PMID-sentid Pub_year Sent_text comp_official_name comp_offsetprotein_name organism prot_offset 1318745-1 1992 The reversible folding of cytochrome c in urea at pH 4.0 was investigated by repetitive pressure perturbation kinetics and by equilibrium spectroscopic methods. Urea 42-46 cytochrome c, somatic Homo sapiens 26-38 10029541-3 1999 We propose a practical solution to this problem and use it to test the dependence of DeltaGD of lysozyme, ribonuclease-A, and cytochrome-c on [urea], the molar urea concentration. Urea 143-147 cytochrome c, somatic Homo sapiens 126-138 10029541-3 1999 We propose a practical solution to this problem and use it to test the dependence of DeltaGD of lysozyme, ribonuclease-A, and cytochrome-c on [urea], the molar urea concentration. Urea 160-164 cytochrome c, somatic Homo sapiens 126-138 8206882-1 1994 Denaturations of ribonuclease A, lysozyme, and cytochrome c by guanidine hydrochloride (GdnHCl), urea, and GdnHCl-urea mixture were studied at constant temperature and pH to assess the functional dependence of denaturational free energy change (delta GD) on denaturant concentration over an extended GdnHCl concentration range. Urea 97-101 cytochrome c, somatic Homo sapiens 47-59 8206882-1 1994 Denaturations of ribonuclease A, lysozyme, and cytochrome c by guanidine hydrochloride (GdnHCl), urea, and GdnHCl-urea mixture were studied at constant temperature and pH to assess the functional dependence of denaturational free energy change (delta GD) on denaturant concentration over an extended GdnHCl concentration range. Urea 114-118 cytochrome c, somatic Homo sapiens 47-59 1322462-4 1992 Using the calorimetric data, the number of apparent binding sites for urea and guanidinium chloride have been estimated for three proteins in their unfolded and native states (ribonuclease A, hen egg white lysozyme and cytochrome c). Urea 70-74 cytochrome c, somatic Homo sapiens 219-231 35079752-1 2022 Electrochemical, spectroscopic and computational methods are used to demonstrate that electrified aqueous organic interfaces are a suitable bio-mimetic platform to study and contrast the accelerated electrocatalytic activity of cytochrome c towards the production of reactive oxygen species (ROS) in the presence of denaturing agents such as guanidinium chloride and urea. Urea 367-371 cytochrome c, somatic Homo sapiens 228-240 2992394-4 1985 In contrast, the broadening of the NMR signals for the heme and methionine-80 methyl groups and the conformational transition in the vicinity of the heme moiety on change from the native to the cyanide-bound or urea-denatured form of cytochrome c showed a similar binding-ratio dependence to the rate constants for the oxidation and reduction reactions. Urea 211-215 cytochrome c, somatic Homo sapiens 234-246 240823-4 1975 Denaturation studies with urea, the absence of any reaction with cyanide, and the evidence from other lines would appear to indicate that the heme group of cytochrome c1 was reduced by ascorbate at approximately 5% of the rate of reduction of cytochrome c but this rate dramatically increased with increasing pH concomitant with the disappearance of the 690 nm absorbance band. Urea 26-30 cytochrome c, somatic Homo sapiens 156-168 6279160-9 1982 Succinylation of the 19th, and final, lysine residue of cytochrome c produced unfolding even in the absence of urea, whereas reaction of the first 18 had very little effect. Urea 111-115 cytochrome c, somatic Homo sapiens 56-68 28735170-4 2017 Therefore, atomistic molecular dynamics (MD) simulations have been carried out to investigate the effect of different solvents (water, urea/water, MeOH and DMSO) on the structure and conformations of apoptotic cyt-c (Fe3+). Urea 135-139 cytochrome c, somatic Homo sapiens 210-215 