Phosphate Transfer Research Articles

Intermolecular phosphotransfer is crucial for efficient catalytic activity of nucleoside diphosphate kinase

NDK (nucleoside diphosphate kinase) is primarily involved in maintaining cellular nucleotide pools in both prokaryotes and eukaryotes. We cloned ndk from Salmonella typhimurium and expressed it in Escherichia coli as a histidine-tagged protein. The Ni-NTA (Ni(2+)-nitrilotriacetate)-purified protein (sNDK) was found to be tetrameric with a monomeric unit molecular mass of approximately 18 kDa. The sNDK exhibited bivalent-cation-dependent autophosphorylation at a wide range of pH values and the phosphorylation withstands acid or alkali treatment. Surprisingly, nucleoside diphosphates did not behave as 'true inhibitors' of autophosphorylation activity. The sNDK displayed phosphotransfer activity from nucleoside triphosphates to nucleoside diphosphates; however, it was Mg(2+)/Mn(2+)-dependent. Mutational analysis established His(117) as the predominantly phosphorylating residue in sNDK. Although it is a histidine kinase, we found that substitution of Ser(119) with alanine/glutamate significantly affected the autophosphorylation, as well as the NTP-synthesizing ability of sNDK. Interestingly, the mixture of inactive (H117A) and partially active (S119A) proteins was found to be catalytically more efficient than the presence of corresponding amounts of active population, advocating transfer of phosphate from phospho-His(117) to Ser(119). Consistent with this observation, the Ni-NTA-purified H117A protein, obtained following co-expression of both of the mutant constructs [His-tagged H117A and GST (glutathione transferase)-tagged S119A] in E. coli, exhibited autophosphorylation, thereby alluding to intermolecular phosphotransfer between His(117) and Ser(119). Although this housekeeping enzyme has long been discovered and characterized from different sources, the results of the present study portray how Ser(119) in sNDK is phosphorylated. Furthermore, our findings illustrate for the first time that the intermolecular phosphotransfer is mandatory for the efficient NTP synthesis in any NDK.

Developments in Defining dif

Developments in Defining <i>dif</i>

Structural Basis for Adenylate Kinase Activity in ABC ATPases

ATP-binding cassette (ABC) enzymes are involved in diverse biological processes ranging from transmembrane transport to chromosome cohesion and DNA repair. They typically use ATP hydrolysis to conduct energy-dependent biological reactions. However, the cystic fibrosis transmembrane conductance regulator and the DNA repair protein Rad50 can also catalyze the adenylate kinase reaction (ATP+AMP↔2ADP). To clarify and provide a mechanistic basis for the adenylate kinase activity of ABC enzymes, we report the crystal structure of the nucleotide-binding domain of the Pyrococcus furiosus structural maintenance of chromosome protein (pfSMCnbd) in complex with the adenylate kinase inhibitor P1,P5-di(adenosine-5′)pentaphosphate. We show that pfSMCnbd possesses reverse adenylate kinase activity. Our results suggest that in adenylate kinase reactions, ATP binds to its canonical binding site while AMP binds to the Q-loop glutamine and a hydration water of the Mg2+ ion. Furthermore, mutational analysis indicates that adenylate kinase reaction occurs in the engaged pfSMCnbd dimer and requires the Signature motif for phosphate transfer. Our results explain how ATP hydrolysis and adenylate kinase reactions can be catalyzed by the same functional motifs within the structural framework of ABC enzymes. Thus, adenylate kinase activity is likely to be a latent activity in many ABC enzymes.

Effect of increasing dialysate flow rate on diffusive mass transfer of urea, phosphate and 2-microglobulin during clinical haemodialysis

