| Records |
| Author |
Polverini, E.; Cugini, G.; Annoni, F.; Abbruzzetti, S.; Viappiani, C.; Gensch, T. |
| Title |
Molten globule formation in apomyoglobin monitored by the fluorescent probe Nile Red |
Type |
Journal Article |
| Year |
2006 |
Publication |
Biochemistry |
Abbreviated Journal |
Biochemistry |
| Volume |
45 |
Issue |
16 |
Pages |
5111-5121 |
| Keywords |
Animals; Apoproteins/*chemistry/*metabolism; Binding Sites; Computer Simulation; Fluorescent Dyes/analysis; Horses; Hydrogen-Ion Concentration; Models, Molecular; Myoglobin/*chemistry/*metabolism; Oxazines/*analysis/chemistry; Protein Binding; Protein Folding; Protein Structure, Tertiary |
| Abstract |
The interaction of nile red (NR) with apomyoglobin (ApoMb) in the native (pH 7) and molten globule (pH 4) states was investigated using experimental and computational methods. NR binds to hydrophobic locations in ApoMb with higher affinity (K(d) = 25 +/- 5 microM) in the native state than in the molten globule state (K(d) = 52 +/- 5 microM). In the molten globule state, NR is located in a more hydrophobic environment. The dye does not bind to the holoprotein, suggesting that the binding site is located at the heme pocket. In addition to monitoring steady-state properties, the fluorescence emission of NR is capable of tracking submillisecond, time-resolved structural rearrangements of the protein, induced by a nanosecond pH jump. Molecular dynamics simulations were run on ApoMb at neutral pH and at pH 4. The structure obtained for the molten globule state is consistent with the experimentally available structural data. The docking of NR with the crystal structure shows that the ligand binds into the binding pocket of the heme group, with an orientation bringing the planar ring system of NR to overlap with the position of two of the heme porphyrin rings in Mb. The docking of NR with the ApoMb structure at pH 4 shows that the dye binds to the heme pocket with a slightly less favorable binding energy, in keeping with the experimental K(d) value. Under these conditions, NR is positioned in a different orientation, reaching a more hydrophobic environment in agreement with the spectroscopic data. |
| Address |
Dipartimento di Fisica, Universita degli Studi di Parma, Viale G. P. Usberti 7/A, 43100 Parma, Italy |
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English |
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Abbreviated Series Title |
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Edition |
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ISSN  |
0006-2960 |
ISBN |
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Expedition |
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Conference |
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| Notes |
PMID:16618100 |
Approved |
no |
| Call Number |
Equine Behaviour @ team @ |
Serial |
3763 |
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| Author |
Haruta, N.; Kitagawa, T. |
| Title |
Time-resolved UV resonance Raman investigation of protein folding using a rapid mixer: characterization of kinetic folding intermediates of apomyoglobin |
Type |
Journal Article |
| Year |
2002 |
Publication |
Biochemistry |
Abbreviated Journal |
Biochemistry |
| Volume |
41 |
Issue |
21 |
Pages |
6595-6604 |
| Keywords |
Animals; Apoproteins/*chemistry; Circular Dichroism; Holoenzymes/chemistry; Horses; Hydrochloric Acid/chemistry; Hydrogen-Ion Concentration; Imidazoles/chemistry; Kinetics; Models, Molecular; Myoglobin/*chemistry; Peptide Fragments/chemistry; *Protein Folding; Protein Structure, Secondary; Spectrum Analysis, Raman/*methods; Tryptophan/*chemistry; Ultraviolet Rays; Whales |
| Abstract |
The 244-nm excited transient UV resonance Raman spectra are observed for the refolding intermediates of horse apomyoglobin (h-apoMb) with a newly constructed mixed flow cell system, and the results are interpreted on the basis of the spectra observed for the equilibrium acid unfolding of the same protein. The dead time of mixing, which was determined with the appearance of UV Raman bands of imidazolium upon mixing of imidazole with acid, was 150 micros under the flow rate that was adopted. The pH-jump experiments of h-apoMb from pH 2.2 to 5.6 conducted with this device demonstrated the presence of three folding intermediates. On the basis of the analysis of W3 and W7 bands of Trp7 and Trp14, the first intermediate, formed before 250 micros, involved incorporation of Trp14 into the alpha-helix from a random coil. The frequency shift of the W3 band of Trp14 observed for this process was reproduced with a model peptide of the A helix when it forms the alpha-helix. In the second intermediate, formed around 1 ms after the start of refolding, the surroundings of both Trp7 and Trp14 were significantly hydrophobic, suggesting the formation of the hydrophobic core. In the third intermediate appearing around 3 ms, the hydrophobicity was relaxed to the same level as that of the pH 4 equilibrium intermediate, which was investigated in detail with the stationary state technique. The change from the third intermediate to the native state needs more time than 40 ms, while the appearance of the native spectrum after the mixing of the same solutions was confirmed separately. |
