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Denaturation
Kinds of Denaturation Terms modified by Denaturation Selected AbstractsEffect of Heat Treatment on Bovine Lactoperoxidase Activity in Skim Milk: Kinetic and Thermodynamic AnalysisJOURNAL OF FOOD SCIENCE, Issue 1 2003E. Marín ABSTRACT: The effect of heat on lactoperoxidase activity in bovine milk was studied over a range of 68 to 76 °C. Values of residual enzymatic activity after different treatments were studied by kinetic analysis, obtaining D-values and the Z-value (3.1 °C). Denaturation of lactoperoxidase, measured by loss in activity, can be described as a 1st-order reaction. Rate constants were calculated, as was the energy of activation, which was 737.69 kJ/mol. Thermodynamic parameters were also calculated. The high value obtained for the variation in enthalpy of activation indicates that a high amount of energy is required to initiate denaturation, probably due to the molecular conformation of lactoperoxidase. [source] Protein Denaturation and Structural Damage During High-Pressure-Shift Freezing of Porcine and Bovine MuscleJOURNAL OF FOOD SCIENCE, Issue 6 2000F. Fernández-Martín ABSTRACT: Pork and beef muscles were subjected to 200 MPa and ,20 °C with or without water freezing. Both tissues responded to the treatment with similar behavior. Protein denaturation was greater when freezing occurred. Pressure-induced cold denaturation was complete for actin and very considerable for myosin and other muscle proteins. Connective proteins remained practically unaltered by pressurization and/or freezing. Structural changes in the muscle at sarcomere levels caused by pressurization were more severe when freezing occurred. Color, drip loss, and textural properties on the pressurized samples also revealed an additional deleterious influence of freezing. Pressurization alone and pressure-shift freezing resulted unsuitable for muscle preservation. [source] Denaturation of replication protein A reveals an alternative conformation with intact domain structure and oligonucleotide binding activityPROTEIN SCIENCE, Issue 5 2004Jonathan E. Nuss Abstract Replication protein A (RPA) is a heterotrimeric, multidomain, single-stranded DNA-binding protein. Using spectroscopic methods and methylene carbene-based chemical modification methods, we have identified conformational intermediates in the denaturation pathway of RPA. Intrinsic protein fluorescence studies reveal unfolding profiles composed of multiple transitions, with midpoints at 1.5, 2.7, 4.2, and 5.3 M urea. CD profiles of RPA unfolding are characterized by a single transition. RPA is stabilized with respect to the CD-monitored transition when bound to a dA15 oligonucleotide. However, oligonucleotide binding appears to exert little, if any, effect on the first fluorescence transition. Methylene carbene chemical modification, coupled with MALDI-TOF mass spectrometry analysis, was also used to monitor unfolding of several specific RPA folds of the protein. The unfolding profiles of the individual structures are characterized by single transitions similar to the CD-monitored transition. Each fold, however, unravels with different individual characteristics, suggesting significant autonomy. Based on results from chemical modification and spectroscopic analyses, we conclude the initial transition observed in fluorescence experiments represents a change in the juxtaposition of binding folds with little unraveling of the domain structures. The second transition represents the unfolding of the majority of fold structure, and the third transition observed by fluorescence correlates with the dissociation of the 70- and 32-kD subunits. [source] Physicochemical properties of thiol proteinase inhibitor isolated from goat pancreasBIOPOLYMERS, Issue 8 2010Medha Priyadarshini Abstract Thiol proteinase inhibitors are crucial to proper functioning of all living tissues consequent to their cathepsin regulatory and myriad important biologic properties. Equilibrium denaturation of dimeric goat pancreas thiol proteinase inhibitor (PTPI), a cystatin superfamily variant has been studied by monitoring changes in the protein's spectroscopic and functional characteristics. Denaturation of PTPI in guanidine hydrochloride and urea resulted in altered intrinsic fluorescence emission spectrum, diminished negative circular dichroism, and loss of its papain inhibitory potential. Native like spectroscopic properties and inhibitory activity are only partially restored when denaturant is diluted from guanidine hydrochloride unfolded samples demonstrating that process is partially reversible. Coincidence of transition curves and dependence of transition midpoint (3.2M) on protein concentration in guanidine hydrochloride-induced denaturation are consistent with a two-state model involving a native like dimer and denatured monomer. On the contrary, urea-induced unfolding of PTPI is a multiphasic process with indiscernible intermediates. The studies demonstrate that functional conformation and stability are governed by both ionic and hydrophobic interactions. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 708,717, 2010. