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1.
Nat Commun ; 15(1): 3850, 2024 May 08.
Article in English | MEDLINE | ID: mdl-38719864

ABSTRACT

The K+ uptake system KtrAB is essential for bacterial survival in low K+ environments. The activity of KtrAB is regulated by nucleotides and Na+. Previous studies proposed a putative gating mechanism of KtrB regulated by KtrA upon binding to ATP or ADP. However, how Na+ activates KtrAB and the Na+ binding site remain unknown. Here we present the cryo-EM structures of ATP- and ADP-bound KtrAB from Bacillus subtilis (BsKtrAB) both solved at 2.8 Å. A cryo-EM density at the intra-dimer interface of ATP-KtrA was identified as Na+, as supported by X-ray crystallography and ICP-MS. Thermostability assays and functional studies demonstrated that Na+ binding stabilizes the ATP-bound BsKtrAB complex and enhances its K+ flux activity. Comparing ATP- and ADP-BsKtrAB structures suggests that BsKtrB Arg417 and Phe91 serve as a channel gate. The synergism of ATP and Na+ in activating BsKtrAB is likely applicable to Na+-activated K+ channels in central nervous system.


Subject(s)
Adenosine Diphosphate , Adenosine Triphosphate , Bacillus subtilis , Bacterial Proteins , Potassium , Sodium , Adenosine Triphosphate/metabolism , Bacillus subtilis/metabolism , Sodium/metabolism , Bacterial Proteins/metabolism , Bacterial Proteins/chemistry , Potassium/metabolism , Crystallography, X-Ray , Adenosine Diphosphate/metabolism , Cryoelectron Microscopy , Binding Sites , Cation Transport Proteins/metabolism , Cation Transport Proteins/chemistry , Models, Molecular , Protein Binding
3.
Diabetes ; 73(6): 849-855, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38768365

ABSTRACT

The canonical model of glucose-induced increase in insulin secretion involves the metabolism of glucose via glycolysis and the citrate cycle, resulting in increased ATP synthesis by the respiratory chain and the closure of ATP-sensitive K+ (KATP) channels. The resulting plasma membrane depolarization, followed by Ca2+ influx through L-type Ca2+ channels, then induces insulin granule fusion. Merrins and colleagues have recently proposed an alternative model whereby KATP channels are controlled by pyruvate kinase, using glycolytic and mitochondrial phosphoenolpyruvate (PEP) to generate microdomains of high ATP/ADP immediately adjacent to KATP channels. This model presents several challenges. First, how mitochondrially generated PEP, but not ATP produced abundantly by the mitochondrial F1F0-ATP synthase, can gain access to the proposed microdomains is unclear. Second, ATP/ADP fluctuations imaged immediately beneath the plasma membrane closely resemble those in the bulk cytosol. Third, ADP privation of the respiratory chain at high glucose, suggested to drive alternating, phased-locked generation by mitochondria of ATP or PEP, has yet to be directly demonstrated. Finally, the approaches used to explore these questions may be complicated by off-target effects. We suggest instead that Ca2+ changes, well known to affect both ATP generation and consumption, likely drive cytosolic ATP/ADP oscillations that in turn regulate KATP channels and membrane potential. Thus, it remains to be demonstrated that a new model is required to replace the existing, mitochondrial bioenergetics-based model.


Subject(s)
Glucose , Insulin-Secreting Cells , KATP Channels , Insulin-Secreting Cells/metabolism , KATP Channels/metabolism , Glucose/metabolism , Humans , Animals , Adenosine Triphosphate/metabolism , Mitochondria/metabolism , Insulin/metabolism , Adenosine Diphosphate/metabolism , Models, Biological , Insulin Secretion/physiology
4.
PLoS Comput Biol ; 20(5): e1012158, 2024 May.
Article in English | MEDLINE | ID: mdl-38768214

ABSTRACT

The self-organization of cells relies on the profound complexity of protein-protein interactions. Challenges in directly observing these events have hindered progress toward understanding their diverse behaviors. One notable example is the interaction between molecular motors and cytoskeletal systems that combine to perform a variety of cellular functions. In this work, we leverage theory and experiments to identify and quantify the rate-limiting mechanism of the initial association between a cargo-bound kinesin motor and a microtubule track. Recent advances in optical tweezers provide binding times for several lengths of kinesin motors trapped at varying distances from a microtubule, empowering the investigation of competing models. We first explore a diffusion-limited model of binding. Through Brownian dynamics simulations and simulation-based inference, we find this simple diffusion model fails to explain the experimental binding times, but an extended model that accounts for the ADP state of the molecular motor agrees closely with the data, even under the scrutiny of penalizing for additional model complexity. We provide quantification of both kinetic rates and biophysical parameters underlying the proposed binding process. Our model suggests that a typical binding event is limited by ADP state rather than physical search. Lastly, we predict how these association rates can be modulated in distinct ways through variation of environmental concentrations and physical properties.


