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Open-tubular capillary electrochromatography with bare gold nanoparticles-based stationary phase applied to separation of trypsin digested proteins
Mikšík, Ivan ; Lacinová, Kateřina ; Zmatlíková, Zdeňka ; Sedláková, Pavla ; Král, V. ; Sýkora, D. ; Řezanka, P. ; Kašička, Václav
Open-tubular capillary electrochromatography (OT-CEC) using bare gold nanoparticles-based stationary phase has been applied to separation of tryptic peptide fragments of native and glycated proteins, bovine serum albumin and human transferrin. OT-CEC with bare gold nanoparticles stationary phase was found to be a suitable technique for separation of complex peptide mixtures originating from enzymatic (tryptic) digestion of native and glycated bovine serum albumin and human transferrin, and for glycation studies of these proteins.
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Does oxidation make the organic aerosol coatings more hydrophilic? Insight from molecular dynamics study of oxidized surfactant monolayers
Roeselová, Martina ; Khabiri, Morteza ; Cwiklik, Lukasz
Organic compounds are ubiquitous in atmospheric aerosols. The morphology and structure of the organic phase affect the optical properties of the aerosols, their heterogeneous reactivity as well as their ability to nucleate cloud droplets and ice particles. It is commonly assumed that atmospheric oxidative ageing of the organic material, leading to the formation of polar groups such as carbonyl (=O), hydroxyl (-OH) and carboxylic acid (-COOH), will render the aerosol particle surfaces increasingly more hydrophilic, hence, able to take up more water. Field measurements have shown that a large fraction of the organic material found in aerosols are surface active compounds, such as fatty acids and lipids(Tervahattu, 2002 and 2005). An inverted micelle structure, with an aqueous core surrounded by an organic surfactant layer, has thus been proposed for aqueous aerosols, both marine and continental (Donaldson, 2006). While recent experiments suggest the existence of more complex structures, such as organic inclusions and surfactant lenses (Dennis-Smither, 2012), a monolayer (ML) of surface active organics on an aqueous subphase (the so called Langmuir monolayers) represents the basic model system used in laboratory studies aimed at elucidating the effect of oxidative processes on structural properties of organic coatings on aerosol particles. In our previous work, we used molecular dynamics computer simulations to study the structure and stability of oxidized phospholipid MLs (Khabiri, 2012). In this contribution, we employed the molecular dynamics simulation technique to investigate – with atomistic resolution – structural changes occuring in a fatty acid ML upon moderate degree of oxidation.
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Molecular simulations unravel preference of haloalkanes for the air/water interface
Habartová, Alena ; Minofar, Babak ; Obisesan, A. ; Roeselová, Martina
Halogenated organics are emitted into the atmosphere from a variety of sources of both natural and anthropogenic origin (Finlayson-Pitts et al., 2000). Their uptake at the surface of aerosols can affect their reactivity, for example in processes which take part in ozone destruction due to production of reactive chlorine, bromine and iodine radicals. This study presents results of molecular dynamic (MD) simulations carried out to investigate the interaction of short-chain haloalkanes with aqueous surfaces. We report on a free energy minimum that the haloalkanes exhibit at the air/water interface.
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Reaction of prion protein with quinacrine
Zawada, Zbigniew ; Šafařík, Martin ; Šebestík, Jaroslav ; Stibor, Ivan ; Bouř, Petr
Prion protein is supposed to cause Creutzfeld–Jakob disease, which can be treated in cell culture by quinacrine. In this work we study acridinylation reaction of prion protein. We also investigate this reaction theoretically on simple models and calculate activation energies for a large ensemble of acridine derivatives. Found correlation between the reactivity and geometry can enhance the design of the new acridine compounds, particularly for medical purposes.
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Expression of osmotin, an antifungal protein from Nicotiana tabacum in Escherichia coli
Viktorová, J. ; Macková, M. ; Macek, Tomáš
Plants have evolved a huge variety of proteins involved in the defense against pathogens and adaptation to stressful environments. Plant proteins whose expression is strongly induced in response to infection by pathogens belong to the group of pathogenesis-related (PR) proteins. The family of PR-5 proteins constitutes a group of cysteine-rich proteins including thaumatin, zeamatin and also osmotin. Osmotin is a cationic protein of 205 residues and molecular weight of 24 kDa. It was discovered and characterized in cells of Nicotiana tabacum var. Wisconsin 38. The plasmid harbouring cDNA of osmotin from Nicotiana tabacum was constructed for transformation of Escherichia coli. The osmotin gene was prepared in fusion with histidine tail to facilitate the isolation and purification from bacterial cells. Selection of transgenic colonies was based on antibiotic resistance. The hexahistidine-tagged osmotin was overexpressed in heterologous system by using pET expression vector and purified using immobilized metal affinity chromatography. The expression of osmotin was detected and antifungal activity was tested.
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Synthetic scan of C-domain from prion proteins
Šebestík, Jaroslav ; Zawada, Zbigniew ; Šafařík, Martin ; Hlaváček, Jan
Prions are suspected as culprits of several neuropathogenic diseases. A combination of chemical and recombinant syntheses is a powerful tool for studying prion role in pathogenesis of neurodegenerative diseases. Due to the presence of “difficult” sequences in the prion protein molecule, chemical ligation procedure using peptide thioesters as key building blocks is a method of choice. Therefore, a synthetic scan of peptides constituting the mouse prion protein (MoPrP) C-domain 93-231 was carried out. The synthesis on chlorotritylchloride resin was the most promising for most peptides. Only the octadecapeptide MoPrP195-212 could not be synthesized by automated peptide synthesis even using the β-sheet breaking dipeptides. This difficulty was overcome by manual peptide synthesis with careful monitoring of coupling and Fmoc removal.
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Study of antimicrobial peptide induction in Brassica napus
Shevchenko, I. ; Neubauerová, Tereza ; Macková, Martina ; Macek, Tomáš
Development of cheap, effective and environmentally friendly protection of industrial plants is a key problem of mankind, where using of antimicrobial peptides could be a reasonable solution. As a source for isolation of these peptides canola (Brassica napus) was chosen, which was treated by functional analog of salicylic acid – benzothiadiazole (BTH) – to stimulate the immune system. To isolate the responsible antimicrobial peptides, crude buffer extract was obtained. Next steps were precipitation, centrifugation and molecular weight filtration. The further isolation procedure comprised hexane extraction, SPE-C18 (Solid Phase Extraction) to separate hydrophobic and hydrophilic fractions and reversed-phase chromatography. Antimicrobial activity was tested by diffusion method. Fractions were tested on gram-positive and gram-negative bacteria and on yeast Candida scotii.
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