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1.
J Biol Chem ; 294(46): 17654-17668, 2019 11 15.
Artigo em Inglês | MEDLINE | ID: mdl-31481464

RESUMO

WT P53-Induced Phosphatase 1 (WIP1) is a member of the magnesium-dependent serine/threonine protein phosphatase (PPM) family and is induced by P53 in response to DNA damage. In several human cancers, the WIP1 protein is overexpressed, which is generally associated with a worse prognosis. Although WIP1 is an attractive therapeutic target, no potent, selective, and bioactive small-molecule modulator with favorable pharmacokinetics has been reported. Phosphatase enzymes are among the most challenging targets for small molecules because of the difficulty of achieving both modulator selectivity and bioavailability. Another major obstacle has been the availability of robust and physiologically relevant phosphatase assays that are suitable for high-throughput screening. Here, we describe orthogonal biochemical WIP1 activity assays that utilize phosphopeptides from native WIP1 substrates. We optimized an MS assay to quantify the enzymatically dephosphorylated peptide reaction product in a 384-well format. Additionally, a red-shifted fluorescence assay was optimized in a 1,536-well format to enable real-time WIP1 activity measurements through the detection of the orthogonal reaction product, Pi We validated these two optimized assays by quantitative high-throughput screening against the National Center for Advancing Translational Sciences (NCATS) Pharmaceutical Collection and used secondary assays to confirm and evaluate inhibitors identified in the primary screen. Five inhibitors were further tested with an orthogonal WIP1 activity assay and surface plasmon resonance binding studies. Our results validate the application of miniaturized physiologically relevant and orthogonal WIP1 activity assays to discover small-molecule modulators from high-throughput screens.


Assuntos
Ativadores de Enzimas/química , Fosfopeptídeos/química , Proteína Fosfatase 2C/química , Bibliotecas de Moléculas Pequenas/química , Ativadores de Enzimas/isolamento & purificação , Ativadores de Enzimas/farmacologia , Ensaios de Triagem em Larga Escala , Humanos , Proteína Fosfatase 2C/antagonistas & inibidores , Bibliotecas de Moléculas Pequenas/isolamento & purificação , Bibliotecas de Moléculas Pequenas/farmacologia , Especificidade por Substrato , Proteína Supressora de Tumor p53/química
2.
PLoS One ; 12(6): e0179547, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28636641

RESUMO

The range of ATP concentrations that can be measured with a fluorescent reagentless biosensor for ATP has been increased by modulating its affinity for this analyte. The ATP biosensor is an adduct of two tetramethylrhodamines with MatB from Rhodopseudomonas palustris. Mutations were introduced into the binding site to modify ATP binding affinity, while aiming to maintain the concomitant fluorescence signal. Using this signal, the effect of mutations in different parts of the binding site was measured. This mutational analysis revealed three variants in particular, each with a single mutation in the phosphate-binding loop, which had potentially beneficial changes in ATP binding properties but preserving a fluorescence change of ~3-fold on ATP binding. Two variants (T167A and T303A) weakened the binding, changing the dissociation constant from the parent's 6 µM to 123 µM and 42 µM, respectively. Kinetic measurements showed that the effect of these mutations on affinity was by an increase in dissociation rate constants. These variants widen the range of ATP concentration that can be measured readily by this biosensor to >100 µM. In contrast, a third variant, S170A, decreased the dissociation constant of ATP to 3.8 µM and has a fluorescence change of 4.2 on binding ATP. This variant has increased selectivity for ATP over ADP of >200-fold. This had advantages over the parent by increasing sensitivity as well as increasing selectivity during ATP measurements in which ADP is present.


Assuntos
Trifosfato de Adenosina/análise , Proteínas de Bactérias/metabolismo , Técnicas Biossensoriais , Coenzima A Ligases/metabolismo , Corantes Fluorescentes/química , Difosfato de Adenosina/química , Difosfato de Adenosina/metabolismo , Trifosfato de Adenosina/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Sítios de Ligação , Coenzima A Ligases/química , Coenzima A Ligases/genética , Cinética , Simulação de Dinâmica Molecular , Mutagênese Sítio-Dirigida , Ligação Proteica , Estrutura Terciária de Proteína , Piruvato Quinase/química , Piruvato Quinase/metabolismo , Rodaminas/química , Rodopseudomonas/enzimologia
3.
ACS Chem Biol ; 10(11): 2650-7, 2015 Nov 20.
Artigo em Inglês | MEDLINE | ID: mdl-26355992

RESUMO

A fluorescent reagentless biosensor for ATP has been developed, based on malonyl-coenzyme A synthetase from Rhodopseudomonas palustris as the protein scaffold and recognition element. Two 5-iodoacetamidotetramethylrhodamines were covalently bound to this protein to provide the readout. This adduct couples ATP binding to a 3.7-fold increase in fluorescence intensity with excitation at 553 nm and emission at 575 nm. It measures ATP concentrations with micromolar sensitivity and is highly selective for ATP relative to ADP. Its ability to monitor enzymatic ATP production or depletion was demonstrated in steady-state kinetic assays in which ATP is a product or substrate, respectively.


