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Saigo, S. (1981). Kinetic and equilibrium studies of alkaline isomerization of vertebrate cytochromes c. Biochim Biophys Acta, 669(1), 13–20.
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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Hasumi, H. (1980). Kinetic studies on isomerization of ferricytochrome c in alkaline and acid pH ranges by the circular dichroism stopped-flow method. Biochim Biophys Acta, 626(2), 265–276.
Abstract: The isomerization of horse-heart ferricytochrome c caused by varying pH was kinetically studied by using circular dichroism (CD) and optical absorption stopped-flow techniques. In the pH range of 7--13, the existence of the three different forms of ferricytochrome c (pH less than 10, pH 10--12, and pH greater than 12) was indicated from the statistical difference CD spectra. On the basis of analyses of the stopped-flow traces in the near-ultraviolet and Soret wavelength regions, the isomerization of ferricytochrome c from neutral form to the above three alkaline forms was interpreted as follows (1) below pH 10, the replacement of the intrinsic ligand of methionine residue by lysine residue occurs; (2) between pH 10 and 12, the uncoupling of the polypeptide chain from close proximity of the heme group occurs first, followed by the interconversion of the intrinsic ligands; and (3) above pH 12, hydroxide form of ferricytochrome c is formed, though the replacement of the intrinsic ligand by extrinsic ligands may occur via different routes from those below pH 12. The CD changes at 288 nm and in the Soret region caused by the pH-jump (down) from pH 6.0 to 1.6 were compared with the appearance of the 620-nm absorption band ascribed to the formation of the high-spin form of ferricytochrome c. Both CD and absorption changes indicated that the isomerization at pH 1.6 consisted of two processes: one proceeded within the dead-time (about 2 ms) of the stopped-flow apparatus and the other proceeded at a determinable rate with the apparatus. On the basis of these results, the isomerization of ferricytochrome c at pH 1.6 was explained as follows: (1) the transition from the low-spin form to the high-spin forms occurs within about 2 ms, the dead-time of the stopped-flow apparatus; and (2) the polypeptide chain is unfolded after the formation of the high-spin form.
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Wilson, M. T., Silvestrini, M. C., Morpurgo, L., & Brunori, M. (1979). Electron transfer kinetics between Rhus vernicifera stellacyanin and cytochrome c (horse heart cytochrome c and Pseudomonas cytochrome c551). J Inorg Biochem, 11(2), 95–100.
Abstract: The electron transfer reactions between Rhus vernicifera stellacyanin and either horse heart cytochrome c or Pseudomonas aeruginosa cytochrome c551 were investigated by rapid reaction techniques. The time course of electron transfer is monophasic under all conditions, and thus consistent with a simple formulation of the reaction. Both stopped-flow and temperature-jump experiments yield equilibrium constants in reasonable agreement with values calculated from the redox potentials. The differences in reaction rate between the two cytochromes and stellacyanin are discussed in terms of the Marcus theory.
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Tsong, T. Y. (1977). Conformational relaxations of urea- and guanidine hydrochloride-unfolded ferricytochrome c. J Biol Chem, 252(24), 8778–8780.
Abstract: Several recent studies of protein the unfolded proteins. In urea- and guanidine HCl-unfolded ferricytochrome c (horse heart), an acid-induced spin state transformation of the heme group has been detected by the heme absorptions, Trp-59 fluorescence, and the intrinsic viscosity of protein. Kinetics of this second conformational transition, by the temperature jump and stopped flow methods, are complex. One rapid reaction (tau1), pH-independent, occurs in a 50-mus range; the second reaction (tau2), in a 1-ms range, depends linearly upon pH and is faster at the alkaline side; a third reaction (tau3), in a 1-s range, shows a sigmoidal transition at pH 5.1 and is faster at the acidic side. The results are consistent with a kinetic scheme which involves protein conformational changes in the transformation of the heme coordination state. The kinetics, along with previous equilibrium studies, indicate that ligand or charge interactions within a protein molecule are not completely prohibited even in strongly denaturing conditions, such as in high concentrations of urea and guanidine HCl. Thus, local structures of peptide chain associated with these interactions can exist in the unfolded protein.
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Paz-y-Miño C. G., Bond, A. B., Kamil, A. C., & Balda, R. P. (2004). Pinyon jays use transitive inference to predict social dominance. Nature, 430(7001), 778–781.
Abstract: Living in large, stable social groups is often considered to favour the evolution of enhanced cognitive abilities, such as recognizing group members, tracking their social status and inferring relationships among them. An individual's place in the social order can be learned through direct interactions with others, but conflicts can be time-consuming and even injurious. Because the number of possible pairwise interactions increases rapidly with group size, members of large social groups will benefit if they can make judgments about relationships on the basis of indirect evidence. Transitive reasoning should therefore be particularly important for social individuals, allowing assessment of relationships from observations of interactions among others. Although a variety of studies have suggested that transitive inference may be used in social settings, the phenomenon has not been demonstrated under controlled conditions in animals. Here we show that highly social pinyon jays (Gymnorhinus cyanocephalus) draw sophisticated inferences about their own dominance status relative to that of strangers that they have observed interacting with known individuals. These results directly demonstrate that animals use transitive inference in social settings and imply that such cognitive capabilities are widespread among social species.
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