Subject(s)
Kinesins , Microtubules , Protein Binding , Kinesins/metabolism , Kinesins/chemistry , Kinetics , Microtubules/metabolism , Microtubules/chemistry , Computational Biology , Adenosine Diphosphate/metabolism , Adenosine Diphosphate/chemistry , Computer Simulation , Models, Biological , Diffusion
5.
Int J Mol Sci ; 25(10)2024 May 13.
Article in English | MEDLINE | ID: mdl-38791359

ABSTRACT

The excessive activation of frog eggs, referred to as overactivation, can be initiated by strong oxidative stress, leading to expedited calcium-dependent non-apoptotic cell death. Overactivation also occurs spontaneously, albeit at a low frequency, in natural populations of spawned frog eggs. Currently, the cytological and biochemical events of the spontaneous process have not been characterized. In the present study, we demonstrate that the spontaneous overactivation of Xenopus frog eggs, similarly to oxidative stress- and mechanical stress-induced overactivation, is characterized by the fast and irreversible contraction of the egg's cortical layer, an increase in egg size, the depletion of intracellular ATP, a drastic increase in the intracellular ADP/ATP ratio, and the degradation of M phase-specific cyclin B2. These events manifest in eggs in the absence of caspase activation within one hour of triggering overactivation. Importantly, substantial amounts of ATP and ADP leak from the overactivated eggs, indicating that plasma membrane integrity is compromised in these cells. The rupture of the plasma membrane and acute depletion of intracellular ATP explicitly define necrotic cell death. Finally, we report that egg overactivation can occur in the frog's genital tract. Our data suggest that mechanical stress may be a key factor promoting egg overactivation during oviposition in frogs.


Subject(s)
Adenosine Triphosphate , Necrosis , Ovum , Animals , Adenosine Triphosphate/metabolism , Ovum/metabolism , Xenopus laevis/metabolism , Female , Oxidative Stress , Adenosine Diphosphate/metabolism , Cell Death , Cell Membrane/metabolism , Stress, Mechanical
6.
Int J Biol Macromol ; 269(Pt 1): 132000, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38697445

ABSTRACT

The sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) transports two Ca2+ ions per ATP hydrolyzed from the cytoplasm to the lumen. However, how the ATP hydrolysis remotely drives the Ca2+ transport is unclear. In the SERCA1a crystal structures, the ATP hydrolysis is accompanied by the notably increasing tilting angle of the central core (CC) and the Ca2+ transport, and the CC tilting angle dramatically decreases in the E2 to E1 transition. We demonstrated that the significantly increasing tilting motion of the CC drove the Ca2+ release in the molecular dynamics simulation of the R836A variant, and the dramatic spontaneous decrease in the CC tilting angle of the E2 state triggers the restart of the SERCA1a's transport cycle. The repulsion between the phosphorylated D351 and the phosphate groups in ADP triggers the release of ADP from the SERCA1a headpiece. We proposed a novel SERCA transport mechanism in which ATP hydrolysis drives a significant tilting motion of the CC, which drives Ca2+ transport and the A domain rotational motion in the E1P-ADP-2Ca2+ to E2P transition. The dramatic spontaneous decrease in the CC tilting angle of the E2 state drives the restart of the transport cycle.


Subject(s)
Adenosine Triphosphate , Calcium , Molecular Dynamics Simulation , Sarcoplasmic Reticulum Calcium-Transporting ATPases , Sarcoplasmic Reticulum Calcium-Transporting ATPases/metabolism , Sarcoplasmic Reticulum Calcium-Transporting ATPases/chemistry , Calcium/metabolism , Adenosine Triphosphate/metabolism , Hydrolysis , Adenosine Diphosphate/metabolism , Humans , Biological Transport
7.
Biosystems ; 240: 105228, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38735525

