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| Author |
Andersen, N.H.; Norgaard, A.; Jensen, T.J.; Ulstrup, J. |
| Title |
Sequential unfolding of the two-domain protein Pseudomonas stutzeri cytochrome c4 |
Type |
Journal Article |
| Year |
2002 |
Publication |
Journal of Inorganic Biochemistry |
Abbreviated Journal |
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| Volume |
88 |
Issue |
3-4 |
Pages |
316-327 |
| Keywords |
P. stutzeri cytochrome c4; Sequential unfolding; Di-haem protein; Unfolding |
| Abstract |
P. stutzeri cytochrome c4 is a di-haem protein, composed of two globular domains each with His-Met coordinated haem, and a hydrogen bond network between the domains. The domain foldings are highly symmetric but with specific differences including structural differences of ligand coordination, and different spin states of the oxidised haem groups. We have studied unfolding of oxidised P. stutzeri cyt c4 induced thermally and by chemical denaturants. Horse heart cyt c was a reference molecule. Isothermal unfolding induced by guanidinium chloride and acid was followed by Soret, α/β, and 701-nm band absorption, and by far-UV circular dichroism spectroscopy. Multifarious patterns emerge, but the two domains clearly unfold sequentially. One phase, assigned to unfolding of the N-terminal domain, proceeds at guanidinium concentrations up to [approximate]1.0 M. This is followed by two overlapping phases at higher concentrations. The intermediate state maintains Fe-Met coordination, assigned to the C-terminal domain. Interdomain interaction is reflected in decreasing values of the cooperativity parameters. Differential scanning calorimetry shows a single peak, but two peaks appear when guanidinium chloride up to 0.4 M is present. This reflects different chemical action in chemical and thermal unfolding. Acid-induced unfolding kinetics was addressed by pH jumps using diode array stopped-flow techniques. Three kinetic phases in the 701 nm Fe-Met marker band, and four phases in the Soret and α/β bands, spanning 4-1000 ms could be distinguished on pH jumps from 7.5 to the range 2.5-3.5. In this range of time and pH cyt c appears to unfold in no more than two phases. Spectral properties of the kinetic intermediates could be identified. Sequential domain unfolding, formation of high-spin states, and an intermediate state with Fe-Met coordination to a single haem group are features of the unfolding kinetics. |
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refbase @ user @ |
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3973 |
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Kordal, R.J.; Parsons, S.M. |
| Title |
Liver alcohol dehydrogenase subunit equivalence studied by rapid sampling of alcohol product formed from sequentially bound [4α-3H]NADH |
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Journal Article |
| Year |
1979 |
Publication |
Archives of Biochemistry and Biophysics |
Abbreviated Journal |
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| Volume |
194 |
Issue |
2 |
Pages |
439-448 |
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| Abstract |
Horse liver alcohol dehydrogenase has been claimed to exhibit presteady-state “half-of-the-sites” reactivity with aromatic substrates under some circumstances. To clarify the role of half-of-the-sites reactivity in liver alcohol dehydrogenase the direct sampling of the alcohol product formed immediately after initiation of the reaction was studied using a rapid sampling device and [4α-3H]NADH. Liver alcohol dehydrogenase which contained a very low mole-ratio of [4α-3H]NADH bound to one subunit of the dimer was rapidly mixed with excess 4-(2'-imidazolylazo)benzaldehyde substrate and nonradioactive NADH to initiate the reaction, which was allowed to proceed for a short time before it was quenched. If strong HClO4 quench was used isolation of total free and bound azoalcohol product was possible. If NaOH quench was used isolation only of the azoalcohol product released by the enzyme was possible since most enzyme-bound azoalcohol was reversed back to azoaldehyde by the base. The pH-jump reversal reaction also was characterized spectroscopically by stopped flow technique. Nearly fullsites reactivity was observed for reaction in either direction. Furthermore (4α-3H]NADH bound firstly to one subunit in the dimer reacted essentially identically to NADH bound secondly to the other subunit. Thus, half-of-the-sites reactivity was not observed in these experiments nor did they give any indication of liver alcohol dehydrogenase active site nonequivalence induced by coenzyme binding or reaction. |
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3983 |
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Wood, F.E.; Cusanovich, M.A. |
| Title |
The reaction of Euglena gracilis cytochrome c-552 with nonphysiological oxidants and reductants |
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Journal Article |
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1975 |
Publication |
Archives of Biochemistry and Biophysics |
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| Volume |
168 |
Issue |
2 |
Pages |
333-342 |
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| Abstract |
The reaction of Euglena gracilis cytochrome c-552 (cytochrome f) with the nonphysiological reactants potassium ferrocyanide, potassium ferricyanide, sodium ascorbate, sodium dithionite, and Chromatium vinosum high potential nonheme iron protein was studied by stopped-flow and temperature-jump kinetic methods. The reaction of the purified, water-soluble protein with the reactants was investigated as a function of ionic strength, pH, and temperature. The results demonstrated that reduction and oxidation takes place at a negatively charged site on the cytochrome c-552 surface. Participation of specific amino acid residues in electron transfer is implicated from the pH results. The results obtained for the nonphysiological reactions of cytochrome c-552 are compared with available data for horse heart cytochrome c and Rhodospirillum rubrum cytochrome c2. The results strongly suggest that Euglena gracilis cytochrome c-552 undergoes nonphysiological oxidation and reduction by a mechanism different from that found for cytochrome c or cytochrome c2. |
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3987 |
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Choleris, E.; Kavaliers, M. |
| Title |
Social Learning in Animals: Sex Differences and Neurobiological Analysis |
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Journal Article |
| Year |
1999 |
Publication |
Pharmacology Biochemistry and Behavior |
Abbreviated Journal |
Pharmacol. Biochem. Behav. |
| Volume |
64 |
Issue |
4 |
Pages |
767-776 |
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Observational learning; Social learning; Individual learning; Imitation; Social constraints; Social facilitation; male-female differences; Gender differences |
| Abstract |
Social learning where an “individual's behavior is influenced by observation of, or interaction with, another animal or its products” has been extensively documented in a broad variety of species, including humans. Social learning occurs within the complex framework of an animal's social interactions that are markedly affected by factors such as dominance hierarchies, family bonds, age, and sex of the interacting individuals. Moreover, it is clear that social learning is influenced not only by important sexually dimorphic social constraints but also that it involves attention, motivational, and perceptual mechanisms, all of which exhibit substantial male-female differences. Although sex differences have been demonstrated in a wide range of cognitive and behavioral processes, investigations of male-female differences in social learning and its neurobiological substrates have been largely neglected. As such, sex differences in social learning and its neurobiological substrates merit increased attention. This review briefly considers various aspects of the study of social learning in mammals, and indicates where male-female differences have either been described, neglected and, or could have a potential impact. It also describes the results of neurobiological investigations of social learning and considers the relevance of these findings to other sexually dimorphic cognitive processes. |
