Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires

Light-induced Trpin/Metout Switching During BLUF Domain Activation in ATP-bound Photoactivatable Adenylate Cyclase OaPAC

The understanding of signal transduction mechanisms in photoreceptor proteins is essential for elucidating how living organisms respond to light as environmental stimuli. In this study, we investigated the ATP binding, photoactivation and signal transduction process in the photoactivatable adenylate cyclase from Oscillatoria acuminata (OaPAC) upon blue light excitation. Structural models with ATP bound in the active site of native OaPAC at cryogenic as well as room temperature are presented. ATP is found in one conformation at cryogenic- and in two conformations at ambient-temperature, and is bound in an energetically unfavorable conformation for the conversion to cAMP. However, FTIR spectroscopic experiments confirm that this conformation is the native binding mode in dark state OaPAC and that transition to a productive conformation for ATP turnover only occurs after light activation. A combination of time-resolved crystallography experiments at synchrotron and X-ray Free Electron Lasers sheds light on the early events around the Flavin Adenine Dinucleotide (FAD) chromophore in the light-sensitive BLUF domain of OaPAC. Early changes involve the highly conserved amino acids Tyr6, Gln48 and Met92. Crucially, the Gln48 side chain performs a 180° rotation during activation, leading to the stabilization of the FAD chromophore. Cryo-trapping experiments allowed us to investigate a late light-activated state of the reaction and revealed significant conformational changes in the BLUF domain around the FAD chromophore. In particular, a Trpin/Metout transition upon illumination is observed for the first time in the BLUF domain and its role in signal transmission via α-helix 3 and 4 in the linker region between sensor and effector domain is discussed.

LncRNA H19 acts as miR-301a-3p sponge to alleviate lung injury in mice with sepsis by regulating Adcy1

BACKGROUND

The abnormal expression of long non-coding RNA (lncRNA) is closely related to disease progression. However, the role and mechanism of lncRNA H19 (lncH19) in sepsis-induced lung injury remain to be elucidated.

METHODS

Cercal ligation and puncture (CLP) mice models and lipopolysaccharide (LPS)-induced cell injury model were used to construct sepsis-induced lung injury in vivo and in vitro. The expression of lncH19, microRNA (miR)-301a-3p and adenylate cyclase 1 (Adcy1) mRNA was assessed using quantitative real-time PCR. The concentrations of inflammatory factors were determined by ELISA assay. Cell proliferation and apoptosis were determined using cell counting kit 8 assay, EdU staining and flow cytometry. The protein expression of apoptosis markers and Adcy1 was examined by western blot analysis. Oxidative stress was assessed by detecting the contents of oxidative stress markers. The interaction between miR-301a-3p and lncH19 or Adcy1 was confirmed using RNA pull-down assay, dual-luciferase reporter assay and RIP assay.

RESULTS

LncH19 was lowly expressed in CLP mice models and LPS-induced cell injury models. Overexpressed lncH19 could alleviate CLP-induced lung injury in mice, as well as LPS-induced cell apoptosis, inflammation and oxidative stress. MiR-301a-3p could be sponged by lncH19, and its overexpression could reverse the inhibition of lncH19 on LPS-induced cell injury. Adcy1 was a target of miR-301a-3p, and its expression was upregulated by lncH19. Silencing of Adcy1 could abolish the suppressive effect of miR-301a-3p inhibitor on LPS-induced cell injury.

CONCLUSION

LncH19 might inhibit sepsis-induced lung injury through acting as a sponge of miR-301a-3p to upregulate Adcy1.Highlights:LncH19 overexpression relieves CLP-induced lung injury and LPS-induced cell injury.LncH19 directly sponges miR-301a-3p.MiR-301a-3p targets Adcy1.

