Current perspectives of oleic acid: Regulation of molecular pathways in mitochondrial and endothelial functioning against insulin resistance and diabetes.

Insulin resistance (IR) and type 2 diabetes mellitus (T2DM) is a leading cause of deaths due to metabolic disorders in recent years. Molecular mechanisms involved in the initiation and development of IR and T2DM are multiples. The major factors include mitochondrial dysfunction which may cause incomplete fatty acid oxidation (FAO). Oleic acid upregulates the expression of genes causing FAO by deacetylation of PGC1α by PKA-dependent activation of SIRT1-PGC1α complex. Another potent factor for the development of IR and T2DM is endothelial dysfunction as damaged endothelium causes increased release of inflammatory mediators such as TNF-α, IL-6, IL-1ß, sVCAM, sICAM, E-selectin and other proinflammatory cytokines. While, on the other hand, oleic acid has the ability to regulate E-selectin, and sICAM expression. Rest of the risk factors may include inflammation, ß-cell dysfunction, oxidative stress, hormonal imbalance, apoptosis, and enzyme dysregulation. Here, we have highlighted how oleic acid regulates underlying causatives factors and hence, keeps surpassing effect in prevention and treatment of IR and T2DM. However, the percentage contribution of these factors in combating IR and ultimately averting T2DM is still debatable. Thus, because of its exceptional protective effect, it can be considered as an improved therapeutic agent in prophylaxis and/or treatment of IR and T2DM.

A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge.

As part of the SAMPL5 blinded experiment, we computed the absolute binding free energies of 22 host-guest complexes employing a novel approach based on the BEDAM single-decoupling alchemical free energy protocol with parallel replica exchange conformational sampling and the AGBNP2 implicit solvation model specifically customized to treat the effect of water displacement as modeled by the Hydration Site Analysis method with explicit solvation. Initial predictions were affected by the lack of treatment of ionic charge screening, which is very significant for these highly charged hosts, and resulted in poor relative ranking of negatively versus positively charged guests. Binding free energies obtained with Debye-Hückel treatment of salt effects were in good agreement with experimental measurements. Water displacement effects contributed favorably and very significantly to the observed binding affinities; without it, the modeling predictions would have grossly underestimated binding. The work validates the implicit/explicit solvation approach employed here and it shows that comprehensive physical models can be effective at predicting binding affinities of molecular complexes requiring accurate treatment of conformational dynamics and hydration.

Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules.

Intermolecular interactions in the aqueous phase must compete with the interactions between the two binding partners and their solvating water molecules. In biological systems, water molecules in protein binding sites cluster at well-defined hydration sites and can form strong hydrogen-bonding interactions with backbone and side-chain atoms. Displacement of such water molecules is only favorable when the ligand can form strong compensating hydrogen bonds. Conversely, water molecules in hydrophobic regions of protein binding sites make only weak interactions, and the requirements for favorable displacement are less stringent. The propensity of water molecules for displacement can be identified using inhomogeneous fluid solvation theory (IFST), a statistical mechanical method that decomposes the solvation free energy of a solute into the contributions from different spatial regions and identifies potential binding hotspots. In this study, we employed IFST to study the displacement of water molecules from the ATP binding site of Hsp90, using a test set of 103 ligands. The predicted contribution of a hydration site to the hydration free energy was found to correlate well with the observed displacement. Additionally, we investigated if this correlation could be improved by using the energetic scores of favorable probe groups binding at the location of hydration sites, derived from a multiple copy simultaneous search (MCSS) method. The probe binding scores were not highly predictive of the observed displacement and did not improve the predictivity when used in combination with IFST-based hydration free energies. The results show that IFST alone can be used to reliably predict the observed displacement of water molecules in Hsp90. However, MCSS can augment IFST calculations by suggesting which functional groups should be used to replace highly displaceable water molecules. Such an approach could be very useful in improving the hit-to-lead process for new drug targets.

Cigarette smoking and nicotine exposure contributes for aberrant insulin signaling and cardiometabolic disorders.

