The metal-ion selectivity in biomolecules represents one of the most important phenomena in bioinorganic chemistry. The open question to what extent is the selectivity in the complex bioinorganic structures such as metallopeptides determined by the first-shell ligands of the metal ion is answered herein using six model peptides complexed with the set of divalent metal ions (Mn(2+), Fe(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), and Hg(2+)) and their various first-shell representations. By calculating the differences among the free energies of complexation of metal ions in these peptides and their model (truncated) systems it is quantitatively shown that the definition of the first shell is paramount to this discussion and revolves around the chemical nature of the binding site. Despite the vast conceivable diversity of peptidic structures, that suggest certain fluidity of this definition, major contributing factors are identified and assessed based on their importance for capturing metal-ion selectivity. These factors include soft/hard character of ligands and various non-covalent interactions in the vicinity of the binding site. The relative importance of these factors is considered and specific suggestions for effective construction of the models are made. The relationship of first-shell models and their corresponding parent peptides is discussed thoroughly, both with respect to their chemical similarity and potential disparity introduced by generally "non-alignable" conformational flexibility of the two systems. It is concluded that, in special cases, this disparity can be negligible and that heeding the chemical factors contributing to selectivity during construction of the model can successfully result in models that retain the affinity profile for various metal ions with high fidelity.

• MeSH
• chemické modely * MeSH
• ionty chemie   MeSH
• konformace proteinů MeSH
• kovy chemie   MeSH
• peptidy chemie   MeSH
• počítačová simulace MeSH
• simulace molekulového dockingu * MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• ionty MeSH
• kovy MeSH
• peptidy MeSH

Parallel reaction monitoring (PRM) has emerged as a popular approach for targeted protein quantification. With high ion utilization efficiency and first-in-class acquisition speed, the timsTOF Pro provides a powerful platform for PRM analysis. However, sporadic chromatographic drift in peptide retention time represents a fundamental limitation for the reproducible multiplexing of targets across PRM acquisitions. Here, we present PRM-LIVE, an extensible, Python-based acquisition engine for the timsTOF Pro, which dynamically adjusts detection windows for reproducible target scheduling. In this initial implementation, we used iRT peptides as retention time standards and demonstrated reproducible detection and quantification of 1857 tryptic peptides from the cell lysate in a 60 min PRM-LIVE acquisition. As an application in functional proteomics, we use PRM-LIVE in an activity-based protein profiling platform to assess binding selectivity of small-molecule inhibitors against 220 endogenous human kinases.

• MeSH
• hmotnostní spektrometrie MeSH
• iontová mobilní spektrometrie * MeSH
• lidé MeSH
• peptidy MeSH
• proteiny MeSH
• proteomika * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• peptidy MeSH
• proteiny MeSH

Ion-pairing reversed-phase liquid chromatography was utilized for the analysis of native and phosphorothioated oligonucleotides differing in the length (2-6mers and 21mer) and the number and position of phosphorothioate modifications. We investigated the influence of counterion (acetate vs. hexafluoroisopropanol) on the adsorption of eleven alkylamines on the stationary phases. A stronger adsorption of charged alkylamines on octadecyl- and phenyl-based stationary phases led to greater retention of oligonucleotides, and the adsorption of alkylamines was promoted with greater concentration of hexafluoroisopropanol in the mobile phase. Selected amines (triethylamine, dipropylamine, hexylamine) were used to study the resolution of n and n-x mers (main peak and its impurities shortened at 5´end), and diastereomeric separation of phosphorothioated oligonucleotides. The results confirmed a crucial role of alkylamine and counterion choice on the diastereomeric separation. The increasing hydrophobicity of alkylamine led to diminished diastereomeric selectivity which produced narrower phosphorothioated oligonucleotides peaks and led to improved n/n-x separation. Using hexafluoroisopropanol instead of acetate as counterion further enhances this effect (except for 100 mM concentration of hexafluoroisopropanol in combination with highly hydrophobic hexylamine). The elevated column temperature led to suppression of the diastereomeric resolution and improved resolution of n and n-x mers oligonucleotides. Baseline separation of oligonucleotides with different number of phosphorothioate linkages was achieved; this may be useful for therapeutic oligonucleotide analysis.

