| 1. |
- Bergqvist, Björn, 1965, et al.
(författare)
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Effect of microwave radiation on permeability of liposomes. Evidence against non-thermal leakage
- 1994
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Ingår i: Biochimica et Biophysica Acta - General Subjects. - : Elsevier BV. - 1872-8006 .- 0304-4165. ; 1201:1, s. 51-54
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Tidskriftsartikel (refereegranskat)abstract
- The effect of 2.45 GHz microwave radiation on the permeability of unilamellar phosphatidylcholine liposomes has been studied. Leakage of 5(6)-calboxyfluorescein from the liposomes was measured using spectrofluorimetry after exposure to either microwaves or thermal heating for 5-20 min intervals. The exposure temperature, 37.6 +/- 0.5 degrees C, was well above the phase transition temperature of the lipid membrane. The microwave exposure did not result in any non-thermal increase in permeability above that produced by thermal heating. This study refutes the results reported by Saalman et al. [1] in which an increased liposome permeability due to microwave exposure was reported. The refined analysis in the present study shows that this increased liposome permeability was not a non-thermal microwave effect.
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| 2. |
- Breccia, Javier D, et al.
(författare)
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The role of poly(ethyleneimine) in stabilization against metal-catalyzed oxidation of proteins: a case study with lactate dehydrogenase.
- 2002
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Ingår i: Biochimica et Biophysica Acta. General Subjects. - 0304-4165. ; 1570:3, s. 165-173
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Tidskriftsartikel (refereegranskat)abstract
- The protection provided by poly(ethyleneimine) (PEI) to muscle lactate dehydrogenase (LDH) in metal-catalyzed oxidation (MCO) systems (CuSO(4) or FeCl(2) combined with H(2)O(2)) was studied, and comparisons were made with the chelators EDTA and desferal, respectively. The analytical chelating capacity of PEI was estimated to be around 1 mol Cu(2+)/10 mol ethyleneimine for all molecular weights of the polymer. The effect of [PEI monomer]/[metal ion] molar ratio on the oxidatively induced aggregation of LDH exhibited a similar trend as that of the other chelators; aggregation was enhanced at lower ratios and subsequently decreased until it was undetectable with increasing ratio. In contrast, the LDH activity showed a monotonic increase with increasing concentrations of the chelator. Total protection to the enzyme by PEI was provided at concentrations lower than that needed for full chelation of the copper ions, i.e. at [PEI monomer]/[Cu(2+)] ratio above 9 in case of PEI 2000, and above 7 for PEI 25000 and 2.6 x 10(6), respectively. The polymer also provided protection against oxidation in an iron-based MCO system. Hydroxyl radical formation during the MCO reaction was inhibited in the presence of PEI. The polymer of higher molecular weights also exhibited a stronger free radical scavenging effect.
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| 3. |
- Johansson, Hans-Olof, et al.
(författare)
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Effects of ions on partitioning of serum albumin and lysozyme in aqueous two-phase systems containing ethylene oxide/propylene oxide co-polymers
- 1996
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Ingår i: Biochimica et Biophysica Acta. General Subjects. - : Elsevier BV. - 0304-4165. ; 1290:3, s. 289-298
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Tidskriftsartikel (refereegranskat)abstract
- Aqueous two-phase systems composed of ethylene oxide/propylene oxide random co-polymers, EO30/PO70 or Ucon (EO50/PO50), in the top phase and dextran T500 in the bottom phase, have been studied. The cloud point diagram for EO30/PO70 in water solution was determined. EO30/PO70 has a cloud point of 32oC at a concentration of 10% (w/w). The phase diagram for the system EO30/PO70-dextran T500-water was determined. Salt effects have been studied on the partitioning of two model proteins, bovine serum albumin and hen egg white lysozyme, in EO30/PO70-dextran and Ucon-dextran systems. Ions with different hydrophobicity, i.e., with different position in the Hofmeister or lyotropic series, were investigated with reference to their effect on protein partition. The counterion hydrophobicity was shown to have a strong influence on the partitioning of BSA and lysozyme. Most extreme partitioning was obtained with hydrophobic (chaotropic) ions like ClO-4 and I-. A comparison of protein partitioning between PEG-dextran and EO30/PO70-dextran has been done. A more extreme protein partitioning was obtained in the EO30/PO70-dextran containing system. Temperature-induced phase separation was studied with EO30/PO70 at 45oC. Both BSA and lysozyme were completely partitioned to the water phase formed above the cloud point of EO30/PO70. Model calculations, based on Flory-Huggins theory of polymer solutions, have been done which could reproduce the salt effect on the protein partitioning in aqueous-two phase system.
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| 4. |
- Johansson, Hans-Olof, et al.
(författare)
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Temperature-induced phase partitioning of peptides in water solutions of ethylene oxide and propylene oxide random copolymers
- 1997
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Ingår i: Biochimica et Biophysica Acta. General Subjects. - 0304-4165. ; 1335:3, s. 315-325
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Tidskriftsartikel (refereegranskat)abstract
- A thermoseparating random copolymer (Ucon 50-HB-5100) composed of (50%) ethylene oxide and (50%) propylene oxide has been used to form an aqueous two-phase system by heating the polymer-water solution above the cloud point of the copolymer. In the formed two-phase system a water rich top phase is in equilibrium with an aqueous polymer rich bottom phase. The partitioning of amino acids and peptides in this aqueous two-phase system has been studied. Hydrophobic peptides (containing aromatic amino acids) were strongly partitioned to the polymer rich phase, while hydrophilic peptides were enriched in the water rich phase. The effect of temperature on the partitioning was investigated and a decreased partitioning to the polymer rich phase was obtained upon temperature increase. The effect of two salts (NaClO4 and Na2SO4) on the partitioning of a positively charged polypeptide, poly(Lys, Trp), was very strong. With NaClO4 the polypeptide was quantitatively partitioned to the polymer rich phase while with Na2SO4 the polypeptide was partitioned to the water rich phase. Model calculations based on a modified Flory-Huggins theory have been performed to better understand the experimental behavior.
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| 5. |
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| 6. |
- Lohmander, Stefan, et al.