| Address |
School of Mathematical and Physical Sciences, The Graduate University for Advanced Studies, Myodaiji, Okazaki 444-8585, Japan |
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English |
Summary Language |
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Abbreviated Series Title |
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Series Issue |
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Edition |
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0006-2960 |
ISBN |
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Conference |
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| Notes |
PMID:12022863 |
Approved |
no |
| Call Number |
Equine Behaviour @ team @ |
Serial |
3785 |
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| Author |
Gulotta, M.; Gilmanshin, R.; Buscher, T.C.; Callender, R.H.; Dyer, R.B. |
| Title |
Core formation in apomyoglobin: probing the upper reaches of the folding energy landscape |
Type |
Journal Article |
| Year |
2001 |
Publication |
Biochemistry |
Abbreviated Journal |
Biochemistry |
| Volume |
40 |
Issue |
17 |
Pages |
5137-5143 |
| Keywords |
Animals; Apoproteins/*chemistry; Computer Simulation; Horses; Hydrogen-Ion Concentration; Kinetics; Models, Molecular; Myoglobin/*chemistry; *Protein Folding; Protein Structure, Secondary; Protein Structure, Tertiary; Spectrometry, Fluorescence/instrumentation/methods; Thermodynamics; Tryptophan/chemistry |
| Abstract |
An acid-destabilized form of apomyoglobin, the so-called E state, consists of a set of heterogeneous structures that are all characterized by a stable hydrophobic core composed of 30-40 residues at the intersection of the A, G, and H helices of the protein, with little other secondary structure and no other tertiary structure. Relaxation kinetics studies were carried out to characterize the dynamics of core melting and formation in this protein. The unfolding and/or refolding response is induced by a laser-induced temperature jump between the folded and unfolded forms of E, and structural changes are monitored using the infrared amide I' absorbance at 1648-1651 cm(-1) that reports on the formation of solvent-protected, native-like helix in the core and by fluorescence emission changes from apomyoglobin's Trp14, a measure of burial of the indole group of this residue. The fluorescence kinetics data are monoexponential with a relaxation time of 14 micros. However, infrared kinetics data are best fit to a biexponential function with relaxation times of 14 and 59 micros. These relaxation times are very fast, close to the limits placed on folding reactions by diffusion. The 14 micros relaxation time is weakly temperature dependent and thus represents a pathway that is energetically downhill. The appearance of this relaxation time in both the fluorescence and infrared measurements indicates that this folding event proceeds by a concomitant formation of compact secondary and tertiary structures. The 59 micros relaxation time is much more strongly temperature dependent and has no fluorescence counterpart, indicating an activated process with a large energy barrier wherein nonspecific hydrophobic interactions between helix A and the G and H helices cause some helix burial but Trp14 remains solvent exposed. These results are best fit by a multiple-pathway kinetic model when U collapses to form the various folded core structures of E. Thus, the results suggest very robust dynamics for core formation involving multiple folding pathways and provide significant insight into the primary processes of protein folding. |
| Address |
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA |
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English |
Summary Language |
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Abbreviated Series Title |
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Series Issue |
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Edition |
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| ISSN |
0006-2960 |
ISBN |
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Expedition |
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Conference |
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| Notes |
PMID:11318635 |
Approved |
no |
| Call Number |
Equine Behaviour @ team @ |
Serial |
3789 |
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| Author |
Ridge, J.A.; Baldwin, R.L.; Labhardt, A.M. |
| Title |
Nature of the fast and slow refolding reactions of iron(III) cytochrome c |
Type |
Journal Article |
| Year |
1981 |
Publication |
Biochemistry |
Abbreviated Journal |
Biochemistry |
| Volume |
20 |
Issue |
6 |
Pages |
1622-1630 |
| Keywords |
Animals; Ascorbic Acid; *Cytochrome c Group; Guanidines; Horses; Kinetics; Oxidation-Reduction; Protein Conformation; Spectrum Analysis |
| Abstract |