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Structure and lability of archaeal dehydroquinaseACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 10 2008Natasha N. Smith Multiple sequence alignments of type I 3-dehydroquinate dehydratases (DQs; EC 4.2.1.10) show that archaeal DQs have shorter helical regions than bacterial orthologs of known structure. To investigate this feature and its relation to thermostability, the structure of the Archaeoglobus fulgidus (Af) DQ dimer was determined at 2.33,Ĺ resolution and its denaturation temperature was measured in vitro by circular dichroism (CD) and differential scanning calorimetry (DSC). This structure, a P212121 crystal form with two 45,kDa dimers in the asymmetric unit, is the first structural representative of an archaeal DQ. Denaturation occurs at 343 ± 3,K at both low and high ionic strength and at 349,K in the presence of the substrate analog tartrate. Since the growth optimum of the organism is 356,K, this implies that the protein maintains its folded state through the participation of additional factors in vivo. The (,,)8 fold is compared with those of two previously determined type I DQ structures, both bacterial (Salmonella and Staphylococcus), which had sequence identities of ,30% with AfDQ. Although the overall folds are the same, there are many differences in secondary structure and ionic features; the archaeal protein has over twice as many salt links per residue. The archaeal DQ is smaller than its bacterial counterparts and lower in regular secondary structure, with its eight helices being an average of one turn shorter. In particular, two of the eight normally helical regions (the exterior of the barrel) are mostly nonhelical in AfDQ, each having only a single turn of 310 -helix flanked by ,-strand and coil. These `protohelices' are unique among evolutionarily close members of the (,,)8 -fold superfamily. Structural features that may contribute to stability, in particular ionic factors, are examined and the implications of having a Tm below the organism's growth temperature are considered. [source] A subclass of myosin XI is associated with mitochondria, plastids, and the molecular chaperone subunit TCP-1, in maizeCYTOSKELETON, Issue 4 2004Zhengyuan Wang Abstract The role and regulation of specific plant myosins in cyclosis is not well understood. In the present report, an affinity-purified antibody generated against a conserved tail region of some class XI plant myosin isoforms was used for biochemical and immunofluorescence studies of Zea mays. Myosin XI co-localized with plastids and mitochondria but not with nuclei, the Golgi apparatus, endoplasmic reticulum, or peroxisomes. This suggests that myosin XI is involved in the motility of specific organelles. Myosin XI was more than 50% co-localized with tailless complex polypeptide-1, (TCP-1,) in tissue sections of mature tissues located more than 1.0 mm from the apex, and the two proteins co-eluted from gel filtration and ion exchange columns. On Western blots, TCP-1, isoforms showed a developmental shift from the youngest 5.0 mm of the root to more mature regions that were more than 10.0 mm from the apex. This developmental shift coincided with a higher percentage of myosin XI /TCP-1, co-localization, and faster degradation of myosin XI by serine protease. Our results suggest that class XI plant myosin requires TCP-1, for regulating folding or providing protection against denaturation. Cell Motil. Cytoskeleton 57:218,232, 2004. © 2004 Wiley-Liss, Inc. [source] Determination of flurbiprofen enantiomers in plasma using a single-isomer amino cyclodextrin derivative in nonaqueous capillary electrophoresis,ELECTROPHORESIS, Issue 17 2008Anne Rousseau Abstract A nonaqueous capillary electrophoresis (NACE) assay was developed for the separation and determination of flurbiprofen enantiomers in plasma samples using 6-monodeoxy-6-mono(3-hydroxy)propylamino-,-cyclodextrin as chiral selector. The nonaqueous background electrolyte was made up of 40,mM ammonium acetate in methanol (MeOH), and flufenamic acid was employed as internal standard. Solid-phase extraction was used for sample cleanup prior to the NACE separation. The NACE method reproducibility was optimized by evaluating different capillary washing sequences between runs. After having tested various conditions, trifluoroacetic acid (1,M) in MeOH was finally selected. Concerning the solid-phase extraction procedure, good and reproducible analyte recoveries were obtained using MeOH for protein denaturation and a polymeric phase combining hydrophobic interactions with anion exchange properties (Oasis® MAX) was selected as extraction sorbent. The method selectivity was not only demonstrated toward a blank plasma sample but also toward other non-steroidal anti-inflammatory drugs. The method was then successfully validated with respect to response function, trueness, precision, accuracy, linearity and limit of quantification. [source] Capillary electrophoresis versus differential scanning calorimetry for the analysis of free enzyme versus enzyme-ligand complexes: In the search of the ligand-free status of cholinesterasesELECTROPHORESIS, Issue 2 2006Daniel Rochu Dr. Abstract Cholinesterases (ChEs) are highly efficient biocatalysts whose active site is buried in a deep, narrow gorge. The talent of CE to discover inhibitors in the gorge of highly purified preparations has fairly altered the meaning of a ChE ligand-free status. To attempt at a description of this one, we investigated the stability of Bungarus fasciatus acetylcholinesterase (AChE), alone or complexed with different inhibitors. Determination of midtransition temperature for thermal denaturation, using differential scanning calorimetry (DSC) and CE, provided conflicting results. Discrepancies strongly question the reality of a ligand-free AChE state. DSC allowed estimation of the stability of AChE-ligands complexes, and to rank the stabilizing effect of different inhibitors. CE acted as a detector of hidden ligands, provided that they were charged, reversibly bound, and thus dissociable upon action of electric fields. Then, CE allowed quantification of the stability of ligand-free AChE. CE and DSC providing each fractional and nonredundant information, cautious attention must be paid for actual estimation of the conformational stability of ChEs. Because inhibitors used in purification of ChEs by affinity chromatography are