Papers by Andrzej Ejchart
Acta Biochimica Polonica, 2007
In the solution structure of the ribosome-associated cold shock response protein Yfia of Escheric... more In the solution structure of the ribosome-associated cold shock response protein Yfia of Escherichia coli in the free state two structural segments can be distinguished: a well structured, rigid N-terminal part displaying a betaalphabetabetabetaalpha topology and a flexible C-terminal tail comprising last 20 amino-acid residues. The backbone dynamics of Yfia protein was studied by (15)N nuclear magnetic relaxation at three magnetic fields and analyzed using model-free approach. The overall diffusional tumbling of the N-terminal part is strongly anisotropic with a number of short stretches showing increased mobility either on a subnanosecond time scale, or a micro- to millisecond time scale, or both. In contrast, the unstructured polypeptide chain of the C-terminal part, which cannot be regarded as a rigid structure, shows the predominance of fast local motions over slower ones, both becoming faster closer to the C-terminus.
Physical Chemistry Chemical Physics, 2019
Complex formation between quinine and natural cyclodextrins (CD) was studied using NMR spectroscopy.
Polimery, 2007
In the review (63 references) the nuclear magnetic relaxation which is a unique experimental meth... more In the review (63 references) the nuclear magnetic relaxation which is a unique experimental method giving insight into dynamic processes existing in proteins and covering a broad range of time scales was presented. This method, however, is demanding experimentally and theoretically. Exprimental methods limited to 15 N nuclei are briefly presented and their limitations discussed. Analysis of experimental relaxation data for proteins can be done in the frame of model-free approach or applying spectral density mapping. Both those approaches are difficult for the physical interpretation of results. Besides motional parameters, some structural parameters influence relaxation rates and have to be estimated or determined. Hopefully, many problems connected with the analysis of relaxation data in proteins can be overcome with relaxation measurements at multiple magnetic fields for different isotopes like 15 N, 13 C, and 2 H.
Journal of biomolecular NMR, Apr 1, 2018
Simple and convenient method of protein dynamics evaluation from the insufficient experimental N ... more Simple and convenient method of protein dynamics evaluation from the insufficient experimental N relaxation data is presented basing on the ratios, products, and differences of longitudinal and transverse N relaxation rates obtained at a single magnetic field. Firstly, the proposed approach allows evaluating overall tumbling correlation time (nanosecond time scale). Next, local parameters of the model-free approach characterizing local mobility of backbone amide N-H vectors on two different time scales, S and R , can be elucidated. The generalized order parameter, S, describes motions on the time scale faster than the overall tumbling correlation time (pico- to nanoseconds), while the chemical exchange term, R , identifies processes slower than the overall tumbling correlation time (micro- to milliseconds). Advantages and disadvantages of different methods of data handling are thoroughly discussed.
International journal of biological macromolecules, 2018
BacSp222 is a multifunctional bacteriocin produced by Staphylococcus pseudintermedius strain 222,... more BacSp222 is a multifunctional bacteriocin produced by Staphylococcus pseudintermedius strain 222, an opportunistic pathogen of domestic animals. At micromolar concentrations, BacSp222 kills Gram-positive bacteria and is cytotoxic toward mammalian cells, while at nanomolar doses, it acts as an immunomodulatory factor, enhancing nitric oxide release in macrophage-like cell lines. The bacteriocin is a cationic, N-terminally formylated, 50-amino-acid-long linear peptide that is rich in tryptophan residues. In this study, the solution structure of BacSp222 was determined and compared to the currently known structures of similar bacteriocins. BacSp222 was isolated from a liquid culture medium in a uniformly 13C- and 15N-labeled form, and NMR data were collected. The structure was calculated based on NMR-derived constraints and consists of a rigid and tightly packed globular bundle of four alpha-helices separated by three short turns. Although the amino acid sequence of BacSp222 has no sig...