(författare)
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Chemical and metabolic heterogeneity of chondroitin sulfate and keratan sulfate in guinea pig cartilage and nucleus pulposus
- 1973
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Ingår i: Biochimica et Biophysica Acta. General Subjects. - : Elsevier BV. - 0304-4165. ; 304:2, s. 430-448
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Tidskriftsartikel (refereegranskat)abstract
- Chondroitin sulfate and keratan sulfate in guinea pig costal cartilage, nasal septum cartilage and nucleus pulposus were separated and fractionated by chromatography on CPC-cellulose, ECTEOLA-cellulose and Sephadex G-200 columns. Characterization of the chondroitin sulfates included determination of molecular weight and of the number, and position, of sulfate groups of the disaccharide units. Distinct chemical differences were found between the total fractions of chondroitin sulfate from the three tissues. Within the total fractions a marked heterogeneity was also apparent. The turnover of the two glycosaminoglycans was studied by using radioactive sulfate as precursor. The guinea pigs were killed at eight intervals, ranging from 30 min to 40 days after injection of the isotope. Total fractions of chondroitin sulfate from rib, nasal septum and nucleus pulposus showed half-lives of about 80, 40 and 30 days, respectively. In addition, the existence of a second metabolic component with a faster turnover (half-life about 3 days) was indicated in chondroitin sulfate from all three tissues. Similarly, keratan sulfate from the rib contained a 'slow' component with a half-life of about 90 days and a 'fast' component with a half-life of 4 days. For keratan sulfate from nucleus pulposus only a single component was demonstrable; it had a half-life of about 30 days. Within the total fractions of both chondroitin sulfate and keratan sulfate from the three tissues studied, a considerable degree of metabolic heterogeneity was apparent between, and within, subfractions of differing molecular weight.
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| 7. |
- Lohmander, Stefan
(författare)
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Ion exchange chromatography of glucosamine and galactosamine in microgram amounts with quantitative determination and specific radioactivity assay
- 1972
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Ingår i: Biochimica et Biophysica Acta. General Subjects. - : Elsevier BV. - 0304-4165. ; 264:3, s. 411-417
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Tidskriftsartikel (refereegranskat)abstract
- A rapid method for the separation and quantitative determination, including radioassay, of glucosamine and galactosamine in microgram amounts is described. It is based upon the use of a column of Aminex A-5 ion exchange resin eluted with a phosphate buffer at pH 7.00 and 60 °C. From each fraction half the volume is used for a scaled down Elson-Morgan procedure and other half for liquid scintillation counting. Amounts of about 0.01-1 μmole of hexosamine may be separated and determined.
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| 8. |
- Lohmander, Stefan, et al.
(författare)
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Proteoglycans of mineralizing rib and epiphyseal cartilage
- 1975
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Ingår i: Biochimica et Biophysica Acta. General Subjects. - : Elsevier BV. - 0304-4165. ; 404:1, s. 93-109
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Tidskriftsartikel (refereegranskat)abstract
- Rib cartilage from growing guinea pigs and epiphyseal cartilage from Beagle puppie were separated into three fractions, representing non-mineralized, low mineralized, and high mineralized, tissue, by centrifuging finely ground material in acetone/bromoform density gradients. Following extraction under dissociative conditions, the proteoglycans were fractionated by density gradient ultracentrifugation under associative and dissociative conditions. With the onset of mineralization, the cartilage lost approximately half its content of proteoglycans. The proteoglycans remaining in the calcified cartilage differed in composition and in size from those of nonmineralized tissue. With the increased mineral content of the tissues the ratios of protein to polysaccharide, of chondroitin sulfate to keratan sulfate, and of 4-sulfated to 6-sulfated chondroitin sulfate increased in the proteoglycan fraction. Furthermore, gel chromatograms indicated decreased proportions of very high molecular weight proteoglycans, in mineralized tissue.
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| 9. |
- Pettersson, Gösta
(författare)
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Error associated with experimental flux control coefficient determinations in the Calvin cycle
- 1996
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Ingår i: Biochimica et Biophysica Acta. General Subjects. - 0304-4165. ; 1289:2, s. 169-174
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Tidskriftsartikel (refereegranskat)abstract
- Model studies of photosynthetic carbohydrate formation in the chloroplast of C3 plants have been performed to examine the expected response of the steady-state reaction flux to finite changes in concentration or activity of individual enzymes in a central metabolic network. The results indicate that flux control coefficients in this system cannot be reliably estimated experimentally even for the two enzymes that do exert predominant control under the examined conditions. Reduction of the mathematical error of the estimates to a satisfactorily low level requires such small enzyme concentration changes that presently available assay methods do not allow for a determination of the corresponding flux changes with satisfactory precision.It is concluded from these observations and general methodological considerations that experimental flux control coefficient estimates cannot be trusted unless evidence is presented to show that the mathematical error associated with their determination is of insignificant magnitude.
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| 10. |
- Shipovskov, S, et al.
(författare)
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Stabilisation of tyrosinase by reversed micelles for bioelectrocatalysis in dry organic media
- 2003
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Ingår i: Biochimica et Biophysica Acta. General Subjects. - 0304-4165. ; 1620:1-3, s. 119-124
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Tidskriftsartikel (refereegranskat)abstract
- The enzymatic and bioelectrocatalytic activity of tyrosinase from mushrooms was studied in a system of reversed micelles formed by Aerosol OT (AOT) in hexane. The optimal catechol oxidising activity of tyrosinase incorporated in reversed micelles was found at a hydration degree of w(0) = 25. The catalytic activity was comparable with tyrosinase activity in aqueous media. When immobilized at an Au electrode, either directly or in reversed micelles, tyrosinase exhibited a similar efficiency of the bioelectrocatalytic reduction of O-2 mediated by catechol; however, a rapid decrease in the activity correlated with the destruction of reversed micelles and/or the removal of tyrosinase from the electrode surface. The system containing tyrosinase in reversed micelles with caoutchouk, spread on the surface of the An electrode and successively covered with a Nafion(R) membrane layer, was found to result in stable tyrosinase-modified electrodes, which were resistant to inactivation in dry acetonitrile. The proposed technique offers possibilities for further development of highly active and stable surfactant/enzyme-modified electrodes for measurements carried out in organic solvents. (C) 2002 Elsevier Science B.V. All rights reserved.