charged, CE remains a leading method to estimate enzyme stability and detect the presence of bound hidden ligands. [source] The biotin-streptavidin interaction can be reversibly broken using water at elevated temperaturesELECTROPHORESIS, Issue 3 2005Anders Holmberg Abstract The biotin-streptavidin system is the strongest noncovalent biological interaction known, having a dissociation constant, Kd, in the order of 4×10,14 M. The strength and specificity of the interaction has led it to be one of the most widely used affinity pairs in molecular, immunological, and cellular assays. However, it has previously been impossible to re-use any streptavidin solid support, since the conditions needed to break the interaction with biotin has led to the denaturation of the streptavidin. Here, we show that a short incubation in nonionic aqueous solutions at temperatures above 70°C can efficiently break the interaction without denaturing the streptavidin tetramer. Both biotin and the streptavidin remain active after dissociation and both molecules can therefore be re-used. The efficiency of the regeneration allowed solid supports with streptavidin to be used many times, here exemplified with the multiple re-use of streptavidin beads used for sample preparation prior to automated DNA sequencing. The results suggest that streptavidin regeneration can be introduced as an improvement in existing methods and assays based on the streptavidin system as well as emerging solid phase applications in fields, such as microfluidics and nanotechnology. [source] Compatible solutes of organisms that live in hot saline environmentsENVIRONMENTAL MICROBIOLOGY, Issue 9 2002Helena Santos Summary The accumulation of organic solutes is a prerequisite for osmotic adjustment of all microorganisms. Thermophilic and hyperthermophilic organisms generally accumulate very unusual compatible solutes namely, di- myo -inositol-phosphate, di-mannosyl-di- myo -inositol-phosphate, di-glycerol-phosphate, mannosylglycerate and mannosylglyceramide, which have not been identified in bacteria or archaea that grow at low and moderate temperatures. There is also a growing awareness that some of these compatible solutes may have a role in the protection of cell components against thermal denaturation. Mannosylglycerate and di-glycerol-phosphate have been shown to protect enzymes and proteins from thermal denaturation in vitro as well, or better, than compatible solutes from mesophiles. The pathways leading to the synthesis of some of these compatible solutes from thermophiles and hyperthermophiles have been elucidated. However, large numbers of questions remain unanswered. Fundamental and applied interest in compatible solutes and osmotic adjustment in these organisms, drives research that, will, in the near future, allow us to understand the role of compatible solutes in osmotic protection and thermoprotection of some of the most fascinating organisms known on Earth. [source] Stress for maintaining memory: HSP70 as a mobile messenger for innate and adaptive immunityEUROPEAN JOURNAL OF IMMUNOLOGY, Issue 6 2010Taoyong Chen Abstract HSP are abundant and conserved proteins present in all cells. Upon temperature shock or other stress stimuli, HSP are synthesized intracellularly, which may protect cells from protein denaturation or from death. Although HSP are synthesized intracellularly, HSP can also be mobilized to the plasma membrane or even be released under stress conditions. Elucidating the roles of cell surface and extracellular HSP in immune regulation has attracted much attention in recent years. Extracellularly, HSP can serve a cytokine function to initiate both innate and adaptive immunity through activation of APC. HSP serves also a chaperone function and facilitates presentation of antigen peptide to T cells. Similarly, cell surface HSP may activate APC and promote antigen presentation through cell,cell contact. A study in this issue of the European Journal of Immunology demonstrates that cell surface HSP70 on DC induced by stress can upregulate membrane-associated IL-15, which in turn promotes the proliferation of CD4+CD45RA memory T cells. Moreover, a DC-CD4+ T-cell interacting circuit formed by CD40L on T cells and CD40 on DC is proposed to play a role in the maintenance of memory homeostasis. This study has widened our view of HSP in adaptive immunity as well as their classical functions such as APC activator and antigen carrier. [source] A fluorescence energy transfer-based mechanical stress sensor for specific proteins in situFEBS JOURNAL, Issue 12 2008Fanjie Meng To measure mechanical stress in real time, we designed a fluorescence resonance energy transfer (FRET) cassette, denoted stFRET, which could be inserted into structural protein hosts. The probe was composed of a green fluorescence protein pair, Cerulean and Venus, linked with a stable ,-helix. We measured the FRET efficiency of the free cassette protein as a function of the length of the linker, the angles of the fluorophores, temperature and urea denaturation, and protease treatment. The linking helix was stable to 80 °C, unfolded in 8 m urea, and rapidly digested by proteases, but in all cases the fluorophores were unaffected. We modified the ,-helix linker by adding and subtracting residues to vary the angles and distance between the donor and acceptor, and assuming that the cassette was a rigid body, we calculated its geometry. We tested the strain sensitivity of stFRET by linking both ends to a rubber sheet subjected to equibiaxial stretch. FRET decreased proportionally to the substrate strain. The naked cassette expressed well in human embryonic kidney-293 cells and, surprisingly, was concentrated in the nucleus. However, when the cassette was located into host proteins such ,-actinin, nonerythrocyte