Covalent modification of the non-catalytic sites of the H+-ATPase from chloroplasts with 2-azido-[α-32P]ATP and its effect on ATP synthesis and ATP hydrolysis

Incubation of the isolated H⁺-ATPase from chloroplasts, CF₀F₁, with 2-azido-[α-³²P]ATP leads to the binding of this nucleotide to different sites. These sites were identified after removal of free nucleotides, UV-irradiation and trypsin treatment by separation of the tryptic peptides by ion exchange chromatography. The nitreno-AMP, nitreno-ADP and nitreno-ATP peptides were further separated on a reversed phase column, the main fractions were subjected to amino acid sequence analysis and the derivatized tyrosines were used to distinguish between catalytic (β-Tyr362) and non-catalytic (β-Tyr385) sites. Several incubation procedures were developed which allow a selective occupation of each of the three non-catalytic sites. The non-catalytic site with the highest dissociation constant (site 6) becomes half maximally filled at 50 μM 2-azido-[α-³²P]ATP, that with the intermediate dissociation constant (site 5) at 2 μM. The ATP at the site with the lowest dissociation constant had to be hydrolyzed first to ADP before a replacement by 2-azido-[α-³²P]ATP was possible. CF₀F₁ with non-covalently bound 2-azido-[α-³²P]ATP and after covalent derivatization was reconstituted into liposomes and the rates of ATP synthesis as well as ATP hydrolysis were measured after energization of the proteoliposomes by ΔpH/Δϕ. Non-covalent binding of 2-azido-ATP to any of the three non-catalytic sites does not influence ATP synthesis and ATP hydrolysis, whereas covalent derivatization of any of the three sites inhibits both, the degree being proportional to the degree of derivatization. Extrapolation to complete inhibition indicates that derivatization of one site (either 4 or 5 or 6) is sufficient to block completely multi-site catalysis. The rates of ATP synthesis and ATP hydrolysis were measured as a function of the ADP and ATP concentration from uni-site to multi-site conditions with covalently derivatized and non-derivatized CF₀F₁. Uni-site ATP synthesis and ATP hydrolysis were not inhibited by covalent derivatization of any of the non-catalytic sites, whereas multi-site catalysis is inhibited. These results indicate that multi-site catalysis requires some flexibility between β- and α-subunits which is abolished by covalent derivatization of β-Tyr385 with a 2-nitreno-adenine nucleotide. Conformational changes connected with energy transduction between the F₀-part and the F₁-part are either not required for uni-site ATP synthesis or they are not impaired by the derivatization of any of the three β-Tyr385.     

ATP binding to the ϵ subunit of thermophilic ATP synthase is crucial for efficient coupling of ATPase and H+ pump activities

ATP binding to the ? subunit of F1-ATPase, a soluble subcomplex of TFoF1 (FoF1-ATPase synthase from the thermophilic Bacillus strain PS3), affects the regulation of F1-ATPase activity by stabilizing the compact, ATPase-active, form of the ? subunit [Kato, S., Yoshida, M. and Kato-Yamada, Y. (2007) J. Biol. Chem. 282, 37618-37623]. In the present study, we report how ATP binding to the ? subunit affects ATPase and H+ pumping activities in the holoenzyme TFoF1. Wild-type TFoF1 showed significant H+ pumping activity when ATP was used as the substrate. However, GTP, which bound poorly to the ? subunit, did not support efficient H+ pumping. Addition of small amounts of ATP to the GTP substrate restored coupling between GTPase and H+ pumping activities. Similar uncoupling was observed when TFoF1 contained an ATP-binding-deficient ? subunit, even with ATP as a substrate. Further analysis suggested that the compact conformation of the ? subunit induced by ATP binding was required to couple ATPase and H+ pumping activities in TFoF1 unless the ? subunit was in its extended-state conformation. The present study reveals a novel role of the ? subunit as an ATP-sensitive regulator of the coupling of ATPase and H+ pumping activities of TFoF1.     