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| 11. |
- Sivars, Ulf, et al.
(författare)
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Mechanisms of phase behaviour and protein partitioning in detergent/polymer aqueous two-phase systems for purification of integral membrane proteins1
- 2000
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Ingår i: Biochimica et Biophysica Acta. General Subjects. - 0304-4165. ; 1474:2, s. 133-146
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Tidskriftsartikel (refereegranskat)abstract
- Detergent/polymer aqueous two-phase systems are studied as a fast, mild and efficient general separation method for isolation of labile integral membrane proteins. Mechanisms for phase behaviour and protein partitioning of both membrane-bound and hydrophilic proteins have been examined in a large number of detergent/polymer aqueous two-phase systems. Non-ionic detergents such as the Triton series (polyoxyethylene alkyl phenols), alkyl polyoxyethylene ethers (CmEOn), Tween series (polyoxyethylene sorbitol esters) and alkylglucosides form aqueous two-phase systems in mixtures with hydrophilic polymers, such as PEG or dextran, at low and moderate temperatures. Phase diagrams for these mixtures are shown and phase behaviour is discussed from a thermodynamic model. Membrane proteins, such as bacteriorhodopsin and cholesterol oxidase, were partitioned strongly to the micelle phase, while hydrophilic proteins, BSA and lysozyme, were partitioned to the polymer phase. The partitioning of membrane protein is mainly determined by non-specific hydrophobic interactions between detergent and membrane protein. An increased partitioning of membrane proteins to the micelle phase was found with an increased detergent concentration difference between the phases, lower polymer molecular weight and increased micelle size. Partitioning of hydrophilic proteins is mainly related to excluded volume effects, i.e. increased phase component size made the hydrophilic proteins partition more to the opposite phase. Addition of ionic detergent to the system changed the partitioning of membrane proteins slightly, but had a strong effect on hydrophilic proteins, and can be used for enhanced separation between hydrophilic proteins and membrane protein.
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| 12. |
- Tejler, L, et al.
(författare)
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Production of protein HC by human fetal liver explants
- 1978
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Ingår i: Biochimica et Biophysica Acta. - : Elsevier BV. - 0006-3002 .- 0304-4165. ; 542:3, s. 14-506
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Tidskriftsartikel (refereegranskat)abstract
- Human fetal lever explants were found to secrete protein HC into the medium in molar amounts comparable to those of albumin, alpha 1-antitrypsin and orosomucoid. Incorporation of a radioactive amino acid from the medium into the secreted protein HC demonstrated de novo synthesis. The secreted protein HC had the same size and electrophoretic mobility as protein HC of plasma and urine and gave a reaction of immunochemical identity with the protein in these biological fluids.
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| 13. |
- Wingren, Christer, et al.
(författare)
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A new approach to examine conformational changes occurring upon binding of ligand by biomolecules
- 1995
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Ingår i: Biochimica et Biophysica Acta. General Subjects. - 0304-4165. ; 1244:1, s. 209-215
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Tidskriftsartikel (refereegranskat)abstract
- Liquid-liquid partition chromatography in an aqueous poly(ethylene glycol)/dextran two-phase system (LLPC) is shown to be a quick and sensitive method for detecting conformational changes occurring upon binding of ligands by biospecific molecules. Two groups of well-characterized proteins, enzymes and monoclonal antibodies, were employed. As an example, LLPC demonstrated that isoforms of lactate dehydrogenase as well as of hexokinase existed in a ligand-dependent equilibrium between two forms and that conformational changes occurred when monoclonal antibodies bound haptens. We also demonstrate that the method could be used to detect and separate subfractions in preparations of unliganded proteins that appeared to be homogeneous when analysed by other techniques.
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| 14. |
- Yang, Hong, et al.
(författare)
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The enantiomeric purity of alcohols formed by enzymatic reduction of ketones can be improved by optimisation of the temperature and by using a high co-substrate concentration
- 1997
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Ingår i: Biochimica et Biophysica Acta - General Subjects. - 0304-4165. ; 1336:1, s. 51-58
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Tidskriftsartikel (refereegranskat)abstract
- The stereoselective reduction of ketones by alcohol dehydrogenase from Thermoanaerobium brockii was studied in organic reaction media, 2-Propanol was used as co-substrate to regenerate the coenzyme NADPH. The enantiomeric excess of the alcohol formed from the ketone decreased during the course of the reaction (from 53 to 0% e.e. in the formation of (R)-2-butanol). This was interpreted as being due to the reversibility of all the reactions involved. By using a large excess of 2-propanol this effect was suppressed. In the reduction of 2-butanone to (R)-2-butanol, the enantiomeric excess increased with increasing temperature, but in the reduction of a-pentanone to (S)-2-pentanol the enantiomeric excess decreased with increasing temperature, The data were evaluated in terms of free energy of activation of the reaction pathways leading to the different possible products.
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| 15. |
- Belyaev, I Y, et al.
(författare)
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Effects of ethidium bromide on DNA loop organisation in human lymphocytes measured by anomalous viscosity time dependence and single cell gel electrophoresis
- 1999
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Ingår i: Biochimica et Biophysica Acta - General Subjects. - 0304-4165 .- 1872-8006. ; 1428:2-3, s. 348-356
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Tidskriftsartikel (refereegranskat)abstract
- The effects of ethidium bromide (EtBr) on human lymphocytes were studied by the method of anomalous viscosity time dependence (AVTD) and by the comet assay. EtBr at low concentrations increased the maximum viscosity and time of radial migration as measured with AVTD at neutral conditions of lysis. A pronounced relaxation of DNA loops was observed with the neutral comet assay. The maximal comet length corresponded to 2 Mb DNA loops. At high concentrations of EtBr, 2. mg/ml, significant reduction in AVTD below control level was seen that suggested hypercondensation of chromatin. The hypercondensation was directly observed with the neutral comet assay. EtBr did not induce DNA strand breaks as measured by the alkaline comet assay. The hypercondensed nuclei could be decondensed by irradiation with gamma-rays or exposure to light. The data provide evidence that EtBr at high concentrations resulted in hypercondensation of chromatin below control level. The comet assay confirmed that the increase in AVTD peaks deals with relaxation of loops and AVTD decrease is caused by chromatin condensation. The prediction of the AVTD theory for a correlation between time of radial migration and condensation of chromatin was verified. Further, the data show that the comet assay at neutral conditions of lysis is rather sensitive to DNA loop relaxation in the absence of DNA damage. Finally, donor specificity was found for the hypercondensation.
