Electron spin-echo envelope modulation (ESEEM) spectroscopy of phospholipids spin-labeled systematically down the sn-2 chain was used to detect the penetration of water (D2O) into bilayer membranes of dipalmitoyl phosphatidylcholine with and without 50 mol % cholesterol. Three-pulse stimulated echoes allow the resolution of two superimposed 2H-ESEEM spectral components of different widths, for spin labels located in the upper part of the lipid chains. Quantum chemical calculations (DFT) and ESEEM simulations assign the broad spectral component to one or two D2O molecules that are directly hydrogen bonded to the N-O group of the spin label. Classical ESEEM simulations establish that the narrow spectral component arises from nonbonded water (D2O) molecules that are free in the hydrocarbon chain region of the bilayer membrane. The amplitudes of the broad 2H-ESEEM spectral component correlate directly with those of the narrow component for spin labels at different positions down the lipid chain, reflecting the local H-bonding equilibria. The D2O-ESEEM amplitudes decrease with position down the chain toward the bilayer center, displaying a sigmoidal dependence on position that is characteristic of transmembrane polarity profiles established by other less direct spin-labeling methods. The midpoint of the sigmoidal profile is shifted toward the membrane center for membranes without cholesterol, relative to those with cholesterol, and the D2O-ESEEM amplitude in the outer regions of the chain is greater in the presence of cholesterol than in its absence. For both membrane types, the D2O amplitude is almost vanishingly small at the bilayer center. The water-penetration profiles reverse correlate with the lipid-chain packing density, as reflected by 1H-ESEEM intensities from protons of the membrane matrix. An analysis of the H-bonding equilibria provides essential information on the binding of water molecules to H-bond acceptors within the hydrophobic interior of membranes. For membranes containing cholesterol, approximately 40% of the nitroxides in the region adjacent to the lipid headgroups are H bonded to water, of which ca. 15% are doubly H bonded. Corresponding H-bonded populations in membranes without cholesterol are ca. 20%, of which ca. 6% are doubly bonded.

The thermal denaturation of azurin from Pseudomonas aeruginosa was investigated by means of differential scanning calorimetry (DSC), electron spin resonance (ESR), and optical density (OD) experiments, with the aim of determining its thermodynamic stability and the thermally induced conformational changes of its active site. DSC experiments have shown an irreversible and complex unfolding path. In order to characterize the kinetically controlled step, DSC measurements were carried out at different scan rates. An extrapolation of the experimental heat capacity data to infinite scan rate allowed all the kinetic and thermodynamic parameters related to the process to be obtained. All these parameters extracted from the calorimetric data were verified by means of a curve-fitting program using an equation containing all information necessary to fully describe the unfolding process in details. Thermal denaturation, followed up to 82 °C by ESR and OD measurements, allowed us to study the structural variations of the copper environment at different temperatures. The A/fu thermodynamic, together with the value of ACp calculated according to an approach taking into account the common features of protein unfolding and dissolution of hydrophobic compounds, was used to evaluate the thermodynamic stability (AG) for the reversible process over the entire temperature range of denaturation. The high value of the maximum stability thus calculated was explained by the stabilizing effect of copper.

Two-pulse, echo-detected (ED) electron paramagnetic resonance (EPR) spectroscopy was used to study the librational motions of spin-labeled lipids in membranes of dipalmitoylphosphatidylcholine + 50 mol % cholesterol. The temperature dependence, over the range 77-240 K, and the dependence on position of spin-labeling in the sn-2 chain (n=5, 7, 10, 12, and 14) of the phospholipid, were characterized in detail. The experimental ED-spectra were corrected for instantaneous spin diffusion arising from static spin-spin interactions, by using spectra recorded at 77 K, where motional contributions are negligible. Simulations according to a model of rapid, small-amplitude librations about an axis whose direction is randomly distributed are able to describe the experimental spectra. Calibrations, in terms of the amplitude-correlation time product, alpha2tauc, were constructed for diagnostic spectral line-height ratios at different echo delay times, and for relaxation spectra obtained from the ratio of ED-spectra recorded at two different echo delays. The librational amplitude, alpha2, was determined for a spin label at the 14-C position of the lipid chain from the partially motionally averaged hyperfine splitting in the conventional EPR spectra. The librational correlation time, tauc, which is deduced from combination of the conventional and ED-EPR results, lies in the subnanosecond regime and depends only weakly on temperature. The temperature dependence of the ED-EPR spectra arises mainly from an increase in librational amplitude with increasing temperature, and position down the lipid chain. A gradual transition takes place at higher temperatures, from a situation in which segmental torsional librations are cumulative, i.e., the contributions of the individual segments add up progressively upon going down the chain, to one of concerted motion only weakly dependent on chain position. Such librational motions are important for glass-like states and are generally relevant to high lipid packing densities, e.g., in cholesterol-containing raft domains and condensed complexes.