Assuntos
Trifosfato de Adenosina/análise , Proteínas de Bactérias/química , Técnicas Biossensoriais , Coenzima A Ligases/química , Corantes Fluorescentes/química , Trifosfato de Adenosina/química , Proteínas de Bactérias/metabolismo , Coenzima A Ligases/metabolismo , Modelos Biológicos , Piruvato Quinase/química , Piruvato Quinase/farmacologia
4.
Biochemistry ; 54(32): 5054-62, 2015 Aug 18.
Artigo em Inglês | MEDLINE | ID: mdl-26199994

RESUMO

A fluorescent reagentless biosensor for inorganic phosphate (Pi), based on the E. coli PstS phosphate binding protein, was redesigned to allow measurements of higher Pi concentrations and at low, substoichiometric concentrations of biosensor. This was achieved by weakening Pi binding of the previous biosensor, and different approaches are described that could enable this change in properties. The readout, providing response to the Pi concentration, is delivered by tetramethylrhodamine fluorescence. In addition to two cysteine mutations for rhodamine labeling at positions 17 and 197, the final variant had an I76G mutation in the hinge region between the two lobes that make up the protein. Upon Pi binding, the lobes rotate on this hinge and the mutation on the hinge lowers affinity ∼200-fold, with a dissociation constant now in the tens to hundreds micromolar range, depending on solution conditions. The signal change on Pi binding was up to 9-fold, depending on pH. The suitability of the biosensor for steady-state ATPase assays was demonstrated with low biosensor usage and its advantage in ability to cope with Pi contamination.


Assuntos
Técnicas Biossensoriais/métodos , Fosfatos/análise , Substituição de Aminoácidos , Sítios de Ligação/genética , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Corantes Fluorescentes/química , Modelos Moleculares , Mutagênese Sítio-Dirigida , Proteínas Periplásmicas de Ligação/química , Proteínas Periplásmicas de Ligação/genética , Proteínas de Ligação a Fosfato/química , Proteínas de Ligação a Fosfato/genética , Conformação Proteica , Engenharia de Proteínas , Estabilidade Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Rodaminas/química , Espectrometria de Fluorescência
5.
Antimicrob Agents Chemother ; 59(1): 186-92, 2015 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-25331707

RESUMO

The development of deoxynucleoside triphosphate (dNTP)-based drugs requires a quantitative understanding of any inhibition, activation, or hydrolysis by off-target cellular enzymes. SAMHD1 is a regulatory dNTP-triphosphohydrolase that inhibits HIV-1 replication in human myeloid cells. We describe here an enzyme-coupled assay for quantifying the activation, inhibition, and hydrolysis of dNTPs, nucleotide analogues, and nucleotide analogue inhibitors by triphosphohydrolase enzymes. The assay facilitates mechanistic studies of triphosphohydrolase enzymes and the quantification of off-target effects of nucleotide-based antiviral and chemotherapeutic agents.


Assuntos
Hidrolases Anidrido Ácido/análise , Bioensaio/métodos , Avaliação Pré-Clínica de Medicamentos/métodos , Proteínas Monoméricas de Ligação ao GTP/análise , Proteínas Monoméricas de Ligação ao GTP/metabolismo , Hidrolases Anidrido Ácido/genética , Hidrolases Anidrido Ácido/metabolismo , Aciclovir/química , Aciclovir/metabolismo , Aciclovir/farmacologia , Nucleotídeos de Adenina/química , Nucleotídeos de Adenina/farmacologia , Antivirais/química , Antivirais/metabolismo , Antivirais/farmacologia , Arabinonucleosídeos/química , Arabinonucleosídeos/farmacologia , Catálise/efeitos dos fármacos , Clofarabina , Desoxirribonucleotídeos/química , Desoxirribonucleotídeos/metabolismo , Relação Dose-Resposta a Droga , Ganciclovir/química , Ganciclovir/farmacologia , HIV-1 , Hidrólise , Proteína 1 com Domínio SAM e Domínio HD
6.
J Biol Chem ; 288(35): 25183-25193, 2013 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-23839989

