| Records |
| Author |
Chiba, K.; Ikai, A.; Kawamura-Konishi, Y.; Kihara, H. |
| Title |
Kinetic study on myoglobin refolding monitored by five optical probe stopped-flow methods |
Type |
Journal Article |
Year  |
1994 |
Publication |
Proteins |
Abbreviated Journal |
Proteins |
| Volume |
19 |
Issue |
2 |
Pages |
110-119 |
| Keywords |
Animals; Chromatography, Gel; Circular Dichroism; Horses; Kinetics; Metmyoglobin/analogs & derivatives/chemistry; Myoglobin/*chemistry; *Protein Folding; Spectrometry, Fluorescence; Spectrophotometry, Ultraviolet; Urea |
| Abstract |
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. |
| Address |
Laboratory of Biodynamics, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Kanagawa, Japan |
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Thesis |
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Place of Publication |
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Editor |
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| Language |
English |
Summary Language |
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Original Title |
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| Series Editor |
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Series Title |
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Abbreviated Series Title |
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| Series Volume |
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Series Issue |
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Edition |
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| ISSN |
0887-3585 |
ISBN |
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Medium |
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| Area |
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Expedition |
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Conference |
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| Notes |
PMID:8090705 |
Approved |
no |
| Call Number |
Equine Behaviour @ team @ |
Serial |
3799 |
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| Author |
Ballew, R.M.; Sabelko, J.; Gruebele, M. |
| Title |
Direct observation of fast protein folding: the initial collapse of apomyoglobin |
Type |
Journal Article |
| Year |
1996 |
Publication |
Proceedings of the National Academy of Sciences of the United States of America |
Abbreviated Journal |
Proc. Natl. Acad. Sci. U.S.A. |
| Volume |
93 |
Issue |
12 |
Pages |
5759-5764 |
| Keywords |
Animals; Apoproteins/*chemistry; Circular Dichroism; Horses; Kinetics; Muscle, Skeletal/chemistry; Myoglobin/*chemistry; *Protein Folding; Spectrometry, Fluorescence; Spectrophotometry, Infrared; Temperature |
| Abstract |
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. |
| Address |
School of Chemical Sciences and Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, 61801, USA |
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Thesis |
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Place of Publication |
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Editor |
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| Language |
English |
Summary Language |
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Original Title |
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Series Title |
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Abbreviated Series Title |
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| Series Volume |
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Series Issue |
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Edition |
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| ISSN |
0027-8424 |
ISBN |
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Medium |
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| Area |
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Expedition |
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Conference |
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| Notes |
PMID:8650166 |
Approved |
no |
| Call Number |
Equine Behaviour @ team @ |
Serial |
3798 |
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| Author |
Gilmanshin, R.; Callender, R.H.; Dyer, R.B. |
| Title |
The core of apomyoglobin E-form folds at the diffusion limit |
Type |
Journal Article |
| Year |
1998 |
Publication |
Nature Structural Biology |
Abbreviated Journal |
Nat Struct Biol |
| Volume |
5 |
Issue |
5 |
Pages |
363-365 |
| Keywords |
Animals; Apoproteins/*chemistry; Diffusion; Horses; Myoglobin/*chemistry; *Protein Folding; Spectroscopy, Fourier Transform Infrared; Temperature |
| 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. |
| Address |
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Thesis |
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Place of Publication |
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Editor |
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| Language |
English |
Summary Language |
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Original Title |
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| Series Editor |
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Series Title |
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Abbreviated Series Title |
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| Series Volume |
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Series Issue |
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Edition |
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| ISSN |
1072-8368 |
ISBN |
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Medium |
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| Area |
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Expedition |
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Conference |
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| Notes |
PMID:9586997 |
Approved |
no |
| Call Number |
Equine Behaviour @ team @ |
Serial |
3795 |
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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 |
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Thesis |
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Place of Publication |
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Editor |
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| Language |
English |
Summary Language |
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Original Title |
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Series Title |
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Abbreviated Series Title |
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| Series Volume |
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Series Issue |
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Edition |
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| ISSN |
0022-2836 |
ISBN |
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Medium |
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| Area |
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Expedition |
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Conference |
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| Notes |
PMID:10966803 |
Approved |
no |
| Call Number |
Equine Behaviour @ team @ |
Serial |
3790 |
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| Author |
Abbruzzetti, S.; Crema, E.; Masino, L.; Vecli, A.; Viappiani, C.; Small, J.R.; Libertini, L.J.; Small, E.W. |
| Title |
Fast events in protein folding: structural volume changes accompanying the early events in the N-->I transition of apomyoglobin induced by ultrafast pH jump |
Type |
Journal Article |
| Year |
2000 |
Publication |
Biophysical Journal |
Abbreviated Journal |
Biophys J |
| Volume |
78 |
Issue |
1 |
Pages |
405-415 |
| Keywords |
Animals; Apoproteins/*chemistry; Horses; *Hydrogen-Ion Concentration; Kinetics; Models, Molecular; Myoglobin/*chemistry; Protein Conformation; *Protein Folding; Protein Structure, Secondary; Spectrometry, Fluorescence |
| Abstract |
