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Li J, Li H. New insights into the folding–unfolding mechanism and conformations of cytochrome C. Chem Sci 2022; 13:7498-7508. [PMID: 35872809 PMCID: PMC9241957 DOI: 10.1039/d2sc01126c] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/29/2022] [Indexed: 11/21/2022] Open
Abstract
Optical trapping experiments offer new insights into the folding and unfolding of cytochrome C.
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Affiliation(s)
- Jiayu Li
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
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2
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Naidu KT, Rao DK, Prabhu NP. Cryo vs Thermo: Duality of Ethylene Glycol on the Stability of Proteins. J Phys Chem B 2020; 124:10077-10088. [PMID: 33143422 DOI: 10.1021/acs.jpcb.0c06247] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Osmolytes are known to stabilize proteins under stress conditions. Thermal denaturation studies on globular proteins (β-lactoglobulin, cytochrome c, myoglobin, α-chymotrypsin) in the presence of ethylene glycol (EG), a polyol class of osmolyte, demonstrate a unique property of EG. EG stabilizes proteins against cold denaturation and destabilizes them during heat-induced denaturation. Further, chemical denaturation experiments performed at room temperature and at a sub-zero temperature (-10 °C) show that EG stabilizes the proteins at subzero temperature but destabilizes them at room temperature. The experiments carried out in the presence of glycerol, however, showed that glycerol stabilizes proteins against all of the denaturing conditions. This differential effect has not been reported for any other polyol class of osmolyte and might be specific to EG. Moreover, molecular dynamics simulations of all of the four proteins were carried out at three different temperatures, 240, 300, and 340 K, in the absence and presence of EG (20 and 40%). The results suggest that EG preferably accumulates around the hydrophobic residues and reduces the hydrophobic hydration of the proteins at a low temperature leading to stabilization of the proteins. At 340 K, the preferential hydration of the proteins is significantly reduced and the preferential binding of EG destabilizes the proteins like common denaturants.
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Affiliation(s)
- K Tejaswi Naidu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - D Krishna Rao
- Tata Institute of Fundamental Research (TIFR) Centre for Interdisciplinary Sciences, Hyderabad 500107, India
| | - N Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
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3
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Osawa K, Kossowska D, Park K, Kwak K, Cho M. Two-dimensional infrared spectroscopic study of cytochrome c peroxidase activity in deep eutectic solvent. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:064703. [PMID: 31867407 PMCID: PMC6920052 DOI: 10.1063/1.5130940] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
Deep eutectic solvents (DESs) prepared by mixing hydrogen-bond donor and acceptor molecules have been found to be of use in several applications. Recently, it was shown that DESs can enhance the peroxidation activity of cytochrome c. Here, to elucidate the effects of DESs on the peroxidase activity of cytochrome c, we carried out linear and nonlinear infrared spectroscopic studies of the CO stretch mode of carbon monoxide cytochrome c (COCytc) in ethylammonium chloride (EAC)/urea DES. The FTIR spectrum of COCytc shows a significant spectral shift upon addition of the DES. The broadening and red-shifting of the CO band are observed in both urea and DES solutions, which are induced by the change of the distal ligands around the heme. Although the FTIR study is sensitive to structural changes in the active site, it does not provide quantitative information about structural dynamics related to the catalytic activity itself. Thus, we carried out two-dimensional IR spectroscopy of the CO mode, which suggests that there is a different conformer that could be related to the enhanced catalytic activity in DES. In particular, the spectral diffusion dynamics of that conformer exhibits quite different behavior. The experimental results lead us to propose a hypothesis that the DES increases the population of the conformer with distal ligand lysines close to the reaction center through the combining effect of urea and EAC, which results in the enhancement of the peroxidase activity of cytochrome c. We anticipate that the present experimental work stimulates future investigations of the effects of DES on biocatalysis.