spectrin and filamin A, the labeled hosts expressed well and distributed normally in cell lines such as 3T3, where they were stressed at the leading edge of migrating cells and relaxed at the trailing edge. When collagen-19 was labeled near its middle with stFRET, it expressed well in Caenorhabditis elegans, distributing similarly to hosts labeled with a terminal green fluorescent protein, and the worms behaved normally. [source] Effects of the G376E and G157D mutations on the stability of yeast enolase , a model for human muscle enolase deficiencyFEBS JOURNAL, Issue 1 2008Songping Zhao The first known human enolase deficiency was reported in 2001 [Comi GP, Fortunato F, Lucchiari S, Bordoni A, Prelle A, Jann S, Keller A, Ciscato P, Galbiati S, Chiveri L et al. (2001) Ann Neurol50, 202,207]. The subject had inherited two mutated genes for ,-enolase. These mutations changed glycine 156 to aspartate and glycine 374 to glutamate. In order to study the effects of these changes on the structure and stability of enolase, we have introduced the corresponding changes (G157D and G376E) into yeast enolase. The two variants are correctly folded. They are less stable than wild-type enolase with respect to thermal denaturation, and both have increased Kd values for subunit dissociation. At 37 °C, in the presence of salt, both are partially dissociated and are extensively cleaved by trypsin. Under the same conditions, wild-type enolase is fully dimeric and is only slightly cleaved by trypsin. However, wild-type enolase is also extensively cleaved if it is partially dissociated. The identification of the cleavage sites and spectral studies of enolase have revealed some of the structural differences between the dimeric and monomeric forms of this enzyme. [source] Small heat shock protein Hsp27 prevents heat-induced aggregation of F-actin by forming soluble complexes with denatured actinFEBS JOURNAL, Issue 22 2007Anastasia V. Pivovarova Previously, we have shown that the small heat shock protein with apparent molecular mass 27 kDa (Hsp27) does not affect the thermal unfolding of F-actin, but effectively prevents aggregation of thermally denatured F-actin [Pivovarova AV, Mikhailova VV, Chernik IS, Chebotareva NA, Levitsky DI & Gusev NB (2005) Biochem Biophys Res Commun331, 1548,1553], and supposed that Hsp27 prevents heat-induced aggregation of F-actin by forming soluble complexes with denatured actin. In the present work, we applied dynamic light scattering, analytical ultracentrifugation and size exclusion chromatography to examine the properties of complexes formed by denatured actin with a recombinant human Hsp27 mutant (Hsp27,3D) mimicking the naturally occurring phosphorylation of this protein at Ser15, Ser78, and Ser82. Our results show that formation of these complexes occurs upon heating and accompanies the F-actin thermal denaturation. All the methods show that the size of actin,Hsp27-3D complexes decreases with increasing Hsp27-3D concentration in the incubation mixture and that saturation occurs at approximately equimolar concentrations of Hsp27-3D and actin. Under these conditions, the complexes exhibit a hydrodynamic radius of ,,16 nm, a sedimentation coefficient of 17,20 S, and a molecular mass of about 2 MDa. It is supposed that Hsp27-3D binds to denatured actin monomers or short oligomers dissociated from actin filaments upon heating and protects them from aggregation by forming relatively small and highly soluble complexes. This mechanism might explain how small heat shock proteins prevent aggregation of denatured actin and by this means protect the cytoskeleton and the whole cell from damage caused by accumulation of large insoluble aggregates under heat shock conditions. [source] Human proteoglycan testican-1 inhibits the lysosomal cysteine protease cathepsin LFEBS JOURNAL, Issue 19 2003Jeffrey P. Bocock Testican-1, a secreted proteoglycan enriched in brain, has a single thyropin domain that is highly homologous to domains previously shown to inhibit cysteine proteases. We demonstrate that purified recombinant human testican-1 is a strong competitive inhibitor of the lysosomal cysteine protease, cathepsin L, with a Ki of 0.7 nm, but it does not inhibit the structurally related lysosomal cysteine protease cathepsin B. Testican-1 inhibition of cathepsin L is independent of its chondroitin sulfate chains and is effective at both pH 5.5 and 7.2. At neutral pH, testican-1 also stabilizes cathepsin L, slowing pH-induced denaturation and allowing the protease to remain active longer, although the rate of proteolysis is reduced. These data indicate that testican-1 is capable of modulating cathepsin L activity both in intracellular vesicles and in the extracellular milieu. [source] ORF6 from the clavulanic acid gene cluster of Streptomyces clavuligerus has ornithine acetyltransferase activityFEBS JOURNAL, Issue 8 2002Nadia J. Kershaw The clinically used beta-lactamase inhibitor clavulanic acid is produced by fermentation of Streptomyces clavuligerus. The orf6 gene of the clavulanic acid biosynthetic gene cluster in S. clavuligerus encodes a protein that shows sequence homology to ornithine acetyltransferase (OAT), the fifth enzyme of the arginine biosynthetic pathway. Orf6 was overexpressed in Escherichia coli (at ,,15% of total soluble protein by SDS/PAGE analysis) indicating it was not toxic to the host cells. The recombinant protein was purified (to >,95% purity) by a one-step technique. Like other OATs it was synthesized as a precursor protein which underwent autocatalytic internal cleavage in E. coli to generate , and , subunits. Cleavage was shown to occur between the alanine and threonine residues in a KGXGMXXPX--(M/L)AT (M/L)L motif conserved within all identified OAT sequences. Gel filtration and native electrophoresis