Conformational analysis and design of cross-strand disulfides in antiparallel β-sheets

Cross‐strand disulfides bridge two cysteines in a registered pair of antiparallel β‐strands. A nonredundant data set comprising 5025 polypeptides containing 2311 disulfides was used to study cross‐strand disulfides. Seventy‐six cross‐strand disulfides were found of which 75 and 1 occurred at non‐hydrogen‐bonded (NHB) and hydrogen‐bonded (HB) registered pairs, respectively. Conformational analysis and modeling studies demonstrated that disulfide formation at HB pairs necessarily requires an extremely rare and positive χ¹ value for at least one of the cysteine residues. Disulfides at HB positions also have more unfavorable steric repulsion with the main chain. Thirteen pairs of disulfides were introduced in NHB and HB pairs in four model proteins: leucine binding protein (LBP), leucine, isoleucine, valine binding protein (LIVBP), maltose binding protein (MBP), and Top7. All mutants LIVBP T247C V331C showed disulfide formation either on purification, or on treatment with oxidants. Protein stability in both oxidized and reduced states of all mutants was measured. Relative to wild type, LBP and MBP mutants were destabilized with respect to chemical denaturation, although the sole exposed NHB LBP mutant showed an increase of 3.1°C in T _m . All Top7 mutants were characterized for stability through guanidinium thiocyanate chemical denaturation. Both exposed and two of the three buried NHB mutants were appreciably stabilized. All four HB Top7 mutants were destabilized (ΔΔG ⁰ = ?3.3 to ?6.7 kcal/mol). The data demonstrate that introduction of cross‐strand disulfides at exposed NHB pairs is a robust method of improving protein stability. All four exposed Top7 disulfide mutants showed mild redox activity. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Increase in synthesis and stability of σ 32 on treatment with inhibitors of DNA gyrase in Escherichia coli

We report here that in Escherichia coli, the anti-bacterial agent nalidixic acid induces transient stabilization and increased synthesis of σ³², accompanied by the induction of heat shock proteins (Dnak and GroEL proteins). The induction of heat shock proteins, increased synthesis of σ³², and stabilization of σ³² observed on treatment of wild-type cells with nalidixic acid were not observed in a nalA26 mutant, a strain that is resistant to nalidixic acid as the result of a mutation in the gyrA gene. Not only oxolinic acid, but also novobiocin, whose targets are the A and B subunits of DNA gyrase, respectively, also induced stabilization and increased synthesis of σ³². Thus, inhibition of the activity of DNA gyrase may cause stabilization and increased synthesis of σ³², resulting in turn in induction of heat shock proteins.     

Chemoenzymatic synthesis of 3′-phosphoadenosine-5′-phosphosulfate coupling with an ATP regeneration system

Applied Microbiology and Biotechnology - 3′-Phosphoadenosine-5′-phosphosulfate (PAPS) is the obligate cosubstrate and source of the sulfonate group in the chemoenzymatic synthesis of...     

Reasons causing a lag period in the oxidative phosphorylation process. Isn't ATP an internal uncoupler of ATP synthetase?]

The kinetics of oxidative phosphorylation catalyzed by bovine heart submitochondrial particles was studied in a range of MgATP and MgADP concentrations from 0.3 to 10 mM. It is shown that, at a low uncoupler concentration (0.9 microM of tetrachlorotrifluoromethylbenzimidazole, the lag period of the reaction increases from 12 s to 2-3 min, and KM for Pi increases severalfold; the value of Vmax remains practically unchanged. Increasing the [MgATP]/[MgADP] concentration ratio, with their total concentration being unchanged, leads to similar changes in the kinetics of oxidative phosphorylation. The value of delta pH generated on the membrane of AS particles at delta microH+ = 60 delta pH was measured using 9-aminoacridine. It was found that the electrochemical potential of H+ ions shows the same thermodynamic shift in the reaction of energy-dependent Pi -ATP exchange throughout the [MgATP]/[MgADP] concentration range studied, from 0.1 to 10: the synthesis on the ATP molecule is provided by the transmembrane transfer of two H+ ions. It was shown that the binding of ATP and/or ADP in the allosteric site, whose saturation is necessary for the functioning of ATP synthase, occurs with equal constants, 1-2 mM. It is concluded that the lag period in the synthesis of ATP indicates the monomolecular transition ATP hydrolase-->ATP sysnthase, which comes about by the action of transmembrane potential. The binding of MgADP or MgATP renders the enzyme structure "more coupled" or "less coupled", respectively. Structural distinctions manifest themselves in a kinetically different behavior of mitochondrial ATP synthase at [MgATP] > [MgADP] and [MgATP] < [MgADP] and do not suggest futile leakage of H+ through the membrane.     