RESUMO

The superfamily 1 helicase, RecD2, is a monomeric, bacterial enzyme with a role in DNA repair, but with 5'-3' activity unlike most enzymes from this superfamily. Rate constants were determined for steps within the ATPase cycle of RecD2 in the presence of ssDNA. The fluorescent ATP analog, mantATP (2'(3')-O-(N-methylanthraniloyl)ATP), was used throughout to provide a complete set of rate constants and determine the mechanism of the cycle for a single nucleotide species. Fluorescence stopped-flow measurements were used to determine rate constants for adenosine nucleotide binding and release, quenched-flow measurements were used for the hydrolytic cleavage step, and the fluorescent phosphate biosensor was used for phosphate release kinetics. Some rate constants could also be measured using the natural substrate, ATP, and these suggested a similar mechanism to that obtained with mantATP. The data show that a rearrangement linked to Mg(2+) coordination, which occurs before the hydrolysis step, is rate-limiting in the cycle and that this step is greatly accelerated by bound DNA. This is also shown here for the PcrA 3'-5' helicase and so may be a general mechanism governing superfamily 1 helicases. The mechanism accounts for the tight coupling between translocation and ATPase activity.


Assuntos
Trifosfato de Adenosina/química , Proteínas de Bactérias/química , DNA Helicases/química , DNA Bacteriano/química , DNA de Cadeia Simples/química , Deinococcus/enzimologia , Trifosfato de Adenosina/genética , Trifosfato de Adenosina/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , DNA Helicases/genética , DNA Helicases/metabolismo , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , DNA de Cadeia Simples/genética , DNA de Cadeia Simples/metabolismo , Deinococcus/genética , Hidrólise , Magnésio/química , Magnésio/metabolismo
7.
PLoS One ; 7(6): e38270, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22701618

RESUMO

The superfamily 2 bacterial helicase, RecG, is a monomeric enzyme with a role in DNA repair by reversing stalled replication forks. The helicase must act specifically and rapidly to prevent replication fork collapse. We have shown that RecG binds tightly and rapidly to four-strand oligonucleotide junctions, which mimic a stalled replication fork. The helicase unwinds such DNA junctions with a step-size of approximately four bases per ATP hydrolyzed. To gain an insight into this mechanism, we used fluorescent stopped-flow and quenched-flow to measure individual steps within the ATPase cycle of RecG, when bound to a DNA junction. The fluorescent ATP analogue, mantATP, was used throughout to determine the rate limiting steps, effects due to DNA and the main states in the cycle. Measurements, when possible, were also performed with unlabeled ATP to confirm the mechanism. The data show that the chemical step of hydrolysis is the rate limiting step in the cycle and that this step is greatly accelerated by bound DNA. The ADP release rate is similar to the cleavage rate, so that bound ATP and ADP would be the main states during the ATP cycle. Evidence is provided that the main structural rearrangements, which bring about DNA unwinding, are linked to these states.


Assuntos
Adenosina Trifosfatases/metabolismo , DNA Helicases/metabolismo , DNA/metabolismo , Thermotoga maritima/enzimologia , Trifosfato de Adenosina/análogos & derivados , Trifosfato de Adenosina/metabolismo , DNA/química , Fluorescência , Hidrólise , Cinética , Modelos Biológicos , Oxigênio/metabolismo , Thermotoga maritima/genética , ortoaminobenzoatos/metabolismo
8.
Nano Lett ; 11(12): 5482-8, 2011 Dec 14.
Artigo em Inglês | MEDLINE | ID: mdl-22023515

RESUMO

Single molecule detection is useful for characterizing nanoscale objects such as biological macromolecules, nanoparticles and nanodevices with nanometer spatial resolution. Fluorescence resonance energy transfer (FRET) is widely used as a single-molecule assay to monitor intramolecular dynamics in the distance range of 3-8 nm. Here we demonstrate that self-quenching of two rhodamine derivatives can be used to detect small conformational dynamics corresponding to subnanometer distance changes in a FRET-insensitive short-range at the single molecule level. A ParM protein mutant labeled with two rhodamines works as a single molecule adenosine 5'-diphosphate (ADP) sensor that has 20 times brighter fluorescence signal in the ADP bound state than the unbound state. Single molecule time trajectories show discrete transitions between fluorescence on and off states that can be directly ascribed to ADP binding and dissociation events. The conformational changes observed with 20:1 contrast are only 0.5 nm in magnitude and are between crystallographic distances of 1.6 and 2.1 nm, demonstrating exquisite sensitivity to short distance scale changes. The systems also allowed us to gain information on the photophysics of self-quenching induced by rhodamine stacking: (1) photobleaching of either of the two rhodamines eliminates quenching of the other rhodamine fluorophore and (2) photobleaching from the highly quenched, stacked state is only 2-fold slower than from the unstacked state.


