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Author |
Uzawa, T.; Akiyama, S.; Kimura, T.; Takahashi, S.; Ishimori, K.; Morishima, I.; Fujisawa, T. |
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Title |
Collapse and search dynamics of apomyoglobin folding revealed by submillisecond observations of alpha-helical content and compactness |
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Journal Article |
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Year |
2004 |
Publication |
Proceedings of the National Academy of Sciences of the United States of America |
Abbreviated Journal |
Proc. Natl. Acad. Sci. U.S.A. |
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Volume |
101 |
Issue |
5 |
Pages |
1171-1176 |
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Keywords |
Animals; Apoproteins/*chemistry; Circular Dichroism; Cytochromes c/chemistry; Horses; Myoglobin/*chemistry; *Protein Folding; *Protein Structure, Secondary; Scattering, Radiation |
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Abstract |
The characterization of protein folding dynamics in terms of secondary and tertiary structures is important in elucidating the features of intraprotein interactions that lead to specific folded structures. Apomyoglobin (apoMb), possessing seven helices termed A-E, G, and H in the native state, has a folding intermediate composed of the A, G, and H helices, whose formation in the submillisecond time domain has not been clearly characterized. In this study, we used a rapid-mixing device combined with circular dichroism and small-angle x-ray scattering to observe the submillisecond folding dynamics of apoMb in terms of helical content (f(H)) and radius of gyration (R(g)), respectively. The folding of apoMb from the acid-unfolded state at pH 2.2 was initiated by a pH jump to 6.0. A significant collapse, corresponding to approximately 50% of the overall change in R(g) from the unfolded to native conformation, was observed within 300 micros after the pH jump. The collapsed intermediate has a f(H) of 33% and a globular shape that involves >80% of all its atoms. Subsequently, a stepwise helix formation was detected, which was interpreted to be associated with a conformational search for the correct tertiary contacts. The characterized folding dynamics of apoMb indicates the importance of the initial collapse event, which is suggested to facilitate the subsequent conformational search and the helix formation leading to the native structure. |
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Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo, Kyoto 615-8510, Japan |
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0027-8424 |
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PMID:14711991 |
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Call Number |
Equine Behaviour @ team @ |
Serial |
3779 |
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Author |
Hirota, S.; Suzuki, M.; Watanabe, Y. |
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Title |
Hydrophobic effect of trityrosine on heme ligand exchange during folding of cytochrome c |
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Journal Article |
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Year |
2004 |
Publication |
Biochemical and Biophysical Research Communications |
Abbreviated Journal |
Biochem Biophys Res Commun |
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Volume |
314 |
Issue |
2 |
Pages |
452-458 |
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Keywords |
Amino Acids/chemistry; Animals; Cytochromes c/*chemistry; Heme/*chemistry; Histidine/chemistry; Horses; Hydrogen-Ion Concentration; Kinetics; Ligands; Myocardium/chemistry; Peptides/chemistry; Protein Folding; Spectrophotometry; Spectrum Analysis, Raman; Tyrosine/*analogs & derivatives/*chemistry |
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Abstract |
Effect of a hydrophobic peptide on folding of oxidized cytochrome c (cyt c) is studied with trityrosine. Folding of cyt c was initiated by pH jump from 2.3 (acid-unfolded) to 4.2 (folded). The Soret band of the 2-ms transient absorption spectrum during folding decreased its intensity and red-shifted from 397 to 400 nm by interaction with trityrosine, whereas tyrosinol caused no significant effect. The change in the transient absorption spectrum by interaction with trityrosine was similar to that obtained with 100 mM imidazole, which showed that the population of the intermediate His/His coordinated species increased during folding of cyt c by interaction with trityrosine. The absorption change was biphasic, the fast phase (82+/-9s(-1)) corresponding to the transition from the His/H(2)O to the His/Met coordinated species, whereas the slow phase (24+/-3s(-1)) from His/His to His/Met. By addition of trityrosine, the relative ratio of the slow phase increased, due to increase of the His/His species at the initial stage of folding. According to the resonance Raman spectra of cyt c, the high-spin 6-coordinate and low-spin 6-coordinate species were dominated at pH 2.3 and 4.2, respectively, and these species were not affected by addition of trityrosine. These results demonstrated that the His/His species increased by interaction with trityrosine at the initial stage of cyt c folding, whereas the heme coordination structure was not affected by trityrosine when the protein was completely unfolded or folded. Hydrophobic peptides thus may be useful to study the effects of hydrophobic interactions on protein folding. |
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Department of Physical Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, 607-8414 Kyoto, Japan. hirota@mb.kyoto-phu.ac.jp |
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0006-291X |
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PMID:14733927 |
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Call Number |
Equine Behaviour @ team @ |
Serial |
3777 |
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Author |
Polverini, E.; Cugini, G.; Annoni, F.; Abbruzzetti, S.; Viappiani, C.; Gensch, T. |
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Title |
Molten globule formation in apomyoglobin monitored by the fluorescent probe Nile Red |
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Journal Article |
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Year |
2006 |
Publication |
Biochemistry |
Abbreviated Journal |
Biochemistry |
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45 |
Issue |
16 |
Pages |
5111-5121 |
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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 |
