Hyaluronan random coils in electrolyte solutions—a molecular dynamics study

A computational method of modeling random coils of hyaluronan was developed based on the molecular-dynamics simulations. An oligosaccharide of 48 monosaccharide units was equilibrated within a 70–100 ns simulation and randomly chosen pieces of this molecule from different simulation frames were combined to constitute a long polysaccharide chain, both for hyaluronan and its non-ionic analog containing glucose instead of glucuronic acid. The dihedral angles of the glycoside connections of the pieces obeyed the statistics deduced from the simulation. The simulations were performed at various concentrations of NaCl and MgCl2. The calculated radii of gyration show a striking agreement with experimental data from the literature and indicate a key importance of the polymer-ion interactions for the random-coil conformation, but a low influence of the excluded volume of the chain and the carboxylate-groups repulsion. The method has thus the potential to become a versatile tool of modeling macromolecules of various semirigid polymers. © 2017 Elsevier LtdNational Grid Infrastructure MetaCentrum, provided under the program "Projects of Large Research, Development, and Innovations Infrastructures" [CESNET LM2015042

Equilibria of oligomeric proteins under high pressure – A theoretical description

High pressure methods have become a useful tool for studying protein structure and stability. Using them, various physico-chemical processes including protein unfolding, aggregation, oligomer dissociation or enzyme-activity decrease were studied on many different proteins. Oligomeric protein dissociation is a process that can perfectly utilize the potential of high-pressure techniques, as the high pressure shifts the equilibria to higher concentrations making them better observable by spectroscopic methods. This can be especially useful when the oligomeric form is highly stable at atmospheric pressure. These applications may be, however, hindered by less intensive experimental response as well as interference of the oligomerization equilibria with unfolding or aggregation of the subunits, but also by more complex theoretical description. In this study we develop mathematical models describing different kinds of oligomerization equilibria, both closed (equilibrium of monomer and the highest possible oligomer without any intermediates) and consecutive. Closed homooligomer equilibria are discussed for any oligomerization degree, while the more complex heterooligomer equilibria and the consecutive equilibria in both homo- and heterooligomers are taken into account only for dimers and trimers. In all the cases, fractions of all the relevant forms are evaluated as functions of pressure and concentration. Significant points (inflection points and extremes) of the resulting transition curves, that can be determined experimentally, are evaluated as functions of pressure and/or concentration. These functions can be further used in order to evaluate the thermodynamic parameters of the system, i.e. atmospheric-pressure equilibrium constants and volume changes of the individual steps of the oligomer-dissociation processes. © 2016 Elsevier LtdP208-12-G016, GACR, Grant Agency of the Czech RepublicGrant Agency of the Czech Republic [P208-12-G016

Pressure induced structural changes and dimer destabilization of HIV-1 protease studied by molecular dynamics simulations

High-pressure methods have become attractive tools for investigation of the structural stability of proteins. Besides protein unfolding, dimerization can be studied this way, too. HIV-1 protease is a convenient target of experimental and theoretical high-pressure studies. In this study molecular-dynamics simulations are used to predict the response of HIV-1 protease to the pressure of 0.1 to 600 MPa. The protease conformation of both the monomer and the dimer is highly rigid changing insignificantly with growing pressure. Hydrophobicity of the protease decreases with increasing pressure. Water density inside the active-site cavity grows from 87% to 100% of the bulk water density within the pressure range. The dimer-dissociation volume change is negative for most of the pressure ranges with the minimum of -105 ml mol-1, except for a short interval of positive values at low pressures. The dimer is thus slightly stabilized up to 160 MPa, but strongly destabilized by higher pressures.P41-RR005969, NIH, National Institutes of HealthNational Institutes of Health [P41-RR005969

Inhibitor and substrate binding induced stability of HIV-1 protease against sequential dissociation and unfolding revealed by high pressure spectroscopy and kinetics