• Klíčová slova
• C18 column, Hexafluoroisopropanol, Ion-pairing reversed-phase chromatography, Phenyl column, Phosphorothioated oligonucleotides,
• MeSH
• adsorpce MeSH
• aminy chemie   MeSH
• chromatografie s reverzní fází * metody   MeSH
• fluorované uhlovodíky MeSH
• fosforothioátové oligonukleotidy * chemie   izolace a purifikace   MeSH
• hydrofobní a hydrofilní interakce MeSH
• propanoly chemie   MeSH
• stereoizomerie MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• aminy MeSH
• fluorované uhlovodíky MeSH
• fosforothioátové oligonukleotidy * MeSH
• hexafluoroisopropanol MeSH Prohlížeč
• propanoly MeSH

We constructed a sensor for the determination of Fe2+ and/or Fe3+ ions that consists of a polyaniline layer as an ion-to-electron transducer; on top of it, chelating molecules are deposited (which can selectively chelate specific ions) and protected with a non-biofouling poly(2-methyl-2-oxazoline)s layer. We have shown that our potentiometric sensing layers show a rapid response to the presence of Fe2+ or Fe3+ ions, do not experience interference with other ions (such as Cu2+), and work in a biological environment in the presence of bovine serum albumin (as a model serum protein). The sensing layers detect iron ions in the concentration range from 5 nM to 50 µM.

• Klíčová slova
• analysis, non-biofouling layer, poly(2-methyl-2-oxazoline)s, potentiometry, sensor of Fe2+ or Fe3+ ions,
• MeSH
• aniliny MeSH
• chelátory * MeSH
• elektrody MeSH
• iontově selektivní elektrody * MeSH
• ionty MeSH
• koncentrace vodíkových iontů MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• aniliny MeSH
• chelátory * MeSH
• ionty MeSH
• polyaniline MeSH Prohlížeč

The functionalized molecules with specific molecular sites appear to be a promising approach for detection of cation in UV-visible and fluorescence spectroscopy. The synthesized receptor 4-((5-methylfuran-2-yl)methylene)hydrazono)methyl)phenol MFMHMP was found selective for La3+ among Ag+, K+, Na+, Be2+, Mg2+, Ca2+, Eu3+, Al3+, La3+, Zr4+, Th4+, UO22+, Fe3+, Fe2+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+ and Hg2+ metal ions used as their nitrates by UV-visible spectroscopy and fluorescence spectroscopy. The binding nature of MFMHMP with La3+ ion was analyzed by UV-visible, fluorescence, IR, mass spectroscopy and cyclic voltammetric studies. The stoichiometry was established to be 1:1 by Benesi-Hildebrand, mole-ratio method and method of continuous variation (Job's method) with good association affinity K = 6.245 × 104 M-1. Computational studies and Density functional theory (DFT) calculation gives the proof of electron transfer during excitation and emission. Binding energy of complex through Density Function Theory -62.387 kcal/mol has also indication of strong binding. The electron transfer energy of Higher occupied molecular orbital (HOMO) to Lower unoccupied molecular orbital (LUMO) is about 4.662 eV for MFMHMP+La3+ Complex. Among that all transitions HOMO → LUMO + 8 and HOMO → LUMO + 9 play a key role for the blue shift transition during complexation.

• Klíčová slova
• DFT, IR, La(3+), Mass spectroscopy, Sensor, UV–visible,
• Publikační typ
• časopisecké články MeSH

• MeSH
• draslík krev   MeSH
• iontově selektivní elektrody * MeSH
• lidé MeSH
• sodík krev   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• draslík MeSH
• sodík MeSH

The ion selective electrode (ISE)-based potentiometric approach is shown to be an effective means of characterizing the anion recognition sites in the molecular receptor calix[2]pyridino[2]pyrrole (CPP). In particular, potentiometric pH-measurements involving the use of experimental PVC-membranes based on CPP revealed the existence of both mono- and diprotonated forms of the receptor under readily accessible conditions. Based on these analyses, apparent surface protonation constants for this heterocalixarene were found to lie between 8.5-8.9 (pK(B1)) and 3.3-3.8 (pK(B2)). CPP was found to interact with targeted anionic analytes based on both coulombic and hydrogen bond interactions, as inferred from varying the kinds of ionic sites present within the membrane phase. Potentiometric selectivity studies revealed that CPP preferred "Y-shaped" anions (e.g. acetate, lactate, benzoate) over spherical anions (e.g. fluoride and chloride), fluoride over chloride within the set of spherical anions, and the ortho-isomer over the corresponding meta- and para-isomers in the case of hydroxybenzoate (salicylate and congeners). In the context of this study, the advantages of potentiometric determinations of acetylsalicylic acid using optimized PVC-membranes based on CPP relative to more conventional PVC-membrane ISEs based on traditional anion exchanger were also demonstrated.