analyses implied that the ORF6 protein was an ,2,2 heterotetramer and direct evidence for this came from mass spectrometric analyses. Although anomalous migration of the , subunit was observed by standard SDS/PAGE analysis, which indicated the presence of two bands (as previously observed for other OATs), mass spectrometric analyses did not reveal any evidence for post-translational modification of the , subunit. Extended denaturation with SDS before PAGE resulted in observation of a single major , subunit band. Purified ORF6 was able to catalyse the reversible transfer of an acetyl group from N -acetylornithine to glutamate, but not the formation of N -acetylglutamate from glutamate and acetyl-coenzyme A, nor (detectably) the hydrolysis of N -acetylornithine. Mass spectrometry also revealed the reaction proceeds via acetylation of the , subunit. [source] The refolding of type II shikimate kinase from Erwinia chrysanthemi after denaturation in ureaFEBS JOURNAL, Issue 8 2002Eleonora Cerasoli Shikimate kinase was chosen as a convenient representative example of the subclass of ,/, proteins with which to examine the mechanism of protein folding. In this paper we report on the refolding of the enzyme after denaturation in urea. As shown by the changes in secondary and tertiary structure monitored by far UV circular dichroism (CD) and fluorescence, respectively, the enzyme was fully unfolded in 4 m urea. From an analysis of the unfolding curve in terms of the two-state model, the stability of the folded state could be estimated as 17 kJ·mol,1. Approximately 95% of the enzyme activity could be recovered on dilution of the urea from 4 to 0.36 m. The results of spectroscopic studies indicated that refolding occurred in at least four kinetic phases, the slowest of which (k = 0.009 s,1) corresponded with the regain of shikimate binding and of enzyme activity. The two most rapid phases were associated with a substantial increase in the binding of 8-anilino-1-naphthalenesulfonic acid with only modest changes in the far UV CD, indicating that a collapsed intermediate with only partial native secondary structure was formed rapidly. The relevance of the results to the folding of other ,/, domain proteins is discussed. [source] The cytochrome cbb3 from Pseudomonas stutzeri displays nitric oxide reductase activityFEBS JOURNAL, Issue 24 2001Elena Forte The cytochrome cbb3 is an isoenzyme in the family of cytochrome c oxidases. This protein purified from Pseudomonas stutzeri displays a cyanide-sensitive nitric oxide reductase activity (Vmax=100±9 mol NO·mol ·min,1 and Km=12±2.5 µm), which is lost upon denaturation. This enzyme is only partially reduced by ascorbate, and readily re-oxidized by NO under anaerobic conditions at a rate consistent with the turnover number for NO consumption. As shown by transient spectroscopy experiments and singular value decomposition (SVD) analysis, these results suggest that the cbb3 -type cytochromes, sharing structural features with bacterial nitric oxide reductases, are the enzymes retaining the highest NO reductase activity within the heme-copper oxidase superfamily. [source] Comparison of the specificity, stability and individual rate constants with respective activation parameters for the peptidase activity of cruzipain and its recombinant form, cruzain, from Trypanosoma cruziFEBS JOURNAL, Issue 24 2001Wagner A. S. Judice The Trypanosoma cruzi cysteine protease cruzipain contains a 130-amino-acid C-terminal extension, in addition to the catalytic domain. Natural cruzipain is a complex of isoforms, because of the simultaneous expression of several genes, and the presence of either high mannose-type, hybrid monoantennary-type or complex biantenary-type oligosacharide chains at Asn255 of the C-terminal extension. Cruzipain and its recombinant form without this extension (cruzain) were studied comparatively in this work. S2 to S2, subsite specificities of these enzymes were examined using four series of substrates derived from the internally quenched fluorescent peptide Abz-KLRFSKQ-EDDnp (Abz, ortho -aminobenzoic acid; EDDnp, N -(2,4-dinitrophenyl)-ethylenediamine). Large differences in the kinetic parameters were not observed between the enzymes; however, Km values were consistently lower for the hydrolysis of most of the substrates by cruzain. No difference in the pH,activity profile between the two enzymes was found, but in 1 m NaCl cruzipain presented a kcat value significantly higher than that of cruzain. The activation energy of denaturation for the enzymes did not differ significantly; however, a negative entropy value was observed for cruzipain denaturation whereas the value for cruzain was positive. We determined the individual rate constants (k1, substrate diffusion; k,1, substrate dissociation; k2, acylation; k3, deacylation) and the respective activation energies and entropies for hydrolysis of Abz-KLRFSKQ-EDDnp determining the temperature dependence of the Michaelis,Menten parameters kcat/Km and kcat as previously described [Ayala, Y.M. & Di Cera, E. (2000) Protein Sci.9, 1589,1593]. Differences between the two enzymes were clearly detected in the activation energies E1 and E,1, which are significantly higher for cruzipain. The corresponding ,S1 and ,S,1 were positive and significantly higher for cruzipain than for cruzain. These results indicate the presence of a larger energy barrier for cruzipain relating to substrate diffusion and dissociation, which could be related to the C-terminal extension and/or glycosylation state of cruzipain. [source] Complete primary structure of rainbow trout type I collagen consisting of ,1(I),2(I),3(I) heterotrimersFEBS JOURNAL, Issue 10 2001Masataka Saito The subunit compositions of skin and muscle type I collagens from rainbow trout were found to be ,1(I),2(I),3(I) and [,1(I)]2,2(I), respectively. The occurrence of ,3(I) has been observed only for bonyfish. The skin collagen exhibited more susceptibility to both heat denaturation and MMP-13 digestion than the muscle counterpart; the former had a lower denaturation temperature by about 0.5 °C than the latter. The lower stability of skin collagen, however, is not due to the low levels of imino acids because the contents of Pro and Hyp were almost constant in both collagens. On the other hand, some cDNAs coding for the N-terminal and/or a part of triple-helical domains of pro,(I) chains were cloned from the cDNA library of rainbow trout fibroblasts. These cDNAs together with the previously cloned collagen cDNAs gave information about the complete primary structure of type I procollagen. The main triple-helical domain of each pro,(I) chain had 338 uninterrupted Gly-X-Y triplets consisting of 1014 amino acids and was unique in its high content of Gly-Gly doublets. In particular, the bonyfish-specific ,(I) chain, pro,3(I) was characterized by the small number of Gly-Pro-Pro triplets, 19, and the large number of Gly-Gly doublets, 38, in the triple-helical domain, compared to 23 and 22, respectively, for pro,1(I). The small number of Gly-Pro-Pro and the large number of Gly-Gly in pro,3(I) was assumed to partially loosen the triple-helical structure of skin collagen, leading to the lower stability of skin collagen mentioned above. Finally, phylogenetic analyses revealed that pro,3(I) had diverged from pro,1(I). This study is the first report of the complete primary structure of fish type I procollagen. [source] Pressure-exploration of the 33-kDa protein from the spinach photosystem II particleFEBS JOURNAL, Issue 9 2001Kangcheng Ruan The 33-kDa protein isolated from the spinach photosystem II particle is an ideal model to explore high-pressure protein-unfolding. The protein has a very low free energy as previously reported by chemical unfolding studies, suggesting that it must be easy to modulate its unfolding transition by rather mild pressure. Moreover, the protein molecule consists of only one tryptophan residue (Trp241) and eight tyrosine residues, which can be conveniently used to probe the protein conformation and structural changes under pressure using either fluorescence spectroscopy or fourth derivative UV absorbance spectroscopy. The different experimental methods used in the present study indicate that at 20 °C and pH 6, the 33-kDa protein shows a reversible two-state unfolding transition from atmospheric pressure to about 180 MPa. This value is much lower than those found for the unfolding of most proteins studied so far. The unfolding transition induces a large red shift of the maximum fluorescence emission of 34 nm (from 316 nm to 350 nm). The change in standard free energy (,Go) and in volume (,V) for the transition at pH 6.0 and 20 °C are ,14.6 kJ·mol,1 and ,120 mL·mol,1, respectively, in which the ,Go value is consistent with that obtained by chemical denaturation. We found that pressure-induced protein unfolding is promoted by elevated temperatures, which seem largely attributed to the decrease in the absolute value of ,Go (only a minor variation was observed for the ,V value). However, the promotion of the unfolding by alkaline pH seems mainly related to the increase in ,V without any significant changes in ,Go. It was also found that NaCl significantly protects the protein from pressure-induced unfolding. In the presence of 1 m NaCl, the pressure needed to induce the half-unfold of the protein is shifted to a higher value (shift of 75 MPa) in comparison with that observed without NaCl. Interestingly, in the presence of NaCl, the value of ,V is significantly reduced whilst that of ,Go remains as before. The unfolding-refolding kinetics of the protein has also been studied by pressure-jump, in which it was revealed that both reactions are a two-state transition process with a relatively slow relaxation time of about 102 s. [source] Structural and catalytic properties and homology modelling of the human nucleoside diphosphate kinase C, product of the DRnm23 geneFEBS JOURNAL, Issue 7 2001Muriel Erent The human DRnm23 gene was identified by differential screening of a cDNA library obtained from chronic myeloid leukaemia-blast crisis primary cells. The over-expression of this gene inhibits differentiation and induces the apoptosis of myeloid precursor cell lines. We overproduced in bacteria a truncated form of the encoded protein lacking the first 17 N-terminal amino acids. This truncated protein was called nucleoside diphosphate (NDP) kinase C,. NDP kinase C, had similar kinetic properties to the major human NDP kinases A and B, but was significantly more stable to denaturation by urea and heat. Analysis of denaturation by urea, using size exclusion chromatography, indicated unfolding without the dissociation of subunits, whereas renaturation occurred via a folded monomer. The stability of the protein depended primarily on subunit interactions. Homology modelling of the structure of NDP kinase C,, based on the crystal structure of NDP kinase B, indicated that NDP kinase C, had several additional stabilizing interactions. The overall structure of the two enzymes appears to be identical because NDP kinase C, readily formed mixed hexamers with NDP kinase A. It is possible that mixed hexamers can be observed in vivo. [source] Characterization of carbonic anhydrase from Neisseria gonorrhoeaeFEBS JOURNAL, Issue 6 2001Björn Elleby We have investigated the steady state and equilibrium kinetic properties of carbonic anhydrase from Neisseria gonorrhoeae (NGCA). Qualitatively, the enzyme shows the same kinetic behaviour as the well studied human carbonic anhydrase II (HCA II). This is reflected in the similar pH dependencies of