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| 16. |
- Cao, Jun, et al.
(författare)
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Helicobacter pylori-antigen-binding fragments expressed on the filamentous M13 phage prevent bacterial growth
- 2000
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Ingår i: Biochimica et Biophysica Acta - General Subjects. - 0304-4165 .- 1872-8006. ; 1474:1, s. 107-113
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Tidskriftsartikel (refereegranskat)abstract
- Colonization of the human stomach by Helicobacter pylori is associated with the development of gastritis, duodenal ulcer, mucosa-associated lymphoid tissue (MALT) lymphoma, and gastric cancer. H. pylori-antigen-binding single-chain variable fragments (ScFv) were derived from murine hybridomas producing monoclonal antibodies and expressed as a g3p-fusion protein on a filamentous M13 phage. The recombinant ScFv-phage reacted specifically with a 30-kDa monomeric protein of a H. pylori surface antigen preparation and by means of immunofluorescence microscopy the phage was shown to bind to both the spiral and coccoid forms of the bacterium. In vitro, the recombinant phage exhibited a bacteriocidal effect and inhibited specifically the growth of all the six strains of H. pylori tested. When H. pylori was pretreated with the phage 10 min before oral inoculation of mice, the colonization of the mouse stomachs by the bacterium was significantly reduced (P<0.01). The results suggest that genetic engineering may be used to generate therapy-effective phages.
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| 17. |
- Dahlqvist, Ulla, et al.
(författare)
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Endogenous substrates of protein kinase in rat liver cell sap under different dietary conditions
- 1978
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Ingår i: Biochimica et Biophysica Acta. - : Elsevier BV. - 0006-3002 .- 1878-2434 .- 0304-4165. ; 540:1, s. 13-23
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Tidskriftsartikel (refereegranskat)abstract
- Liver cell sap from normally fed rats, rats fed with a high-carbohydrate diet and fasted rats was chromatographed on DEAE-cellulose (pH 7.0). The chromatogram from each diet group was analyzed for pyruvate kinase activity and endogenous substrates of cyclic AMP-stimulated protein kinase. The materials were pooled into five phosphorylatable fractions, in each of which phosphate incorporation at 0.1 mM and 1.0 mM [32P]ATP in the presence of cyclic AMP and protein kinase was determined. For characterization of the phosphorylatable components, thin-layer gel chromatography on Sephadex G-200 and polyacrylamide gel electrophoresis in detergent were used for determination of native and minimal molecular weights, respectively. Except for pyruvate kinase, eight components which incorporated at least 0.05 nmol of [32P]phosphate/g of liver were detected. The phosphorylation of four of them was stimulated by cyclic AMP. Their minimal molecular weights were 42000, 21000, 52000 and 49000. The component with a minimal molecular weight of 42000 seemed to have a native molecular weight of 160000. Both the 21000 and the 52000 component had a native molecular weight of about 110000-120000. The protein with a minimal molecular weight of 49000 could not be correlated with certainty to a native molecular weight. The proteins whose phosphorylation was not stimulated by cyclic AMP had minimal molecular weights of 54000, 39000, 34000 and 22000.
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| 18. |
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| 19. |
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| 20. |
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| 21. |
- Ramström, Olof, et al.
(författare)
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Chemical biology of dynamic combinatorial libraries
- 2002
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Ingår i: Biochimica et Biophysica Acta - General Subjects. - 0304-4165 .- 1872-8006. ; 1572:03-feb, s. 178-186
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Forskningsöversikt (refereegranskat)abstract
- Dynamic combinatorial chemistry (DCC) is a recently introduced supramolecular approach to generate libraries of chemical compounds based on reversible exchange processes. The building elements are spontaneously and reversibly assembled to virtually encompass all possible combinations, allowing for simple one-step generation of complex libraries. The method has been applied to a variety of combinatorial systems, ranging from synthetic models to materials science and drug discovery, and enables the establishment of adaptive processes due to the dynamic interchange of the library constituents and its evolution toward the best fit to the target. In particular, it has the potential to become a useful tool in the direct screening of ligands to a chosen receptor without extensive prior knowledge of the site structure, and several biological systems have been targeted. In the vast field of glycoscience, the concept may find special perspective in response to the highly complex nature of carbohydrate-protein interactions. This chapter summarises studies that have been performed using DCC in biological systems, with special emphasis on glycoscience.
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| 22. |
- Ahmadpour, Doryaneh, 1973, et al.
(författare)
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Yeast reveals unexpected roles and regulatory features of aquaporins and aquaglyceroporins
- 2014
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Ingår i: Biochimica et Biophysica Acta. General Subjects. - : Elsevier BV. - 0304-4165 .- 1872-8006 .- 0006-3002. ; 1840:5, s. 1482-1491
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Forskningsöversikt (refereegranskat)abstract
- Background: The yeast Saccharomyces cerevisiae provides unique opportunities to study roles and regulation of aqua/glyceroporins using frontline tools of genetics and genomics as well as molecular cell and systems biology. Scope of review: S. cerevisiae has two similar orthodox aquaporins. Based on phenotypes mediated by gene deletion or overexpression as well as on their expression pattern, the yeast aquaporins play important roles in key aspects of yeast biology: establishment of freeze tolerance, during spore formation as well as determination of cell surface properties for substrate adhesion and colony formation. Exactly how the aquaporins perform those roles and the mechanisms that regulate their function under such conditions remain to be elucidated. S. cerevisiae also has two different aquaglyceroporins. While the role of one of them, Yfl054c, remains to be determined, Fps1 plays critical roles in osmoregulation by controlling the accumulation of the osmolyte glycerol. Fpsl communicates with two osmo-sensing MAPK signalling pathways to perform its functions but the details of Fps1 regulation remain to be determined. Major conclusions: Several phenotypes associated with aqua/glyceroporin function in yeasts have been established. However, how water and glycerol transport contribute to the observed effects is not understood in detail. Also many of the basic principles of regulation of yeast aqua/glyceroporins remain to be elucidated. General significance: Studying the yeast aquaporins and aquaglyceroporins offers rich insight into the life style, evolution and adaptive responses of yeast and rewards us with discoveries of unexpected roles and regulatory mechanisms of members of this ancient protein family. This article is part of a Special Issue entitled Aquaporins. (c) 2013 Elsevier B.V. All rights reserved.
