Absolute nutrient concentration measurements in cell culture media: (1)H q-NMR spectra and data to compare the efficiency of pH-controlled protein precipitation versus CPMG or post-processing filtering approaches.

The NMR spectra and data reported in this article refer to the research article titled "A simple and accurate protocol for absolute polar metabolite quantification in cell cultures using q-NMR" [1]. We provide the (1)H q-NMR spectra of cell culture media (DMEM) after removal of serum proteins, which show the different efficiency of various precipitating solvents, the solvent/DMEM ratios, and pH of the solution. We compare the data of the absolute nutrient concentrations, measured by PULCON external standard method, before and after precipitation of serum proteins and those obtained using CPMG (Carr-Purcell-Meiboom-Gill) sequence or applying post-processing filtering algorithms to remove, from the (1)H q-NMR spectra, the proteins signal contribution.

A simple and accurate protocol for absolute polar metabolite quantification in cell cultures using quantitative nuclear magnetic resonance.

Absolute analyte quantification by nuclear magnetic resonance (NMR) spectroscopy is rarely pursued in metabolomics, even though this would allow researchers to compare results obtained using different techniques. Here we report on a new protocol that permits, after pH-controlled serum protein removal, the sensitive quantification (limit of detection [LOD] = 5-25 μM) of hydrophilic nutrients and metabolites in the extracellular medium of cells in cultures. The method does not require the use of databases and uses PULCON (pulse length-based concentration determination) quantitative NMR to obtain results that are significantly more accurate and reproducible than those obtained by CPMG (Carr-Purcell-Meiboom-Gill) sequence or post-processing filtering approaches.

All-Purpose Containers? Lipid-Binding Protein - Drug Interactions.

The combined use of in vitro (19F-NMR) and in silico (molecular docking) procedures demonstrates the affinity of a number of human calycins (lipid-binding proteins from ileum, liver, heart, adipose tissue and epidermis, and retinol-binding protein from intestine) for different drugs (mainly steroids and vastatins). Comparative evaluations on the complexes outline some of the features relevant for interaction (non-polar character of the drugs; amino acids and water molecules in the protein calyx most often involved in binding). Dissociation constants (Ki) for drugs typically lie in the same range as Ki for natural ligands; in most instances (different proteins and docking conditions), vastatins are the strongest interactors, with atorvastatin ranking top in half of the cases.

Bovine beta-lactoglobulin acts as an acid-resistant drug carrier by exploiting its diverse binding regions.

Binding of fluorine-containing drugs to bovine beta-lactoglobulin, the most abundant whey protein in bovine milk, was investigated by means of (19)F NMR and mass spectrometry. The stoichiometry of the binding and its stability in acidic medium, where beta-lactoglobulin is folded and stable, were also studied, along with competition from molecules that can be regarded as analogs of physiological ligands to bovine beta-lactoglobulin. Conditional binding data were combined with protein structural information derived from circular dichroism and limited proteolysis studies.

Structural and dynamic roles of permanent water molecules in ligand molecular recognition by chicken liver bile acid binding protein.

Chicken liver bile acid binding protein (cL-BABP) crystallizes with water molecules in its binding site. To obtain insights on the role of internal water, we performed two 100 ns molecular dynamics (MD) simulations in explicit solvent for cL-BABP, as apo form and as a complex with two molecules of cholic acid, and analyzed in detail the dynamics properties of all water molecules. The diffusion coefficients of the more persistent internal water molecules are significantly different from the bulk, but similar between the two protein forms.

Computational and experimental approaches assess the interactions between bovine beta-lactoglobulin and synthetic compounds of pharmacological interest.

Extending a previous investigation, the ability of binding to the model calycin beta-lactoglobulin (BLG) was evaluated both in silico and in vitro for several fluorine-containing (semi-)synthetic molecules of pharmacological and pharmaceutical interest (antibiotics, vastatins, steroid drugs). Simulation procedures included molecular docking according to a Montecarlo-simulated annealing protocol and molecular dynamics; heteronuclear NMR and denaturant gradient gel electrophoresis were the selected experimental techniques. For the tested drugs, ranking of the binding affinity was consistently assessed by computation and by experiment.