ABSTRACT

The nonequilibrium coupled processes of oxidation and ATP synthesis in the fundamental process of oxidative phosphorylation (OXPHOS) are of vital importance in biosystems. These coupled chemical reaction and transport bioenergetic processes using the OXPHOS pathway meet >90% of the ATP demand in aerobic systems. On the basis of experimentally determined thermodynamic OXPHOS flux-force relationships and biochemical data for the ternary system of oxidation, ion transport, and ATP synthesis, the Onsager phenomenological coefficients have been computed, including an estimate of error. A new biothermokinetic theory of energy coupling has been formulated and on its basis the thermodynamic parameters, such as the overall degree of coupling, q and the phenomenological stoichiometry, Z of the coupled system have been evaluated. The amount of ATP produced per oxygen consumed, i.e. the actual, operating P/O ratio in the biosystem, the thermodynamic efficiency of the coupled reactions, η, and the Gibbs free energy dissipation, Φ have been calculated and shown to be in agreement with experimental data. At the concentration gradients of ADP and ATP prevailing under state 3 physiological conditions of OXPHOS that yield Vmax rates of ATP synthesis, a maximum in Φ of ∼0.5J(hmgprotein)-1, corresponding to a thermodynamic efficiency of ∼60% for oxidation on succinate, has been obtained. Novel mechanistic insights arising from the above have been discussed. This is the first report of a 3 × 3 system of coupled chemical reactions with transport in a biological context in which the phenomenological coefficients have been evaluated from experimental data.


Subject(s)
Adenosine Triphosphate , Energy Metabolism , Oxidative Phosphorylation , Thermodynamics , Adenosine Triphosphate/metabolism , Energy Metabolism/physiology , Oxidation-Reduction , Models, Biological , Kinetics , Adenosine Diphosphate/metabolism , Humans
8.
Nat Commun ; 15(1): 4655, 2024 May 31.
Article in English | MEDLINE | ID: mdl-38821922

ABSTRACT

The human AAA-ATPase Bcs1L translocates the fully assembled Rieske iron-sulfur protein (ISP) precursor across the mitochondrial inner membrane, enabling respiratory Complex III assembly. Exactly how the folded substrate is bound to and released from Bcs1L has been unclear, and there has been ongoing debate as to whether subunits of Bcs1L act in sequence or in unison hydrolyzing ATP when moving the protein cargo. Here, we captured Bcs1L conformations by cryo-EM during active ATP hydrolysis in the presence or absence of ISP substrate. In contrast to the threading mechanism widely employed by AAA proteins in substrate translocation, subunits of Bcs1L alternate uniformly between ATP and ADP conformations without detectable intermediates that have different, co-existing nucleotide states, indicating that the subunits act in concert. We further show that the ISP can be trapped by Bcs1 when its subunits are all in the ADP-bound state, which we propose to be released in the apo form.


Subject(s)
ATPases Associated with Diverse Cellular Activities , Adenosine Diphosphate , Adenosine Triphosphate , Cryoelectron Microscopy , Electron Transport Complex III , Adenosine Triphosphate/metabolism , Hydrolysis , Electron Transport Complex III/metabolism , Electron Transport Complex III/chemistry , Humans , Adenosine Diphosphate/metabolism , ATPases Associated with Diverse Cellular Activities/metabolism , ATPases Associated with Diverse Cellular Activities/chemistry , Iron-Sulfur Proteins/metabolism , Iron-Sulfur Proteins/chemistry , Protein Conformation , Protein Folding , Models, Molecular , Protein Transport
9.
Nat Commun ; 15(1): 4491, 2024 May 27.
Article in English | MEDLINE | ID: mdl-38802374

ABSTRACT

Actin nucleotide-dependent actin remodeling is essential to orchestrate signal transduction and cell adaptation. Rapid energy starvation requires accurate and timely reorganization of the actin network. Despite distinct treadmilling mechanisms of ADP- and ATP-actin filaments, their filament structures are nearly identical. How other actin-binding proteins regulate ADP-actin filament assembly is unclear. Here, we show that Spa2 which is the polarisome scaffold protein specifically remodels ADP-actin upon energy starvation in budding yeast. Spa2 triggers ADP-actin monomer nucleation rapidly through a dimeric core of Spa2 (aa 281-535). Concurrently, the intrinsically disordered region (IDR, aa 1-281) guides Spa2 undergoing phase separation and wetting on the surface of ADP-G-actin-derived F-actin and bundles the filaments. Both ADP-actin-specific nucleation and bundling activities of Spa2 are actin D-loop dependent. The IDR and nucleation core of Spa2 are evolutionarily conserved by coexistence in the fungus kingdom, suggesting a universal adaptation mechanism in the fungal kingdom in response to glucose starvation, regulating ADP-G-actin and ADP-F-actin with high nucleotide homogeneity.


