Vladimir V. Klochkov

p-tert-Butyl thiacalix[4]arenes functionalized at the lower rim by amide, hydroxyl and ester groups as anion receptors

New p-tert-butyl thiacalix[4]arenes differently substituted at the lower rim with amide, hydroxyl and ester groups were synthesized. Binding properties of the compounds toward some tetrabutylammonium salts n-Bu(4)NX (X = F(-), Cl(-), Br(-), I(-), CH(3)CO(2)(-), H(2)PO(4)(-), NO(3)(-)) were studied by UV spectroscopy. It was found that the stoichiometry of the complexes, generally, is 1 : 1, and the association constants are in the range of 10(3)-10(5) M(-1). The p-tert-butyl thiacalix[4]arenes containing secondary amide groups trisubstituted at the lower rim bind the studied anions most effectively. Selective receptors for fluoride and dihydrogen phosphate salts of tetrabutylammonium were found.

High-resolution NMR structure of the antimicrobial peptide protegrin-2 in the presence of DPC micelles

AbstractPG-1 adopts a dimeric structure in dodecylphosphocholine (DPC) micelles, and a channel is formed by the association of several dimers but the molecular mechanisms of the membrane damage by non-α-helical peptides are still unknown. The formation of the PG-1 dimer is important for pore formation in the lipid bilayer, since the dimer can be regarded as the primary unit for assembly into the ordered aggregates. It was supposed that only 12 residues (RGGRL-CYCRR-RFCVC-V) are needed to endow protegrin molecules with strong antibacterial activity and that at least four additional residues are needed to add potent antifungal properties. Thus, the 16-residue protegrin (PG-2) represents the minimal structure needed for broad-spectrum antimicrobial activity encompassing bacteria and fungi. As the peptide conformation and peptide-to-membrane binding properties are very sensitive to single amino acid substitutions, the solution structure of PG-2 in solution and in a membrane mimicking environment are crucial. In order to find evidence if the oligomerization state of PG-1 in a lipid environment will be the same or not for another protegrins, we investigate in the present work the PG-2 NMR solution structure in the presence of perdeuterated DPC micelles. The NMR study reported in the present work indicates that PG-2 form a well-defined structure (PDB: 2MUH) composed of a two-stranded antiparallel β-sheet when it binds to DPC micelles.

Antimicrobial peptide protegrin-3 adopt an antiparallel dimer in the presence of DPC micelles: a high-resolution NMR study.

A tendency to dimerize in the presence of lipids was found for the protegrin. The dimer formation by the protegrin-1 (PG-1) is the first step for further oligomeric membrane pore formation. Generally there are two distinct model of PG-1 dimerization in either a parallel or antiparallel β-sheet. But despite the wealth of data available today, protegrin dimer structure and pore formation is still not completely understood. In order to investigate a more detailed dimerization process of PG-1 and if it will be the same for another type of protegrins, in this work we used a high-resolution NMR spectroscopy for structure determination of protegrin-3 (RGGGL-CYCRR-RFCVC-VGR) in the presence of perdeuterated DPC micelles and demonstrate that PG-3 forms an antiparallel NCCN dimer with a possible association of these dimers. This structural study complements previously published solution, solid state and computational studies of PG-1 in various environments and validate the potential of mean force simulations of PG-1 dimers and association of dimers to form octameric or decameric β-barrels.

Spatial structure of peptides determined by residual dipolar couplings analysis.

The gated decoupled 13C NMR spectra of a dipeptide (Glu‐Trp) and a tetrapeptide (NAc‐Ser‐Phe‐Val‐Gly‐OMe) were recorded in D2O and in a lyotropic alignment medium (pentaethylene glycol monododecyl ether/n‐hexanol). The residual dipolar couplings were extracted as the differences between the observed couplings for the magnetic nuclei dissolved in the latter and former media. Using a computational optimization, the spatial structures of the compounds were calculated starting from their respective low energy conformations obtained on a semiempirical basis. The uniformity of each conformation was confirmed by the solid‐state 13C NMR spectra of powder samples. Differences between the starting structures and final ones, optimized when employing residual dipolar couplings, are discussed. Copyright

Changes in the Nitrocellulose Molecule Induced by Sulfate-Reducing Bacteria Desulfovibrio desulfuricans 1388. The Enzymes Participating in This Process