Double Proton Transfer during a Novel Tertiary α-Ketol Rearrangement in Ketol-Acid Reductoisomerase: A Water-Mediated, Metal-Catalyzed, Base-Induced Mechanism

(KARI) catalyzes the conversion of (S)-2-acetolactate or (S)-2-aceto-2-hydroxybutyrate to 2,3-dihydroxy-3-alkylbutyrate, the second step in the biosynthesis of branched chain amino acids (BCAAs). Because the BCAA biosynthetic pathway is present in bacteria, plants, and fungi, but absent in animals, it is an excellent target for the development of new-generation antibiotics and herbicides. Nevertheless, the mechanism of the KARI-catalyzed reaction has not yet been fully solved. In this study, we used iterative molecular dynamics (MD) flexible fitting-Rosetta techniques to optimize the three-dimensional solution structure of archaea KARI from Sulfolobus solfataricus (Sso-KARI) determined from cryo-electron microscopy. On the basis of the structure of the Sso-KARI/2Mg²⁺/NADH/(S)-2-acetolactate complex, we deciphered the catalytic mechanism of the KARI-mediated reaction through hybrid quantum mechanics/molecular mechanics MD simulations in conjunction with umbrella sampling. With an activation energy of only 6.06 kcal/mol, a water-mediated, metal-catalyzed, base-induced (WMMCBI) mechanism was preferred for deprotonation of the tertiary OH group of (S)-2-acetolactate in Sso-KARI. The WMMCBI mechanism for double proton transfer occurred within a proton wire route with two steps involving the formation of hydroxide: (i) Glu233 served as a general base to deprotonate the Mg²⁺-bound water, forming a hydroxide-coordinated Mg²⁺ ion; (ii) this hydroxide ion acted as a strong base that rapidly deprotonated the ternary OH group of the substrate. In contrast, the direct deprotonation of the substrate by Glu233 was kinetically unfavorable. This mechanism suggests a novel approach for designing catalysts for deprotonation and provides clues for the development of new-generation antibiotics and herbicides.

RNA-Inspired and Accelerated Degradation of Polylactide in Seawater

Marine plastic pollution is a worldwide challenge making advances in the field of biodegradable polymer materials necessary. Polylactide (PLA) is a promising biodegradable polymer used in various applications; however, it has a very slow seawater degradability. Herein, we present the first library of PLA derivatives with incorporated "breaking points" to vary the speed of degradation in artificial seawater from years to weeks. Inspired by the fast hydrolysis of ribonucleic acid (RNA) by intramolecular transesterification, we installed phosphoester breaking points with similar hydroxyethoxy side groups into the PLA backbone to accelerate chain scission. Sequence-controlled anionic ring-opening copolymerization of lactide and a cyclic phosphate allowed PLA to be prepared with controlled distances of the breaking points along the backbone. This general concept could be translated to other slowly degrading polymers and thereby be able to prevent additional marine pollution in the future.

Model of the RNA Polymerase Complex of the SARS-CoV-2 Virus with Favipiravir

A model of a multidomain complex is constructed using molecular modeling methods to explain the mechanism of the inhibitory effect of favipiravir on RNA-dependent RNA polymerase (RdRp) of the SARS-CoV-2 coronavirus. As the initial atomic coordinates, we use cryoelectron microscopy data for the apo form of RdRp of the SARS-CoV-2 virus and data on the structure of RdRp of the hepatitis C virus. After appropriate substitutions, an RdRp complex containing RNA chains and a potential enzyme inhibitor, favipiravir in the form of ribosatriphosphate, are constructed. The structure of the complex in aqueous shells, which includes more than 100 000 atoms, is optimized by molecular dynamics methods. Analysis of the active site with the incorporated favipiravir molecule makes it possible to explain the chemical reaction of the enzyme with the inhibitor.

