) (maltol)3 which is more resistant to reduction. On the other hand ascorbate is a stronger reducing agent at higher pH. The rates are also found to be inversely dependent on the concentration of free ligand. These observations are explained by the following rate law:Rate = ((k0 +k1[H+])k2 [Asc-]/ (k-1[HMal] + k2[Asc-])) + k3 [Asc-] ) [FeIII(Mal)3] Here k1 is the rate constant for acid hydrolysis of the Fe(maltol)3 complex to Fe(maltol)2 complex and is directly controlled by H+, k0 is the rate constant for hydrolysis of the Fe(maltol)3 complex to Fe(maltol)2 complex and is an intrinsic process, k-1 is the rate constant of reformation of the tris complex by reaction of the bis complex and the free ligand, k2 is the rate constant for reduction of the bis complex by ascorbate and k3 is the rate constant for the reduction of the tris complex by ascorbate.

Increased dynamics in the 40-57 Ω-loop of the G41S variant of human cytochrome c promote its pro-apoptotic conformation.

Thrombocytopenia 4 is an inherited autosomal dominant thrombocytopenia, which occurs due to mutations in the human gene for cytochrome c that results in enhanced mitochondrial apoptotic activity. The Gly41Ser mutation was the first to be reported. Here we report stopped-flow kinetic studies of azide binding to human ferricytochrome c and its Gly41Ser variant, together with backbone amide H/D exchange and 15N-relaxation dynamics using NMR spectroscopy, to show that alternative conformations are kinetically and thermodynamically more readily accessible for the Gly41Ser variant than for the wild-type protein. Our work reveals a direct conformational link between the 40–57 Ω-loop in which residue 41 resides and the dynamical properties of the axial ligand to the heme iron, Met80, such that the replacement of glycine by serine promotes the dissociation of the Met80 ligand, thereby increasing the population of a peroxidase active state, which is a key non-native conformational state in apoptosis.

Construction of Functional Monomeric Type 2 Isopentenyl Diphosphate:Dimethylallyl Diphosphate Isomerase.

Type 2 isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IDI-2) catalyzes the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) in the isoprenoid biosynthetic pathway. The enzyme from Streptomyces pneumoniae (spIDI-2) is a homotetramer in solution with behavior, including a substantial increase in the rate of FMN reduction by NADPH in the presence of IPP, suggesting that substrate binding at one subunit alters the kinetic and binding properties of another. We now report the construction of catalytically active monomeric spIDI-2. The monomeric enzyme contains a single-point mutation (N37A) and a six-residue C-terminal deletion that preserves the secondary structure of the subunits in the wild-type (wt) homotetramer. UV-vis spectra of the enzyme-bound flavin mononucleotide (FMN) cofactor in FMNox, FMNred, and FMNred·IPP/DMAPP states are the same for monomeric and wt homotetrameric spIDI-2. The mutations in monomeric IDI-2 lower the melting temperature of the protein by 20 °C and reduce the binding affinities of FMN and IDI by 40-fold but have a minimal effect on kcat. Stopped-flow kinetic studies of monomeric spIDI-2 showed that the rate of reduction of FMN by NADH (k = 1.64 × 10(-3) s(-1)) is substantially faster when IPP is added to the monomeric enzyme (k = 0.57 s(-1)), similar to behavior seen for wt-spIDI-2. Our results indicate that cooperative interactions among subunits in the wt homotetramer are not responsible for the increased rate of reduction of spIDI-2·FMN by NADH, and two possible scenarios for the enhancement are suggested.

Peroxo and Superoxo Moieties Bound to Copper Ion: Electron-Transfer Equilibrium with a Small Reorganization Energy.

Oxygenation of [Cu2(UN-O(-))(DMF)](2+) (1), a structurally characterized dicopper Robin-Day class I mixed-valent Cu(II)Cu(I) complex, with UN-O(-) as a binucleating ligand and where dimethylformamide (DMF) binds to the Cu(II) ion, leads to a superoxo-dicopper(II) species [Cu(II)2(UN-O(-))(O2(•-))](2+) (2). The formation kinetics provide that kon = 9 × 10(-2) M(-1) s(-1) (-80 °C), ΔH(‡) = 31.1 kJ mol(-1) and ΔS(‡) = -99.4 J K(-1) mol(-1) (from -60 to -90 °C data). Complex 2 can be reversibly reduced to the peroxide species [Cu(II)2(UN-O(-))(O2(2-))](+) (3), using varying outer-sphere ferrocene or ferrocenium redox reagents. A Nernstian analysis could be performed by utilizing a monodiphenylamine substituted ferrocenium salt to oxidize 3, leading to an equilibrium mixture with Ket = 5.3 (-80 °C); a standard reduction potential for the superoxo-peroxo pair is calculated to be E° = +130 mV vs SCE. A literature survey shows that this value falls into the range of biologically relevant redox reagents, e.g., cytochrome c and an organic solvent solubilized ascorbate anion. Using mixed-isotope resonance Raman (rRaman) spectroscopic characterization, accompanied by DFT calculations, it is shown that the superoxo complex consists of a mixture of μ-1,2- (2(1,2)) and μ-1,1- (2(1,1)) isomers, which are in rapid equilibrium. The electron transfer process involves only the μ-1,2-superoxo complex [Cu(II)2(UN-O(-))(μ-1,2-O2(•-))](2+) (2(1,2)) and μ-1,2-peroxo structures [Cu(II)2(UN-O(-))(O2(2-))](+) (3) having a small bond reorganization energy of 0.4 eV (λin). A stopped-flow kinetic study results reveal an outer-sphere electron transfer process with a total reorganization energy (λ) of 1.1 eV between 2(1,2) and 3 calculated in the context of Marcus theory.