Background. Diffusive clearance depends on blood and dialysate flow rates and the overall mass transfer area coefficient (KoA) of the dialyzer. Although KoA should be constant for a given dialyzer, urea KoA has been reported to vary with dialysate flow rate possibly because of improvements in flow distribution. This study examined the dependence of KoA for urea, phosphate and β2-microglobulin on dialysate flow rate in dialyzers containing undulating fibers to promote flow distribution and two different fiber packing densities.Methods. Twelve stable haemodialysis patients underwent dialysis with four different dialyzers, each used with a blood flow rate of 400 mL/min and dialysate flow rates of 350, 500 and 800 mL/min. Clearances of urea, phosphate and β2-microglobulin were measured and KoA values calculated.Results. Clearances of urea and phosphate, but not β2-microglobulin, increased significantly with increasing dialysate flow rate. However, increasing dialysate flow rate had no significant effect on KoA or Ko for any of the three solutes examined, although Ko for urea and phosphate increased significantly as the average flow velocity in the dialysate compartment increased.Conclusions. For dialyzers with features that promote good dialysate flow distribution, increasing dialysate flow rate beyond 600 mL/min at a blood flow rate of 400 mL/min is likely to have only a modest impact on dialyzer performance, limited to the theoretical increase predicted for a constant KoA.

Structural basis for the efficient phosphorylation of AZT-MP (3′-azido-3′-deoxythymidine monophosphate) and dGMP by Plasmodium falciparum type I thymidylate kinase

Plasmodium falciparum is the causative agent of malaria, a disease where new drug targets are required due to increasing resistance to current anti-malarials. TMPK (thymidylate kinase) is a good candidate as it is essential for the synthesis of dTTP, a critical precursor of DNA and has been much studied due to its role in prodrug activation and as a drug target. Type I TMPKs, such as the human enzyme, phosphorylate the substrate AZT (3'-azido-3'-deoxythymidine)-MP (monophosphate) inefficiently compared with type II TMPKs (e.g. Escherichia coli TMPK). In the present paper we report that eukaryotic PfTMPK (P. falciparum TMPK) presents sequence features of a type I enzyme yet the kinetic parameters for AZT-MP phosphorylation are similar to those of the highly efficient E. coli enzyme. Structural information shows that this is explained by a different juxtaposition of the P-loop and the azide of AZT-MP. Subsequent formation of the transition state requires no further movement of the PfTMPK P-loop, with no steric conflicts for the azide moiety, allowing efficient phosphate transfer. Likewise, we present results that confirm the ability of the enzyme to uniquely accept dGMP as a substrate and shed light on the basis for its wider substrate specificity. Information resulting from two ternary complexes (dTMP-ADP and AZT-MP-ADP) and a binary complex with the transition state analogue AP5dT [P1-(5'-adenosyl)-P5-(5'-thymidyl) pentaphosphate] all reveal significant differences with the human enzyme, notably in the lid region and in the P-loop which may be exploited in the rational design of Plasmodium-specific TMPK inhibitors with therapeutic potential.

Phosphoenolpyruvate and Mg2+ Binding to Pyruvate Kinase Monitored by Infrared Spectroscopy

Structural changes in rabbit muscle pyruvate kinase (PK) induced by phosphoenolpyruvate (PEP) and Mg2+ binding were studied by attenuated total reflection Fourier transform infrared spectroscopy in combination with a dialysis accessory. The experiments indicated a largely preserved secondary structure upon PEP and Mg2+ binding but also revealed small backbone conformational changes of PK involving all types of secondary structure. To assess the effect of the protein environment on the bound PEP, we assigned and evaluated the infrared absorption bands of bound PEP. These were identified using 2,3-13C2-labeled PEP. We obtained the following assignments: 1589 cm−1 (antisymmetric carboxylate stretching vibration); 1415 cm−1 (symmetric carboxylate stretching vibration); 1214 cm−1 (C-O stretching vibration); 1124 and 1110 cm−1 (asymmetric PO32- stretching vibrations); and 967 cm−1 (symmetric PO32- stretching vibration). The corresponding band positions in solution are 1567, 1407, 1229, 1107, and 974 cm−1. The differences for bound and free PEP indicate specific interactions between ligand and protein. Quantification of the interactions with the phosphate group indicated that the enzyme environment has little influence on the P-O bond strengths, and that the bridging P-O bond, which is broken in the catalytic reaction, is weakened by <3%. Thus, there is only little distortion toward a dissociative transition state of the phosphate transfer reaction when PEP binds to PK. Therefore, our results are in line with an associative transition state. Carboxylate absorption bands indicated a maximal shortening of the length of the shorter C-O bond by 1.3 pm. PEP bound to PK in the presence of the monovalent ion Na+ exhibited the same band positions as in the presence of K+, indicating very similar interaction strengths between ligand and protein in both cases.