Assuntos
Actinas/química , Difosfato de Adenosina/metabolismo , Proteínas de Escherichia coli/química , Escherichia coli/química , Transferência Ressonante de Energia de Fluorescência/métodos , Rodaminas/química , Actinas/metabolismo , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , Modelos Moleculares , Conformação Proteica
9.
Methods Mol Biol ; 778: 161-74, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-21809206

RESUMO

The interconversion of nucleoside triphosphate (NTP) and diphosphate occurs in some of the most -important cellular reactions. It is catalyzed by diverse classes of enzymes, such as nucleoside triphosphatases, kinases, and ATP synthases. Triphosphatases include helicases, myosins, and G-proteins, as well as many other energy-transducing enzymes. The transfer of phosphate by kinases is involved in many metabolic pathways and in control of enzyme activity through protein phosphorylation. To understand the processes catalyzed by these enzymes, it is important to measure the kinetics of individual elementary steps and conformation changes. Fluorescent nucleotides can directly report on the binding and release steps, and conformational changes associated with these processes. In single-molecule studies, fluorescent nucleotides can allow their role to be explored by following precisely the temporal and spatial changes in the bound nucleotide. Here, the selection of fluorophores and nucleotide modifications are discussed and methods are described to prepare ATP analogs with examples of two alternate fluorophores, diethylaminocoumarin and Cy3.


Assuntos
Microscopia de Fluorescência/métodos , Trifosfato de Adenosina/metabolismo , Guanosina Trifosfato/metabolismo
10.
Biophys J ; 99(7): 2163-9, 2010 Oct 06.
Artigo em Inglês | MEDLINE | ID: mdl-20923650

RESUMO

Fluorescence lifetime imaging microscopy is used to demonstrate that different loads applied to a muscle fiber change the microenvironment of the nucleotide binding pocket of myosin. Permeabilized skeletal muscle fibers in rigor were labeled with a fluorescent ATP analog, 3'-DEAC-propylenediamine (pda)-ATP (3'-O-{N-[3-(7-diethylaminocoumarin-3-carboxamido)propyl]carbamoyl}ATP), which was hydrolyzed to the diphosphate. Cycles of small-amplitude stretches and releases (<1% of muscle segment length) were synchronized with fluorescence lifetime imaging and force measurements to correlate the effect of force on the lifetime of the ATP analog bound to the actomyosin complex. Analysis of the fluorescence decay resolved two lifetimes, corresponding to the free nucleotide DEAC-pda-ATP (τ(1) = 0.47 ± 0.03 ns; mean ± SD) and nucleotide bound to the actomyosin complex (τ(2) = 2.21 ± 0.06 ns at low strain). Whereas τ(1) did not change with force, τ(2) showed a linear dependence with the force applied to the muscle of 0.43 ± 0.05 ps/kPa. Hence, the molecular environment of the nucleotide binding pocket of myosin is directly affected by a change of length applied at the ends of the fiber segments. These changes may help explain how force modulates the actomyosin ATPase cycle and thus the physiology and energetics of contraction.


Assuntos
Trifosfato de Adenosina/metabolismo , Imageamento Tridimensional/métodos , Músculos/metabolismo , Miosinas/metabolismo , Animais , Sítios de Ligação , Fenômenos Biomecânicos/fisiologia , Fluorescência , Fibras Musculares Esqueléticas/metabolismo , Coelhos , Fatores de Tempo
11.
Nucleic Acids Res ; 38(13): 4448-57, 2010 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-20350930

RESUMO

DNA helicases are motor proteins that catalyze the unwinding of double-stranded DNA into single-stranded DNA using the free energy from ATP hydrolysis. Single molecule approaches enable us to address detailed mechanistic questions about how such enzymes move processively along DNA. Here, an optical method has been developed to follow the unwinding of multiple DNA molecules simultaneously in real time. This was achieved by measuring the accumulation of fluorescent single-stranded DNA-binding protein on the single-stranded DNA product of the helicase, using total internal reflection fluorescence microscopy. By immobilizing either the DNA or helicase, localized increase in fluorescence provides information about the rate of unwinding and the processivity of individual enzymes. In addition, it reveals details of the unwinding process, such as pauses and bursts of activity. The generic and versatile nature of the assay makes it applicable to a variety of DNA helicases and DNA templates. The method is an important addition to the single-molecule toolbox available for studying DNA processing enzymes.