Cigarette smoking- and nicotine-mediated dysregulation in insulin-signaling pathways are becoming leading health issues associated with morbidity and mortality worldwide. Many cardiometabolic disorders particularly insulin resistance, polycystic ovary syndrome (PCOS), central obesity and cardiovascular diseases are initiated from exposure of exogenous substances which augment by disturbances in insulin signaling cascade. Among these exogenous substances, nicotine and cigarette smoking are potential triggers for impairment of insulin-signaling pathways. Further, this aberrant insulin signaling is associated with many metabolic complications, which consequently give rise to initiation as well as progression of these metabolic syndromes. Hence, understanding the underlying molecular mechanisms responsible for cigarette smoking- and nicotine-induced altered insulin signaling pathways and subsequent participation in several health hazards are quite essential for prophylaxis and combating these complications. In this article, we have focused on the role of nicotine and cigarette smoking mediated pathological signaling; for instance, nicotine-mediated inhibition of nuclear factor erythroid 2-related factor 2 and oxidative damage, elevated cortisol that may promote central obesity, association PCOS and oxidative stress via diminished nitric oxide which may lead to endothelial dysfunction and vascular inflammation. Pathological underlying molecular mechanisms involved in mediating these metabolic syndromes via alteration of insulin signaling cascade and possible molecular mechanism responsible for these consequences on nicotine exposure have also been discussed.

The 1.5-A structure of XplA-heme, an unusual cytochrome P450 heme domain that catalyzes reductive biotransformation of royal demolition explosive.

XplA is a cytochrome P450 of unique structural organization, consisting of a heme-domain that is C-terminally fused to its native flavodoxin redox partner. XplA, along with flavodoxin reductase XplB, has been shown to catalyze the breakdown of the nitramine explosive and pollutant hexahydro-1,3,5-trinitro-1,3,5-triazine (royal demolition explosive) by reductive denitration. The structure of the heme domain of XplA (XplA-heme) has been solved in two crystal forms: as a dimer in space group P2(1) to a resolution of 1.9 A and as a monomer in space group P2(1)2(1)2 to a resolution of 1.5 A, with the ligand imidazole bound at the heme iron. Although it shares the overall fold of cytochromes P450 of known structure, XplA-heme is unusual in that the kinked I-helix that traverses the distal face of the heme is broken by Met-394 and Ala-395 in place of the well conserved Asp/Glu plus Thr/Ser, important in oxidative P450s for the scission of the dioxygen bond prior to substrate oxygenation. The heme environment of XplA-heme is hydrophobic, featuring a cluster of three methionines above the heme, including Met-394. Imidazole was observed bound to the heme iron and is in close proximity to the side chain of Gln-438, which is situated over the distal face of the heme. Imidazole is also hydrogen-bonded to a water molecule that sits in place of the threonine side-chain hydroxyl exemplified by Thr-252 in Cyt-P450cam. Both Gln-438 --> Ala and Ala-395 --> Thr mutants of XplA-heme displayed markedly reduced activity compared with the wild type for royal demolition explosive degradation when combined with surrogate electron donors.

Naringenin downregulates inflammation-mediated nitric oxide overproduction and potentiates endogenous antioxidant status during hyperglycemia.

Nitric oxide is a key regulating factor for physiological functions, when elevated during inflammatory conditions, NO, can lower endogenous antioxidants level. Naringenin, a bioflavonoid has shown to possess anti-inflammatory action. However, its role in NO-mediated responses has not been elucidated till date. This study was designed to investigate antioxidant potential of naringenin against inflammation-mediated nitric oxide overproduction and antioxidant status with an improved glycemic profile in diabetic rats. From total rats, Group 1 received normal saline, while remaining received single intraperitoneal injection of alloxan and were then equally divided into group 2, 3, and 4, which latter received no-treatment, metformin (50 mg kg-1  day-1 ) and naringenin (50 mg kg-1  day-1 ), respectively, for 1 month. Results showed that naringenin significantly downregulated levels of glucose (p < .05), lipid profile, inflammatory biomarkers, and nitric oxide (p < .01) in alloxan-induced diabetic rats. It also improved SOD level as compared to that of metformin treatment. This work delivers that naringenin exerts antioxidant effect by downregulating inflammation-mediated nitric oxide overproduction. PRACTICAL APPLICATIONS: Naringenin is a well-recognized member of bioflavonoids and is commonly present in citrus fruits like oranges, grapes, and berries. The foremost property of naringenin is its antioxidant potential, which aids in decreasing the burden of oxidative stress by declining the generation of free radicals. The overproduction of these oxygen or nitrogen reactive species are considered as underlying cause of undesired biological activities like O 2 - ∙ or nitrite-mediated inflammation and altered metabolic parameters. Hence, this study was designed to investigate the antioxidant potential of naringenin as natural flavone to downregulate the inflammation-mediated nitric oxide overproduction and improve glycemic profile. The therapeutic perspective of naringenin from current study against nitric oxide overproduction and to eradicate inflammation via controlling of levels of pro-inflammatory mediators suggests that naringenin holds the forthcoming vision as a supportive constituent alone or in combination with some other conventional medicinal agents against conditions like metabolic disorders.