Chirality, 2017
Gibbs energies of complex formation between enantiomers of bicyclic terpenoid, fenchone, and natu... more Gibbs energies of complex formation between enantiomers of bicyclic terpenoid, fenchone, and naturally occurring cyclodextrins, βCD and γCD, were determined by means of 13 C and 1 H nuclear magnetic resonance (NMR) titration data. These results were compared with the corresponding data obtained previously for the diastereomeric fenchone/αCD complexes. The size of the inner cavity of host molecules significantly influences stoichiometry, association constants, and enantiomeric differentiation of the studied complexes. These complementary data allow us to discuss qualitatively the influence of the host size on the guest-host interactions. A method of the simultaneous use of titration data collected for several resonances of different isotopes in the determination of association constants was worked out and thoroughly analyzed. Comparison of the results of global data analyses with weighted means of individual ones revealed that both these approaches are equally trustworthy.
Scientific Reports, 2016
The binding of metal ions at the interface of protein complexes presents a unique and poorly unde... more The binding of metal ions at the interface of protein complexes presents a unique and poorly understood mechanism of molecular assembly. A remarkable example is the Rad50 zinc hook domain, which is highly conserved and facilitates the Zn2+-mediated homodimerization of Rad50 proteins. Here, we present a detailed analysis of the structural and thermodynamic effects governing the formation and stability (logK12 = 20.74) of this evolutionarily conserved protein assembly. We have dissected the determinants of the stability contributed by the small β-hairpin of the domain surrounding the zinc binding motif and the coiled-coiled regions using peptides of various lengths from 4 to 45 amino acid residues, alanine substitutions and peptide bond-to-ester perturbations. In the studied series of peptides, an >650 000-fold increase of the formation constant of the dimeric complex arises from favorable enthalpy because of the increased acidity of the cysteine thiols in metal-free form and the s...
Journal of peptide science : an official publication of the European Peptide Society, 2016
The synthesis of new dermorphin analogues is described. The (R)-alanine or phenylalanine residues... more The synthesis of new dermorphin analogues is described. The (R)-alanine or phenylalanine residues of natural dermorphin were substituted by the corresponding α-methyl-β-azidoalanine or α-benzyl-β-azido(1-piperidinyl)alanine residues. The potency and selectivity of the new analogues were evaluated by a competitive receptor binding assay in rat brain using [(3) H]DAMGO (a μ ligand) and [(3) H]DELT (a δ ligand). The most active analogue in this series, Tyr-(R)-Ala-(R)-α-benzyl-β-azidoAla-Gly-Tyr-Pro-Ser-NH2 and its epimer were analysed by (1) H and (13) C NMR spectroscopy and restrained molecular dynamics simulations. The dominant conformation of the investigated peptides depended on the absolute configuration around C(α) in the α-benzyl-β-azidoAla residue in position 3. The (R) configuration led to the formation of a type I β-turn, whilst switching to the (S) configuration gave rise to an inverse β-turn of type I', followed by the formation of a very short β-sheet. The selectivity...
Chemical Biology & Drug Design, 2016
This article is dedicated to the memory of Andrzej Lipkowski (deceased November 27, 2014). The pe... more This article is dedicated to the memory of Andrzej Lipkowski (deceased November 27, 2014). The peptide community has lost an excellent scientist and a dear friend, and he will be missed by all of us who were fortunate enough to know him and work with him. This article describes new deltorphin I analogs in which phenylalanine residues were replaced by the corresponding (R) or (S)-a-benzyl-b-azidoalanine, a-benzyl-b-(1-pyrrolidinyl)alanine, a-benzyl-b-(1-piperidinyl)alanine, and a-benzyl-b-(4-morpholinyl)-alanine residues. The potency and selectivity of the new analogs were evaluated by a competitive receptor binding assay in the rat brain using [ 3 H]DAMGO (a l ligand) and [ 3 H]DELT (a d ligand). The affinity of analogs containing (R) or (S)-abenzyl-b-azidoalanine in position 3 to d-receptors strongly depended on the chirality of the a,a-disubstituted residue. The conformational behavior of peptides modified with (R) or (S)-a-benzyl-b-(1-piperidinyl)Ala, which displays the opposite selectivity, was analyzed by 1 H and 13 C NMR. The l-selective Tyr-D-Ala-(R)a-benzyl-b-(1-piperidinyl)Ala-Asp-Val-Val-Gly-NH 2 lacks the helical conformation observed in the d-selective Tyr-D-Ala-(S)-a-benzyl-b-(1-piperidinyl)Ala-Asp-Val-Val-Gly-NH 2. Our results support the proposal that differences between d-and l-selective opioid peptides are attributable to the presence or absence of a spatial overlap between the N-terminal message domain and the C-terminal address domain.