Subject(s)
Actins , Adenosine Diphosphate , Glucose , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Actin Cytoskeleton/metabolism , Actins/metabolism , Adenosine Diphosphate/metabolism , Adenosine Diphosphate/analogs & derivatives , Glucose/metabolism , Microfilament Proteins/metabolism , Microfilament Proteins/genetics , Microfilament Proteins/chemistry , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/chemistry
10.
Front Immunol ; 15: 1328306, 2024.
Article in English | MEDLINE | ID: mdl-38590528

ABSTRACT

CD39 is the major enzyme controlling the levels of extracellular adenosine triphosphate (ATP) via the stepwise hydrolysis of ATP to adenosine diphosphate (ADP) and adenosine monophosphate (AMP). As extracellular ATP is a strong promoter of inflammation, monoclonal antibodies (mAbs) blocking CD39 are utilized therapeutically in the field of immune-oncology. Though anti-CD39 mAbs are highly specific for their target, they lack deep penetration into the dense tissue of solid tumors, due to their large size. To overcome this limitation, we generated and characterized nanobodies that targeted and blocked human CD39. From cDNA-immunized alpacas we selected 16 clones from seven nanobody families that bind to two distinct epitopes of human CD39. Among these, clone SB24 inhibited the enzymatic activity of CD39. Of note, SB24 blocked ATP degradation by both soluble and cell surface CD39 as a 15kD monomeric nanobody. Dimerization via fusion to an immunoglobulin Fc portion further increased the blocking potency of SB24 on CD39-transfected HEK cells. Finally, we confirmed the CD39 blocking properties of SB24 on human PBMCs. In summary, SB24 provides a new small biological antagonist of human CD39 with potential application in cancer therapy.


Subject(s)
Single-Domain Antibodies , Humans , Single-Domain Antibodies/pharmacology , Adenosine Triphosphate/metabolism , Adenosine Monophosphate , Adenosine Diphosphate/metabolism
11.
Biochem J ; 481(8): 587-599, 2024 Apr 24.
Article in English | MEDLINE | ID: mdl-38592738

ABSTRACT

The AMP-activated protein kinase (AMPK) is a sensor of cellular energy status. When activated by increases in ADP:ATP and/or AMP:ATP ratios (signalling energy deficit), AMPK acts to restore energy balance. Binding of AMP to one or more of three CBS repeats (CBS1, CBS3, CBS4) on the AMPK-γ subunit activates the kinase complex by three complementary mechanisms: (i) promoting α-subunit Thr172 phosphorylation by the upstream kinase LKB1; (ii) protecting against Thr172 dephosphorylation; (iii) allosteric activation. Surprisingly, binding of ADP has been reported to mimic the first two effects, but not the third. We now show that at physiologically relevant concentrations of Mg.ATP2- (above those used in the standard assay) ADP binding does cause allosteric activation. However, ADP causes only a modest activation because (unlike AMP), at concentrations just above those where activation becomes evident, ADP starts to cause competitive inhibition at the catalytic site. Our results cast doubt on the physiological relevance of the effects of ADP and suggest that AMP is the primary activator in vivo. We have also made mutations to hydrophobic residues involved in binding adenine nucleotides at each of the three γ subunit CBS repeats of the human α2ß2γ1 complex and examined their effects on regulation by AMP and ADP. Mutation of the CBS3 site has the largest effects on all three mechanisms of AMP activation, especially at lower ATP concentrations, while mutation of CBS4 reduces the sensitivity to AMP. All three sites appear to be required for allosteric activation by ADP.