33705282-5 2021 The alkaline isomerization of cyt c in the presence of 8 M urea, measured by Trp59 fluorescence, implied an existence of a high-affinity non-native ligand for the heme iron even in a partially denatured protein conformation. Urea 59-63 cytochrome c, somatic Homo sapiens 30-35 33705282-6 2021 The conformation of the cyt c alkaline state in 8 M urea was considerably modulated by the specific effect of anions. Urea 52-56 cytochrome c, somatic Homo sapiens 24-29 30775200-0 2019 Uncovering dehydration in cytochrome c refolding from urea- and guanidine hydrochloride-denatured unfolded state by high pressure spectroscopy. Urea 54-58 cytochrome c, somatic Homo sapiens 26-38 30775200-2 2019 DeltaV u values for the unfolding to urea- and guanidine hydrochloride (GdnHCl)-denatured Cyt c were estimated to be 56+-5 and 29+-1 mL mol-1, respectively. Urea 37-41 cytochrome c, somatic Homo sapiens 90-95 30775200-4 2019 Because of the marked tendency of guanidium ions to interact with hydrophobic groups, a smaller number of water molecules were hydrated with hydrophobic groups in GdnHCl-denatured Cyt c than in urea-denatured Cyt c, resulting in the smaller positive DeltaV u. Urea 194-198 cytochrome c, somatic Homo sapiens 180-185 30775200-4 2019 Because of the marked tendency of guanidium ions to interact with hydrophobic groups, a smaller number of water molecules were hydrated with hydrophobic groups in GdnHCl-denatured Cyt c than in urea-denatured Cyt c, resulting in the smaller positive DeltaV u. Urea 194-198 cytochrome c, somatic Homo sapiens 209-214 30775200-5 2019 On the other hand, urea is a relatively weak denaturant and urea-denatured Cyt c is not completely hydrated, which retains the partially folded structures. Urea 19-23 cytochrome c, somatic Homo sapiens 75-80 30775200-5 2019 On the other hand, urea is a relatively weak denaturant and urea-denatured Cyt c is not completely hydrated, which retains the partially folded structures. Urea 60-64 cytochrome c, somatic Homo sapiens 75-80 30775200-6 2019 To unfold such partial structures, we introduced a mutation near the heme binding site, His26, to Gln, resulting in a negatively shifted DeltaV u (4+-2 mL mol-1) in urea-denatured Cyt c. Urea 165-169 cytochrome c, somatic Homo sapiens 180-185 29239171-6 2018 The smart MALDI plate shows high performance for mass spectrometric analysis of cytochrome c and neurotensin in the presence of 1 M urea and 100 mM NaHCO3, as well as improved detection sensitivity and high sequence coverage for alpha-casein and cytochrome c digests in femtomole range. Urea 132-136 cytochrome c, somatic Homo sapiens 80-92 31867407-3 2019 Here, to elucidate the effects of DESs on the peroxidase activity of cytochrome c, we carried out linear and nonlinear infrared spectroscopic studies of the CO stretch mode of carbon monoxide cytochrome c (COCytc) in ethylammonium chloride (EAC)/urea DES. Urea 246-250 cytochrome c, somatic Homo sapiens 69-81 31867407-3 2019 Here, to elucidate the effects of DESs on the peroxidase activity of cytochrome c, we carried out linear and nonlinear infrared spectroscopic studies of the CO stretch mode of carbon monoxide cytochrome c (COCytc) in ethylammonium chloride (EAC)/urea DES. Urea 246-250 cytochrome c, somatic Homo sapiens 192-204 31867407-9 2019 The experimental results lead us to propose a hypothesis that the DES increases the population of the conformer with distal ligand lysines close to the reaction center through the combining effect of urea and EAC, which results in the enhancement of the peroxidase activity of cytochrome c. Urea 200-204 cytochrome c, somatic Homo sapiens 277-289 30048628-3 2018 Thermodynamic analysis of thermal and urea-unfolding curves of cytochrome c (Cyt c) and myoglobin (Mb) measured at different [GdnHCl] in presence of crowding agents reveals that crowder presence counterbalances and strengthens the destabilizing action of GdnHCl on stability of Cyt c and Mb, respectively. Urea 38-42 cytochrome c, somatic Homo sapiens 63-75 30048628-3 2018 Thermodynamic analysis of thermal and urea-unfolding curves of cytochrome c (Cyt c) and myoglobin (Mb) measured at different [GdnHCl] in presence of crowding agents reveals that crowder presence counterbalances and strengthens the destabilizing action of GdnHCl on stability of Cyt c and Mb, respectively. Urea 38-42 cytochrome c, somatic Homo sapiens 77-82 28735170-11 2017 Essential dynamics analysis implies that the overall motions of cyt-c in water, MeOH and urea/water are involved in three to four eigenvectors and in first eigenvector in DMSO. Urea 89-93 cytochrome c, somatic Homo sapiens 64-69 23337638-0 2013 Urea-induced modification of cytochrome c flexibility as probed by cyanide binding. Urea 0-4 cytochrome c, somatic Homo sapiens 29-41 25869364-6 2015 The m value (a measure of dependence of DeltaGD on denaturant concentration) for Cyt c and Mb is lower when it is denatured with urea compared to GdnHCl. Urea 129-133 cytochrome c, somatic Homo sapiens 81-86 24514269-1 2014 The K72A/K73H/K79A variant of cytochrome c undergoes a reversible change from a His/Met to a His/His axial heme ligation upon urea-induced unfolding slightly below neutral pH. Urea 126-130 cytochrome c, somatic Homo sapiens 30-42 26931726-0 2016 Interaction-component analysis of the hydration and urea effects on cytochrome c. Urea 52-56 cytochrome c, somatic Homo sapiens 68-80 23337638-1 2013 Cyanide binding to cytochrome c was monitored by absorption spectroscopy from neutral to acidic pH in the presence of urea. Urea 118-122 cytochrome c, somatic Homo sapiens 19-31 17696324-0 2007 A solution study on the local and global structure changes of cytochrome c: an unfolding process induced by urea. Urea 108-112 cytochrome c, somatic Homo sapiens 62-74 23005031-7 2012 In aqueous buffer upon increasing urea concentrations, cyt c underwent unfolding, at [urea] of 9-10 M, which was analyzed under the framework of the equilibrium between two states (native-unfolded). Urea 34-38 cytochrome c, somatic Homo sapiens 55-60 23005031-7 2012 In aqueous buffer upon increasing urea concentrations, cyt c underwent unfolding, at [urea] of 9-10 M, which was analyzed under the framework of the equilibrium between two states (native-unfolded). Urea 86-90 cytochrome c, somatic Homo sapiens 55-60 23005031-8 2012 In the presence of polymers, the native folding of cyt c was preserved at low concentrations of urea (typically <4M). Urea 96-100 cytochrome c, somatic Homo sapiens 51-56 18326641-1 2008 Equilibrium unfolding behaviors of cytochrome c and lysozyme induced by the presence of urea (0-10 M) as well as changes in temperature (295-363 K) or pH (1.8-7) are examined via small-angle x-ray scattering and spectroscopic techniques, including circular dichroism and optical absorption. Urea 88-92 cytochrome c, somatic Homo sapiens 35-47 18326641-3 2008 Results indicate that there are at least four unfolding groups in the temperature-, urea-, or pH-induced unfolding of cytochrome c: two of these are related to the prosthetic heme group, and the other two correspond, respectively, to the unfolding of alpha-helices and global changes in protein morphology that are largely unaccounted for by the first two groups. Urea 84-88 cytochrome c, somatic Homo sapiens 118-130 17718500-2 2007 We have found that a calix[6]areneacetic acid derivative forms a supramolecular complex with urea-denatured cytochrome c at the oil-water interface, which enables quantitative transfer of the protein from an 8 M urea