Solanum anguivi Lam. Fruits: Their Potential Effects on Type 2 Diabetes Mellitus

Type 2 diabetes mellitus (T2DM) is a complex metabolic disorder of glucose homeostasis associated with a status of insulin resistance, impaired insulin signaling, β-cell dysfunction, impaired glucose and lipid metabolism, sub-clinical inflammation, and increased oxidative stress. Consuming fruits and vegetables rich in phytochemicals with potential antidiabetic effects may prevent T2DM and/or support a conservative T2DM treatment while being safer and more affordable for people from low-income countries. Solanum anguivi Lam. fruits (SALF) have been suggested to exhibit antidiabetic properties, potentially due to the presence of various phytochemicals, including saponins, phenolics, alkaloids, ascorbic acid, and flavonoids. For the saponin fraction, antidiabetic effects have already been reported. However, it remains unclear whether this is also true for the other phytochemicals present in SALF. This review article covers information on glucose homeostasis, T2DM pathogenesis, and also the potential antidiabetic effects of phytochemicals present in SALF, including their potential mechanisms of action.

Light-Induced Change of Arginine Conformation Modulates the Rate of Adenosine Triphosphate to Cyclic Adenosine Monophosphate Conversion in the Optogenetic System Containing Photoactivated Adenylyl Cyclase

We report the first computational characterization of an optogenetic system composed of two photosensing BLUF (blue light sensor using flavin adenine dinucleotide) domains and two catalytic adenylyl cyclase (AC) domains. Conversion of adenosine triphosphate (ATP) to the reaction products, cyclic adenosine monophosphate (cAMP) and pyrophosphate (PPi), catalyzed by ACs initiated by excitation in photosensing domains has emerged in the focus of modern optogenetic applications because of the request in photoregulated enzymes that modulate cellular concentrations of signaling messengers. The photoactivated AC from the soil bacterium Beggiatoa sp. (bPAC) is an important model showing a considerable increase in the ATP to cAMP conversion rate in the catalytic domain after the illumination of the BLUF domain. The 1 μs classical molecular dynamics simulations reveal that the activation of the BLUF domain leading to tautomerization of Gln49 in the chromophore-binding pocket results in switching of the position of the side chain of Arg278 in the active site of AC. Allosteric signal transmission pathways between Gln49 from BLUF and Arg278 from AC were revealed by the dynamical network analysis. The Gibbs energy profiles of the ATP → cAMP + PPi reaction computed using QM(DFT(ωB97X-D3/6-31G**))/MM(CHARMM) molecular dynamics simulations for both Arg278 conformations in AC clarify the reaction mechanism. In the light-activated system, the corresponding arginine conformation stabilizes the pentacoordinated phosphorus of the α-phosphate group in the transition state, thus lowering the activation energy. Simulations of the bPAC system with the Tyr7Phe replacement in the BLUF demonstrate occurrence of both arginine conformations in an equal ratio, explaining the experimentally observed intermediate catalytic activity of the bPAC-Y7F variant as compared with the dark and light states of the wild-type bPAC.

Two Faces of Water in the Formation and Stabilization of Multicomponent Crystals of Zwitterionic Drug-Like Compounds

Two new hydrated multicomponent crystals of zwitterionic 2-aminonicotinic acid with maleic and fumaric acids have been obtained and thoroughly characterized by a variety of experimental (X-ray analysis and terahertz Raman spectroscopy) and theoretical periodic density functional theory calculations, followed by Bader analysis of the crystalline electron density) techniques. It has been found that the Raman-active band in the region of 300 cm−1 is due to the vibrations of the intramolecular O-H...O bond in the maleate anion. The energy/enthalpy of the intermolecular hydrogen bonds was estimated by several empirical approaches. An analysis of the interaction networks reflects the structure-directing role of the water molecule in the examined multicomponent crystals. A general scheme has been proposed to explain the proton transfer between the components during the formation of multicomponent crystals in water. Water molecules were found to play the key role in this process, forming a “water wire” between the COOH group of the dicarboxylic acid and the COO– group of the zwitterion and the rendering crystal lattice of the considered multicomponent crystals.