The fast and slow refolding reactions of iron(III) cytochrome c (Fe(III) cyt c), previously studied by Ikai et al. (Ikai, A., Fish, W. W., & Tanford, C. (1973) J. Mol. Biol. 73, 165--184), have been reinvestigated. The fast reaction has the major amplitude (78%) and is 100-fold faster than the slow reaction in these conditions (pH 7.2, 25 degrees C, 1.75 M guanidine hydrochloride). We show here that native cyt c is the product formed in the fast reaction as well as in the slow reaction. Two probes have been used to test for formation of native cyt c. absorbance in the 695-nm band and rate of reduction of by L-ascorbate. Different unfolded species (UF, US) give rise to the fast and slow refolding reactions, as shown both by refolding assays at different times after unfolding (“double-jump” experiments) and by the formation of native cyt c in each of the fast and slow refolding reactions. Thus the fast refolding reaction is UF leads to N and the slow refolding reaction is Us leads to N, where N is native cyt c, and there is a US in equilibrium UF equilibrium in unfolded cyt c. The results are consistent with the UF in equilibrium US reaction being proline isomerization, but this has not yet been tested in detail. Folding intermediates have been detected in both reactions. In the UF leads to N reaction, the Soret absorbance change precedes the recovery of the native 695-nm band spectrum, showing that Soret absorbance monitors the formation of a folding intermediate. In the US leads to N reaction an ascorbate-reducible intermediate has been found at an early stage in folding and the Soret absorbance change occurs together with the change at 695 nm as N is formed in the final stage of folding. |
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English |
Summary Language |
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Series Title |
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Abbreviated Series Title |
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Series Issue |
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Edition |
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| ISSN |
0006-2960 |
ISBN |
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Medium |
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Conference |
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| Notes |
PMID:6261802 |
Approved |
no |
| Call Number |
Equine Behaviour @ team @ |
Serial |
3809 |
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| Author |
Dunn, M.F.; Branlant, G. |
| Title |
Roles of zinc ion and reduced coenzyme in horse liver alcohol dehydrogenase catalysis. The mechanism of aldehyde activation |
Type |
Journal Article |
| Year |
1975 |
Publication |
Biochemistry |
Abbreviated Journal |
Biochemistry |
| Volume |
14 |
Issue |
14 |
Pages |
3176-3182 |
| Keywords |
*Alcohol Oxidoreductases/metabolism; Aldehydes/*pharmacology; Animals; Binding Sites; Enzyme Activation/drug effects; Horses; Hydrogen-Ion Concentration; Kinetics; Liver/enzymology; *NAD/analogs & derivatives/pharmacology; Oxidation-Reduction; Protein Binding; Spectrophotometry; Spectrophotometry, Ultraviolet; Temperature; *Zinc/pharmacology |
| Abstract |
1,4,5,6-Tetrahydronicotinamide adenine dinucleotide (H2NADH) has been investigated as a reduced coenzyme analog in the reaction between trans-4-N,N-dimethylaminocinnamaldehyde (I) (lambdamax 398 nm, epsilonmax 3.15 X 10-4 M-minus 1 cm-minus 1) and the horse liver alcohol dehydrogenase-NADH complex. These equilibrium binding and temperature-jump kinetic studies establish the following. (i) Substitution of H2NADH for NADH limits reaction to the reversible formation of a new chromophoric species, lambdamax 468 nm, epsilonmax 5.8 x 10-4 M-minus 1 cm-minus 1. This chromophore is demonstrated to be structurally analogous to the transient intermediate formed during the reaction of I with the enzyme-NADH complex [Dunn, M. F., and Hutchison, J. S. (1973), Biochemistry 12, 4882]. (ii) The process of intermediate formation with the enzyme-NADH complex is independent of pH over the range 6.13-10.54. Although studies were limited to the pH range 5.98-8.72, a similar pH independence appears to hold for the H2NADH system. (iii) Within the ternary complex, I is bound within van der Waal's contact distance of the coenzyme nicotinamide ring. (iv) Formation of the transient intermediate does not involve covalent modification of coenzyme. Based on these findings, we conclude that zinc ion has a Lewis acid function in facilitating the chemical activation of the aldehyde carbonyl for reduction, and that reduced coenzyme plays a noncovalent effector role in this substrate activating step. |
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English |
Summary Language |
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Series Title |
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Abbreviated Series Title |
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Series Issue |
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Edition |
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| ISSN |
0006-2960 |
ISBN |
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Conference |
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| Notes |
PMID:238585 |
Approved |
no |
| Call Number |
Equine Behaviour @ team @ |
Serial |
3817 |
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| Author |
Steinhoff, H.J.; Schrader, J.; Schlitter, J. |
| Title |
Temperature-jump studies and polarized absorption spectroscopy of methemoglobin-thiocyanate single crystals |
Type |
Journal Article |
| Year |
1992 |
Publication |
Biochimica et Biophysica Acta |
Abbreviated Journal |
Biochim Biophys Acta |
| Volume |
1121 |