Assuntos
DNA Helicases/análise , Microscopia de Fluorescência/métodos , Trifosfato de Adenosina/metabolismo , DNA/química , DNA/metabolismo , DNA Helicases/metabolismo , DNA de Cadeia Simples/metabolismo , Proteínas de Ligação a DNA/análise , Exodesoxirribonucleases/análise , Proteínas Imobilizadas/análise
12.
ACS Chem Biol ; 5(4): 415-25, 2010 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-20158267

RESUMO

Fluorescence assays for ADP detection are of considerable current interest, both in basic research and in drug discovery, as they provide a generic method for measuring the activity of ATPases and kinases. The development of a novel fluorescent biosensor is described that is based on a tetramethylrhodamine-labeled, bacterial actin homologue, ParM. The design of the biosensor takes advantage of the large conformational change of ParM on ADP binding and the strong quenching of the tetramethylrhodamine fluorescence by stacking of the dye. ParM was labeled with two tetramethylrhodamines in close proximity, whereby the fluorophores are able to interact with each other. ADP binding alters the distance and relative orientation of the tetramethylrhodamines, which leads to a change in this stacking interaction and so in the fluorescence intensity. The final ADP biosensor shows approximately 15-fold fluorescence increase in response to ADP binding. It has relatively weak affinity for ADP (K(d) = 30 microM), enabling it to be used at substoichiometric concentrations relative to ADP, while reporting ADP concentration changes in a wide range around the K(d) value, namely, submicromolar to tens of micromolar. The biosensor strongly discriminates against ATP (>100-fold), allowing ADP detection against a background of millimolar ATP. At 20 degrees C, the labeled ParM binds ADP with a rate constant of 9.5 x 10(4) M(-1) s(-1) and the complex dissociates at 2.9 s(-1). Thus, the biosensor is suitable for real-time measurements, and its performance in such assays is demonstrated using a sugar kinase and a mammalian protein kinase.


Assuntos
Actinas/metabolismo , Difosfato de Adenosina/análise , Proteínas de Bactérias/metabolismo , Técnicas Biossensoriais/métodos , Corantes Fluorescentes/química , Rodaminas/química , Actinas/genética , Difosfato de Adenosina/metabolismo , Adenilato Quinase/metabolismo , Animais , Proteínas de Bactérias/genética , Hexoquinase/metabolismo , Ligação Proteica , Saccharomyces cerevisiae/enzimologia , Sensibilidade e Especificidade
13.
J Biol Chem ; 284(48): 33130-8, 2009 Nov 27.
Artigo em Inglês | MEDLINE | ID: mdl-19801632

RESUMO

Nearly every cellular process requires the presence of ATP. This is reflected in the vast number of enzymes like kinases or ATP hydrolases, both of which cleave the terminal phosphate from ATP, thereby releasing ADP. Despite the fact that ATP hydrolysis is one of the most fundamental reactions in biological systems, there are only a few methods available for direct measurements of enzymatic-driven ATP conversion. Here we describe the development of a reagentless biosensor for ADP, the common product of all ATPases and kinases, which allows the real-time detection of ADP, produced enzymatically. The biosensor is derived from a bacterial actin homologue, ParM, as protein framework. A single fluorophore (a diethylaminocoumarin), attached to ParM at the edge of the nucleotide binding site, couples ADP binding to a >3.5-fold increase in fluorescence intensity. The labeled ParM variant has high affinity for ADP (0.46 mum) and a fast signal response, controlled by the rate of ADP binding to the sensor (0.65 microm(-1)s(-1)). Amino acids in the active site were mutated to reduce ATP affinity and achieve a >400-fold discrimination against triphosphate binding. A further mutation ensured that the final sensor did not form filaments and, as a consequence, has extremely low ATPase activity. The broad applicability of N-[2-(1-maleimidyl)ethyl]-7-diethylaminocoumarin-3-carboxamide (MDCC)-ParM as a sensitive probe for ADP is demonstrated in real-time kinetic assays on two different ATPases and a protein kinase.


Assuntos
Difosfato de Adenosina/análise , Trifosfato de Adenosina/metabolismo , Técnicas Biossensoriais/métodos , Espectrometria de Fluorescência/métodos , Actinas/química , Actinas/genética , Actinas/metabolismo , Difosfato de Adenosina/química , Difosfato de Adenosina/metabolismo , Adenosina Trifosfatases/metabolismo , Ligação Competitiva , Técnicas Biossensoriais/instrumentação , Cumarínicos/química , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Hidrólise , Cinética , Modelos Moleculares , Mutação , Ligação Proteica , Proteínas Quinases/metabolismo , Estrutura Terciária de Proteína , Reprodutibilidade dos Testes
14.
J Mol Biol ; 392(4): 1020-32, 2009 Oct 02.
Artigo em Inglês | MEDLINE | ID: mdl-19647000