the kinetic parameters for CO2 hydration and the similar behaviour of the kinetics of 18O exchange between CO2 and water at chemical equilibrium. The pH profile of the turnover number, kcat, can be described as a titration curve with an exceptionally high maximal value of 1.7 × 106 s,1 at alkaline pH and a pKa of 7.2. At pH 9, kcat is buffer dependent in a saturable manner, suggesting a ping-pong mechanism with buffer as the second substrate. The ratio kcat/Km is dependent on two ionizations with pKa values of 6.4 and 8.2. However, an 18O-exchange assay identified only one ionizable group in the pH profile of kcat/Km with an apparent pKa of 6.5. The results of a kinetic analysis of a His66,Ala variant of the bacterial enzyme suggest that His66 in NGCA has the same function as a proton shuttle as His64 in HCA II. The kinetic defect in the mutant can partially be overcome by certain buffers, such as imidazole and 1,2-dimethylimidazole. The bacterial enzyme shows similar Ki values for the inhibitors NCO,, SCN, and N3, as HCA II, while CN, and the sulfonamide ethoxzolamide are considerably weaker inhibitors of the bacterial enzyme than of HCA II. The absorption spectra of the adducts of Co(II)-substituted NGCA with acetazolamide, NCO,, SCN,, CN, and N3, resemble the corresponding spectra obtained with human Co(II)-isozymes I and II. Measurements of guanidine hydrochloride (GdnHCl)-induced denaturation reveal a sensitivity of the CO2 hydration activity to the reducing agent tris(2-carboxyethyl)phosphine (TCEP). However, the A292/A260 ratio was not affected by the presence of TCEP, and a structural transition at 2.8,2.9 m GdnHCl was observed. [source] Thermally induced conformational changes in horseradish peroxidaseFEBS JOURNAL, Issue 1 2001David G. Pina Detailed differential scanning calorimetry (DSC), steady-state tryptophan fluorescence and far-UV and visible CD studies, together with enzymatic assays, were carried out to monitor the thermal denaturation of horseradish peroxidase isoenzyme c (HRPc) at pH 3.0. The spectral parameters were complementary to the highly sensitive but integral method of DSC. Thus, changes in far-UV CD corresponded to changes in the overall secondary structure of the enzyme, while that in the Soret region, as well as changes in intrinsic tryptophan fluorescence emission, corresponded to changes in the tertiary structure of the enzyme. The results, supported by data about changes in enzymatic activity with temperature, show that thermally induced transitions for peroxidase are irreversible and strongly dependent upon the scan rate, suggesting that denaturation is under kinetic control. It is shown that the process of HRPc denaturation can be interpreted with sufficient accuracy in terms of the simple kinetic scheme where k is a first-order kinetic constant that changes with temperature, as given by the Arrhenius equation; N is the native state, and D is the denatured state. On the basis of this model, the parameters of the Arrhenius equation were calculated. [source] Effects of cadmium on manganese peroxidaseFEBS JOURNAL, Issue 6 2000Competitive inhibition of MnII oxidation, thermal stabilization of the enzyme Inhibition of manganese peroxidase by cadmium was studied under steady-state and transient-state kinetic conditions. CdII is a reversible competitive inhibitor of MnII in the steady state with Ki , 10 µm. CdII also inhibits enzyme-generated MnIII,chelate-mediated oxidation of 2,6-dimethoxyphenol with Ki , 4 µm. CdII does not inhibit direct oxidation of phenols such as 2,6-dimethoxyphenol or guaiacol (2-methoxyphenol) in the absence of MnII. CdII alters the heme Soret on binding manganese peroxidase and exhibits a Kd , 8 µm, similar to Mn (Kd , 10 µm). Under transient-state conditions, CdII inhibits reduction of compound I and compound II by MnII at pH 4.5. However, CdII does not inhibit formation of compound I nor does it inhibit reduction of the enzyme intermediates by phenols in the absence of MnII. Kinetic analysis suggests that CdII binds at the MnII -binding site, preventing oxidation of MnII, but does not impair oxidation of substrates, such as phenols, which do not bind at the MnII -binding site. Finally, at pH 4.5 and 55 °C, MnII and CdII both protect manganese peroxidase from thermal denaturation more efficiently than CaII, extending the half-life of the enzyme by more than twofold. Furthermore, the combination of half MnII and half CdII nearly quadruples the enzyme half-life over either metal alone or either metal in combination with CaII. [source] Assignment of a single disulfide bridge in rat liver methionine adenosyltransferaseFEBS JOURNAL, Issue 1 2000María L. Martínez-Chantar Rat liver methionine adenosyltransferase incorporated 8 mol of N -ethylmaleimide per mol of subunit upon denaturation in the presence of 8 m urea, whereas 10 such groups were labelled when dithiothreitol was also included. This observation prompted a re-examination of the state of the thiol groups, which was carried out using peptide mapping, amino acid analysis and N-terminal sequencing. The results obtained revealed a disulfide bridge between Cys35 and Cys61. This disulfide did not appear to be conserved because cysteines homologous to residue 61 do not exist in methionine adenosyltransferases of other origins, therefore suggesting its importance for the differential aspects of the liver-specific enzyme. [source] Characterization of active-site mutants of Schizosaccharomyces pombe phosphoglycerate mutaseFEBS JOURNAL, Issue 24 2000Elucidation of the roles of amino acids involved in substrate binding, catalysis The roles of a number of amino acids present at the active site of the monomeric phosphoglycerate mutase from the fission yeast Schizosaccharomyces pombe have been explored by site-directed mutagenesis. The