Gas-Phase Rearrangements Do Not Affect Site Localization Reliability in Phosphoproteomics Data Sets

Intramolecular transfer of phosphate during collision-induced dissociation (CID) in ion-trap mass spectrometers has recently been described. Because phosphorylation events are assigned to discrete serine, threonine, and tyrosine residues based on the presence of site-determining ions in MS/MS spectra, phosphate transfer may invalidate or confound site localization in published large-scale phosphorylation data sets. Here, we present evidence for the occurrence of this phenomenon using synthetic phosphopeptide libraries, specifically for doubly charged species. We found, however, that the extent of the transfer reaction was insufficient to cause localization of phosphorylation sites to incorrect residues. We further compared CID to electron-transfer dissociation (ETD) for site localization using synthetic libraries and a large-scale yeast phosphoproteome experiment. The agreement in site localization was >99.5 and 93%, respectively, suggesting that ETD-based site localization is no more reliable than CID. We conclude that intramolecular phosphate transfer does not affect the reliability of current or past phosphorylation data sets.

From Creatine Kinase-MB to Troponin

From Creatine Kinase-MB to Troponin

Interaction analysis of TcrX/Y two component system from Mycobacterium tuberculosis

TcrX/Y is one of the twelve two component system (TCS) present in Mycobacterium tuberculosis. The objective was to investigate the TcrX/Y interaction by in silico studies, pull down assay, radioactive phosphotransfer, surface plasmon resonance as well as crosstalk analysis of TcrY with TcrA ‐ a non‐cognate response regulator. Sequence alignment of TcrY with other histidine kinases revealed His256 as the residue responsible for autophosphorylation. Modeled structure of TcrX predicts that Asp59 may be involved in phosphotransfer with His256 of TcrY. Docking analysis pointed to the interaction of TcrY/His256 with TcrX/Asp54. TcrY/Y dimerisation was also observed by in silico and crosslinking studies. Autophosphorylation of TcrY has been observed followed by the phosphate transfer to TcrX. The phosphorylation process required divalent metal ions like Mg2+ or Ca2+ ions as evident from the radioactive phosphorylation studies. Interaction was not observed in TcrY/A suggesting the signal transduction process is specific in TcrX/Y system. TcrY hydrolyzes ATP and the Km value has been found to be 10 mM. TcrX/Y interaction has been determined by surface plasmon resonance and dissociation constant (KD) was evaluated to be 3.6 μM. We conclude from our results that TcrX/Y are part of the same signal transduction pathway without their involvement in crosstalk with non‐cognate counterpart.The work was funded by Department of Biotechnology, Govt. of India.

Three (and more) component regulatory systems – auxiliary regulators of bacterial histidine kinases

Two-component signal transduction (TCST) is the most prevalent mechanism employed by microbes to sense and respond to environmental changes. It is characterized by the signal-induced transfer of phosphate from a sensor histidine kinase (HK) to a response regulator (RR), resulting in a cellular response. An emerging theme in the field of TCST signalling is the discovery of auxiliary factors, distinct from the HK and RR, which are capable of influencing phosphotransfer. One group of TCST auxiliary proteins accomplishes this task by acting on HKs. Auxiliary regulators of HKs are widespread and have been identified in all cellular compartments, where they can influence HK activity through interactions with the sensing, transmembrane or enzymatic domains of the HK. The effects of an auxiliary regulator are controlled by its regulated expression, modification and/or through ligand binding. Ultimately, auxiliary regulators can connect a given TCST system to other regulatory networks in the cell or result in regulation of the TCST system in response to an expanded range of stimuli. The studies highlighted in this review draw attention to an emerging view of bacterial TCST systems as core signalling units upon which auxiliary factors act.

Characterization of the rice PHO1 gene family reveals a key role for OsPHO1;2 in phosphate homeostasis and the evolution of a distinct clade in dicotyledons.