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.

Network analysis of a proposed exit pathway for protons to the P-side of cytochrome c oxidase.

Cytochrome c Oxidase (CcO) reduces O2, the terminal electron acceptor, to water in the aerobic, respiratory electron transport chain. The energy released by O2 reductions is stored by removing eight protons from the high pH, N-side, of the membrane with four used for chemistry in the active site and four pumped to the low pH, P-side. The proton transfers must occur along controllable proton pathways that prevent energy dissipating movement towards the N-side. The CcO N-side has well established D- and K-channels to deliver protons to the protein interior. The P-side has a buried core of hydrogen-bonded protonatable residues designated the Proton Loading Site cluster (PLS cluster) and many protonatable residues on the P-side surface, providing no obvious unique exit. Hydrogen bond pathways were identified in Molecular Dynamics (MD) trajectories of Rb. sphaeroides CcO prepared in the PR state with the heme a3 propionate and Glu286 in different protonation states. Grand Canonical Monte Carlo sampling of water locations, polar proton positions and residue protonation states in trajectory snapshots identify a limited number of water mediated, proton paths from PLS cluster to the surface via a (P-exit) cluster of residues. Key P-exit residues include His93, Ser168, Thr100 and Asn96. The hydrogen bonds between PLS cluster and P-exit clusters are mediated by a water wire in a cavity centered near Thr100, whose hydration can be interrupted by a hydrophobic pair, Leu255B (near CuA) and Ile99. Connections between the D channel and PLS via Glu286 are controlled by a second, variably hydrated cavity. SIGNIFICANCE STATEMENT: Cytochrome C oxidase plays a crucial role in cellular respiration and energy generation. It reduces O2 to water and uses the released free energy to move protons across mitochondrial and bacterial cell membranes adding to the essential electrochemical gradient. Energy storage requires that protons are taken up from the high pH, N-side and released to the low pH, P-side of the membrane. We identify a potential proton exit from a buried cluster of polar residues (the proton loading site) to the P-side of CcO via paths made up of waters and conserved residues. Two water cavities connect the proton exit pathway to the surface only when hydrated. Changing the degree of hydration may control otherwise energetically favorable proton backflow from the P-side.

Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces.

The principles underlying water reorganization around simple nonpolar solutes are well understood and provide the framework for the classical hydrophobic effect, whereby water molecules structure themselves around solutes so that they maintain favorable energetic contacts with both the solute and the other water molecules. However, for certain solute surface topographies, water molecules, due to their geometry and size, are unable to simultaneously maintain favorable energetic contacts with both the surface and neighboring water molecules. In this study, we analyze the solvation of ligand-binding sites for six structurally diverse proteins using hydration site analysis and measures of local water structure, in order to identify surfaces at which water molecules are unable to structure themselves in a way that maintains favorable enthalpy relative to bulk water. These surfaces are characterized by a high degree of enclosure, weak solute-water interactions, and surface constraints that induce unfavorable pair interactions between neighboring water molecules. Additionally, we find that the solvation of charged side chains in an active site generally results in favorable enthalpy but can also lead to pair interactions between neighboring water molecules that are significantly unfavorable relative to bulk water. We find that frustrated local structure can occur not only in apolar and weakly polar pockets, where overall enthalpy tends to be unfavorable, but also in charged pockets, where overall water enthalpy tends to be favorable. The characterization of local water structure in these terms may prove useful for evaluating the displacement of water from diverse protein active-site environments.

Sonic hedgehog signalling pathway: a complex network.

Sonic Hedgehog (Shh) signalling cascade is one of the intricate signal transduction mechanisms that govern the precisely regulated developmental processes of multicellular organisms. Along with establishing the patterns of cellular differentiation to direct complex organ formation, it also has an important role in post-embryonic tissue regeneration and repair processes. Especially, Shh signalling is implicated in the induction of multifarious neuronal populations in central nervous system. There is compelling evidence of the involvement of Shh protein in the signalling network that regulates various morphogenetic processes such as the exquisite neural tube pattern formation. In the morphogenetic field, the activation of Shh signalling processes is intricately linked to the alterations at the molecular level in the structure of Shh protein that leads to its altered biophysical and biochemical reactivity. This brief article gives an overview of such complex cascade of events in Shh signalling and its transduction pathways.