Subject(s)
AMP-Activated Protein Kinases , Adenosine Diphosphate , Adenosine Monophosphate , Adenosine Diphosphate/metabolism , Adenosine Monophosphate/metabolism , Humans , Allosteric Regulation , AMP-Activated Protein Kinases/metabolism , AMP-Activated Protein Kinases/genetics , AMP-Activated Protein Kinases/chemistry , Ligands , Phosphorylation , Adenosine Triphosphate/metabolism , Enzyme Activation , Protein Binding
12.
Arch Biochem Biophys ; 756: 109998, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38641233

ABSTRACT

The kinesin-5 family member, Eg5, plays very important role in the mitosis. As a mitotic protein, Eg5 is the target of various mitotic inhibitors. There are two targeting pockets in the motor domain of Eg5, which locates in the α2/L5/α3 region and the α4/α6 region respectively. We investigated the interactions between the different inhibitors and the two binding pockets of Eg5 by using all-atom molecular dynamics method. Combined the conformational analysis with the free-energy calculation, the binding patterns of inhibitors to the two binding pockets are shown. The α2/L5/α3 pocket can be divided into 4 regions. The structures and binding conformations of inhibitors in region 1 and 2 are highly conserved. The shape of α4/α6 pocket is alterable. The space of this pocket in ADP-binding state of Eg5 is larger than that in ADP·Pi-binding state due to the limitation of a hydrogen bond formed in the ADP·Pi-binding state. The results of this investigation provide the structural basis of the inhibitor-Eg5 interaction and offer a reference for the Eg5-targeted drug design.


Subject(s)
Kinesins , Molecular Dynamics Simulation , Protein Binding , Kinesins/antagonists & inhibitors , Kinesins/chemistry , Kinesins/metabolism , Binding Sites , Humans , Adenosine Diphosphate/metabolism , Adenosine Diphosphate/chemistry , Hydrogen Bonding
13.
J Biol Chem ; 300(5): 107279, 2024 May.
Article in English | MEDLINE | ID: mdl-38588808

ABSTRACT

Actin bundling proteins crosslink filaments into polarized structures that shape and support membrane protrusions including filopodia, microvilli, and stereocilia. In the case of epithelial microvilli, mitotic spindle positioning protein (MISP) is an actin bundler that localizes specifically to the basal rootlets, where the pointed ends of core bundle filaments converge. Previous studies established that MISP is prevented from binding more distal segments of the core bundle by competition with other actin-binding proteins. Yet whether MISP holds a preference for binding directly to rootlet actin remains an open question. By immunostaining native intestinal tissue sections, we found that microvillar rootlets are decorated with the severing protein, cofilin, suggesting high levels of ADP-actin in these structures. Using total internal reflection fluorescence microscopy assays, we also found that purified MISP exhibits a binding preference for ADP- versus ADP-Pi-actin-containing filaments. Consistent with this, assays with actively growing actin filaments revealed that MISP binds at or near their pointed ends. Moreover, although substrate attached MISP assembles filament bundles in parallel and antiparallel configurations, in solution MISP assembles parallel bundles consisting of multiple filaments exhibiting uniform polarity. These discoveries highlight nucleotide state sensing as a mechanism for sorting actin bundlers along filaments and driving their accumulation near filament ends. Such localized binding might drive parallel bundle formation and/or locally modulate bundle mechanical properties in microvilli and related protrusions.


Subject(s)
Actins , Protein Binding , Actins/metabolism , Animals , Actin Cytoskeleton/metabolism , Microvilli/metabolism , Microfilament Proteins/metabolism , Cell Cycle Proteins/metabolism , Humans , Adenosine Diphosphate/metabolism , Actin Depolymerizing Factors/metabolism
14.
Int J Artif Organs ; 47(4): 269-279, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38506302

ABSTRACT

Centrifugal blood pumps can be used for treating heart failure patients. However, pump thrombosis has remained one of the complications that trouble clinical treatment. This study analyzed the effect of impeller shroud on the thrombosis risk of the blood pump, and predicted areas prone to thrombosis. Multi-constituent transport equations were presented, considering mechanical activation and biochemical activation. It was found that activated platelets concentration can increase with shear stress and adenosine diphosphate(ADP) concentration increasing, and the highest risk of thrombosis inside the blood pump was under extracorporeal membrane oxygenation (ECMO) mode. Under the same condition, ADP concentration and thrombosis index of semi-shroud impeller can increase by 7.3% and 7.2% compared to the closed-shroud impeller. The main reason for the increase in thrombosis risk was owing to elevated scalar shear stress and more coagulation promoting factor-ADP released. The regions with higher thrombosis potential were in the center hole, top and bottom clearance. As a novelty, the findings revealed that impeller shroud can influence mechanical and biochemical activation factors. It is useful for identifying potential risk regions of thrombus formation based on relative comparisons.