Ultrafast, laser-induced pH jump with time-resolved photoacoustic detection has been used to investigate the early protonation steps leading to the formation of the compact acid intermediate (I) of apomyoglobin (ApoMb). When ApoMb is in its native state (N) at pH 7.0, rapid acidification induced by a laser pulse leads to two parallel protonation processes. One reaction can be attributed to the binding of protons to the imidazole rings of His24 and His119. Reaction with imidazole leads to an unusually large contraction of -82 +/- 3 ml/mol, an enthalpy change of 8 +/- 1 kcal/mol, and an apparent bimolecular rate constant of (0.77 +/- 0.03) x 10(10) M(-1) s(-1). Our experiments evidence a rate-limiting step for this process at high ApoMb concentrations, characterized by a value of (0. 60 +/- 0.07) x 10(6) s(-1). The second protonation reaction at pH 7. 0 can be attributed to neutralization of carboxylate groups and is accompanied by an apparent expansion of 3.4 +/- 0.2 ml/mol, occurring with an apparent bimolecular rate constant of (1.25 +/- 0.02) x 10(11) M(-1) s(-1), and a reaction enthalpy of about 2 kcal/mol. The activation energy for the processes associated with the protonation of His24 and His119 is 16.2 +/- 0.9 kcal/mol, whereas that for the neutralization of carboxylates is 9.2 +/- 0.9 kcal/mol. At pH 4.5 ApoMb is in a partially unfolded state (I) and rapid acidification experiments evidence only the process assigned to carboxylate protonation. The unusually large contraction and the high energetic barrier observed at pH 7.0 for the protonation of the His residues suggests that the formation of the compact acid intermediate involves a rate-limiting step after protonation. |
| Address |
Dipartimento di Fisica, Universita di Parma, 43100 Parma, Italia |
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Thesis |
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Place of Publication |
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Editor |
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| Language |
English |
Summary Language |
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Original Title |
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Series Title |
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Abbreviated Series Title |
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| Series Volume |
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Series Issue |
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Edition |
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| ISSN |
0006-3495 |
ISBN |
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Medium |
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| Area |
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Expedition |
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Conference |
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| Notes |
PMID:10620304 |
Approved |
no |
| Call Number |
Equine Behaviour @ team @ |
Serial |
3792 |
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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 |
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Place of Publication |
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Editor |
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| Language |
English |
Summary Language |
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Original Title |
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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 |
0022-2836 |
ISBN |
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Medium |
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| Area |
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Expedition |
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Conference |
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| Notes |
PMID:10801361 |
Approved |
no |
| Call Number |
refbase @ user @ |
Serial |
3853 |
| Permanent link to this record |
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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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Thesis |
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Place of Publication |
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Editor |
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| Language |
English |
Summary Language |
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Original Title |
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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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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 |
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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Place of Publication |
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Editor |
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English |
Summary Language |
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Original Title |
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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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0006-2960 |
ISBN |
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Medium |
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Expedition |
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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 |
Miksovska, J.; Larsen, R.W. |
| Title |
Photothermal studies of pH induced unfolding of apomyoglobin |
Type |
Journal Article |
| Year |
2003 |
Publication |
Journal of Protein Chemistry |
Abbreviated Journal |
J Protein Chem |
| Volume |
22 |
Issue |
4 |
Pages |
387-394 |
| Keywords |
Acoustics; Animals; Apoproteins/*chemistry/metabolism; Circular Dichroism; Horses; Myocardium/chemistry; Myoglobin/*chemistry/metabolism; Photolysis; Protein Conformation/radiation effects; Protein Denaturation/radiation effects; *Protein Folding; Temperature; Thermodynamics |
| Abstract |
Conformational dynamic and enthalpy changes associated with pH induced unfolding of apomyoglobin were studied using photoacoustic calorimetry and photothermal beam deflection methods. The transition between the native state and the I intermediate was induced by a nanosecond pH jump from o-nitrobenzaldehyde photolysis. Deconvolution of photoacoustic waves indicates two kinetic processes. The fast phase (T < 50 ns) is characterized by a volume expansion of 8.8 ml mol(-1). This process is followed by a volume contraction of about -22 ml mol(-1) (tau approximately 500 ns). Photothermal beam deflection measurements do not reveal any volume changes on the time scale between approximately 100 micros and 5 ms. We associate the volume contraction with structural changes occurring during the transition between the native state and the I intermediate. The lack of any processes on the ms time scale may indicate the absence of structural events involving larger conformational changes of apomyoglobin after the pH jump. |
| Address |
Department of Chemistry, University of South Florida, Tampa, Florida 33620, USA |
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Place of Publication |
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| Language |
English |
Summary Language |
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Original Title |
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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 |
0277-8033 |
ISBN |
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Medium |
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Expedition |
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Conference |
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| Notes |
PMID:13678303 |
Approved |
no |
| Call Number |
Equine Behaviour @ team @ |
Serial |
3780 |
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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 |
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Place of Publication |
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English |
Summary Language |
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Original Title |
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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 |
0022-2836 |
ISBN |
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Medium |
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Expedition |
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Conference |
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| Notes |
PMID:12875834 |
Approved |
no |
| Call Number |
Equine Behaviour @ team @ |
Serial |
3781 |
| Permanent link to this record |