• MeSH
• anionty chemie   MeSH
• Aspirin analýza   MeSH
• chemické modely MeSH
• chemické techniky analytické metody   MeSH
• iontově selektivní elektrody * MeSH
• ionty MeSH
• kalixareny chemie   MeSH
• koncentrace vodíkových iontů MeSH
• kyselina salicylová chemie   MeSH
• polymery chemie   MeSH
• potenciometrie metody   MeSH
• vazebná místa MeSH
• vodíková vazba MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• anionty MeSH
• Aspirin MeSH
• ionty MeSH
• kalixareny MeSH
• kyselina salicylová MeSH
• polymery MeSH

The aim of the present study was to develop an ion-selective electrode method for the continuous determination of the intracellular pH in Lactobacillus plantarum using a small-scale bioreactor. This method employed a salicylate-selective electrode basing on the distribution of salicylic acid across the cytoplasmic membrane. This developed electrode responded to salicylate concentrations above 20 μmol/L with a Nernstian sensitivity. The energized and concentrated cells were added into a thermostated small-scale bioreactor that contained the salicylate anions dissolved in a 100 mmol/L potassium phosphate buffer at different pH values. The changes in salicylate concentration that occurred in the medium containing bacterial suspension were measured as a voltage change. The cells of Lactobacillus plantarum showed maintenance of pH homeostasis at the studied pH ranging from 4.0 to 7.0, and they kept a neutral intracellular pH up to 5.8. The simplicity of the measuring preparation and the relatively low cellular concentration, as well as the advantages of the small-scale bioreactor, lead us to believe that the described method can facilitate the study of the physicochemical factors on the intracellular pH of lactic acid bacteria using a single pH probe in one method.

• MeSH
• anionty MeSH
• bioreaktory * MeSH
• cytoplazma chemie   MeSH
• iontově selektivní elektrody * MeSH
• koncentrace vodíkových iontů MeSH
• Lactobacillus plantarum chemie   fyziologie   MeSH
• salicylany analýza   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• anionty MeSH
• salicylany MeSH

• MeSH
• iontové kanály metabolismus   MeSH
• permeabilita MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• iontové kanály MeSH

Colicin U is a protein produced by the bacterium Shigella boydii (serovars 1 and 8). It exerts antibacterial activity against strains of the enterobacterial genera Shigella and Escherichia Here, we report that colicin U forms voltage-dependent pores in planar lipid membranes; its single-pore conductance was found to be about 22 pS in 1 M KCl at pH 6 under 80 mV in asolectin bilayers. In agreement with the high degree of homology between their C-terminal domains, colicin U shares some pore characteristics with the related colicins A and B. Colicin U pores are strongly pH dependent, and as we deduced from the activity of colicin U in planar membranes at different protein concentrations, they have a monomeric pore structure. However, in contrast to related colicins, we observed a very low cationic selectivity of colicin U pores (1.5/1 of K+/Cl- at pH 6) along with their atypical voltage gating. Finally, using nonelectrolytes, we determined the inner diameter of the pores to be in the range of 0.7 to 1 nm, which is similar to colicin Ia, but with a considerably different inner profile.IMPORTANCE Currently, a dramatic increase in antibiotic resistance is driving researchers to find new antimicrobial agents. The large group of toxins called bacteriocins appears to be very promising from this point of view, especially because their narrow killing spectrum allows specific targeting against selected bacterial strains. Colicins are a subgroup of bacteriocins that act on Gram-negative bacteria. To date, some colicins are commercially used for the treatment of animals (1) and tested as a component of engineered species-specific antimicrobial peptides, which are studied for the potential treatment of humans (2). Here, we present a thorough single-molecule study of colicin U which leads to a better understanding of its mode of action. It extends the range of characterized colicins available for possible future medical applications.

• Klíčová slova
• Shigella boydii, black lipid membrane, colicin U, ion-selectivity, membrane pores,
• MeSH
• buněčná membrána metabolismus   MeSH
• chlorid draselný farmakologie   MeSH
• gating iontového kanálu MeSH
• koliciny metabolismus   MeSH
• koncentrace vodíkových iontů MeSH
• lipidové dvojvrstvy metabolismus   MeSH
• permeabilita MeSH
• Shigella boydii metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• chlorid draselný MeSH
• koliciny MeSH
• lipidové dvojvrstvy MeSH