The Proteomics Protocols Handbook, 2005
Nuclear magnetic resonance (NMR) spectroscopy is well suited to play an important part in proteom... more Nuclear magnetic resonance (NMR) spectroscopy is well suited to play an important part in proteomics programs because this method provides structural information at the atomic level. Nuclei of isotopes of biologically important elements display narrow reso- nance lines. Internuclear interactions, modulated by even small structural and confor- mational changes, influence line position, line shape, and intensity of signals in NMR spectra. Last but not least, NMR provides high-resolution structures in solution, allow- ing the study of proteins that fail to crystallize or comparison of differences between their crystal and solution structure (1). The potential of the NMR method, however, has not been reflected by the present number of deposited structures; less than 14% of the protein structures in the Protein Data Bank (PDB) have been determined by NMR spec- troscopy (2).
European Biophysics Journal, 2014
Journal of Peptide Science, 2014
New analogues of deltorphin I (DT I, Tyr-D-Ala-Phe-Asp-Val-Val-Gly-NH2 ), with the D-Ala residue ... more New analogues of deltorphin I (DT I, Tyr-D-Ala-Phe-Asp-Val-Val-Gly-NH2 ), with the D-Ala residue in position 2 replaced by α-methyl-β-azido(amino, 1-pyrrolidinyl, 1-piperidinyl or 4-morpholinyl)alanine, were synthesized by a combination of solid-phase and solution methods. All ten new analogues were tested for receptor affinity and selectivity to μ- and δ-opioid receptors. The affinity of analogues containing (R) or (S)-α-methyl-β-azidoalanine in position 2 to δ-receptors strongly depended on the chirality of the α,α-disubstituted residue. Peptide II, containing (S)-α-methyl-β-azidoalanine in position 2, displayed excellent δ-receptor selectivity with its δ-receptor affinity being only three times lower than that of DT I.
Toxicology Letters, 2010
Zinc is known to be involved in colon carcinogenesis. Higher external as well as internal zinc co... more Zinc is known to be involved in colon carcinogenesis. Higher external as well as internal zinc concentrations may activate stress signaling in colon cancer cells, thus inhibiting their growth and proliferation and leading to their demise. Despite growing evidence about intracellular targets of zinc toxicity in various cells, its mechanisms and biology in progressive of colon cancer stages remain relatively underexplored. Thus in this study we investigated the effects of zinc ionophore on behavior of colon cancer cell lines SW-620 and SW620-r. Exposure to zinc ionophore produced timedependent influx of zinc ions into the cytoplasm of treated cells. This influx was accompanied by enhanced oxidative stress, changes in mitochondrial topography and inhibition of ATP production with resulting cell death. The analyses of various cell death markers suggested that it combined features of apoptosis and autophagic demise which was much more expressed in aggressive SW620-r cells. Our findings thus point at interesting aspects of zinc toxicity in colon cancer cells while drawing attention to autophagic mechanisms whereby exposed cells may reduce or ultimately escape cell death.
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Papers by Andrzej Ejchart