Phosphate homeostasis was studied in a monocotyledonous model plant through the characterization of the PHO1 gene family in rice (Oryza sativa). Bioinformatics and phylogenetic analysis showed that the rice genome has three PHO1 homologs, which cluster with the Arabidopsis (Arabidopsis thaliana) AtPHO1 and AtPHO1;H1, the only two genes known to be involved in root-to-shoot transfer of phosphate. In contrast to the Arabidopsis PHO1 gene family, all three rice PHO1 genes have a cis-natural antisense transcript located at the 5 ' end of the genes. Strand-specific quantitative reverse transcription-PCR analyses revealed distinct patterns of expression for sense and antisense transcripts for all three genes, both at the level of tissue expression and in response to nutrient stress. The most abundantly expressed gene was OsPHO1;2 in the roots, for both sense and antisense transcripts. However, while the OsPHO1;2 sense transcript was relatively stable under various nutrient deficiencies, the antisense transcript was highly induced by inorganic phosphate (Pi) deficiency. Characterization of Ospho1;1 and Ospho1;2 insertion mutants revealed that only Ospho1;2 mutants had defects in Pi homeostasis, namely strong reduction in Pi transfer from root to shoot, which was accompanied by low-shoot and high-root Pi. Our data identify OsPHO1;2 as playing a key role in the transfer of Pi from roots to shoots in rice, and indicate that this gene could be regulated by its cis-natural antisense transcripts. Furthermore, phylogenetic analysis of PHO1 homologs in monocotyledons and dicotyledons revealed the emergence of a distinct clade of PHO1 genes in dicotyledons, which include members having roles other than long-distance Pi transport.

Anion Translocation in a Brush-Like Nanopore: Simulations of the Outer Membrnae Protein OprP

The outer membrane protein OprP from Pseudomonas aeruginosa forms an anion-selective pore, especially selective for phosphate ions. The protein is homo-trimeric, with each pore lined by three positively charged loops (L3, L5, and T7) folded into its lumen. OprP plays a key role in high-affinity phosphate uptake under the condition of phosphate starvation. To better understand the mechanism of phosphate-selective permeation, we employed three simulation techniques: (i) equilibrium molecular dynamics simulations (MD); (ii) steered MD (SMD); (iii) umbrella sampling to calculate a potential of mean force (PMF) for phosphate and chloride ions. The PMFs reveal a deep energy well midway along the OprP channel. Two adjacent phosphate-binding sites (W1 and W2), each with a well depth of ∼8kT, are identified close to the L3 loop in the most constricted region of the pore. The transfer of phosphate between sites W1 and W2 is correlated with changes in conformation of the sidechain of K121, which serves as a ‘charged brush’ to facilitate phosphate passage between the two subsites. The PMF for chloride has also been computed and can be compared with that of phosphate. Our simulations suggest that OprP does not conform to the conventional picture of a channel with a relatively flat energy landscape for permeant ions, but rather resembles a membrane-inserted binding protein with a high specificity that allows access to a centrally located binding site from both the extracellular and the periplasmic spaces.

Semisynthesis of human thymidine monophosphate kinase

Protein semisynthesis based on native chemical ligation has become a major protein engineering tool that allows manipulation of domains of proteins of all sizes. It helps to overcome limitations in chemical protein synthesis set by the inherent size limits of solid phase peptide synthesis. Here we present a semisynthesis approach that provides access to N-terminally-modified variants of human thymidine monophosphate kinase (TMPK). This enzyme is intimately involved in activating nucleoside-based drugs directed against viral infections such as HIV and against certain types of cancers. The option to chemically synthesize and manipulate the first 30 amino acids of this enzyme via protein semisynthesis allows direct substitution of vital amino acids in the P-loop of this enzyme for probing the mechanism of phosphate transfer and direct observation of substrate or inhibitor binding. Efficient native chemical ligation of two N-terminal segments, one comprising the wild type sequence and one containing a small fluorescent probe, provides milligram amounts of two semisynthetic TMPK variants. An efficient folding procedure in the presence of substrate nucleotides provides access to active semisynthetic TMPK variants.

Using Difference Infrared Spectroscopy to Investigate the Effects of pH on PGK-Substrate Complexes

Yeast phosphoglycerate kinase catalyzes the reversible phosphate transfer in the reaction: ADP +1,3-bis-phosphoglycerate ↔ ATP + 3-phosphoglycerate. Prior research indicates a hinge-bending mechanism occurs during catalysis to bring the substrates into closer proximity. Domain closure is only initiated in ternary complexes, in which both substrates are simultaneously bound to the enzyme. The activity and conformation of PGK is directly influenced by substrate and salt concentrations as well as pH.

Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate

The outer membrane protein OprP from Pseudomonas aeruginosa forms a phosphate selective pore. To understand the mechanism of phosphate permeation and selectivity, we used three simulation techniques [equilibrium molecular dynamics simulations, steered molecular dynamics, and calculation of a potential of mean force (PMF)]. The PMF for phosphate reveals a deep free energy well midway along the OprP channel. Two adjacent phosphate-binding sites (W1 and W2), each with a well depth of approximately 8 kT, are identified close to the L3 loop in the most constricted region of the pore. A dissociation constant for phosphate of 6 microM is computed from the PMF, within the range of reported experimental values. The transfer of phosphate between sites W1 and W2 is correlated with changes in conformation of the sidechain of K121, which serves as a "charged brush" to facilitate phosphate passage between the two subsites. OprP also binds chloride, but less strongly than phosphate, as calculated from a Cl(-) PMF. The difference in affinity and hence selectivity is due to the "Lys-cluster" motif, the positive charges of which interact strongly with a partially dehydrated phosphate ion but are shielded from a Cl(-) by the hydration shell of the smaller ion. Our simulations suggest that OprP does not conform to the conventional picture of a channel with relatively flat energy landscape for permeant ions, but rather resembles a membrane-inserted binding protein with a high specificity that allows access to a centrally located binding site from both the extracellular and the periplasmic spaces.

Interaction analysis of TcrX/Y two component system from Mycobacterium tuberculosis

TcrX/Y is one of the twelve two component system (TCS) present in Mycobacterium tuberculosis. We have investigated the TcrX/Y interaction by in silico studies, pull down assay, radioactive phosphotransfer, surface plasmon resonance as well as crosstalk analysis of TcrY with TcrA – a non-cognate response regulator. Sequence alignment of TcrY with other histidine kinases revealed His256 as the residue responsible for autophosphorylation. The modeled structure of TcrX/Y was docked with each other by GRAMM-X revealing the interaction of TcrY/His256 with TcrX/Asp54. TcrY dimerization via the formation of four helix bundle was also observed by protein–protein docking. Autophosphorylation of TcrY has been observed followed by the phosphate transfer from TcrY to TcrX. The phosphorylation process required divalent metal ions like Mg 2+ or Ca 2+ ions as evident from the radioactive phosphorylation studies. Interaction was not observed between TcrY and TcrA suggesting the signal transduction process is specific in TcrX/Y system. TcrY hydrolyzes ATP and the K m value has been found to be 10 mM which is comparable to that of Hsp104. TcrX/Y interaction has been determined by surface plasmon resonance and dissociation constant ( K D) was evaluated to be 3.6 μM. We conclude from our results that TcrX and TcrY are part of the same signal transduction pathway without their involvement in crosstalk with non-cognate counterpart.

A Non-hydrolyzable ATP Derivative Generates a Stable Complex in a Light-inducible Two-component System

Isothermal calorimetry (ITC) measurements yielded the binding constants during complex formation of light-inducible histidine kinases (HK) and their cognate CheY-type response regulators (RR). HK-RR interactions represent the core function of the bacterial two-component system, which is also present in many bacterial phytochromes. Here, we have studied the recombinant forms of phytochromes CphA and CphB from the cyanobacterium Tolypothrix PCC7601 and their cognate RRs RcpA and RcpB. The interaction between the two reaction partners (HK and RR) was studied in the presence and absence of ATP. A complex formation was observable in the presence of ATP, but specific interactions were only found when a non-hydrolyzable ATP derivative was added to the mixture. Also, the incubation of the HK domain alone (expressed as a recombinant protein) with the RR did not yield specific interactions, indicating that the HK domain is only active as a component of the full-length phytochrome. Considering also previous studies on the same proteins (Hübschmann, T., Jorissen, H. J. M. M., Börner, T., Gärtner, W., and de Marsac, N. (2001) Eur. J. Biochem. 268, 3383-3389) we now conclude that the HK domains of these phytochromes are active only when the chromophore domain is in its Pr form. The formerly documented phosphate transfer between the HK domain and the RR takes place via a transiently formed protein-protein complex, which becomes detectable by ITC in the presence of a non-hydrolyzable ATP derivative. This finding is of interest also in relation to the function of some (blue light-sensitive) photoreceptors that carry the HK domain and the RR fused together in one single protein.