The carboxyl-terminal helical domain of the ATP synthase γ subunit is involved in ε subunit conformation and energy coupling

The γ subunit located at the center of ATP synthase (F_OF₁) plays critical roles in catalysis. Escherichia coli mutant with Pro substitution of the γ subunit residue γLeu218, which are located the rotor shaft near the c subunit ring, decreased NADH-driven ATP synthesis activity and ATP hydrolysis-dependent H⁺ transport of membranes to ~60% and ~40% of the wild type, respectively, without affecting F_OF₁ assembly. Consistently, the mutant was defective in growth by oxidative phosphorylation, indicating that energy coupling is impaired by the mutation. The ε subunit conformations in the γLeu218Pro mutant enzyme were investigated by cross-linking between cysteine residues introduced into both the ε subunit (εCys118 and εCys134, in the second helix and the hook segment, respectively) and the γ subunit (γCys99 and γCys260, located in the globular domain and the carboxyl-terminal helix, respectively). In the presence of ADP, the two γ260 and ε134 cysteine residues formed a disulfide bond in both the γLeu218Pro mutant and the wild type, indicating that the hook segment of ε subunit penetrates into the α₃β₃-ring along with the γ subunits in both enzymes. However, γ260/ε134 cross-linking in the γLeu218Pro mutant decreased significantly in the presence of ATP, whereas this effect was small in the wild type. These results suggested that the γ subunit carboxyl-terminal helix containing γLeu218 is involved in the conformation of the ε subunit hook region during ATP hydrolysis and, therefore, is required for energy coupling in F_OF₁.     

How does protein architecture facilitate the transduction of ATP chemical-bond energy into mechanical work? The cases of nitrogenase and ATP binding-cassette proteins

Transduction of adenosine triphosphate (ATP) chemical-bond energy into work to drive large-scale conformational changes is common in proteins. Two specific examples of ATP-utilizing proteins are the nitrogenase iron protein and the ATP binding-cassette transporter protein, BtuCD. Nitrogenase catalyzes biological nitrogen fixation whereas BtuCD transports vitamin B(12) across membranes. Both proteins drive their reactions with ATP. To interpret how the mechanical force generated by ATP binding and hydrolysis is propagated in these proteins, a coarse-grained elastic network model is employed. The analysis shows that subunits of the proteins move against each other in a concerted manner. The lowest-frequency modes of the nitrogenase iron protein and of the ATP binding-cassette transporter BtuCD protein are found to link the functionally critical domains, and these modes are suggested to be responsible for (at least the initial stages) large-scale ATP-coupled conformational changes.     

Standard magnetic resonance-based measurements of the Pi→ATP rate do not index the rate of oxidative phosphorylation in cardiac and skeletal muscles

Magnetic resonance spectroscopy-based magnetization transfer techniques (MT) are commonly used to assess the rate of oxidative (i.e., mitochondrial) ATP synthesis in intact tissues. Physiologically appropriate interpretation of MT rate data depends on accurate appraisal of the biochemical events that contribute to a specific MT rate measurement. The relative contributions of the specific enzymatic reactions that can contribute to a MT P(i)→ATP rate measurement are tissue dependent; nonrecognition of this fact can bias the interpretation of MT P(i)→ATP rate data. The complexities of MT-based measurements of mitochondrial ATP synthesis rates made in striated muscle and other tissues are reviewed, following which, the adverse impacts of erroneous P(i)→ATP rate data analyses on the physiological inferences presented in selected published studies of cardiac and skeletal muscle are considered.     

Irreversibility of the interaction of human growth hormone with its receptor and analysis of irreversible reactions in radioreceptor assays—Theoretical considerations

Kinetic studies of the binding and dissociation of [¹²⁵I]-human growth hormone to rabbit liver and mammary gland membrane receptors have showed that the binding of [¹²⁵I]-human growth hormone was largely irreversible to liver membrane receptors and completely to the solubilised mammary gland receptor. As Scatchard analysis assumes complete reversibility of the hormone-receptor interaction the validity of estimates of affinity and capacity of receptors derived by this analysis may be questionable. Theoretical considerations show that in unimolecular irreversible interactions of hormone and receptor, a nonlinear (concave) or a linear Scatchard plot can be obtained. In linear Scatchard plots the capacity of the receptor obtained by extrapolation represents an overestimation of true capacity. This overestimation correlates with the value of the intercept in the Scatchard plot.     

Serum prolidase activity and oxidative–antioxidative status in patients with developmental dysplasia of the hip and its relationship with radiographic severity

Background: We aimed to investigate serum prolidase activity and to investigate its association with oxidative–antioxidative status in patients with developmental dysplasia of the hip (DDH).

Methods: Oxidative status parameters, including lipid hydroperoxide (LOOH), total oxidant status (TOS), and the oxidative stress index (OSI), and antioxidative status parameters, free sulfhydryl groups (Total –SH), and total antioxidative capacity (TAC), as well as serum prolidase activity were assessed in patients with DDH (n?=?93), and in healthy controls (n?=?82). The severity of dysplasia was evaluated according to the Tonnis grading system.

