In certain structural or functional contexts, RNA structures can contain protonated nucleotides. However, a direct role for stably protonated nucleotides in ligand binding and ligand recognition has not yet been demonstrated unambiguously. Previous X-ray structures of c-GAMP binding riboswitch aptamer domains in complex with their near-cognate ligand c-di-GMP suggest that an adenine of the riboswitch either forms two hydrogen bonds to a G nucleotide of the ligand in the unusual enol tautomeric form or that the adenine in its N1 protonated form binds the G nucleotide of the ligand in its canonical keto tautomeric state.
By using NMR spectroscopy we demonstrate that the c-GAMP riboswitches bind c-di-GMP using a stably protonated adenine in the ligand binding pocket. Thereby, we provide novel insights into the putative biological functions of protonated nucleotides in RNA, which in this case influence the ligand selectivity in a riboswitch.
Intracellular and extracelluar cyclic GMP in the brain and the hippocampus
- Cyclic Guanosine-Monophosphate (cGMP) is implicated as second messenger in a plethora of pathways and its effects are executed mainly by cGMP-dependent protein kinases (PKG). It is involved in both peripheral (cardiovascular regulation, intestinal secretion, phototransduction, etc.) and brain (hippocampal synaptic plasticity, neuroinflammation, cognitive function, etc.) processes. Stimulation of hippocampal cGMP signaling have been proved to be beneficial in animal models of aging, Alzheimer’s disease or hepatic encephalopathy, restoring different cognitive functions such as passive avoidance, object recognition or spatial memory.
- However, even when some inhibitors of cGMP-degrading enzymes (PDEs) are already used against peripheral pathologies, their utility as neurological treatments is still under clinical investigation. Additionally, it has been demonstrated a list of cGMP roles as not second but first messenger.
- The role of extracellular cGMP has been specially studied in hippocampal function and cognitive impairment in animal models and it has emerged as an important modulator of neuroinflammation-mediated cognitive alterations and hippocampal synaptic plasticity malfunction. Specifically, it has been demonstrated that extracellular cGMP decreases hippocampal IL-1β levels restoring membrane expression of glutamate receptors in the hippocampus and cognitive function in hyperammonemic rats.
- The mechanisms implicated are still unclear and might involve complex interactions between hippocampal neurons, astrocytes and microglia. Membrane targets for extracellular cGMP are still poorly understood and must be addressed in future studies.
Nitroxyl Donor CXL-1020 Lowers Blood Pressure by Targeting C195 in Cyclic Guanosine-3′,5′-Monophosphate-Dependent Protein Kinase I
Background: We previously demonstrated that nitroxyl causes vasodilation, at least in part, by inducing the formation of an intradisulfide bond between C117 and C195 in the high affinity cyclic guanosine monophosphate-binding site of PKGI (cyclic guanosine monophosphate-dependent protein kinase I). The aim of this study was to determine whether nitroxyl donors lower blood pressure via this novel PKGI activation mechanism in vivo.
Methods: To determine this, a C195S PKGI knock-in mouse model was generated that ubiquitously and constitutively expresses a mutant kinase resistant to nitroxyl-induced intradisulfide activation.
Results: Knock-in and wild-type littermates did not differ in appearance, body weight, in PKGI protein expression or blood gas content. Organ weight was similar between genotypes apart from the cecum that was significantly enlarged in knock-in animals. Mean arterial pressure and heart rate monitored in vivo over 24 hours by radio-telemetry revealed neither a significant difference between genotypes at baseline nor during angiotensin II-induced hypertension or sepsis. CXL-1020, a clinically relevant nitroxyl donor, did not lower blood pressure in normotensive animals. In contrast, administering CXL-1020 to hypertensive wild-type mice reduced their blood pressure by 10±4 mm Hg (P=0.0184), whereas the knock-in littermates were unaffected.