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Affiliation(s)
- Koji Osawa
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
| | | | - Kwanghee Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
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4
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Kumar R, Kumar R, Sharma D, Garg M, Kumar V, Agarwal MC. Macromolecular crowding-induced molten globule states of the alkali pH-denatured proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1102-1114. [DOI: 10.1016/j.bbapap.2018.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/07/2018] [Accepted: 08/30/2018] [Indexed: 11/26/2022]
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5
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Kumar R. Analysis of the pH-dependent thermodynamic stability, local motions, and microsecond folding kinetics of carbonmonoxycytochrome c. Arch Biochem Biophys 2016; 606:16-25. [DOI: 10.1016/j.abb.2016.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 06/11/2016] [Accepted: 07/13/2016] [Indexed: 10/21/2022]
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6
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Jain R, Kumar R, Kumar S, Chhabra R, Agarwal MC, Kumar R. Analysis of the pH-dependent stability and millisecond folding kinetics of horse cytochrome c. Arch Biochem Biophys 2015; 585:52-63. [DOI: 10.1016/j.abb.2015.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 11/26/2022]
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7
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Kubo T, Arimura S, Tominaga Y, Naito T, Hosoya K, Otsuka K. Molecularly Imprinted Polymers for Selective Adsorption of Lysozyme and Cytochrome c Using a PEG-Based Hydrogel: Selective Recognition for Different Conformations Due to pH Conditions. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b00834] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Takuya Kubo
- Graduate
School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Shunsuke Arimura
- Graduate
School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yuichi Tominaga
- Structural
Materials Research Institute, National Institute of Advanced Industrial Science and Technology, 2266-98 Anagahora, Shimoshidami, Moriyama-ku, Nagoya 463-8560, Japan
| | - Toyohiro Naito
- Graduate
School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Ken Hosoya
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamo
Hangicho, Kyoto 606-8522, Japan
| | - Koji Otsuka
- Graduate
School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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8
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Jain R, Sharma D, Kumar S, Kumar R. Factor Defining the Effects of Glycine Betaine on the Thermodynamic Stability and Internal Dynamics of Horse Cytochrome c. Biochemistry 2014; 53:5221-35. [DOI: 10.1021/bi500356c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Rishu Jain
- School
of Chemistry and Biochemistry, Thapar University, Patiala 147004, India
| | - Deepak Sharma
- Council
of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Sandeep Kumar
- School
of Chemistry and Biochemistry, Thapar University, Patiala 147004, India
| | - Rajesh Kumar
- School
of Chemistry and Biochemistry, Thapar University, Patiala 147004, India
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9
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Kumar S, Sharma D, Kumar R. Effect of urea and alkylureas on the stability and structural fluctuation of the M80-containing Ω-loop of horse cytochrome c. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:641-55. [DOI: 10.1016/j.bbapap.2014.01.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 01/10/2014] [Accepted: 01/22/2014] [Indexed: 11/27/2022]
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10
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Kumar R, Jain R, Kumar R. Viscosity-dependent structural fluctuation of the M80-containing Ω-loop of horse ferrocytochrome c. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Jain R, Kaur S, Kumar R. Guanidine hydrochloride-induced alkali molten globule model of horse ferrocytochrome c. J Biochem 2012; 153:161-77. [DOI: 10.1093/jb/mvs134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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12
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Choi J, Yang C, Kim J, Ihee H. Protein Folding Dynamics of Cytochrome c Seen by Transient Grating and Transient Absorption Spectroscopies. J Phys Chem B 2011; 115:3127-35. [DOI: 10.1021/jp106588d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jungkweon Choi
- Center for Time-Resolved Diffraction, Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
| | - Cheolhee Yang
- Center for Time-Resolved Diffraction, Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
| | - Jeongho Kim
- Center for Time-Resolved Diffraction, Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
| | - Hyotcherl Ihee
- Center for Time-Resolved Diffraction, Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
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13
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Bhuyan AK. The Off-Pathway Status of the Alkali Molten Globule Is Unrelated to Heme Misligation and Trans-pH Effects: Experiments with Ferrocytochrome c. Biochemistry 2010; 49:7774-82. [DOI: 10.1021/bi100881n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Abani K. Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
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14
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Abstract
To understand the mechanism of ionic detergent-induced protein denaturation, this study examines the action of sodium dodecyl sulfate on ferrocytochrome c conformation under neutral and strongly alkaline conditions. Equilibrium and stopped-flow kinetic results consistently suggest that tertiary structure unfolding in the submicellar and chain expansion in the micellar range of SDS concentrations are the two major and discrete events in the perturbation of protein structure. The nature of interaction between the detergent and the protein is predominantly hydrophobic in the submicellar and exclusively hydrophobic at micellar levels of SDS concentration. The observation that SDS also interacts with a highly denatured and negatively charged form of ferrocytochrome c suggests that the interaction is independent of structure, conformation, and ionization state of the protein. The expansion of the protein chain at micellar concentration of SDS is driven by coulombic repulsion between the protein-bound micelles, and the micelles and anionic amino acid side chains.