High-pressure methods have become an interesting tool of investigation of structural stability of proteins. They are used to study protein unfolding, but dissociation of oligomeric proteins can be addressed this way, too. HIV-1 protease, although an interesting object of biophysical experiments, has not been studied at high pressure yet. In this study HIV-1 protease is investigated by high pressure (up to 600 MPa) fluorescence spectroscopy of either the inherent tryptophan residues or external 8-anilino-1-naphtalenesulfonic acid at 25°C. A fast concentration-dependent structural transition is detected that corresponds to the dimer-monomer equilibrium. This transition is followed by a slow concentration independent transition that can be assigned to the monomer unfolding. In the presence of a tight-binding inhibitor none of these transitions are observed, which confirms the stabilizing effect of inhibitor. High-pressure enzyme kinetics (up to 350 MPa) also reveals the stabilizing effect of substrate. Unfolding of the protease can thus proceed only from the monomeric state after dimer dissociation and is unfavourable at atmospheric pressure. Dimer-destabilizing effect of high pressure is caused by negative volume change of dimer dissociation of -32.5 mL/mol. It helps us to determine the atmospheric pressure dimerization constant of 0.92 μM. High-pressure methods thus enable the investigation of structural phenomena that are difficult or impossible to measure at atmospheric pressure. © 2015 Ingr et al.INSERM; Grant Agency of the Czech Republic [P208-12-G016

Assessing aerobic biodegradability of plastics in aqueous environment by GC-analyzing composition of equilibrium gaseous phase

Byl zpracován matematický model acidobazické rovnováhy CO2 v systému plyn - kapalina umožňující stanovit množství produkovaného CO2 chromatografickou analýzou plynné fáze. Za vytipovaných podmínek byla sledována biologická rozložitelnost modelových vzorků, průběh biorozkladu byl sledován podle produkce CO2 stanovované GC analýzou plynné fáze a standardním "titračním" postupem. Jedná se o "zastupitelné" postupy sledování průběhu aerobního biologického rozkladu látek ve vodním prostředí.A mathematical model of acid-basic CO2 equilibrium in a gas - liquid system was worked out, enabling to determine quantity of produced CO2 through chromatographic analysis of gaseous phase. Under appropriate test conditions, biodegradability of model samples was explored. Course of biodegradation was studied through produced CO2 determined by analyzing gaseous phase through GC on the one hand, and through customary "titration" procedure on the other. The procedures in question are "substituting" procedures for observing course of aerobic biodegradation of substances in an aqueous environment

Physical recycling of PET bottles - possibilities of the next aplications

The authors have assessed various sources of recycled PET (washed dry flakes, ground preforms etc.) using the proper methods (TG, viscometry, filtration test of the melt, DSC, ESM etc.). They have evaluated the most harmful impurities. The data presented could help those interested in the other potential applications of the recycled PET materials. This publication is one of the results based on the Grant sponsored by Czech Ministry of Industry and Trade "The new possibilities of the textile application of the recycled PET bottles"

Assessing aerobic biodegradability in aqueous environment by analyzing composition of equilibrium gaseous phase

Cílem práce bylo posouzení možnosti využití plynově chromatografické analýzy plynné fáze pro hodnocení aerobní biologické rozložitelnosti látek ve dvoufázovém systému plyn-kapalina. Příspěvek je rozdělen do dvou částí: v první části je diskutována acidobazická rovnováha CO2 v reálných podmínkách biologických testů; druhá část příspěvku pak zahrnuje experimentální ověření teoretických závěrů bilance CO2.The objective of this study was to verify potential use of chromatographic analysis of gaseous phase composition in an enclosed two-phase gas-liquid system to study course of biodegradation. This contribution is divided into the two parts: in the first part acidobasic equilibrium states of CO2 in a real biological system is discussed; the second part of this contribution includes experimental verification of the theoretical conclusions

Effect of solvent and ions on the structure and dynamics of a hyaluronan molecule