Subject(s)
Heart-Assist Devices , Stress, Mechanical , Thrombosis , Thrombosis/etiology , Thrombosis/physiopathology , Thrombosis/blood , Humans , Heart-Assist Devices/adverse effects , Platelet Activation , Models, Cardiovascular , Adenosine Diphosphate/metabolism , Prosthesis Design , Extracorporeal Membrane Oxygenation/adverse effects , Risk Factors , Blood Platelets/metabolism
15.
Proteomics ; 24(11): e2300391, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38556629

ABSTRACT

Arterial thrombosis manifesting as heart attack and stroke is the leading cause of death worldwide. Platelets are central mediators of thrombosis that can be activated through multiple activation pathways. Platelet-derived extracellular vesicles (pEVs), also known as platelet-derived microparticles, are granular mixtures of membrane structures produced by platelets in response to various activating stimuli. Initial studies have attracted interest on how platelet agonists influence the composition of the pEV proteome. In the current study, we used physiological platelet agonists of varying potencies which reflect the microenvironments that platelets experience during thrombus formation: adenosine diphosphate, collagen, thrombin as well as a combination of thrombin/collagen to induce platelet activation and pEV generation. Proteomic profiling revealed that pEVs have an agonist-dependent altered proteome in comparison to their cells of origin, activated platelets. Furthermore, we found that various protein classes including those related to coagulation and complement (prothrombin, antithrombin, and plasminogen) and platelet activation (fibrinogen) are attributed to platelet EVs following agonist stimulation. This agonist-dependent altered proteome suggests that protein packaging is an active process that appears to occur without de novo protein synthesis. This study provides new information on the influence of physiological agonist stimuli on the biogenesis and proteome landscape of pEVs.


Subject(s)
Blood Platelets , Extracellular Vesicles , Platelet Activation , Proteome , Proteomics , Thrombin , Blood Platelets/metabolism , Blood Platelets/drug effects , Humans , Proteome/metabolism , Extracellular Vesicles/metabolism , Extracellular Vesicles/drug effects , Platelet Activation/drug effects , Thrombin/pharmacology , Thrombin/metabolism , Proteomics/methods , Adenosine Diphosphate/pharmacology , Adenosine Diphosphate/metabolism , Collagen/metabolism
16.
J Thromb Haemost ; 22(6): 1715-1726, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38508397

ABSTRACT

BACKGROUND: Protease-activated receptor 4 (PAR4) mediates thrombin signaling on platelets and other cells. Our recent structural studies demonstrated that a single nucleotide polymorphism in extracellular loop 3 and PAR4-P310L (rs2227376) leads to a hyporeactive receptor. OBJECTIVES: The goal of this study was to determine how the hyporeactive PAR4 variant in extracellular loop 3 impacts platelet function in vivo using a novel knock-in mouse model (PAR4-322L). METHODS: A point mutation was introduced into the PAR4 gene F2rl3 via CRISPR/Cas9 to create PAR4-P322L, the mouse homolog to human PAR4-P310L. Platelet response to PAR4 activation peptide (AYPGKF), thrombin, ADP, and convulxin was monitored by αIIbß3 integrin activation and P-selectin translocation using flow cytometry or platelet aggregation. In vivo responses were determined by the tail bleeding assay and the ferric chloride-induced carotid artery injury model. RESULTS: PAR4-P/L and PAR4-L/L platelets had a reduced response to AYPGKF and thrombin measured by P-selectin translocation or αIIbß3 activation. The response to ADP and convulxin was unchanged among genotypes. In addition, both PAR4-P/L and PAR4-L/L platelets showed a reduced response to thrombin in aggregation studies. There was an increase in the tail bleeding time for PAR4-L/L mice. The PAR4-P/L and PAR4-L/L mice both showed an extended time to arterial thrombosis. CONCLUSION: PAR4-322L significantly reduced platelet responsiveness to AYPGKF and thrombin, which is in agreement with our previous structural and cell signaling studies. In addition, PAR4-322L had prolonged arterial thrombosis time. Our mouse model provides a foundation to further evaluate the role of PAR4 in other pathophysiological contexts.