RESUMO

The superfamily 1 bacterial helicase PcrA has a role in the replication of certain plasmids, acting with the initiator protein (RepD) that binds to and nicks the double-stranded origin of replication. PcrA also translocates single-stranded DNA with discrete steps of one base per ATP hydrolyzed. Individual rate constants have been determined for the DNA helicase PcrA ATPase cycle when bound to either single-stranded DNA or a double-stranded DNA junction that also has RepD bound. The fluorescent ATP analogue 2'(3')-O-(N-methylanthraniloyl)ATP was used throughout all experiments to provide a complete ATPase cycle for a single nucleotide species. Fluorescence intensity and anisotropy stopped-flow measurements were used to determine rate constants for binding and release. Quenched-flow measurements provided the kinetics of the hydrolytic cleavage step. The fluorescent phosphate sensor MDCC-PBP was used to measure phosphate release kinetics. The chemical cleavage step is the rate-limiting step in the cycle and is essentially irreversible and would result in the bound ATP complex being a major component at steady state. This cleavage step is greatly accelerated by bound DNA, producing the high activation of this protein compared to the protein alone. The data suggest the possibility that ADP is released in two steps, which would result in bound ADP also being a major intermediate, with bound ADP.P(i) being a very small component. It therefore seems likely that the major transition in structure occurs during the cleavage step, rather than P(i) release. ATP rebinding could then cause reversal of this structural transition. The kinetic mechanism of the PcrA ATPase cycle is very little changed by potential binding to RepD, supporting the idea that RepD increases the processivity of PcrA by increasing affinity to DNA rather than affecting the enzymatic properties per se.


Assuntos
Adenosina Trifosfatases/metabolismo , Proteínas de Bactérias/metabolismo , DNA Helicases/metabolismo , DNA Bacteriano/metabolismo , Geobacillus stearothermophilus/enzimologia , Trifosfato de Adenosina/metabolismo , Sequência de Bases , DNA/metabolismo , Geobacillus stearothermophilus/genética , Geobacillus stearothermophilus/metabolismo , Hidrólise , Modelos Biológicos , Dados de Sequência Molecular , Oxigênio/metabolismo , Fosfatos/metabolismo , Ligação Proteica , Transporte Proteico
15.
Cell ; 137(5): 849-59, 2009 May 29.
Artigo em Inglês | MEDLINE | ID: mdl-19490894

RESUMO

Superfamily 1B (SF1B) helicases translocate in a 5'-3' direction and are required for a range of cellular activities across all domains of life. However, structural analyses to date have focused on how SF1A helicases achieve 3'-5' movement along nucleic acids. We present crystal structures of the complex between the SF1B helicase RecD2 from Deinococcus radiodurans and ssDNA in the presence and absence of an ATP analog. These snapshots of the reaction pathway reveal a nucleotide binding-induced conformational change of the two motor domains that is broadly reminiscent of changes observed in other SF1 and SF2 helicases. Together with biochemical data, the structures point to a step size for translocation of one base per ATP hydrolyzed. Moreover, the structures also reveal a mechanism for nucleic acid translocation in the 5'-3' direction by SF1B helicases that is surprisingly different from that of 3'-5' translocation by SF1A enzymes, and explains the molecular basis of directionality.


Assuntos
DNA Helicases/química , DNA Helicases/metabolismo , Deinococcus/enzimologia , Trifosfato de Adenosina/análogos & derivados , Cristalografia por Raios X , DNA de Cadeia Simples/metabolismo , Modelos Moleculares , Estrutura Terciária de Proteína
16.
Biochemistry ; 48(27): 6326-34, 2009 Jul 14.
Artigo em Inglês | MEDLINE | ID: mdl-19473041

RESUMO

The plasmid replication initiator protein, RepD, greatly stimulates the ability of the DNA helicase, PcrA, to unwind plasmid lengths of DNA. Unwinding begins at oriD, the double-stranded origin of replication that RepD recognizes and covalently binds to initiate replication. Using a combination of plasmids containing oriD and oligonucleotide structures that mimic parts of oriD, the kinetics of DNA nicking and separation have been determined, along with the coupling ratio between base separation and ATP hydrolysis. At 30 degrees C, the rate of nicking is 1.0 s(-1), and translocation is approximately 30 bp s(-1). During translocation, the coupling ratio is one ATP hydrolyzed per base pair separated, the same as the value previously reported for ATP hydrolyzed per base moved by PcrA along single-stranded DNA. The data suggest that processivity is high, such that several thousand base-pair plasmids are unwound by a single molecule of PcrA. In the absence of RepD, a single PcrA is unable to separate even short lengths (10 to 40 bp) of double stranded DNA.