Results: Serum prolidase activity and the oxidant parameters (LOOH, TOS, and OSI) were significantly higher and the antioxidant parameters (Total –SH and TAC) were significantly lower in patients with DDH compared to the controls (P?P?P?Conclusion: Increased levels of serum prolidase activity, LOOH, TOS, and OSI, and decreased levels of total –SH and TAC, may be associated with DDH, and these parameters may be useful adjunctive tools to assess the severity of DDH.     

Salmonella typhimurium with γ-radiation induced H2AX phosphorylation and apoptosis in melanoma

To investigate the combinatorial effects using Salmonella and γ-radiation, the Salmonella typhimurium infection in combination with γ-radiation was investigated on melanoma. We showed that ROS expression and H₂AX phosphorylation increased during stress by γ-radiation irrespective of Salmonella infection, inducing apoptosis by caspase-3 and bcl2 in tumor cells. In addition, tumor growth was suppressed by this combinatory therapy suggesting candidates for radiation therapy against melanoma.     

Conformational and Structural Analysis of Bovine β Lactoglobulin-A Upon Interaction with Cr+3

Thermodynamic studies have been made on the effect of Cr⁺³ on the conformation and structure of bovine β lactoglobulin-A, (Blg-A) in 50 mM sodium chloride solution at 27°C using isothermal titration calorimetry (ITC), circular dichroism (CD) and fluorescence spectroscopy. There is a set of six identical and independent binding sites for Cr⁺³ by a dissociation binding constant of 124 μM and the molar enthalpy of binding −17.8 kJ/mol. Circular dichroism studies do not show any significant change in the secondary structure of the protein after the binding of chromium ion on the Blg-A. Fluorescence spectroscopy studies do not show any considerable change in the tertiary structure of Blg-A due to the increasing of Cr⁺³ in low concentration. However, occupation of fourth and fifth binding sites for chromium ions induce partially unfolding in the tertiary structure of the protein resulted from solvent – exposed hydrophobic patches on BLG-A.     

Conformational energy analysis of the substitution of Val for Gly 233 in a functional region of platelet GPIbα in platelet-type von Willebrand disease

Platelet-type von Willebrand disease (PT-vWD) is an autosomal dominant bleeding disorder in which patient platelets exhibit an abnormally increased binding of circulating von Willebrand factor (vWF). We have recently shown that this abnormality is associated with a point mutation resulting in substitution of Val for Gly 233 in platelet membrane glycoprotein Ibα (GPIbga), a major component of the platelet (GPIb/IX receptor for vWF. To investigate the effect of this substitution on the three-dimensional structure of this region of the protein, we have generated the allowed (low energy) conformations of the region of the GPIα protein containing residues 228–238 (with 5 residues on either side of the critical residue 233) with Gly 233 (wild type) and Val 233 (PT-vWD) using the computer program ECEPP (Empirical Conformational Energies of Peptides Program). The wild-type sequence is Tyr-Val-Trp-Lys-Gln-Gly-Val-Asp-Val-Lys-Ala. We find that the Gly 233-containing peptide can exist in two low energy conformers. The lowest energy conformer is a structure containing a β-turn at Gln 232-Gly 233 while the alternative conformation is an amphipathic helical structure. Only the amphipathic helical structure is allowed for the Val 233-containing peptide which contains a hydrophobic ‘face’ consisting of Val 229, Val 233 and Val 236 and another hydrophilic surface composed of such residues as Lys 231 and Asp 235. No such surfaces exist for the lowest energy bend conformer for the Gly 233-containing peptide, but do exist in the higher energy helical structure. The amphiphatic surfaces in the 228–238 region of the Val 233-containing GPIbα protein may associate strongly with complementary surfaces during vWF binding to the GPIb/IX receptor complex and may help explain heightened association of vWF with this receptor in PT-vWD.     

The coupling of electron flow to ATP synthesis in pea chloroplasts stored in the presence of glycerol at −70°C

A method is described for preserving coupling activity in isolated chloroplasts stored in the frozen state for periods up to 16 weeks. Pea chloroplasts stored in a high osmolarity medium supplemented with 50% (v/v) glycerol and 10 mg/ml bovine serum albumin show high rates of photophosphorylation, good coupling efficiencies, photosynthetic control, and modulation of the high energy state by adenine nucleotides.     