Subject(s)
Blood Platelets , Mice, Inbred C57BL , Platelet Aggregation , Platelet Glycoprotein GPIIb-IIIa Complex , Receptors, Thrombin , Thrombin , Animals , Blood Platelets/metabolism , Receptors, Thrombin/genetics , Receptors, Thrombin/metabolism , Thrombin/metabolism , Platelet Glycoprotein GPIIb-IIIa Complex/metabolism , Platelet Glycoprotein GPIIb-IIIa Complex/genetics , Disease Models, Animal , Crotalid Venoms/pharmacology , Crotalid Venoms/toxicity , Adenosine Diphosphate/metabolism , Adenosine Diphosphate/pharmacology , P-Selectin/metabolism , P-Selectin/genetics , Point Mutation , Gene Knock-In Techniques , Signal Transduction , Thrombosis/genetics , Thrombosis/blood , Male , Chlorides , Mice , Platelet Activation , CRISPR-Cas Systems , Humans , Phenotype , Ferric Compounds , Oligopeptides , Lectins, C-Type , Receptors, Proteinase-Activated
17.
Nucleic Acids Res ; 52(7): 3911-3923, 2024 Apr 24.
Article in English | MEDLINE | ID: mdl-38364872

ABSTRACT

Double-strand DNA breaks are the severest type of genomic damage, requiring rapid response to ensure survival. RecBCD helicase in prokaryotes initiates processive and rapid DNA unzipping, essential for break repair. The energetics of RecBCD during translocation along the DNA track are quantitatively not defined. Specifically, it's essential to understand the mechanism by which RecBCD switches between its binding states to enable its translocation. Here, we determine, by systematic affinity measurements, the degree of coupling between DNA and nucleotide binding to RecBCD. In the presence of ADP, RecBCD binds weakly to DNA that harbors a double overhang mimicking an unwinding intermediate. Consistently, RecBCD binds weakly to ADP in the presence of the same DNA. We did not observe coupling between DNA and nucleotide binding for DNA molecules having only a single overhang, suggesting that RecBCD subunits must both bind DNA to 'sense' the nucleotide state. On the contrary, AMPpNp shows weak coupling as RecBCD remains strongly bound to DNA in its presence. Detailed thermodynamic analysis of the RecBCD reaction mechanism suggests an 'energetic compensation' between RecB and RecD, which may be essential for rapid unwinding. Our findings provide the basis for a plausible stepping mechanism' during the processive translocation of RecBCD.


Subject(s)
DNA , Exodeoxyribonuclease V , Exodeoxyribonuclease V/metabolism , Binding Sites , DNA/metabolism , DNA/chemistry , Protein Binding , Adenosine Diphosphate/metabolism , Nucleotides/metabolism , Escherichia coli Proteins/metabolism , Escherichia coli Proteins/chemistry , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli/enzymology , DNA Repair
18.
Proteins ; 92(7): 808-818, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38333996

ABSTRACT

Isopentenyl phosphate kinases (IPKs) have recently garnered attention for their central role in biocatalytic "isoprenol pathways," which seek to reduce the synthesis of the isoprenoid precursors to two enzymatic steps. Furthermore, the natural promiscuity of IPKs toward non-natural alkyl-monophosphates (alkyl-Ps) as substrates has hinted at the isoprenol pathways' potential to access novel isoprenoids with potentially useful activities. However, only a handful of IPK crystal structures have been solved to date, and even fewer of these contain non-natural substrates bound in the active site. The current study sought to elucidate additional ternary complexes bound to non-natural substrates using the IPK homolog from Thermococcus paralvinellae (TcpIPK). Four such structures were solved, each bound to a different non-natural alkyl-P and the phosphoryl donor substrate/product adenosine triphosphate (ATP)/adenosine diphosphate (ADP). As expected, the quaternary, tertiary, and secondary structures of TcpIPK closely resembled those of IPKs published previously, and kinetic analysis of a novel alkyl-P substrate highlighted the potentially dramatic effects of altering the core scaffold of the natural substrate. Even more interesting, though, was the discovery of a trend correlating the position of two α helices in the active site with the magnitude of an IPK homolog's reaction rate for the natural reaction. Overall, the current structures of TcpIPK highlight the importance of continued structural analysis of the IPKs to better understand and optimize their activity with both natural and non-natural substrates.