The dynamics of spin-labeled lipid chains in the low-temperature phases of dipalmitoyl phosphatidylcholine (DPPC) membranes, with and without equimolar cholesterol, have been investigated by pulsed electron paramagnetic resonance (EPR) spectroscopy. Echo-detected spectra from the two-pulse, primary spin-echo (pulse sequence: π/2-τ-π-τ-echo) are used to detect rapid angular motions, on the time scale of the phase memory time (T 2M ) that is in the nanosecond regime. Echo-detected spectra from the three-pulse, stimulated spin-echo (pulse sequence: π/2-τ-π/2-T-π/2-τ-echo) are used to detect slow angular motions, on the time scale of the spin-lattice relaxation time (T 1 ) that is in the microsecond regime. Spectra recorded at very low temperature (77 K) are used to correct the two-pulse echo spectra for instantaneous diffusion that arises from dipolar spin-spin interactions between different spin labels. Echo-detected inversion recovery spectra are used to correct the three-pulse echo spectra for intrinsic spin-lattice relaxation and large-scale spectral diffusion induced by nitrogen nuclear spin flips. The dependence of the echo-detected spectral line shapes on the two time delays, τ and T, can be simulated adequately by using a simple two-state model to represent the small-amplitude librational motions in the low-temperature membrane phases. The fast librational motion has isotropic character, no singly defined direction of the librational axis, and is segmental in nature, depending on chain position and also on the presence of cholesterol. The slow librational motion is of a more global, cooperative nature, being independent of chain position and cholesterol content.

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Background: Hypoxia plays a relevant role in tumor-related inflammation toward the metastatic spread and cancer aggressiveness. The pro-inflammatory cytokine interleukin-1β (IL-β) and its cognate receptor IL1R1 contribute to the initiation and progression of breast cancer determining pro-tumorigenic inflammatory responses. The transcriptional target of the hypoxia inducible factor-1α (HIF-1α) namely the G protein estrogen receptor (GPER) mediates a feedforward loop coupling IL-1β induction by breast cancer-associated fibroblasts (CAFs) to IL1R1 expression by breast cancer cells toward the regulation of target genes and relevant biological responses. Methods: In order to ascertain the correlation of IL-β with HIF-1α and further hypoxia-related genes in triplenegative breast cancer (TNBC) patients, a bioinformatics analysis was performed using the information provided by The Invasive Breast Cancer Cohort of The Cancer Genome Atlas (TCGA) project and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) datasets. Gene expression correlation, statistical analysis and gene set enrichment analysis (GSEA) were carried out with R studio packages. Pathway enrichment analysis was evaluated with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. TNBC cells and primary CAFs were used as model system. The molecular mechanisms implicated in the regulation of IL-1β by hypoxia toward a metastatic gene expression profile and invasive properties were assessed performing gene and protein expression studies, PCR arrays, gene silencing and immunofluorescence analysis, co-immunoprecipitation and ChiP assays, ELISA, cell spreading, invasion and spheroid formation.

Human serum albumin possesses multiple binding sites and transports a wide range of ligands that include the anti-inflammatory drug ibuprofen. A complete map of the binding sites of ibuprofen in albumin is difficult to obtain in traditional experiments, because of the structural adaptability of this protein in accommodating small ligands. In this work, we provide a set of predictions covering the geometry, affinity of binding and protonation state for the pharmaceutically most active form (S– isomer) of ibuprofen to albumin, by using absolute binding free energy calculations in combination with classical molecular dynamics (MD) simulations and molecular docking. The most favorable binding modes correctly reproduce several experimentally identified binding locations, which include the two Sudlow's drug sites (DS2 and DS1) and the fatty acid binding sites 6 and 2 (FA6 and FA2). Previously unknown details of the binding conformations were revealed for some of them, and formerly undetected binding modes were found in other protein sites. The calculated binding affinities exhibit trends which seem to agree with the available experimental data, and drastically degrade when the ligand is modeled in a protonated (neutral) state, indicating that ibuprofen associates with albumin preferentially in its charged form. These findings provide a detailed description of the binding of ibuprofen, help to explain a wide range of results reported in the literature in the last decades, and demonstrate the possibility of using simulation methods to predict ligand binding to albumin.