Assuntos
Trifosfato de Adenosina/metabolismo , Proteínas de Bactérias/metabolismo , DNA Helicases/metabolismo , DNA/metabolismo , Geobacillus stearothermophilus/enzimologia , Plasmídeos , Sequência de Bases , Primers do DNA , Hidrólise , Cinética , Reação em Cadeia da Polimerase
17.
Biophys J ; 96(8): 3281-94, 2009 Apr 22.
Artigo em Inglês | MEDLINE | ID: mdl-19383472

RESUMO

A phosphorylated, single cysteine mutant of nucleoside diphosphate kinase, labeled with N-[2-(iodoacetamido)ethyl]-7-diethylaminocoumarin-3-carboxamide (P approximately NDPK-IDCC), was used as a fluorescence probe for time-resolved measurement of changes in [MgADP] during contraction of single permeabilized rabbit psoas fibers. The dephosphorylation of the phosphorylated protein by MgADP occurs within the lattice environment of permeabilized fibers with a second-order rate constant at 12 degrees C of 10(5) M(-1) s(-1). This dephosphorylation is accompanied by a change in coumarin fluorescence. We report the time course of P approximately NDPK-IDCC dephosphorylation during the period of active isometric force redevelopment after quick release of fiber strain at pCa(2+) of 4.5. After a rapid length decrease of 0.5% was applied to the fiber, the extra NDPK-IDCC produced during force recovery, above the value during the approximately steady state of isometric contraction, was 2.7 +/- 0.6 microM and 4.7 +/- 1.5 microM at 12 and 20 degrees C, respectively. The rates of P approximately NDPK-IDCC dephosphorylation during force recovery were 28 and 50 s(-1) at 12 and 20 degrees C, respectively. The time courses of isometric force and P approximately NDPK-IDCC dephosphorylation were simulated using a seven-state reaction scheme. Relative isometric force was modeled by changes in the occupancy of strongly bound A.M.ADP.P(i) and A.M.ADP states. A strain-sensitive A.M.ADP isomerization step was rate-limiting (3-6 s(-1)) in the cross-bridge turnover during isometric contraction. At 12 degrees C, the A.M.ADP.P(i) and the pre- and postisomerization A.M.ADP states comprised 56%, 38%, and 7% of the isometric force-bearing AM states, respectively. At 20 degrees C, the force-bearing A.M.ADP.P(i) state was a lower proportion of the total force-bearing states (37%), whereas the proportion of postisomerization A.M.ADP states was higher (19%). The simulations suggested that release of cross-bridge strain caused rapid depopulation of the preisomerization A.M.ADP state and transient accumulation of MgADP in the postisomerization A.M.ADP state. Hence, the strain-sensitive isomerization of A.M.ADP seems to explain the rate of change of P approximately NDPK-IDCC dephosphorylation during force recovery. The temperature-dependent isometric distribution of myosin states is consistent with the previous observation of a small decrease in amplitude of the P(i) transient during force recovery at 20 degrees C and the current observation of an increase in amplitude of the ADP-sensitive NDPK-IDCC transient.


Assuntos
Difosfato de Adenosina/metabolismo , Contração Muscular/fisiologia , Fibras Musculares Esqueléticas/metabolismo , Animais , Cálcio/metabolismo , Simulação por Computador , Cumarínicos , Feminino , Fluorescência , Cinética , Modelos Lineares , Força Muscular , Mutação de Sentido Incorreto , Núcleosídeo-Difosfato Quinase/genética , Fosforilação , Isoformas de Proteínas/metabolismo , Músculos Psoas/metabolismo , Coelhos
18.
J Biol Chem ; 284(4): 2138-49, 2009 Jan 23.
Artigo em Inglês | MEDLINE | ID: mdl-19008235

RESUMO

We have determined the kinetic mechanism and motile properties of the switch 1 mutant S217A of myosin Va. Phosphate dissociation from myosin V-ADP-Pi (inorganic phosphate) and actomyosin V-ADP-Pi and the rate of the hydrolysis step (myosin V-ATP-->myosin V-ADP-Pi) were all approximately 10-fold slower in the S217A mutant than in wild type (WT) myosin V, resulting in a slower steady-state rate of basal and filamentous actin (actin)-activated ATP hydrolysis. Substrate binding and ADP dissociation kinetics were all similar to or slightly faster in S217A than in WT myosin V and mechanochemical gating of the rates of dissociation of ADP between trail and lead heads is maintained. The reduction in the rate constants of the hydrolysis and phosphate dissociation steps reduces the duty ratio from approximately 0.85 in WT myosin V to approximately 0.25 in S217A and produces a motor in which the average run length on actin at physiological concentrations of ATP is reduced 10-fold. Thus we demonstrate that, by mutational perturbation of the switch 1 structure, myosin V can be converted into a low duty ratio motor that is processive only at low substrate concentrations.