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| 23. |
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| 24. |
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| 25. |
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| 26. |
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| 27. |
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| 28. |
- Bergström, Tobias, et al.
(författare)
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Developmentally regulated collagen/integrin interactions confer adhesive properties to early postnatal neural stem cells
- 2014
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Ingår i: Biochimica et Biophysica Acta - General Subjects. - : Elsevier BV. - 0304-4165 .- 1872-8006. ; 1840:8, s. 2526-2532
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Tidskriftsartikel (refereegranskat)abstract
- Background:It is becoming increasingly apparent that the extracellular matrix acts as an important regulator of the neural stem niche. Previously we found that neural stem and progenitor cells (NSPCs) derived from the early postnatal subventricular zone of mice adhere to a collagen/hyaluronan hydrogel, whereas NSPCs from the adult and embryonic brain do not.Methods:To examine the specific adhesive properties of young stem cells in more detail, NSPCs isolated from embryonic, postnatal day 6 (P6), and adult mouse brains were cultured on collagen I.Results:Early postnatal NSPCs formed paxillin-positive focal adhesions on collagen I, and these adhesions could be prevented by an antibody that blocked integrin beta 1. Furthermore, we found the corresponding integrin alpha subunits alpha 2 and alpha 11 levels to be highest at the postnatal stage. Gene ontology analysis of differentially expressed genes showed higher expression of transcripts involved in vasculature development and morphogenesis in P6 stem cells, compared to adult.Conclusions:The ability to interact with the extracellular matrix differs between postnatal and adult NSPCs.General significance:Our observations that the specific adhesive properties of early postnatal NSPCs, which are lost in the adult brain, can be ascribed to the integrin subunits expressed by the former furthering our understanding of the developing neurogenic niche. This article is part of a Special Issue entitled Matrix-mediated cell behaviour and properties.
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| 29. |
- Blikstad, Cecilia, et al.
(författare)
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Emergence of a novel highly specific and catalytically efficient enzyme from a naturally promiscuous glutathione transferase
- 2008
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Ingår i: Biochimica et Biophysica Acta. - : Elsevier BV. - 0006-3002 .- 1878-2434 .- 0304-4165. ; 1780:12, s. 1458-63
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Tidskriftsartikel (refereegranskat)abstract
- Redesign of glutathione transferases (GSTs) has led to enzymes with remarkably enhanced catalytic properties. Exchange of substrate-binding residues in GST A1-1 created a GST A4-4 mimic, called GIMFhelix, with >300-fold improved activity with nonenal and suppressed activity with other substrates. In the present investigation GIMFhelix was compared with the naturally-evolved GSTs A1-1 and A4-4 by determining catalytic efficiencies with nine alternative substrates. The enzymes can be represented by vectors in multidimensional substrate-activity space, and the vectors of GIMFhelix and GST A1-1, expressed in kcat/Km values for the alternative substrates, are essentially orthogonal. By contrast, the vectors of GIMFhelix and GST A4-4 have approximately similar lengths and directions. The broad substrate acceptance of GST A1-1 contrasts with the high selectivity of GST A4-4 and GIMFhelix for alkenal substrates. Multivariate analysis demonstrated that among the diverse substrates used, nonenal, cumene hydroperoxide, and androstenedione are major determinants in the portrayal of the three enzyme variants. These GST substrates represent diverse chemistries of naturally occurring substrates undergoing Michael addition, hydroperoxide reduction, and steroid double-bond isomerization, respectively. In terms of function, GIMFhelix is a novel enzyme compared to its progenitor GST A1-1 in spite of 94% amino-acid sequence identity between the enzymes. The redesign of GST A1-1 into GIMFhelix therefore serves as an illustration of divergent evolution leading to novel enzymes by minor structural modifications in the active site. Notwithstanding low sequence identity (60%), GIMFhelix is functionally an isoenzyme of GST A4-4.
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| 30. |
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| 31. |
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| 32. |
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| 33. |
- Carlsson, Michael, et al.
(författare)
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Different fractions of human serum glycoproteins bind galectin-1 or galectin-8, and their ratio may provide a refined biomarker for pathophysiological conditions in cancer and inflammatory disease
- 2012
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Ingår i: Biochimica et Biophysica Acta - General Subjects. - : Elsevier. - 0304-4165 .- 1872-8006 .- 0006-3002. ; 1820:9, s. 1366-1372
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Tidskriftsartikel (refereegranskat)abstract
- Background: Changes in glycosylation of serum proteins are common, and various glycoforms are being explored as biomarkers in cancer and inflammation. We recently showed that glycoforms detected by endogenous galectins not only provide potential biomarkers, but also have different functions when they encounter galectins in tissue cells. Now we have explored the use of a combination of two galectins with different specificities, to further increase biomarker sensitivity and specificity. less thanbrgreater than less thanbrgreater thanMethods: Sera from 14 women with metastatic breast cancer, 12 healthy controls, 14 patients with IgA-nephritis (IgAN), and 12 patients with other glomerulonephritis were fractionated by affinity chromatography on immobilized human galectin-1 or galectin-8N, and the protein amounts of the bound and unbound fractions for each galectin were determined. less thanbrgreater than less thanbrgreater thanResults: Each galectin bound largely different fractions of the serum glycoproteins, including different glycoforms of haptoglobin. In the cancer sera, the level of galectin-1 bound glycoproteins was higher and galectin-8N bound glycoproteins lower compared to the other patients groups, whereas in IgAN sera the level of galectin-8N bound glycoproteins were higher. less thanbrgreater than less thanbrgreater thanConclusion: The ratio of galectin-1 bound/galectin-8N bound glycoproteins showed high discriminatory power between cancer patients and healthy, with AUC of 0.98 in ROC analysis, and thus provides an interesting novel cancer biomarker candidate. less thanbrgreater than less thanbrgreater thanGeneral significance: The galectin-binding ability of a glycoprotein is not only a promising biomarker candidate but may also have a specific function when the glycoprotein encounters the galectin in tissue cells, and thus be related to the pathophysiological state of the patient. This article is part of a Special Issue entitled Glycoproteomics.