The appearance of unsubstituted glucopyranose residues in nitrocellulose (NC) induced by Desulfovibrio desulfuricans was established by 13C-NMR spectroscopy. After contact with bacterial cells, the degree of substitution by nitro groups in NC decreased from 2.59 to 2.40. The bacteria possess intra- and extracellular nitroesterase activities, which are responsible for denitration of the polymer. The presence of NC in the growth medium influences the extracellular nitroesterase activity. It is shown that inhibition of enzymatic activity in the presence of NC is caused by appearance of nitrates in the culture medium. Nitrate and nitrite reductases of dissimilatory type reduce nitrates. The data suggest consideration of bacteria belonging to the Desulfovibrio genus as the initial agent in utilization of an unnatural polymer—nitrocellulose—in a microbial consortium.

Structure of pravastatin and its complex with sodium dodecyl sulfate micelles studied by NMR spectroscopy

The aim of this work was to study the mechanisms of interaction between pravastatin and cell membranes using model membranes (sodium dodecyl sulfate micelles) by nuclear magnetic resonance spectroscopy methods. On the basis of the nuclear magnetic resonance experiments, it was established that pravastatin can form intermolecular complexes with sodium dodecyl sulfate micelles by the interaction of its hydrophilic groups with the polar surface of the micelle. Conformational features of pravastatin molecule were also studied. Copyright

Inversion of Population Distribution of Felodipine Conformations at Increased Concentration in Dimethyl Sulfoxide Is a Prerequisite to Crystal Nucleation

Knowledge of the preferred conformations of biologically active compounds is of the utmost importance for a better understanding of the structure-activity relationships underlying their biological activity, as well as their mechanism of action. Moreover, investigating the mechanism of nucleation from a saturated solution can facilitate the discovery and preparation of new polymorphic forms. To search regularities in the crystal nucleation of biologically active compounds (drugs) from a saturated solution, we studied the conformational preference of felodipine in dilute and saturated solution in dimethyl sulfoxide. The inversion of conformation distribution at increased concentration occurs: conformers that dominate in a dilute solution become the least abundant in the saturated one. Conformers that dominate in the saturated solution are of the same type as revealed in crystalline state by X-ray.

Spatial structure of heptapeptide Aβ16–22 (beta-amyloid Aβ1–40 active fragment) in solution and in complex with a biological membrane model

The spatial structure of an active fragment of beta‐amyloid Aβ1–40 heptapeptide Aβ16–22 (Lys‐Leu‐Val‐Phe‐Phe‐Ala‐Glu) in aqueous buffer solution and in complex with sodium dodecyl sulfate micelles as a model membrane system was investigated by 1H NMR spectroscopy and two‐dimensional NMR (TOCSY, HSQC‐HECADE (Heteronuclear Couplings from ASSCI‐domain experiments with E.COSY‐type crosspeaks), NOESY) spectroscopy. Complex formation was confirmed by the chemical shift changes of the heptapeptides 1H NMR spectra, as well as by the signs and values of the NOE effects in different environments. We compared the spatial structure of the heptapeptide in borate buffer solution and in complex with a model of the cell surface membrane. Copyright

Dynamic NMR study of cyclic derivatives of pyridoxine.

A series of pyridoxine derivatives was investigated by 1H and 2D nuclear overhauser enhancement spectroscopy (NOESY) NMR. The free energies of activation for the pyridyl‐oxygen rotation of the 2,4‐dinitrophenyl ether of the seven‐membered acetals of pyridoxine were measured by dynamic NMR. A conformational exchange between the chair and twist forms of the seven‐membered acetal ring was confirmed by dynamic NMR and STO3G computations. Copyright

Dynamic NMR study of dinitrophenyl derivatives of seven-membered cyclic ketals of pyridoxine

Two pyridoxine derivatives containing a dinitrophenyl moiety were investigated by 1H NMR spectroscopy. Conformational dynamics in solution were studied for each compound using dynamic NMR experiments. It was shown that both compounds studied are involved into two conformational exchange processes. The first process is a transformation of the seven‐membered cycle conformation between the enantiomeric P‐twist and M‐twist forms, and the second is a rotation of the dinitrophenyl fragment of the molecules around the C–O bond. Energy barriers of both conformational transitions were determined. Copyright