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refbase @ user @ |
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575 |
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Bigiani, A.; Mucignat-Caretta, C.; Montani, G.; Tirindelli, R. |
| Title |
Pheromone reception in mammals |
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Journal Article |
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2005 |
Publication |
Reviews of Physiology, Biochemistry and Pharmacology |
Abbreviated Journal |
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| Volume |
154 |
Issue |
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Pages |
1-35 |
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Pheromonal communication is the most convenient way to transfer information regarding gender and social status in animals of the same species with the holistic goal of sustaining reproduction. This type of information exchange is based on pheromones, molecules often chemically unrelated, that are contained in body fluids like urine, sweat, specialized exocrine glands, and mucous secretions of genitals. So profound is the relevance of pheromones over the evolutionary process that a specific peripheral organ devoted to their recognition, namely the vomeronasal organ of Jacobson, and a related central pathway arose in most vertebrate species. Although the vomeronasal system is well developed in reptiles and amphibians, most mammals strongly rely on pheromonal communication. Humans use pheromones too; evidence on the existence of a specialized organ for their detection, however, is very elusive indeed. In the present review, we will focus our attention on the behavioral, physiological, and molecular aspects of pheromone detection in mammals. We will discuss the responses to pheromonal stimulation in different animal species, emphasizing the complicacy of this type of communication. In the light of the most recent results, we will also discuss the complex organization of the transduction molecules that underlie pheromone detection and signal transmission from vomeronasal neurons to the higher centers of the brain. Communication is a primary feature of living organisms, allowing the coordination of different behavioral paradigms among individuals. Communication has evolved through a variety of different strategies, and each species refined its own preferred communication medium. From a phylogenetic point of view, the most widespread and ancient way of communication is through chemical signals named pheromones: it occurs in all taxa, from prokaryotes to eukaryotes. The release of specific pheromones into the environment is a sensitive and definite way to send messages to other members of the same species. Therefore, the action of an organism can alter the behavior of another organism, thereby increasing the fitness of either or both. Albeit slow in transmission and not easily modulated, pheromones can travel around objects in the dark and over long distances. In addition, they are emitted when necessary and their biosynthesis is usually economic. In essence, they represent the most efficient tool to refine the pattern of social behaviors and reproductive strategies. © Springer-Verlag 2005. |
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Università di Parma, Dipartimento di Neuroscienze, Sezione di Fisiologia, Via Volturno 39, 43100 Parma, Italy |
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Equine Behaviour @ team @ |
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4570 |
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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 |
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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. |
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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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0006-2960 |
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PMID:16618100 |
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no |
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Equine Behaviour @ team @ |
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3763 |
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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 |
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Journal Article |
| Year |
2002 |
Publication |
Biochemistry |
Abbreviated Journal |
Biochemistry |
| Volume |
41 |
Issue |
21 |
Pages |
6595-6604 |
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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. |
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School of Mathematical and Physical Sciences, The Graduate University for Advanced Studies, Myodaiji, Okazaki 444-8585, Japan |
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0006-2960 |
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PMID:12022863 |
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no |
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Equine Behaviour @ team @ |
Serial |
3785 |
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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 |
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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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0006-2960 |
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PMID:11318635 |
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no |
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Equine Behaviour @ team @ |
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3789 |
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Ridge, J.A.; Baldwin, R.L.; Labhardt, A.M. |
| Title |
Nature of the fast and slow refolding reactions of iron(III) cytochrome c |
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Journal Article |
| Year |
1981 |
Publication |
Biochemistry |
Abbreviated Journal |
Biochemistry |
| Volume |
20 |
Issue |
6 |
Pages |
1622-1630 |
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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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0006-2960 |
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PMID:6261802 |
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no |
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Equine Behaviour @ team @ |
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3809 |
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Dunn, M.F.; Branlant, G. |
| Title |
Roles of zinc ion and reduced coenzyme in horse liver alcohol dehydrogenase catalysis. The mechanism of aldehyde activation |
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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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0006-2960 |
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PMID:238585 |
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no |
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Equine Behaviour @ team @ |
Serial |
3817 |
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