Combining Medium Effects and Cofactor Catalysis: Metal‐Coordinated Synzymes Accelerate Phosphate Transfer by 108

The systematic exploration of the modification of polyethylene imine with guanidinium and octyl groups has led to the identification of a catalyst, CD6, which accelerates the phosphate transfer reaction of HPNP (2-hydroxypropyl-4-nitrophenyl phosphate) in the presence of divalent metals such as Zn(2+), Co(2+), Mg(2+) or Ni(2+). CD6 exhibits saturation kinetics that are described by Michaelis-Menten parameters K(m) ranging from 2.5-8 mM and k(cat) ranging from 0.0014-0.09 s(-1). For Zn(II)-CD6 this corresponds to an overall acceleration k(cat)/k(uncat) of 3.8x10(5) and a catalytic proficiency (k(cat)/K(m))/k(uncat) of 1.5x10(8). Catalysis by Zn(II)-CD6 is specifically inhibited by inorganic phosphate, allowing turnover regulation by product inhibition. This effect stands in contrast to Zn(II)-catalysed transesterification of HPNP in water or by the synzymes Co(II)-CD6 and Ni(II)-CD6, with which no such interference by product is observed. These characteristics render synzyme Zn(II)-CD6 an efficient enzyme model that reflects enzyme-like properties in a wide range of features.

Ultrasound Mobilization of Liquid/Liquid/Solid Triple-Phase Boundary Redox Systems

Power ultrasound is used to “mobilize” droplets of 1,2-dichloroethane (DCE) on a glassy carbon electrode surface in an aqueous electrolyte environment. Voltammetric methods are employed to investigate the effect of ultrasound on (i) the mass transport in the aqueous phase, (ii) the mass transport in the DCE−aqueous two-phase system, and (iii) the triple-phase boundary anion extraction reaction coupled to oxidation of n-butylferrocene (nBuFc) in the organic phase. Optimized conditions comprise a 13 mm diameter ultrasonic horn (24 kHz) with 15 W/cm2 power output at a distance of 15 mm from a 2.83 cm2 glassy carbon working electrode in 32 cm3 of aqueous solution. Mass transport in the aqueous phase is probed for the reduction of hexaammineruthenium(III) chloride in aqueous 0.1 M KCl supporting electrolyte, and an increase in mass transport induced by the DCE droplets is observed. Triple-phase-boundary ion transfer reactions are studied for the oxidation of nBuFc in DCE in the presence of aqueous 0.1 M NaBPh4, KPF6, NaClO4, and phosphate buffer pH 1. The hydrophobicity of the transferring electrolyte anion is observed to shift the electrochemical response according to the standard transfer potential. For phosphate electrolyte media, rather than phosphate transfer, n-butylferricenium cation transfer into the aqueous phase and iron(III) phosphate formation occur. The beneficial effect of adding tetrabutylammonium hexafluorophosphate electrolyte into the organic DCE phase is demonstrated; however, triple-phase-boundary processes in the absence of intentionally added electrolyte in the organic phase are feasible.

Oxidative modification and aggregation of creatine kinase from aged mouse skeletal muscle

Creatine kinase catalyzes the reversible transfer of the gamma phosphate from ATP to creatine forming the high energy compound creatine phosphate. Muscle creatine kinase (CKm) activity maintains energetic homeostasis as variations in energy requirements dictate that ATP be readily available. Recent studies suggest that CKm activity is altered during aging. Proteomic analyses have shown that CKm is 3-nitrotyrosine (3-NT) modified and carbonylated in aged rodent skeletal muscle. However, it remains unknown if these modifications affect its structure and activity. To address this we characterized oxidatively modified CKm from the quadriceps of young, middle-aged, and aged mice. Our data indicate that 3-NT modified and carbonylated CKm are found predominantly in aged muscle and that it exists in high molecular weight oligomers and insoluble protein aggregates. CKm from middle-aged and aged mouse quadriceps also exhibits structural instability that may account for its reduction in function. These structural and functional changes correlate with the differential protein modifications. Interestingly, the majority of the age-related changes in enzyme activity and protein stability occurred by middle age. Our studies indicate that the age-associated oxidative and nitrative modification of CKm results in a decrease in its activity and may cause structural changes that promote oligomerization and aggregation.