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| 34. |
- Cederfur, Cecilia, et al.
(författare)
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Glycoproteomic identification of galectin-3 and -8 ligands in bronchoalveolar lavage of mild asthmatics and healthy subjects.
- 2012
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Ingår i: Biochimica et biophysica acta. - : Elsevier BV. - 0006-3002 .- 0304-4165. ; 1820:9, s. 1429-1436
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Galectins, a family of small carbohydrate binding proteins, have been implicated in regulation of inflammatory reactions, including asthma and fibrosis in the lungs. Galectins are found in cells of the airways and in airway secretions, but their glycoprotein ligands there have only been studied to a very limited extent. METHODS: Bronchoalveolar lavage (BAL) fluid from mild asthmatics and healthy volunteers were fractionated by affinity chromatography on the immobilized galectins. Total (10-30μg) and galectin bound (~1-10μg) protein fractions were identified, quantified and compared using shot-gun proteomics and spectral counts. RESULTS: About 175 proteins were identified in unfractionated BAL-fluid, and about 100 bound galectin-3 and 60 bound galectin-8. These included plasma glycoproteins, and typical airway proteins such as SP-A2, PIGR and SP-B. The concentration of galectin-binding proteins was 100-300 times higher than the concentration of galectins in BAL. CONCLUSION: The low relative concentration of galectins in BAL makes it likely that functional interactions with glycoproteins occur at sites rich in galectin, such as cells of the airways, rather than the extracellular fluid itself. The profile of galectin bound proteins differed between samples from asthma patients and healthy subjects and correlated with the presence of fibroblasts or eosinophils. This included appearance of a specific galectin-8-binding glycoform of haptoglobin, previously shown to be increased in serum in other inflammatory conditions. GENERAL SIGNIFICANCE: It is technically feasible to identify galectin-binding glycoproteins in low concentration patient samples such as BAL-fluid, to generate biomedically interesting results. This article is part of a Special Issue entitled Glycoproteomics.
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| 35. |
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| 36. |
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| 37. |
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| 38. |
- Dimarogona, Maria, et al.
(författare)
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Structural and functional studies of a Fusarium oxysporum cutinase with polyethylene terephthalate modification potential
- 2015
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Ingår i: Biochimica et Biophysica Acta - General Subjects. - : Elsevier BV. - 0304-4165 .- 1872-8006. ; 1850:11, s. 2308-2317
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundCutinases are serine hydrolases that degrade cutin, a polyester of fatty acids that is the main component of plant cuticle. These biocatalysts have recently attracted increased biotechnological interest due to their potential to modify and degrade polyethylene terephthalate (PET), as well as other synthetic polymers.MethodsA cutinase from the mesophilic fungus Fusarium oxysporum, named FoCut5a, was expressed either in the cytoplasm or periplasm of Escherichia coli BL21. Its X-ray structure was determined to 1.9 Å resolution using molecular replacement. The activity of the recombinant enzyme was tested on a variety of synthetic esters and polyester analogues.ResultsThe highest production of recombinant FoCut5a was achieved using periplasmic expression at 16οC. Its crystal structure is highly similar to previously determined Fusarium solani cutinase structure. However, a more detailed comparison of the surface properties and amino acid interactions revealed differences with potential impact on the biochemical properties of the two enzymes. FoCut5a showed maximum activity at 40οC and pH 8.0, while it was active on three p-nitrophenyl synthetic esters of aliphatic acids (C2, C4, C12), with the highest catalytic efficiency for the hydrolysis of the butyl ester. The recombinant cutinase was also found capable of hydrolyzing PET model substrates and synthetic polymers.ConclusionsThe first reported expression and crystal structure determination of a functional cutinase from the mesophilic fungus F. oxysporum with potential application in surface modification of PET synthetic polymers.General significanceFoCut5a could be used as a biocatalyst in industrial applications for the environmentally-friendly treatment of synthetic polymers.
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| 39. |
- Dowaidar, Moataz, et al.
(författare)
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Graphene oxide nanosheets in complex with cell penetrating peptides for oligonucleotides delivery
- 2017
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Ingår i: Biochimica et Biophysica Acta - General Subjects. - : Elsevier BV. - 0304-4165 .- 1872-8006. ; 1861:9, s. 2334-2341
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Tidskriftsartikel (refereegranskat)abstract
- A new strategy for gene transfection using the nanocarrier of cell penetrating peptides (CPPs; PepFect14 (PF14) or PepFect14 (PF14) (PF221)) in complex with graphene oxide (GO) is reported. GO complexed with CPPs and plasmid (pGL3), splice correction oligonucleotides (SCO) or small interfering RNA (siRNA) are performed. Data show adsorption of CPPs and oligonucleotides on the top of the graphenic lamellar without any observed change of the particle size of GO. GO mitigates the cytotoxicity of CPPs and improves the material biocompatibility. Complexes of GO-pGL3-CPPs (CPPs; PF14 or PF221) offer 2.1–2.5 fold increase of the cell transfection compared to pGL3-CPPs (CPPs; PF14 or PF221). GO-SCO-PF14 assemblies effectively transfect the cells with an increase of > 10–25 fold compared to the transfection using PF14. The concentration of GO plays a significant role in the material nanotoxicity and the transfection efficiency. The results open a new horizon in the gene treatment using CPPs and offer a simple strategy for further investigations.
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| 40. |
- Duarte, Fernanda, et al.