Assuntos
Miosina Tipo V/metabolismo , Actinas/metabolismo , Difosfato de Adenosina/metabolismo , Trifosfato de Adenosina/metabolismo , Animais , Linhagem Celular , Hidrólise , Cinética , Camundongos , Mutação , Subfragmentos de Miosina/metabolismo , Miosina Tipo V/genética , Fosfatos/metabolismo , Ligação Proteica , Coelhos , Serina/genética , Serina/metabolismo , Spodoptera
19.
Nature ; 455(7209): 128-32, 2008 Sep 04.
Artigo em Inglês | MEDLINE | ID: mdl-18668042

RESUMO

Myosin Va transports intracellular cargoes along actin filaments in cells. This processive, two-headed motor takes multiple 36-nm steps in which the two heads swing forward alternately towards the barbed end of actin driven by ATP hydrolysis. The ability of myosin Va to move processively is a function of its long lever arm, the high duty ratio of its kinetic cycle and the gating of the kinetics between the two heads such that ADP release from the lead head is greatly retarded. Mechanical studies at the multiple- and the single-molecule level suggest that there is tight coupling (that is, one ATP is hydrolysed per power stroke), but this has not been directly demonstrated. We therefore investigated the coordination between the ATPase mechanism of the two heads of myosin Va and directly visualized the binding and dissociation of single fluorescently labelled nucleotide molecules, while simultaneously observing the stepping motion of the fluorescently labelled myosin Va as it moved along an actin filament. Here we show that preferential ADP dissociation from the trail head of mouse myosin Va is followed by ATP binding and a synchronous 36-nm step. Even at low ATP concentrations, the myosin Va molecule retained at least one nucleotide (ADP in the lead head position) when moving. Thus, we directly demonstrate tight coupling between myosin Va movement and the binding and dissociation of nucleotide by simultaneously imaging with near nanometre precision.


Assuntos
Movimento , Cadeias Pesadas de Miosina/metabolismo , Miosina Tipo V/metabolismo , Difosfato de Adenosina/metabolismo , Trifosfato de Adenosina/análogos & derivados , Trifosfato de Adenosina/metabolismo , Animais , Cumarínicos/metabolismo , Corantes Fluorescentes , Cinética , Camundongos , Microscopia de Fluorescência , Cadeias Pesadas de Miosina/ultraestrutura , Subfragmentos de Miosina/metabolismo , Subfragmentos de Miosina/ultraestrutura , Miosina Tipo V/ultraestrutura , Ligação Proteica
20.
J Biol Chem ; 283(2): 766-73, 2008 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-17965414

RESUMO

Myosin V is a cellular motor protein, which transports cargos along actin filaments. It moves processively by 36-nm steps that require at least one of the two heads to be tightly bound to actin throughout the catalytic cycle. To elucidate the kinetic mechanism of processivity, we measured the rate of product release from the double-headed myosin V-HMM using a new ATP analogue, 3'-(7-diethylaminocoumarin-3-carbonylamino)-3'-deoxy-ATP (deac-aminoATP), which undergoes a 20-fold increase in fluorescence emission intensity when bound to the active site of myosin V (Forgacs, E., Cartwright, S., Kovács, M., Sakamoto, T., Sellers, J. R., Corrie, J. E. T., Webb, M. R., and White, H. D. (2006) Biochemistry 45, 13035-13045). The kinetics of ADP and deac-aminoADP dissociation from actomyosin V-HMM, following the power stroke, were determined using double-mixing stopped-flow fluorescence. These used either deac-aminoATP as the substrate with ADP or ATP chase or alternatively ATP as the substrate with either a deac-aminoADP or deac-aminoATP chase. Both sets of experiments show that the observed rate of ADP or deac-aminoADP dissociation from the trail head of actomyosin V-HMM is the same as from actomyosin V-S1. The dissociation of ADP from the lead head is decreased by up to 250-fold.


Assuntos
Actomiosina/metabolismo , Difosfato de Adenosina/metabolismo , Miosina Tipo V/metabolismo , Actinas/isolamento & purificação , Actinas/metabolismo , Animais , Hidrólise , Cinética , Camundongos , Músculo Esquelético/metabolismo , Subfragmentos de Miosina/metabolismo , Coelhos , Espectrometria de Fluorescência
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