Computational and experimental approaches for assessing the interactions between the model calycin beta-lactoglobulin and two antibacterial fluoroquinolones.

Norfloxacin and levofloxacin, two fluoroquinolones of different bulk, rigidity and hydrophobicity taken as model ligands, were docked to one apo and two holo crystallographic structures of bovine beta-lactoglobulin (BLG) using different computational approaches. BLG is a member of the lipocalin superfamily. Lipocalins show a typical b-barrel structure encompassing an internal cavity where small hydrophobic molecules are usually bound.

Hemoglobin and heme scavenging.

Release of hemoglobin into plasma is a physiological phenomenon associated with intravascular hemolysis. In plasma, stable haptoglobin-hemoglobin complexes are formed and these are subsequently delivered to the reticulo-endothelial system by CD163 receptor-mediated endocytosis. Heme arising from the degradation of hemoglobin, myoglobin, and of enzymes with heme prosthetic groups could be delivered in plasma.

Synthesis and reactivity of N-heterocycle-B(C6F5)3 complexes. 4. Competition between pyridine- and pyrrole-type substrates toward B(C6F5)3: structure and dynamics of 7-B(C6F5)3-7-azaindole and [7-Azaindolium]+[HOB(C6F5)3]-.

Reaction between 7-azaindole and B(C6F5)3 quantitatively yields 7-(C6F5)3B-7-azaindole (4), in which B(C6F5)3 coordinates to the pyridine nitrogen of 7-azaindole, leaving the pyrrole ring unreacted even in the presence of a second equivalent of B(C6F5)3. Reaction of 7-azaindole with H2O-B(C6F5)3 initially produces [7-azaindolium]+[HOB(C6F5)3]- (5) which slowly converts to 4 releasing a H2O molecule. Pyridine removes the borane from the known complexes (C6F5)3B-pyrrole (1) and (C6F5)3B-indole (2), with formation of free pyrrole or indole, giving the more stable adduct (C6F5)3B-pyridine (3).

NMR investigation of the dihydrogen-bonding and proton-transfer equilibria between the hydrido carbonyl anion [HRe2(CO)9]- and fluorinated alcohols.

The interaction of fluorinated alcohols with the anionic hydrido complex [HRe2(CO)9]- (1) has been investigated by NMR spectroscopy. According to the acidic strength of the alcohols, the interaction may result not only in the formation of dihydrogen-bonded ROH..

Oxygen-bridged borate anions from tris(pentafluorophenyl)borane: synthesis, NMR characterization, and reactivity.

The previously known anion [(C6F5)3B(mu-OH)B(C6F5)3]- (2) has been prepared by a two-step procedure, involving deprotonation of (C6F5)3BOH2 to give [B(C6F5)3OH]- (1), followed by addition of B(C6F5)3. The solution structure and the dynamics of 2 have been investigated by 1H and 19F NMR spectroscopy. The reaction of [NHEt3]2 with NEt3 resulted in the formation of [NHEt3]+ [(C6F5)3BOH]-, [NHEt3]+ [(C6F5)3BH]-, and (C6F5)3B- (CH2CH=N+ Et2).

Solution conformation and dynamics of the ion pairs originating from the reaction of B(C6F5)3 with bisindenyl dimethyl zirconium complexes.

The two ion pairs [(4,7-Me(2)indenyl)(2)ZrMe](+)[MeB(C(6)F(5))(3)](-) (1 b) and [(indenyl)(2)ZrMe](+) [MeB(C(6)F(5))(3)](-) (2 b) have been generated in situ by reaction of stoichiometric B(C(6)F(5))(3) with the corresponding dimethyl zirconocenes. It has been shown that molecular mechanics computations, guided by experimental (1)H/(1)H NOE correlations, can provide information on the conformers present in solution. The dynamics of the ion pairs has also been investigated, showing the occurrence of both the processes previously characterized for this class of compounds, namely the B(C(6)F(5))(3) migration between the two methyl groups and dissociation-recombination of the whole [MeB(C(6)F(5))(3)](-) anion, the latter process being much faster than the first one (about three order of magnitude).

Reorganization in apo- and holo-beta-lactoglobulin upon protonation of Glu89: molecular dynamics and pKa calculations.