(författare)
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Recent advances in QM/MM free energy calculations using reference potentials
- 2015
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Ingår i: Biochimica et Biophysica Acta - General Subjects. - : Elsevier BV. - 0304-4165 .- 1872-8006. ; 1850:5, s. 954-965
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Forskningsöversikt (refereegranskat)abstract
- Background: Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meaningful become more and more difficult to fulfill. The use of simplified models to describe complex biological systems has long been shown to be an effective way to overcome some of the limitations associated with this computational cost in a rational way. Scope of review: Hybrid QM/MM approaches have rapidly become one of the most popular computational tools for studying chemical reactivity in biomolecular systems. However, the high cost involved in performing high-level QM calculations has limited the applicability of these approaches when calculating free energies of chemical processes. In this review, we present some of the advances in using reference potentials and mean field approximations to accelerate high-level QM/MM calculations. We present illustrative applications of these approaches and discuss challenges and future perspectives for the field. Major conclusions: The use of physically-based simplifications has shown to effectively reduce the cost of high-level QM/MM calculations. In particular, lower-level reference potentials enable one to reduce the cost of expensive free energy calculations, thus expanding the scope of problems that can be addressed. General significance: As was already demonstrated 40 years ago, the usage of simplified models still allows one to obtain cutting edge results with substantially reduced computational cost. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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| 41. |
- Eklund, Birgitta I., et al.
(författare)
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Importance of a hypervariable active-site residue in human Mu class glutathione transferases catalyzing the bioactivation of chemotherapeutic thiopurine prodrugs
- 2007
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Ingår i: Biochimica et Biophysica Acta - General Subjects. - : Elsevier BV. - 0304-4165 .- 1872-8006. ; 1770:8, s. 1098-1103
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Tidskriftsartikel (refereegranskat)abstract
- Glutathione transferases (GSTs) catalyze the bioactivation of the thiopurine prodrugs azathioprine, cis-6-(2-acetylvinylthio)purine (cAVTP) and trans-6-(2-acetylvinylthio)guanine (tAVTG), thereby releasing the antimetabolites 6-mercaptopurine and 6-thioguanine. In the GST Mu class, GST M1-1 has the highest catalytic efficiency, whereas GST M2-2 and other enzymes are less active. In the evolution of Mu class GSTs, residue 210 appears hypervariable and has particular functional significance. We demonstrate that the catalytic activity of GST M1-1 with cAVTP or tAVTG is successively diminished when wild-type Ser-210 is mutated into Ala followed by Thr. Conversely, mutating wild-type Thr-210 in GST M2-2 into Ala and Ser enhanced the corresponding activities. Comparisons were also made with GST M2-2 distinguished by Gly or Pro in position 210, as well as wild-type GSTs M4-4 and M5-5. The results suggest that the hydroxyl group of Ser in position 210 stabilizes the transition state of the GST-catalyzed reaction. The low activity of GSTs containing Thr in position 210 is probably due to steric hindrance caused by the β-methyl group of the side chain. The ratios of the different catalytic efficiencies were translated into differences in the Gibbs free energies of transition state stabilization. The effects of the mutations were qualitatively parallel for the alternative substrates, but vary significantly in magnitude. From the evolutionary perspective the data show that a point mutation can alternatively enhance or attenuate the activity with a particular substrate and illustrate the functional plasticity of GSTs.
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| 42. |
- Ekstrom, TJ
(författare)
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Epigenetic control of gene expression
- 2009
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Ingår i: Biochimica et biophysica acta. - : Elsevier BV. - 0006-3002 .- 0304-4165. ; 1790:9, s. 845-846
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 43. |
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| 44. |
- Ferapontova, Elena, et al.
(författare)
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Bioelectrocatalytic properties of lignin peroxidase from Phanerochaete chrysosporium in reactions with phenols, catechols and lignin-model compounds
- 2006
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Ingår i: Biochimica et Biophysica Acta. General Subjects. - : Elsevier BV. - 0304-4165. ; 1760:9, s. 1343-1354
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Tidskriftsartikel (refereegranskat)abstract
- Bioelectrocatalytic reduction of H2O2 catalysed by lignin peroxidase from Phanerochaete chrysosporium (LiP) was studied with LiP-modified graphite electrodes to elucidate the ability of UP to electro-enzymatically oxidise phenols, catechols, as well as veratryl alcohol (VA) and some other high-redox-potential lignin model compounds (LMC). Flow-through amperometric experiments performed at +0.1 V vs. Ag vertical bar AgCl demonstrated that UP displayed significant bioelectrocatalytic activity for the reduction of H2O2 both directly (i.e., in direct electron transfer (ET) reaction between LiP and the electrode) and using most of studied compounds acting as redox mediators in the UP bioelectrocatalytic cycle, with a pH optimum of 3.0. The bioelectrocatalytic reduction Of H2O2 mediated by VA and effects of VA on the efficiency of bioelectrocatalytic oxidation of other co-substrates acting as mediators were investigated. The bioelectrocatalytic oxidation of phenol- and catechol derivatives and 2,2'-azino-bis(3-ethyl-benzothiazoline-6-sulphonate) by UP was independent of the presence of VA, whereas the efficiency of the UP bioelectrocatalysis with the majority of other LMC acting as mediators increased upon addition of VA. Special cases were phenol and 4-methoxymandelic acid (4-MMA). Both phenol and 4-MMA suppressed the bioelectrocatalytic activity of UP below the direct ET level, which was, however, restored and increased in the presence of VA mediating the ET between UP and these two compounds. The obtained results suggest different mechanisms for the bioelectrocatalysis of UP depending on the chemical nature of the mediators and are of a special interest both for fundamental science and for application of LiP in biotechnological processes as solid-phase bio(electro)catalyst for decomposition/detection of recalcitrant aromatic compounds. (c) 2006 Elsevier B.V All rights reserved.
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| 45. |
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| 46. |
- Ferreira, Silvia A., et al.