Agronomic biofortification of Brassica with selenium—enrichment of SeMet and its identification in Brassica seeds and meal

Selenium (Se) is an essential micronutrient and is circulated to the food chain through crops. Brassica species are efficient in Se accumulation and thus, good species for Se biofortification purposes. The residual fraction obtained after oil processing of Brassica seeds, the meal, is an important protein source in animal diets and used in feed concentrates. The accumulation of soil or foliar applied Se in the seeds and meal of Brassica napus and B. rapa as well as its effects on growth and yield formation was studied in two field experiments. Also, a HPLC-ICP-MS based method for the identification and quantification of Se species in Brassica seeds and meal was developed. Selenium application did not affect the yield or oil content. High accumulation of Se in the seeds and meal (1.92–1.96 μg Se g^?1) was detected. Biotransformation of inorganic Se was evaluated by using HPLC-ICP-MS previous enzymatic hydrolysis for species extraction. The Se speciation studies showed that up to 85% of the total Se was SeMet whereas other Se-species were not detected. We conclude that the agronomic biofortification of Brassica species can improve the nutritive quality of the protein rich meal fraction as it contains significant amount of SeMet.     

Design and synthesis of tricyclic sulfones as γ-secretase inhibitors with greatly reduced Notch toxicity

A novel series of tricyclic γ-secretase inhibitors was designed and synthesized via a conformational analysis of literature compounds. The preliminary results have shown that compounds in this new series have much improved in vitro potency and in vivo profiles. More importantly, they have greatly reduced Notch related toxicity that was associated with previous γ-secretase inhibitors.     

Design and synthesis of piperazine-indole p38α MAP kinase inhibitors with improved pharmacokinetic profiles

Derivatives of the 4-fluorobenzyl dimethylpiperazine-indole class of p38α MAP kinase inhibitors are described. Biological evaluation of these compounds focused on maintaining activity while improving pharmacokinetic (PK) properties. Improved properties were observed for structures bearing substitutions on the benzylic methylene.     

Role of energy metabolic deficits and oxidative stress in excitotoxic spinal motor neuron degeneration in?vivo

MN (motor neuron) death in amyotrophic lateral sclerosis may be mediated by glutamatergic excitotoxicity. Previously, our group showed that the microdialysis perfusion of AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionate) in the rat lumbar spinal cord induced MN death and permanent paralysis within 12 h after the experiment. Here, we studied the involvement of energy metabolic deficiencies and of oxidative stress in this MN degeneration, by testing the neuroprotective effect of various energy metabolic substrates and antioxidants. Pyruvate, lactate, β-hydroxybutyrate, α-ketobutyrate and creatine reduced MN loss by 50–65%, preserved motor function and completely prevented the paralysis. Ascorbate, glutathione and glutathione ethyl ester weakly protected against motor deficits and reduced MN death by only 30–40%. Reactive oxygen species formation and 3-nitrotyrosine immunoreactivity were studied 1.5–2 h after AMPA perfusion, during the initial MN degenerating process, and no changes were observed. We conclude that mitochondrial energy deficiency plays a crucial role in this excitotoxic spinal MN degeneration, whereas oxidative stress seems a less relevant mechanism. Interestingly, we observed a clear correlation between the alterations of motor function and the number of damaged MNs, suggesting that there is a threshold of about 50% in the number of healthy MNs necessary to preserve motor function.     

Crystal structure of subtilisin complexed with its trapped substrateStreptomyces subtilisin inhibitor—Protein-protein interaction and evolution of serine proteinases and their proteinaceous inhibitors

The complex of a bacterial alkaline serine proteinase, subtilisin BPN’, with its proteinaceous inhibitorStreptomyces subtilisin inhibitor is unique in several respects, compared with other similar complexes containing serine proteinases of trypsin family. In addition to the usual antiparallelβ-sheet involving P₁-P₃ residues of the inhibitor, P₄-P₆ residues form antiparallelβ-sheet with a previously unnoticed chain segment (the ‘S4-6 site’) of subtilisin. The ‘S4-6 site’ does not exist in serine proteinases of trypsin family, whether of mammalian or microbial origin. Global induced-fit movement seems to occur on the ‘trapped substrate’Streptomyces subtilisin inhibitor: a channel-like structure in SSI remote from the contact region becomes about 2 Å wider upon complexing with subtilisin. Main role of the secondary contact region ofStreptomyces subtilisin inhibitor seems to support the reactive site loop (primary contact region). Steric homology for the two contact regions is so high between the inhibitors ofStreptomyces subtilisin inhibitor family and those of pancreatic secretory trypsin inhibitor-ovomucoid inhibitor family that it seems to favour a divergent evolution and to support the general notion as to the relationship of prokaryotic and eukaryotic genes put forwarded by Doolittle(Nature (London),272, 581, 1978).