Hyaluronic acid (hyaluronan, HA) is a negatively charged polysaccharide forming highly swollen random coils in aqueous solutions. Their size decreases along with growing salt concentration, but the mechanism of this phenomenon remains unclear. We carry out molecular-dynamics simulations of a 48-monosaccharide HA oligomer in varying salt concentration and temperature. They identify the interaction points of Na+ ions with the HA chain and reveal their influence on the HA solvation-shell structure. The salt-dependent variation of the molecular size does not consist in the distribution of the dihedral angles of the glycosidic connections but is driven by the random flips of individual dihedral angles, which cause the formation of temporary hairpin-like structures effectively shortening the chain. They are induced by the frequency of cation-chain interactions that grow with the salt concentration, but is reduced by the simultaneous decrease of ions’ activities. This leads to an anomalous random-coil shrinkage at 0.6 M salt concentration. © 2020 The AuthorsInternal Funding Agency of Tomas Bata University in Zlin [IGA/FT/2016/011, IGA/FT/2017/009, IGA/FT/2018/010]; Grant Agency of the Czech RepublicGrant Agency of the Czech Republic [P208-12-G016

Contribution to assesing cross-linking of protein hydrolyzate with diepoxides

Bylo studováno sítování hydrolyzátu kolagenu diepoxibutanem nebo (oktanem) při 25oC. Optimální pH pro sítování bylo 9. Rozpustnost vzorku klesala úměrně s množstvím použitého sítovadla. Pro stanovení limitního viskozitního čísla je optimální měřit viskozity vzorku v 1M KCl roztoku. Diepoxyoktan byl účinnější sítovadlo než diepoxybutan. V IR spektrech se sítování projevilo slabě a jen při použití diepoxyoktanu.Colagen hydrolyzate was crosslinked with diepoxibutane or (octane) at 25oC. Suitable conditions for crosslinking were found at pH = 9. Solubility of samples decreased proportionately with increasing concentration of crosslinking agent. Viscosity measurements yielded best results for estimation of intrinsic viscosity in 1M KCl solution. Diepoxyoctane was better crosslinking agent than diepoxybutane. In IR spectra crosslinking demonstrated only weakly with diepoxyoctane

Decelerating weight loss of harvested strawberries by applying edible coatings based on starch-protein hydrolysate of amaranth flour

Cílem práce bylo sledování kvalitativních změn sklizených jahod opatřených ochranným jedlým polymerním povlakem. Povlaky byly vytvořeny máčením jahod do škrobo-proteinového hydrolysátu amarantové mouky o koncentraci 50 % (w/w). Testoval se vliv přídavku změkčovadla ? glycerinu (10 a 30 %) a síťovadla ? dialdehydu škrobu (1 a 4 %) na bariérové vlastnosti povlaků. Tenký ochranný film byl na jahodách vytvořen po 5 min sušení v sušárně; testovaly se teploty 23, 30 a 40 oC. Jahody byly skladovány při teplotách 7?1,5 oC (relativní vlhkost 40?3 %) a 23?1,5 oC (relativní vlhkost 48?2 %). Sledoval se hmotnostní úbytek jahod. Výsledky ukázaly, že ochranný polymerní povlak vytvořený z 50 % roztoku hydrolysátu amarantové mouky s přídavkem 30 % glycerinu má optimální bariérové vlastnosti pro vodní páry. U jahod ošetřených tímto povlakem byly zaznamenány nejnižší hmotnostní ztráty způsobené odpařováním vlhkosti při obou skladovacích teplotách.The work studied weight losses of harvested strawberries provided with protective edible coating. Coatings were produced by dipping strawberries in 50 % (w/w) starch-protein hydrolysate of amaranth flour. Tests investigated influence of added glycerol (10 or 30 %) and dialdehyde starch (1 or 4 %) on barrier properties. A protective film was produced on the strawberries after drying 5 min at 23, 30 or 40 oC. Strawberries were stored at 7?1.5 oC or 23?1.5 oC. The lowest losses in mass caused by humidity evaporating were provided by a protective coating produced with 30 % added glycerol at both storage temperatures.Ministry of Education of The Czech Republic under MSM [7088352102