aqueous solution into an organic phase through a proton-exchange mechanism. Urea 93-97 cytochrome c, somatic Homo sapiens 108-120 17718500-2 2007 We have found that a calix[6]areneacetic acid derivative forms a supramolecular complex with urea-denatured cytochrome c at the oil-water interface, which enables quantitative transfer of the protein from an 8 M urea aqueous solution into an organic phase through a proton-exchange mechanism. Urea 212-216 cytochrome c, somatic Homo sapiens 108-120 19756254-3 2008 Cytochrome c is used as a model protein; comparison of conformational stabilities ( DeltaGH2O ) measured via two chemical denaturants, urea and guanidinium hydrochloride, illustrate important concepts in protein folding and intermolecular interactions. Urea 135-139 cytochrome c, somatic Homo sapiens 0-12 18325656-4 2008 We attempted to monitor the value of this parameter upon the unfolding process of cyt c by urea, during which it was increased sigmoidally from about 0.52 to 0.82 eV for native and unfold protein, respectively. Urea 91-95 cytochrome c, somatic Homo sapiens 82-87 17696324-1 2007 The local and global structural changes of cytochrome c induced by urea in aqueous solution have been studied using X-ray absorption spectroscopy (XAS) and small-angle X-ray scattering (SAXS). Urea 67-71 cytochrome c, somatic Homo sapiens 43-55 17696324-5 2007 The SAXS result reveals a significant morphology change of cytochrome c from a globular shape of a radius of gyration R(g) = 12.8 A of the native protein to an elongated ellipsoid shape of R(g) = 29.7 A for the unfolded protein in the presence of concentrated urea. Urea 260-264 cytochrome c, somatic Homo sapiens 59-71 16888736-8 2006 Multilateral cross-testing of "free" CytC in a native-like, glucose-stabilized and urea-destabilized (molten-globule-like) states revealed novel intrinsic links between local/global structural and functional characteristics. Urea 83-87 cytochrome c, somatic Homo sapiens 37-41 15588700-0 2004 The heme iron coordination of unfolded ferric and ferrous cytochrome c in neutral and acidic urea solutions. Urea 93-97 cytochrome c, somatic Homo sapiens 58-70 15588700-2 2004 The heme iron coordination of unfolded ferric and ferrous cytochrome c in the presence of 7-9 M urea at different pH values has been probed by several spectroscopic techniques including magnetic and natural circular dichroism (CD), electrochemistry, UV-visible (UV-vis) absorption and resonance Raman (RR). Urea 96-100 cytochrome c, somatic Homo sapiens 58-70 15588700-3 2004 In 7-9 M urea at neutral pH, ferric cytochrome c is found to be predominantly a low spin bis-His-ligated heme center. Urea 9-13 cytochrome c, somatic Homo sapiens 36-48 15588700-6 2004 In 9 M urea, ferrous cytochrome c is shown to retain its native ligation structure at pH 7. Urea 7-11 cytochrome c, somatic Homo sapiens 21-33 15588700-8 2004 The formal redox potential of the His/H(2)O complex of cytochrome c in 9 M urea at pH 3 was estimated to be -0.13 V, ca. Urea 75-79 cytochrome c, somatic Homo sapiens 55-67 15588700-9 2004 100 mV more positive than E degrees " estimated for the bis-His complex of cytochrome c in urea solution at pH 7. Urea 91-95 cytochrome c, somatic Homo sapiens 75-87 15362102-4 2004 On the experimental side we study the stability of encapsulated cytochrome c against unfolding induced by the presence of denaturants, such as urea. Urea 143-147 cytochrome c, somatic Homo sapiens 64-76 11699911-3 2001 The [urea]1/2 parameter provides an idea of the stability of the protein at a given pH; in the case of cytochrome c, for example, it shows that at and below pH 2 the protein will spontaneously unfold even in the absence of a denaturant. Urea 5-9 cytochrome c, somatic Homo sapiens 103-115