Issue |
3 |
Pages |
269-278 |
| Keywords |
Animals; Crystallization; Horses; Kinetics; Methemoglobin/*chemistry; Solutions; Spectrum Analysis; Temperature; Thiocyanates/*chemistry |
| Abstract |
Association equilibria and association kinetics of the thiocyanate binding reaction to methemoglobin in single crystals and solution are studied using temperature-jump technique and polarized absorption spectroscopy. Different kinetic constants are found for the reaction in solution and crystal phase for the alpha- and beta-subunits of the methemoglobin tetramer. The reduction of the reactivity of the alpha- and beta-subunits in crystalline phase is 6-fold and 2.4-fold, respectively, compared to the values found in solution. The intramolecular binding reaction of the N epsilon of the distal histidine E7 which is observed in methemoglobin in solution cannot be detected in single crystals. Our results suggest that crystallization of hemoglobin has little influence on small-scale structural fluctuations which are necessary for ligands to get to the binding sites and large-scale structural motions are suppressed. |
| Address |
Institut fur Biophysik, Ruhr-Universitat Bochum, Germany |
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English |
Summary Language |
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Abbreviated Series Title |
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Series Issue |
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Edition |
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| ISSN |
0006-3002 |
ISBN |
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| Notes |
PMID:1627604 |
Approved |
no |
| Call Number |
Equine Behaviour @ team @ |
Serial |
3800 |
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| Author |
Steinhoff, H.J.; Lieutenant, K.; Redhardt, A. |
| Title |
Conformational transition of aquomethemoglobin: intramolecular histidine E7 binding reaction to the heme iron in the temperature range between 220 K and 295 K as seen by EPR and temperature-jump measurements |
Type |
Journal Article |
| Year |
1989 |
Publication |
Biochimica et Biophysica Acta |
Abbreviated Journal |
Biochim Biophys Acta |
| Volume |
996 |
Issue |
1-2 |
Pages |
49-56 |
| Keywords |
Animals; Electron Spin Resonance Spectroscopy; Heme; Histidine; Horses; Humans; Hydrogen-Ion Concentration; Methemoglobin/*ultrastructure; Motion; Protein Conformation; Temperature; Thermodynamics; Water |
| Abstract |
Temperature-dependent EPR and temperature-jump measurements have been carried out, in order to examine the high-spin to low-spin transition of aquomethemogobin (pH 6.0). Relaxation rates and equilibrium constants could be determined as a function of temperature. As a reaction mechanism for the high-spin to low-spin transition, the binding of N epsilon of His E7 to the heme iron had been proposed; the same mechanism had been suggested for the ms-effect, found in temperature-jump experiments on aquomethemoglobin. A comparison of the thermodynamic quantities, deduced form the measurements in this paper, gives evidence that indeed the same reaction is investigated in both cases. Our results and most of the findings of earlier studies on the spin-state transitions of aquomethemoglobin, using susceptibility, optical, or EPR measurements, can be explained by the transition of methemoglobin with H2O as ligand (with high-spin state at all temperatures) and methemoglobin with ligand N epsilon of His E7 (with a low-spin ground state). Thermal fluctuations of large amplitude have to be postulated for the reaction to take place, so this reaction may be understood as a probe for the study of protein dynamics. |
| Address |
Institut fur Biophysik, Ruhr-Universitat Bochum, F.R.G |
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English |
Summary Language |
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Series Title |
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Abbreviated Series Title |
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Series Issue |
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Edition |
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0006-3002 |
ISBN |
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Expedition |
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Conference |
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| Notes |
PMID:2544230 |
Approved |
no |
| Call Number |
Equine Behaviour @ team @ |
Serial |
3803 |
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| Author |
Kihara, H.; Nakatani, H.; Hiromi, K.; Hon-Nami, K. |
| Title |
Kinetic studies on redox reactions of hemoproteins. I. Reduction of thermoresistant cytochrome c-552 and horse heart cytochrome c by ferrocyanide |
Type |
Journal Article |
| Year |
1977 |
Publication |
Biochimica et Biophysica Acta |
Abbreviated Journal |
Biochim Biophys Acta |
| Volume |
460 |
Issue |
3 |
Pages |
480-489 |
| Keywords |
Animals; Bacteria; *Cytochrome c Group; *Ferrocyanides; Horses; Kinetics; Mathematics; Oxidation-Reduction; Spectrophotometry; Spectrophotometry, Ultraviolet; Temperature; Thermodynamics |
| Abstract |
