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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.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language	English	Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0006-3002	ISBN		Medium
	Area		Expedition		Conference
	Notes	PMID:6271238			Approved	no
	Call Number	refbase @ user @			Serial	3871
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	Author	Hasumi, H.
	Title	Kinetic studies on isomerization of ferricytochrome c in alkaline and acid pH ranges by the circular dichroism stopped-flow method			Type	Journal Article
	Year	1980	Publication	Biochimica et Biophysica Acta	Abbreviated Journal	Biochim Biophys Acta
	Volume	626	Issue	2	Pages	265-276
	Keywords	Circular Dichroism; *Cytochrome c Group; Hydrogen-Ion Concentration; Isomerism; Kinetics; Spectrophotometry
	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.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language	English	Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0006-3002	ISBN		Medium
	Area		Expedition		Conference
	Notes	PMID:6260152			Approved	no
	Call Number	refbase @ user @			Serial	3876
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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.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language	English	Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0006-3002	ISBN		Medium
	Area		Expedition		Conference
	Notes	PMID:195599			Approved	no
	Call Number	Equine Behaviour @ team @			Serial	3815
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	Author	Paz-y-Miño C. G.; Bond, A.B.; Kamil, A.C.; Balda, R.P.
	Title	Pinyon jays use transitive inference to predict social dominance			Type	Journal Article
	Year	2004	Publication	Nature	Abbreviated Journal	Nature
	Volume	430	Issue	7001	Pages	778-781
	Keywords	Animals; Cognition/physiology; Group Structure; Male; Social Dominance; Songbirds/*physiology
	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.
	Address	Center for Avian Cognition, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, USA
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language	English	Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1476-4687	ISBN		Medium
	Area		Expedition		Conference
	Notes	PMID:15306809			Approved	no
	Call Number	refbase @ user @; Equine Behaviour @ team @ room B 3.029			Serial	352
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	Author	Shettleworth, S.J.
	Title	Cognitive science: rank inferred by reason			Type	Journal Article
	Year	2004	Publication	Nature	Abbreviated Journal	Nature
	Volume	430	Issue	7001	Pages	732-733
	Keywords	Animals; Cognition/physiology; Group Structure; Male; Social Dominance; Songbirds/*physiology
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language	English	Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1476-4687	ISBN		Medium
	Area		Expedition		Conference
	Notes	PMID:15306792			Approved	no
	Call Number	refbase @ user @			Serial	365
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	Author	Conradt, L.; Roper, T.J.
	Title	Group decision-making in animals			Type	Journal Article
	Year	2003	Publication	Nature	Abbreviated Journal	Nature
	Volume	421	Issue	6919	Pages	155-158
	Keywords	Animals; Behavior, Animal/physiology; Decision Making; Democracy; Group Processes; *Models, Biological; Population Density; Social Behavior
	Abstract	Groups of animals often need to make communal decisions, for example about which activities to perform, when to perform them and which direction to travel in; however, little is known about how they do so. Here, we model the fitness consequences of two possible decision-making mechanisms: 'despotism' and 'democracy'. We show that under most conditions, the costs to subordinate group members, and to the group as a whole, are considerably higher for despotic than for democratic decisions. Even when the despot is the most experienced group member, it only pays other members to accept its decision when group size is small and the difference in information is large. Democratic decisions are more beneficial primarily because they tend to produce less extreme decisions, rather than because each individual has an influence on the decision per se. Our model suggests that democracy should be widespread and makes quantitative, testable predictions about group decision-making in non-humans.
	Address	School of Biological Sciences, University of Sussex, Brighton BN1 9QG, UK. l.conradt@sussex.ac.uk
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language	English	Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0028-0836	ISBN		Medium
	Area		Expedition		Conference
	Notes	PMID:12520299			Approved	no
	Call Number	Equine Behaviour @ team @			Serial	5136
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	Author	Dyer, J.R.G.; Johansson, A.; Helbing, D.; Couzin, I.D.; Krause, J.
	Title	Leadership, consensus decision making and collective behaviour in humans			Type	Journal Article
	Year	2009	Publication	Philosophical Transactions of the Royal Society B: Biological Sciences	Abbreviated Journal	Phil. Trans. Biol. Sci.
	Volume	364	Issue	1518	Pages	781-789
	Keywords	* leadership * consensus decision making * collective behaviour * human group
	Abstract	This paper reviews the literature on leadership in vertebrate groups, including recent work on human groups, before presenting the results of three new experiments looking at leadership and decision making in small and large human groups. In experiment 1, we find that both group size and the presence of uninformed individuals can affect the speed with which small human groups (eight people) decide between two opposing directional preferences and the likelihood of the group splitting. In experiment 2, we show that the spatial positioning of informed individuals within small human groups (10 people) can affect the speed and accuracy of group motion. We find that having a mixture of leaders positioned in the centre and on the edge of a group increases the speed and accuracy with which the group reaches their target. In experiment 3, we use large human crowds (100 and 200 people) to demonstrate that the trends observed from earlier work using small human groups can be applied to larger crowds. We find that only a small minority of informed individuals is needed to guide a large uninformed group. These studies build upon important theoretical and empirical work on leadership and decision making in animal groups.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	no
	Call Number	Equine Behaviour @ team @			Serial	5122
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	Author	Hoang, L.; Maity, H.; Krishna, M.M.G.; Lin, Y.; Englander, S.W.