Molecular dynamics (MD) simulations starting from crystallographic data allowed us to directly account for the effects of the protonation state of Glu89 on the conformational stability of apo- and holo-beta-lactoglobulin (BLG). In apo-BLG simulations starting from the protonated crystal structure, we observe a long-lived H-bond interaction between the protonated Glu89 and Ser116. This interaction, sequestering the proton from the aqueous medium, explains a pK(half) value evaluated at pH 7.

Synthesis and reactivity of (C6F5)3B-N-heterocycle complexes. 1. Generation of highly acidic sp3 carbons in pyrroles and indoles.

The reaction of pyrroles and indoles with B(C(6)F(5))(3) and BCl(3) produces 1:1 B-N complexes containing highly acidic sp(3) carbons, for example, N-[tris(pentafluorophenyl)borane]-5H-pyrrole (1) and N-[tris(pentafluorophenyl)borane]-3H-indole (2), that are formed by a new formal N-to-C hydrogen shift, the mechanism of which is discussed. With some derivatives, restricted rotation around the B-N bond and/or the B-C bonds was observed by NMR techniques, and some rotational barriers were calculated from experimental data. The acidity of the sp(3) carbons in these complexes is shown by their ability to protonate NEt(3), with formation of pyrrolyl- and indolyl-borate ammonium salts.

An intramolecular N-H...(mu-H)Re2 dihydrogen bond and a novel mu 3-eta 2 coordination mode of the pyrazolate anion on a triangular cluster face.

The quantitative addition of pyrazole (Hpz) to the 44 valence-electron, triangular cluster anion [Re3(mu 3-H)-(mu-H)3(CO)9]- gives the novel unsaturated anion [Re3(mu-H)4(CO)9(Hpz)]- (1, 46 valence electrons), which contains a pyrazole molecule that is terminally coordinated on a cluster vertex. Solidstate X-ray and IR analyses reveal a rather weak hydrogen-bonding interaction between the NH proton and one of the hydrides bridging the opposite triangular cluster edge (delta H degree = -3.1 kcal mol-1 from the Iogansen equation).

pH and ionic strength dependence of protein (un)folding and ligand binding to bovine beta-lactoglobulins A and B.

Formation of complexes between bovine beta-lactoglobulins (BLG) and long-chain fatty acids (FAs), effect of complex formation on protein stability, and effects of pH and ionic strength on both complex formation and protein stability were investigated as a function of pH and ionic strength by electrophoretic techniques and NMR spectroscopy. The stability of BLG against unfolding is sharply affected by the pH of the medium: both A and B BLG variants are maximally stabilized against urea denaturation at acidic pH and against SDS denaturation at alkaline pH. The complexes of BLGB with oleic (OA) and palmitic acid (PA) appear more stable than the apoprotein at neutral pH whereas no differential behavior is observed in acidic and alkaline media.

NMR and DFT analysis of [Re(2)H(2)(CO)(9)]: evidence of an eta(2)-H(2) intermediate in a new type of fast mutual exchange between terminal and bridging hydrides.

Protonation of the anion [Re(2)H(CO)(9)](-) (1) with a strong acid at 193 K affords the neutral complex [Re(2)H(2)(CO)(9)] (2), that in THF above 253 K irreversibly loses H(2) to give [Re(2)(CO)(9)(THF)], previously obtained by room-temperature protonation of 1. Treatment of 2 with NEt(4)OH restores the starting anion 1. Variable temperature (1)H and (13)C NMR spectra as well as T(1) measurements agree with the formulation of 2 as a classical [Re(2)H(mu-H)(CO)(9)] complex, in which two dynamic processes takes place.

[Re (μ-H) (CO) ] and [Re (μ-H) (CO) ], Two Isolobal Analogues of Cyclopentane.

The first five-membered rings of metal atoms connected by M-M or M-H-M bonds only have been obtained by a Re +Re condensation in which a polyhydride acts as a bridging bidentate ligand toward a coordinatively unsaturated fragment (see scheme below). In spite of the octahedral coordination of the Re centers, the Re rings display conformations (twisted and envelope) comparable with those observed for organic five-membered rings of tetrahedral carbon atoms.