The oxidation-reduction reaction of horse heart cytochrome c and cytochrome c (552, Thermus thermophilus), which is highly thermoresistant, was studied by temperature-jump method. Ferrohexacyanide was used as reductant. (Formula: see text.) Thermodynamic and activation parameters of the reaction obtained for both cytochromes were compared with each other. The results of this showed that (1) the redox potential of cytochrome c-552, + 0.19 V, is markedly less than that of horse heart cytochrome c. (2) deltaHox of cytochrome c-552 is considerably lower than that of horse heart cytochrome c. (3) deltaSox and deltaSred of cytochrome c-552 are more negative than those of horse heart cytochrome c. (4) kred of cytochrome c-552 is much lower than that of horse heart cytochrome c at room temperature. |
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English |
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Abbreviated Series Title |
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Edition |
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0006-3002 |
ISBN |
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Conference |
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| Notes |
PMID:195599 |
Approved |
no |
| Call Number |
Equine Behaviour @ team @ |
Serial |
3815 |
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| Author |
Saigo, S. |
| Title |
Kinetic and equilibrium studies of alkaline isomerization of vertebrate cytochromes c |
Type |
Journal Article |
| Year |
1981 |
Publication |
Biochimica et Biophysica Acta |
Abbreviated Journal |
Biochim Biophys Acta |
| Volume |
669 |
Issue |
1 |
Pages |
13-20 |
| Keywords |
Amino Acid Sequence; Animals; Cytochrome c Group/*metabolism; Dogs; Hydrogen-Ion Concentration; Isomerism; Kinetics; Vertebrates/metabolism |
| Abstract |
Equilibria and kinetics of alkaline isomerization of seven ferricytochromes c from vertebrates were studied by pH-titration and pH-jump methods in the pH region of 7-12. In the equilibrium behavior, no significant difference was detected among the cytochromes c, whereas marked differences in the kinetic behavior were observed. According to the kinetic behavior of the isomerization, the cytochromes c examined fall into three classes: Group I (horse, sheep, dog and pigeon cytochromes c), Group II (tuna and bonito cytochromes c) and Group III (rhesus monkey cytochrome c). The kinetic results are interpreted in terms of the sequential scheme: Neutral form in equilibrium with fast Transient form in equilibrium with slow Alkaline form where the neutral and alkaline forms are the species stable at neutral and alkaline pH, respectively, and the transient form is a kinetic intermediate. From comparison of the primary sequences of the seven cytochromes c and the classification of these cytochromes c, it is concluded that the amino acid substitution Phe/Tyr at the 46-th position has a major influence on the kinetic behavior. In Group II and III cytochromes c, the ionization of Tyr-46 is suggested to bring about loosening of the heme crevice and thus facilitate the ligand replacement involved in the isomerization. |
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English |
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Abbreviated Series Title |
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Edition |
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0006-3002 |
ISBN |
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Conference |
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| Notes |
PMID:6271238 |
Approved |
no |
| Call Number |
refbase @ user @ |
Serial |
3871 |
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| Author |
Morton, D.B. |
| Title |
Self-consciousness and animal suffering |
Type |
Journal Article |
| Year |
2000 |
Publication |
Biologist (London, England) |
Abbreviated Journal |
Biologist (London) |
| Volume |
47 |
Issue |
2 |
Pages |
77-80 |
| Keywords |
Animal Population Groups/*psychology; Animal Welfare/*standards; Animals; Behavior, Animal; *Consciousness; Dogs; *Ego; Horses/psychology; Pain/psychology/*veterinary; Pan troglodytes/psychology; Parrots; Pongo pygmaeus/psychology; Self Concept |
| Abstract |
Animals with relatively highly developed brains are likely to experience some degree of self-awareness and the ability to think. As well as being interesting in its own right, self-consciousness matters from an ethical point of view, since it can give rise to forms of suffering above and beyond the immediate physical sensations of pain or distress. This article surveys the evidence for animal self-consciousness and its implications for animal welfare. |
| Address |
Division of Primary Care, Public and Occupational Health, School of Medicine, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK. d.b.morton@bham.ac.uk |
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English |
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Series Issue |
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Edition |
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0006-3347 |
ISBN |
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Expedition |
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Conference |
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| Notes |
PMID:11190233 |
Approved |
no |
| Call Number |
refbase @ user @ |
Serial |
618 |
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