	Title	Folding units govern the cytochrome c alkaline transition			Type	Journal Article
	Year	2003	Publication	Journal of Molecular Biology	Abbreviated Journal	J Mol Biol
	Volume	331	Issue	1	Pages	37-43
	Keywords	Animals; Cytochrome c Group/chemistry; Horses; Hydrogen/chemistry; Hydrogen-Ion Concentration; Kinetics; Models, Molecular; Protein Folding; Protein Structure, Tertiary; Spectrum Analysis; Titrimetry
	Abstract	The alkaline transition of cytochrome c is a model for protein structural switching in which the normal heme ligand is replaced by another group. Stopped flow data following a jump to high pH detect two slow kinetic phases, suggesting two rate-limiting structure changes. Results described here indicate that these events are controlled by the same structural unfolding reactions that account for the first two steps in the reversible unfolding pathway of cytochrome c. These and other results show that the cooperative folding-unfolding behavior of protein foldons can account for a variety of functional activities in addition to determining folding pathways.
	Address	Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6059, USA. lhoang@mail.upenn.edu
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language	English	Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-2836	ISBN		Medium
	Area		Expedition		Conference
	Notes	PMID:12875834			Approved	no
	Call Number	Equine Behaviour @ team @			Serial	3781
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	Author	Hagen, S.J.; Eaton, W.A.
	Title	Two-state expansion and collapse of a polypeptide			Type	Journal Article
	Year	2000	Publication	Journal of Molecular Biology	Abbreviated Journal	J Mol Biol
	Volume	301	Issue	4	Pages	1019-1027
	Keywords	Animals; Computer Simulation; Cytochrome c Group/chemistry/metabolism; Horses; Kinetics; Lasers; Models, Chemical; Peptides/chemistry/metabolism; Protein Conformation; Protein Denaturation; *Protein Folding; Spectrometry, Fluorescence; Temperature; Thermodynamics
	Abstract	The initial phase of folding for many proteins is presumed to be the collapse of the polypeptide chain from expanded to compact, but still denatured, conformations. Theory and simulations suggest that this collapse may be a two-state transition, characterized by barrier-crossing kinetics, while the collapse of homopolymers is continuous and multi-phasic. We have used a laser temperature-jump with fluorescence spectroscopy to measure the complete time-course of the collapse of denatured cytochrome c with nanosecond time resolution. We find the process to be exponential in time and thermally activated, with an apparent activation energy approximately 9 k(B)T (after correction for solvent viscosity). These results indicate that polypeptide collapse is kinetically a two-state transition. Because of the observed free energy barrier, the time scale of polypeptide collapse is dramatically slower than is predicted by Langevin models for homopolymer collapse.
	Address	Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Building 5, Bethesda, MD, 20892-0520, USA
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language	English	Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-2836	ISBN		Medium
	Area		Expedition		Conference
	Notes	PMID:10966803			Approved	no
	Call Number	Equine Behaviour @ team @			Serial	3790
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	Author	Pierce, M.M.; Nall, B.T.
	Title	Coupled kinetic traps in cytochrome c folding: His-heme misligation and proline isomerization			Type	Journal Article
	Year	2000	Publication	Journal of Molecular Biology	Abbreviated Journal	J Mol Biol
	Volume	298	Issue	5	Pages	955-969
	Keywords	Amino Acid Sequence; Amino Acid Substitution/genetics; Binding Sites; Cytochrome c Group/chemistry/genetics/metabolism; Cytochromes c; Enzyme Stability/drug effects; Fluorescence; Guanidine/pharmacology; Heme/metabolism; Histidine/genetics/metabolism; Hydrogen-Ion Concentration; Isomerism; Kinetics; Models, Molecular; Molecular Sequence Data; Mutation/genetics; Proline/chemistry/metabolism; Protein Conformation/drug effects; Protein Denaturation/drug effects; *Protein Folding; Protein Renaturation; Saccharomyces cerevisiae/enzymology/genetics; Sequence Alignment; Thermodynamics
	Abstract	The effect of His-heme misligation on folding has been investigated for a triple mutant of yeast iso-2 cytochrome c (N26H,H33N,H39K iso-2). The variant contains a single misligating His residue at position 26, a location at which His residues are found in several cytochrome c homologues, including horse, tuna, and yeast iso-1. The amplitude for fast phase folding exhibits a strong initial pH dependence. For GdnHCl unfolded protein at an initial pH<5, the observed refolding at final pH 6 is dominated by a fast phase (tau(2f)=20 ms, alpha(2f)=90 %) that represents folding in the absence of misligation. For unfolded protein at initial pH 6, folding at final pH 6 occurs in a fast phase of reduced amplitude (alpha(2f) approximately 20 %) but the same rate (tau(2f)=20 ms), and in two slower phases (tau(m)=6-8 seconds, alpha(m) approximately 45 %; and tau(1b)=16-20 seconds, alpha(1b) approximately 35 %). Double jump experiments show that the initial pH dependence of the folding amplitudes results from a slow pH-dependent equilibrium between fast and slow folding species present in the unfolded protein. The slow equilibrium arises from coupling of the His protonation equilibrium to His-heme misligation and proline isomerization. Specifically, Pro25 is predominantly in trans in the unligated low-pH unfolded protein, but is constrained in a non-native cis isomerization state by His26-heme misligation near neutral pH. Refolding from the misligated unfolded form proceeds slowly due to the large energetic barrier required for proline isomerization and displacement of the misligated His26-heme ligand.
	Address	Center for Biomolecular Structure, Department of Biochemistry, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language	English	Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-2836	ISBN		Medium
	Area		Expedition		Conference
	Notes	PMID:10801361			Approved	no
	Call Number	refbase @ user @			Serial	3853
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