(författare)
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Biocompatibility of mannan nanogel-safe interaction with plasma proteins
- 2012
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Ingår i: Biochimica et Biophysica Acta. General Subjects. - : Elsevier BV. - 0304-4165. ; 1820:7, s. 1043-1051
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Tidskriftsartikel (refereegranskat)abstract
- Background: Self-assembled mannan nanogels are designed to provide a therapeutic or vaccine delivery platform based on the bioactive properties of mannan to target mannose receptor expressed on the surface of antigen-presenting cells, combined with the performance of nanogels as carriers of biologically active agents. Methods: Proteins in the corona around mannan nanogel formed in human plasma were identified by mass spectrometry after size exclusion chromatography or centrifugation followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Structural changes and time dependent binding of human apolipoprotein A-I (apoA-I) and human serum albumin (HSA) to mannan nanogel were studied using intrinsic tryptophan fluorescence and circular dichroism spectroscopy. The mannan nanogel effect on blood coagulation and fibrillation of Alzheimer's disease-associated amyloid beta peptide and hemodialysis-associated amyloidosis beta 2 microglobulin was evaluated using thrombin generation assay or thioflavin T fluorescence assay, respectively. Results: The protein corona around mannan nanogel is formed through a slow process, is quite specific comprising apolipoproteins B-100, A-I and E and HSA, evolves over time, and the equilibrium is reached after hours to days. Structural changes and time dependent binding of apoA-I and HSA to mannan nanogel are minor. The mannan nanogel does not affect blood coagulation and retards the fibril formation. Conclusions: Mannan nanogel has a high biosafety and biocompatibility, which is mandatory for nanomaterials to be used in biomedical applications. General Significance: Our research provides a molecular approach to evaluate the safety aspects of nanomaterials, which is of general concern in society and science. (C) 2012 Elsevier B.V. All rights reserved.
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| 47. |
- Gaglione, R., et al.
(författare)
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Insights into the anticancer properties of the first antimicrobial peptide from Archaea
- 2017
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Ingår i: Biochimica et Biophysica Acta - General Subjects. - : Elsevier BV. - 1872-8006 .- 0304-4165. ; 1861:9, s. 2155-2164
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Tidskriftsartikel (refereegranskat)abstract
- Background: The peptide VLL-28, identified in the sequence of an archaeal protein, the transcription factor Stf76 from Sulfolobus islandicus, was previously identified and characterized as an antimicrobial peptide, possessing a broad-spectrum antibacterial activity. Methods: Through a combined approach of NMR and Circular Dichroism spectroscopy, Dynamic Light Scattering, confocal microscopy and cell viability assays, the interaction of VLL-28 with the membranes of both parental and malignant cell lines has been characterized and peptide mechanism of action has been studied. Results: It is here demonstrated that VLL-28 selectively exerts cytotoxic activity against murine and human tumor cells. By means of structural methodologies, VLL-28 interaction with the membranes has been proven and the binding residues have been identified. Confocal microscopy data show that VLL-28 is internalized only into tumor cells. Finally, it is shown that cell death is mainly caused by a time-dependent activation of apoptotic pathways. Conclusions: VLL-28, deriving from the archaeal kingdom, is here found to be endowed with selective cytotoxic activity towards both murine and human cancer cells and consequently can be classified as an ACP.
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| 48. |
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| 49. |
- Genovese, Ilaria, et al.
(författare)
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Profiling calcium-dependent interactions between Sorcin and intrinsically disordered regions of human proteome
- 2020
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Ingår i: Biochimica et Biophysica Acta - General Subjects. - : Elsevier. - 0304-4165 .- 1872-8006. ; 1864:8
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Tidskriftsartikel (refereegranskat)abstract
- Background: Sorcin is a calcium sensor that exerts many calcium-related functions in the cells, e.g. it regulates calcium concentration in the cytoplasm, endoplasmic reticulum (ER) and mitochondria, by interacting with calcium pumps, exchangers and channels. Albeit Sorcin is an interesting potential cancer target, little is known about its interactors upon calcium-mediated activation. Our previous study suggested that Sorcin may recognize short linear binding motifs as the crystal structure revealed a self-interaction with a GYYPGG stretch in its N-terminus, and combinatorial peptide-phage display provided support for peptide-mediated interactions. Methods: In this study we screened for motif-based interactions between Sorcin and intrinsically disordered regions of the human proteome using proteomic peptide phage display (ProP-PD). We identified a peptide belonging to protein phosphatase 1 regulatory subunit 3G (PPP1R3G) as a potential novel interactor and confirm the interaction through biophysical and cell-based approaches, and provide structural information through molecular dynamics simulations. Results: Altogether, we identify a preferred motif in the enriched pool of binders and a peptide belonging to protein phosphatase 1 regulatory subunit 3G (PPP1R3G) as a preferred ligand. Conclusion: Through this study we gain information on a new Sorcin binding partner and profile Sorcin's motif-based interaction. General significance: The interaction between Sorcin and PPP1R3G may suggest a close dependence between glucose homeostasis and calcium concentration in the different cell compartments, opening a completely new and interesting scenery yet to be fully disclosed.
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| 50. |
- Georgoulia, Panagiota S., et al.
(författare)
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The catalytic activity of Abl1 single and compound mutations : Implications for the mechanism of drug resistance mutations in chronic myeloid leukaemia
- 2019
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Ingår i: Biochimica et Biophysica Acta - General Subjects. - : Elsevier. - 0304-4165 .- 1872-8006. ; 1863:4, s. 732-741
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundAbl1 is a protein tyrosine kinase whose aberrant activation due to mutations is the culprit of several cancers, most notably chronic myeloid leukaemia. Several Abl1 inhibitors are used as anti-cancer drugs. Unfortunately, drug resistance limits their effectiveness. The main cause for drug resistance is mutations in the kinase domain (KD) of Abl1 that evolve in patients. The T315I mutation confers resistance against all clinically-available inhibitors except ponatinib. Resistance to ponatinib can develop by compound (double) mutations.MethodsKinetic measurements of the KD of Abl1 and its mutants were carried out to examine their catalytic activity. Specifically, mutants that lead to drug resistance against ponatinib were considered. Molecular dynamics simulations and multiple sequence analysis were used for explanation of the experimental findings.ResultsThe catalytic efficiency of the T315I pan-resistance mutant is more than two times lower than that of the native KD. All ponatinib resistant mutations restore the catalytic efficiency of the enzyme. Two of them (G250E/T315I and Y253H/E255V) have a catalytic efficiency that is more than five times that of the native KD.ConclusionsThe measurements and analysis suggest that resistance is at least partially due to the development of a highly efficient kinase through subsequent mutations. The simulations highlight modifications in two structurally important regions of Abl1, the activation and phosphate binding loops, upon mutations.General significanceExperimental and computational methods were used together to explain how mutations in the kinase domain of Abl1 lead to resistance against the most advanced drug currently in use to treat chronic myeloid leukaemia.
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