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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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0006-2960 |
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PMID:16618100 |
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Call Number |
Equine Behaviour @ team @ |
Serial |
3763 |
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Author |
Chiba, K.; Ikai, A.; Kawamura-Konishi, Y.; Kihara, H. |
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Title |
Kinetic study on myoglobin refolding monitored by five optical probe stopped-flow methods |
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Journal Article |
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Year |
1994 |
Publication |
Proteins |
Abbreviated Journal |
Proteins |
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Volume |
19 |
Issue |
2 |
Pages |
110-119 |
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Keywords |
Animals; Chromatography, Gel; Circular Dichroism; Horses; Kinetics; Metmyoglobin/analogs & derivatives/chemistry; Myoglobin/*chemistry; *Protein Folding; Spectrometry, Fluorescence; Spectrophotometry, Ultraviolet; Urea |
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The refolding kinetics of horse cyanometmyoglobin induced by concentration jump of urea was investigated by five optical probe stopped-flow methods: absorption at 422 nm, tryptophyl fluorescence at around 340 nm, circular dichroism (CD) at 222 nm, CD at 260 nm, and CD at 422 nm. In the refolding process, we detected three phases with rate constants of > 1 x 10(2) s-1, (4.5-9.3) s-1, and (2-5) x 10(-3) s-1. In the fastest phase, a substantial amount of secondary structure (approximately 40%) is formed within the dead time of the CD stopped-flow apparatus (10.7 ms). The kinetic intermediate populated in the fastest phase is shown to capture a hemindicyanide, suggesting that a “heme pocket precursor” recognized by hemindicyanide must be constructed within the dead time. In the middle phase, most of secondary and tertiary structures, especially around the captured hemindicyanide, have been constructed. In the slowest phase, we detected a minor structural rearrangement accompanying the ligand-exchange reaction in the fifth coordination of ferric iron. We present a possible model for the refolding process of myoglobin in the presence of the heme group. |
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Laboratory of Biodynamics, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Kanagawa, Japan |
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0887-3585 |
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PMID:8090705 |
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Equine Behaviour @ team @ |
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3799 |
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Author |
Ballew, R.M.; Sabelko, J.; Gruebele, M. |
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Direct observation of fast protein folding: the initial collapse of apomyoglobin |
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Journal Article |
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1996 |
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Proceedings of the National Academy of Sciences of the United States of America |
Abbreviated Journal |
Proc. Natl. Acad. Sci. U.S.A. |
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Volume |
93 |
Issue |
12 |
Pages |
5759-5764 |
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Keywords |
Animals; Apoproteins/*chemistry; Circular Dichroism; Horses; Kinetics; Muscle, Skeletal/chemistry; Myoglobin/*chemistry; *Protein Folding; Spectrometry, Fluorescence; Spectrophotometry, Infrared; Temperature |
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The rapid refolding dynamics of apomyoglobin are followed by a new temperature-jump fluorescence technique on a 15-ns to 0.5-ms time scale in vitro. The apparatus measures the protein-folding history in a single sweep in standard aqueous buffers. The earliest steps during folding to a compact state are observed and are complete in under 20 micros. Experiments on mutants and consideration of steady-state CD and fluorescence spectra indicate that the observed microsecond phase monitors assembly of an A x (H x G) helix subunit. Measurements at different viscosities indicate diffusive behavior even at low viscosities, in agreement with motions of a solvent-exposed protein during the initial collapse. |
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School of Chemical Sciences and Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, 61801, USA |
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0027-8424 |
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PMID:8650166 |
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Equine Behaviour @ team @ |
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3798 |
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Author |
Gilmanshin, R.; Callender, R.H.; Dyer, R.B. |
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The core of apomyoglobin E-form folds at the diffusion limit |
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Journal Article |
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Year |
1998 |
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Nature Structural Biology |
Abbreviated Journal |
Nat Struct Biol |
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Volume |
5 |
Issue |
5 |
Pages |
363-365 |
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Keywords |
Animals; Apoproteins/*chemistry; Diffusion; Horses; Myoglobin/*chemistry; *Protein Folding; Spectroscopy, Fourier Transform Infrared; Temperature |
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Abstract |
The E-form of apomyoglobin has been characterized using infrared and fluorescence spectroscopies, revealing a compact core with native like contacts, most probably consisting of 15-20 residues of the A, G and H helices of apomyoglobin. Fast temperature-jump, time-resolved infrared measurements reveal that the core is formed within 96 micros at 46 degrees C, close to the diffusion limit for loop formation. Remarkably, the folding pathway of the E-form is such that the formation of a limited number of native-like contacts is not rate limiting, or that the contacts form on the same time scale expected for diffusion controlled loop formation. |
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1072-8368 |
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PMID:9586997 |
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Equine Behaviour @ team @ |
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3795 |
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