Subject(s)
Adenosine Triphosphate , Catalytic Domain , Thermococcus , Substrate Specificity , Thermococcus/enzymology , Adenosine Triphosphate/metabolism , Adenosine Triphosphate/chemistry , Crystallography, X-Ray , Models, Molecular , Protein Binding , Kinetics , Archaeal Proteins/chemistry , Archaeal Proteins/metabolism , Archaeal Proteins/genetics , Hemiterpenes/metabolism , Hemiterpenes/chemistry , Protein Interaction Domains and Motifs , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Recombinant Proteins/genetics , Protein Conformation, alpha-Helical , Adenosine Diphosphate/metabolism , Adenosine Diphosphate/chemistry , Cloning, Molecular , Gene Expression , Protein Conformation, beta-Strand , Amino Acid Sequence , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli/enzymology , Protein Kinases
19.
J Am Chem Soc ; 146(10): 7105-7115, 2024 Mar 13.
Article in English | MEDLINE | ID: mdl-38417151

ABSTRACT

The binding of nucleotides is crucial for signal transduction as it induces conformational protein changes, leading to downstream cellular responses. Synthetic receptors that bind nucleotides and transduce the binding event into global conformational rearrangements are highly challenging to design, especially those that operate in an aqueous solution. Much work is focused on evaluating functionalized dyes to detect nucleotides, whereas coupling of a nucleotide-induced conformational switching to a sensing event has not been reported to date. We disclose synthetic receptors that undergo a global conformational rearrangement upon nucleotide binding. Integrating naphthalimide and the pyridinium ion into the structure enables stabilization of the folded conformation and efficient fluorescence quenching. The binding of a nucleotide rearranges the receptor conformation and alters the strong fluorescence enhancement. The methylpyridinium-containing receptor demonstrated high sensing selectivity for adenosine 5'-triphosphate (ATP) and a record 160-fold fluorescence enhancement. It can detect fluctuations of ATP in HeLa cells and possesses low cytotoxicity. The developed systems present an attractive approach for designing ATP-responsive artificial molecular switches that operate in water and integrate a strong fluorescence response.


Subject(s)
Adenosine Triphosphate , Receptors, Artificial , Humans , Adenosine Triphosphate/chemistry , Fluorescence , HeLa Cells , Nucleotides/metabolism , Positron-Emission Tomography , Spectrometry, Fluorescence , Protein Conformation , Fluorescent Dyes/chemistry , Adenosine Diphosphate/metabolism
20.
Br J Pharmacol ; 181(4): 564-579, 2024 02.
Article in English | MEDLINE | ID: mdl-36694432

ABSTRACT

BACKGROUND AND PURPOSE: Platelet function during inflammation is dependent on activation by endogenous nucleotides. Non-canonical signalling via the P2Y1 receptor is important for these non-thrombotic functions of platelets. However, apart from ADP, the role of other endogenous nucleotides acting as agonists at P2Y1 receptors is unknown. This study compared the effects of ADP, Ap3A, NAD+ , ADP-ribose, and Up4A on platelet functions contributing to inflammation or haemostasis. EXPERIMENTAL APPROACH: Platelets obtained from healthy human volunteers were incubated with ADP, Ap3A, NAD+ , ADP-ribose, or Up4A, with aggregation and fibrinogen binding measured (examples of function during haemostasis) or before exposure to fMLP to measure platelet chemotaxis (an inflammatory function). In silico molecular docking of these nucleotides to the binding pocket of P2Y1 receptors was then assessed. KEY RESULTS: Platelet aggregation and binding to fibrinogen induced by ADP was not mimicked by NAD+ , ADP-ribose, and Up4A. However, these endogenous nucleotides induced P2Y1 -dependent platelet chemotaxis, an effect that required RhoA and Rac-1 activity, but not canonical PLC activity. Analysis of molecular docking of the P2Y1 receptor revealed distinct differences of amino acid interactions and depth of fit within the binding pocket for Ap3A, NAD+ , ADP-ribose, or Up4A compared with ADP. CONCLUSION AND IMPLICATIONS: Platelet function (aggregation vs motility) can be differentially modulated by biased-agonist activation of P2Y1 receptors. This may be due to the character of the ligand-binding pocket interaction. This has implications for future therapeutic strategies aimed to suppress platelet activation during inflammation without affecting haemostasis as is the requirement of current ant-platelet drugs. LINKED ARTICLES: This article is part of a themed issue on Platelet purinergic receptor and non-thrombotic disease. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v181.4/issuetoc.


Subject(s)
Blood Platelets , NAD , Humans , Molecular Docking Simulation , NAD/metabolism , Adenosine Diphosphate/pharmacology , Adenosine Diphosphate/metabolism , Platelet Aggregation , Inflammation/metabolism , Fibrinogen/metabolism , Fibrinogen/pharmacology , Adenosine Diphosphate Ribose/metabolism , Adenosine Diphosphate Ribose/pharmacology , Receptors, Purinergic P2Y1/metabolism , Receptors, Purinergic P2Y12/metabolism
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