Conclusions: Oxidation of C195 in PKGI contributes to the antihypertensive effects observed in response to nitroxyl donors, emphasising the potential importance of nitroxyl donors in pathological scenarios when cyclic guanosine monophosphate levels are reduced and insufficient to activate PKGI.
Molecular descriptors suggest stapling as a strategy for optimizing membrane permeability of cyclic peptides
Cyclic peptides represent a promising class of drug candidates. A significant obstacle limiting their development as therapeutics is the lack of an ability to predict their membrane permeability. We use molecular dynamics simulations to assess the ability of a set of widely used parameters in describing the membrane permeability of a set of model cyclic peptides; the parameters include polar surface area (PSA), the number of hydrogen bonds, and transfer free energy between an aqueous phase and a membrane mimicking phase. These parameters were found to generally correlate with the membrane permeability of the set of cyclic peptides.
We propose two new descriptors, the charge reweighted PSA and the non-polar surface area to PSA ratio; both show enhanced correlation with membrane permeability. This inspired us to explore crosslinking of the peptide to reduce the accessible surface area of the backbone polar atoms, and we find that this can indeed result in reductions in the accessible PSA. This gives reason to speculate that crosslinking may result in increased permeability, thus suggesting a new scaffold for the development of cyclic peptides as potential therapeutics.
Re-engineered BCG overexpressing cyclic di-AMP augments trained immunity and exhibits improved efficacy against bladder cancer
In addition to its role as a TB vaccine, BCG has been shown to elicit heterologous protection against many other pathogens including viruses through a process termed trained immunity. Despite its potential as a broadly protective vaccine, little has been done to determine if BCG-mediated trained immunity levels can be optimized. Here we re-engineer BCG to express high levels of c-di-AMP, a PAMP recognized by stimulator of interferon genes (STING). We find that BCG overexpressing c-di-AMP elicits more potent signatures of trained immunity including higher pro-inflammatory cytokine responses, greater myeloid cell reprogramming toward inflammatory and activated states, and enhances epigenetic and metabolomic changes. In a model of bladder cancer, we also show that re-engineered BCG induces trained immunity and improved functionality. These results indicate that trained immunity levels and antitumor efficacy may be increased by modifying BCG to express higher levels of key PAMP molecules.
DetectX® 3'3'-Cyclic GAMP Antibody, 3ML |
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| C272-3ML | Arbor Assays | 3ML | 289 EUR |
DetectX® 2'3'-Cyclic GAMP Antibody, 2.3ML |
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| C241-2.3ML | Arbor Assays | 2.3ML | 289 EUR |
DetectX® 2'3'-Cyclic GAMP Antibody, 3ML |
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| C241-3ML | Arbor Assays | 3ML | 289 EUR |
DetectX® 3'3'-Cyclic GAMP Antibody, 13ML |
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| C272-13ML | Arbor Assays | 13ML | 1156 EUR |
DetectX® 3'3'-Cyclic GAMP Conjugate, 3ML |
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| C273-3ML | Arbor Assays | 3ML | 289 EUR |
DetectX® 2'3'-Cyclic GAMP Antibody, 13ML |
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| C241-13ML | Arbor Assays | 13ML | 1156 EUR |
DetectX® 2'3'-Cyclic GAMP Conjugate, 2.3ML |
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| C242-2.3ML | Arbor Assays | 2.3ML | 289 EUR |
DetectX® 2'3'-Cyclic GAMP Conjugate, 3ML |
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| C242-3ML | Arbor Assays | 3ML | 289 EUR |
DetectX® 3'3'-Cyclic GAMP Conjugate, 13ML |
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| C273-13ML | Arbor Assays | 13ML | 1156 EUR |
DetectX® 2'3'-Cyclic GAMP Conjugate, 13ML |
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| C242-13ML | Arbor Assays | 13ML | 1156 EUR |
3',3'-Cyclic GAMP ELISA Kit, (1 Plate) |
