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Author (up) 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
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 0006-3495 ISBN Medium
Area Expedition Conference
Notes PMID:10620304 Approved no
Call Number Equine Behaviour @ team @ Serial 3792
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Author (up) Abbruzzetti, S.; Viappiani, C.; Sinibaldi, F.; Santucci, R.
Title Kinetics of histidine dissociation from the heme Fe(III) in N-fragment (residues 1-56) of cytochrome c Type Journal Article
Year 2004 Publication The Protein Journal Abbreviated Journal Protein J
Volume 23 Issue 8 Pages 519-527
Keywords Animals; Cytochromes c/*chemistry; Enzyme Activation; Histidine/*chemistry; Horses; Hydrogen-Ion Concentration; Kinetics; Lasers; Ligands; Peptide Mapping; Photolysis; Spectrophotometry
Abstract We have here investigated the dissociation kinetics of the His side chains axially ligated to the heme-iron in the ferric (1-56 residues) N-fragment of horse cyt c. The ligand deligation induced by acidic pH-jump occurs as a biexponential process with different pre-exponential factors, consistent with a structural heterogeneity in solution and the presence of two differently coordinated species. In analogy with GuHCl-denatured cyt c, our data indicate the presence in solution of two ferric forms of the N-fragment characterized by bis-His coordination, as summarized in the following scheme: His18-Fe(III)-His26 <==> His18-Fe(III)-His33. We have found that the pre-exponential factors depend on the extent of the pH-jump. This may be correlated with the different pKa values shown by His26 and His33; due to steric factors, His26 binds to the heme-Fe(III) less strongly than His33, as recently shown by studies on denatured cyt c. Interestingly, the two lifetimes are affected by temperature but not by the extent of the pH-jump. The lower pKa for the deligation reaction required the use of an improved laser pH-jump setup, capable of inducing changes in H+ concentration as large as 1 mM after the end of the laser pulse. For the ferric N-fragment, close activation entropy values have been determined for the two histidines coordinated to the iron; this result significantly differs from that for GuHCl-denatured cyt c, where largely different values of activation entropy were calculated. This underlines the role played by the missing segment (residues 57-104) peptide chain in discriminating deligation of the “nonnative” His from the sixth coordination position of the metal.
Address Dipartimento di Fisica, Universita degli Studi di Parma, Parco Area delle Scienze 7/A 43100 Parma, Italy
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 1572-3887 ISBN Medium
Area Expedition Conference
Notes PMID:15648974 Approved no
Call Number Equine Behaviour @ team @ Serial 3770
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Author (up) Abbruzzetti, S.; Viappiani, C.; Small, J.R.; Libertini, L.J.; Small, E.W.
Title Kinetics of histidine deligation from the heme in GuHCl-unfolded Fe(III) cytochrome C studied by a laser-induced pH-jump technique Type Journal Article
Year 2001 Publication Journal of the American Chemical Society Abbreviated Journal J Am Chem Soc
Volume 123 Issue 27 Pages 6649-6653
Keywords Animals; *Bacterial Proteins; Cytochrome c Group/*chemistry; Guanidine/*chemistry; Heme/*chemistry; Histidine/*chemistry; Horses; Hydrogen-Ion Concentration; Kinetics; *Lasers; Ligands; Protein Folding
Abstract We have developed an instrumental setup that uses transient absorption to monitor protein folding/unfolding processes following a laser-induced, ultrafast release of protons from o-nitrobenzaldehyde. The resulting increase in [H(+)], which can be more than 100 microM, is complete within a few nanoseconds. The increase in [H(+)] lowers the pH of the solution from neutrality to approximately 4 at the highest laser pulse energy used. Protein structural rearrangements can be followed by transient absorption, with kinetic monitoring over a broad time range (approximately 10 ns to 500 ms). Using this pH-jump/transient absorption technique, we have examined the dissociation kinetics of non-native axial heme ligands (either histidine His26 or His33) in GuHCl-unfolded Fe(III) cytochrome c (cyt c). Deligation of the non-native ligands following the acidic pH-jump occurs as a biexponential process with different pre-exponential factors. The pre-exponential factors markedly depend on the extent of the pH-jump, as expected from differences in the pK(a) values of His26 and His33. The two lifetimes were found to depend on temperature but were not functions of either the magnitude of the pH-jump or the pre-pulse pH of the solution. The activation energies of the deligation processes support the suggestion that GuHCl-unfolded cyt c structures with non-native histidine axial ligands represent kinetic traps in unfolding.
Address Dipartimento di Fisica, Universita di Parma, Istituto Nazionale per la Fisica della Materia, 43100 Parma, Italy
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 0002-7863 ISBN Medium
Area Expedition Conference
Notes PMID:11439052 Approved no
Call Number Equine Behaviour @ team @ Serial 3788
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Author (up) 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 Type 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.
Address Dipartimento di Fisica, Universita degli Studi di Parma, Viale G. P. Usberti 7/A, 43100 Parma, Italy
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 0006-2960 ISBN Medium
Area Expedition Conference
Notes PMID:16618100 Approved no
Call Number Equine Behaviour @ team @ Serial 3763
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