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Author |
Gulotta, M.; Gilmanshin, R.; Buscher, T.C.; Callender, R.H.; Dyer, R.B. |
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Title |
Core formation in apomyoglobin: probing the upper reaches of the folding energy landscape |
Type |
Journal Article |
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Year |
2001 |
Publication |
Biochemistry |
Abbreviated Journal |
Biochemistry |
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Volume |
40 |
Issue ![sorted by Issue field, descending order (down)](img/sort_desc.gif) |
17 |
Pages |
5137-5143 |
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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 |
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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. |
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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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Call Number |
Equine Behaviour @ team @ |
Serial |
3789 |
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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 |
Type |
Journal Article |
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Year |
2006 |
Publication |
Biochemistry |
Abbreviated Journal |
Biochemistry |
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Volume |
45 |
Issue ![sorted by Issue field, descending order (down)](img/sort_desc.gif) |
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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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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0006-2960 |
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PMID:16618100 |
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Call Number |
Equine Behaviour @ team @ |
Serial |
3763 |
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Author |
Ballew, R.M.; Sabelko, J.; Gruebele, M. |
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Title |
Direct observation of fast protein folding: the initial collapse of apomyoglobin |
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Journal Article |
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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. |
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93 |
Issue ![sorted by Issue field, descending order (down)](img/sort_desc.gif) |
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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Call Number |
Equine Behaviour @ team @ |
Serial |
3798 |
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Author |
Hoang, L.; Maity, H.; Krishna, M.M.G.; Lin, Y.; Englander, S.W. |
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Title |
Folding units govern the cytochrome c alkaline transition |
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Journal Article |
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Year |
2003 |
Publication |
Journal of Molecular Biology |
Abbreviated Journal |
J Mol Biol |
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Volume |
331 |
Issue ![sorted by Issue field, descending order (down)](img/sort_desc.gif) |
1 |
Pages |
37-43 |
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Keywords |
Animals; Cytochrome c Group/*chemistry; Horses; Hydrogen/chemistry; Hydrogen-Ion Concentration; Kinetics; Models, Molecular; *Protein Folding; Protein Structure, Tertiary; Spectrum Analysis; Titrimetry |
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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. |
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Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6059, USA. lhoang@mail.upenn.edu |
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0022-2836 |
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PMID:12875834 |
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Equine Behaviour @ team @ |
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3781 |
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Author |
Abbruzzetti, S.; Crema, E.; Masino, L.; Vecli, A.; Viappiani, C.; Small, J.R.; Libertini, L.J.; Small, E.W. |
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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 |
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Year |
2000 |
Publication |
Biophysical Journal |
Abbreviated Journal |
Biophys J |
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78 |
Issue ![sorted by Issue field, descending order (down)](img/sort_desc.gif) |
1 |
Pages |
405-415 |
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Animals; Apoproteins/*chemistry; Horses; *Hydrogen-Ion Concentration; Kinetics; Models, Molecular; Myoglobin/*chemistry; Protein Conformation; *Protein Folding; Protein Structure, Secondary; Spectrometry, Fluorescence |
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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. |
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Dipartimento di Fisica, Universita di Parma, 43100 Parma, Italia |
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0006-3495 |
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PMID:10620304 |
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Equine Behaviour @ team @ |
Serial |
3792 |
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Permanent link to this record |
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Author |
Mizuguchi, M.; Arai, M.; Ke, Y.; Nitta, K.; Kuwajima, K. |
![find record details (via OpenURL) openurl](img/xref.gif)
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Title |
Equilibrium and kinetics of the folding of equine lysozyme studied by circular dichroism spectroscopy |
Type |
Journal Article |
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Year |
1998 |
Publication |
Journal of Molecular Biology |
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283 |
Issue ![sorted by Issue field, descending order (down)](img/sort_desc.gif) |
1 |
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265-277 |
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Keywords |
equine lysozyme; protein folding; molten globule; stopped-flow; folding intermediate |
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The equilibrium unfolding and the kinetics of unfolding and refolding of equine lysozyme, a Ca2+-binding protein, were studied by means of circular dichroism spectra in the far and near-ultraviolet regions. The transition curves of the guanidine hydrochloride-induced unfolding measured at 230 nm and 292.5 nm, and for the apo and holo forms of the protein have shown that the unfolding is well represented by a three-state mechanism in which the molten globule state is populated as a stable intermediate. The molten globule state of this protein is more stable and more native-like than that of α-lactalbumin, a homologous protein of equine lysozyme. The kinetic unfolding and refolding of the protein were induced by concentration jumps of the denaturant and measured by stopped-flow circular dichroism. The observed unfolding and refolding curves both agreed well with a single-exponential function. However, in the kinetic refolding reactions below 3 M guanidine hydrochloride, a burst-phase change in the circular dichroism was present, and the burst-phase intermediate in the kinetic refolding is shown to be identical with the molten globule state observed in the equilibrium unfolding. Under a strongly native condition, virtually all the molecules of equine lysozyme transform the structure from the unfolded state into the molten globule, and the subsequent refolding takes place from the molten globule state. The transition state of folding, which may exist between the molten globule and the native states, was characterized by investigating the guanidine hydrochloride concentration-dependence of the rate constants of refolding and unfolding. More than 80% of the hydrophobic surface of the protein is buried in the transition state, so that it is much closer to the native state than to the molten globule in which only 36% of the surface is buried in the interior of the molecule. It is concluded that all the present results are best explained by a sequential model of protein folding, in which the molten globule state is an obligatory folding intermediate on the pathway of folding. |
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refbase @ user @ |
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3990 |
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