amino acids examined could be divided broadly into those presumed from previous related structural studies to be important in the catalytic process (R14, S62 and E93) and those thought to be important in substrate binding (R94, R120 and R121). Most of these residues have not previously been studied by site-directed mutagenesis. All the mutants except R14 were expressed in an engineered null strain of Saccharomyces cerevisiae (S150-gpm::HIS) in good yield. The R14Q mutant was expressed in good yield in the transformed AH22 strain of S. cerevisiae. The S62A mutant was markedly unstable, preventing purification. The various mutants were purified to homogeneity and characterized in terms of kinetic parameters, CD and fluorescence spectra, stability towards denaturation by guanidinium chloride, and stability of phosphorylated enzyme intermediate. In addition, the binding of substrate (3-phosphoglycerate) to wild-type, E93D and R120,121Q enzymes was measured by isothermal titration calorimetry. The results provide evidence for the proposed roles of each of these amino acids in the catalytic cycle and in substrate binding, and will support the current investigation of the structure and dynamics of the enzyme using multidimensional NMR techniques. [source] Bacterial metabolism in small temperate streams under contemporary and future climatesFRESHWATER BIOLOGY, Issue 12 2007KAJ SAND-JENSEN Summary 1. We examined the detailed temperature dependence (0,40 °C) of bacterial metabolism associated with fine sediment particles from three Danish lowland streams to test if temperature dependence varied between sites, seasons and quality of organic matter and to evaluate possible consequences of global warming. 2. A modified Arrhenius model with reversible denaturation at high temperatures could account for the temperature dependence of bacterial metabolism and the beginning of saturation above 35 °C and it was superior to the unmodified Arrhenius model. Both models overestimated respiration rates at very low temperatures (<5 °C), whereas Ratkowsky's model , the square root of respiration , provided an excellent linear fit between 0 and 30 °C. 3. There were no indications of differences in temperature dependence among samples dominated by slowly or easily degradable organic substrates. Optimum temperature, apparent minimum temperature, Q10 -values for 0,40 °C and activation energies of bacterial respiration were independent of season, stream site and degradability of organic matter. 4. Q10 -values of bacterial respiration declined significantly with temperature (e.g. 3.31 for 5,15 °C and 1.43 for 25,35 °C) and were independent of site and season. Q10 -values of bacterial production behaved similarly, but were significantly lower than Q10 -values of respiration implying that bacterial growth efficiency declined with temperature. 5. A regional warming scenario for 2071,2100 (IPCC A2) predicted that mean annual temperatures will increase by 3.5 °C in the air and 2.2,4.3 °C in the streams compared with the control scenario for 1961,1990. Temperature is expected to rise more in cool groundwater-fed forest springs than in open, summer-warm streams. Mean annual bacterial respiration is estimated to increase by 26,63% and production by 18,41% among streams assuming that established metabolism,temperature relationships and organic substrate availability remain the same. To improve predictions of future ecosystem behaviour, we further require coupled models of temperature, hydrology, organic production and decomposition. [source] Synthesis, DNA-Binding and Photocleavage Studies of the Ruthenium(II) Complexes [Ru(phen)2(ppd)]2+ and [Ru(phen)(ppd)2]2+ (ppd=Pteridino[6,7- f],[1,10]phenanthroline-11,13(10H,12H)-dione, phen=1,10-Phenanthroline)HELVETICA CHIMICA ACTA, Issue 3 2008Feng Gao Abstract Two new complexes, [Ru(phen)2(ppd)]2+ (1) and [Ru(phen)(ppd)2]2+ (2) (ppd=pteridino[6,7- f],[1,10]phenanthroline-11,13(10H,12H)-dione, phen=1,10-phenanthroline) were synthesized and characterized by ES-MS, 1H-NMR spectroscopy, and elemental analysis. The intercalative DNA-binding properties of 1 and 2 were investigated by absorption-spectroscopy titration, luminescence-spectroscopy studies, thermal denaturation, and viscosity measurements. The theoretical aspects were further discussed by comparative studies of 1 and 2 by means of DFT calculations and molecular-orbital theory. Photoactivated cleavage of pBR322 DNA by the two complexes were also studied, and 2 was found to be a much better photocleavage reagent than 1. The mechanism studies revealed that singlet oxygen and the excited-states redox potentials of the complex may play an important role in the DNA photocleavage. [source] Extending the Pressure,Temperature State Diagram of MyoglobinHELVETICA CHIMICA ACTA, Issue 3 2005Filip Meersman The pressure,temperature (P,T) diagram of proteins proposed by Hawley concerns the equilibrium between native and denatured forms. However, the importance of protein aggregation is increasingly recognized, and it has been suggested that certain aggregated states represent alternative folds of the polypeptide chain. Here, we present a P,T -diagram for myoglobin in which we include the aggregated state and suggest to call it a P,T -state diagram, as not all boundaries are true equilibrium transitions. We observe by Fourier transform infrared spectroscopy that increasing temperature causes the protein to aggregate, but that a subsequent further temperature increase results in the dissociation of this aggregate. Moreover, we observe that moderate pressures stabilize myoglobin against thermal denaturation. We hypothesize that this effect originates from the volume changes associated with the aggregation transition. [source] | ||||||||||||||||||||||||||||||||||||||||||||||