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| K073-H1 | Arbor Assays | 1x96 well plate | 598 EUR |
3',3'-Cyclic GAMP ELISA Kit, (5 Plate) |
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| K073-H5 | Arbor Assays | 5x96 well plate | 2390 EUR |
Mouse 2',3'-Cyclic GAMP,cGAMP ELISA KIT |
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| EA0126Mo | Jiaxing Korain Biotech Ltd (BT Labs) | 96 wells | 458 EUR |
2'3'-Cyclic GAMP ELISA Kit, (1 Strip Plate) |
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| K067-H1 | Arbor Assays | 1x96 well plate | 624 EUR |
2'3'-Cyclic GAMP ELISA Kit, (1 Whole Plate) |
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| K067-H1W | Arbor Assays | 1x96 well plate | 572 EUR |
2'3'-Cyclic GAMP ELISA Kit, (5 Strip Plate) |
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| K067-H5 | Arbor Assays | 5x96 well plate | 2494 EUR |
2'3'-Cyclic GAMP ELISA Kit, (5 Whole Plate) |
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| K067-H5W | Arbor Assays | 5x96 well plate | 2342 EUR |
2'3'-Cyclic GAMP ELISA Kit, (384-well Plate) |
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| K067-H1D | Arbor Assays | 1x384 well plate | 1698 EUR |
Cyclic Adenosine Monophosphate (Cyclic AMP) |
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| MBS621824-1mg | MyBiosource | 1mg | 975 EUR |
Cyclic Adenosine Monophosphate (Cyclic AMP) |
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| MBS621824-5x1mg | MyBiosource | 5x1mg | 4240 EUR |
cAMP (Cyclic Adenosine Monophosphate, Cyclic AMP) |
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| MBS6507052-005mL | MyBiosource | 0.05mL | 845 EUR |
cAMP (Cyclic Adenosine Monophosphate, Cyclic AMP) |
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| MBS6507052-5x005mL | MyBiosource | 5x0.05mL | 3660 EUR |
Cyclic AMP |
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| 591136 | MedKoo Biosciences | 1.0g | 410 EUR |
Cyclic AMP |
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| HY-B1511 | MedChemExpress | 500mg | 142.8 EUR |
Cyclic AMP |
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| TCO2745-10mg | TargetMol Chemicals | 10mg | Ask for price |
Cyclic AMP |
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| TCO2745-1g | TargetMol Chemicals | 1g | Ask for price |
Cyclic AMP |
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| TCO2745-1mg | TargetMol Chemicals | 1mg | Ask for price |
Cyclic AMP |
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| TCO2745-50mg | TargetMol Chemicals | 50mg | Ask for price |
Cyclic AMP |
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| TCO2745-5mg | TargetMol Chemicals | 5mg | Ask for price |
Cyclic AMP |
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| MBS342149-05mL | MyBiosource | 0.5mL | 270 EUR |
Yielding transition of a two dimensional glass former under athermal cyclic shear deformation
We study numerically the yielding transition of a two dimensional model glass subjected to athermal quasi-static cyclic shear deformation, with the aim of investigating the effect on the yielding behavior of the degree of annealing, which in turn depends on the preparation protocol. We find two distinct regimes of annealing separated by a threshold energy. Poorly annealed glasses progressively evolve toward the threshold energy as the strain amplitude is increased toward the yielding value.
Well annealed glasses with initial energies below the threshold energy exhibit stable behavior, with a negligible change in energy with increasing strain amplitude, until they yield. Discontinuities in energy and stress at yielding increase with the degree of annealing, consistent with recent results found in three dimensions. We observe a significant structural change with strain amplitude that closely mirrors the changes in energy and stresses. We investigate groups of particles that are involved in plastic rearrangements. We analyze the distributions of avalanche sizes, of clusters of connected rearranging particles, and related quantities, employing finite size scaling analysis. We verify previously investigated relations between exponents characterizing these distributions.