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Affiliation(s)
- Abani K Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India.
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15
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Kumar R, Bhuyan AK. Viscosity scaling for the glassy phase of protein folding. J Phys Chem B 2008; 112:12549-54. [PMID: 18781712 DOI: 10.1021/jp804021d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although commendable progress has been made in the understanding of the physics of protein folding, a key unresolved issue is whether Kramers' diffusion model of chemical reactions is generally applicable to activated barrier crossing events during folding. To examine the solvent viscosity effect on the folding transition of native-like trapped intermediates, laser flash photolysis has been used to measure the microsecond folding kinetics of a natively folded state of CO-liganded ferrocytochrome c (M-state) in the 1-250 cP range of glycerol viscosity at pH 7.0, 20 degrees C. The single rate coefficient for the folding of the M-state to the native state of the protein (i.e., the M --> N folding process) decreases initially when the solvent viscosity is low (<10 cP), but saturates at higher viscosity, indicating that Kramers model is not general enough for scaling the viscosity dependence of post-transition folding involving glassy dynamics. Analysis based on the Grote-Hynes idea of time dependent friction in conjunction with defect diffusion dynamics can account for the observed non-Kramers scaling.
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Affiliation(s)
- Rajesh Kumar
- Schools of Chemistry and Life Sciences, University of Hyderabad, Hyderabad, India
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16
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Latypov RF, Maki K, Cheng H, Luck SD, Roder H. Folding mechanism of reduced Cytochrome c: equilibrium and kinetic properties in the presence of carbon monoxide. J Mol Biol 2008; 383:437-53. [PMID: 18761351 DOI: 10.1016/j.jmb.2008.08.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 08/08/2008] [Accepted: 08/13/2008] [Indexed: 11/26/2022]
Abstract
Despite close structural similarity, the ferric and ferrous forms of cytochrome c differ greatly in terms of their ligand binding properties, stability, folding, and dynamics. The reduced heme iron binds diatomic ligands such as CO only under destabilizing conditions that promote weakening or disruption of native methionine-iron linkage. This makes CO a useful conformational probe for detecting partially structured states that cannot be observed in the absence of endogenous ligands. Heme absorbance, circular dichroism, and NMR were used to characterize the denaturant-induced unfolding equilibrium of ferrocytochrome c in the presence and in the absence of CO. In addition to the native state (N), which does not bind CO, and the unfolded CO complex (U-CO), a structurally distinct CO-bound form (M-CO) accumulates to high levels (approximately 75% of the population) at intermediate guanidine HCl concentrations. Comparison of the unfolding transitions for different conformational probes reveals that M-CO is a compact state containing a native-like helical core and regions of local disorder in the segment containing the native Met80 ligand and adjacent loops. Kinetic measurements of CO binding and dissociation under native, partially denaturing, and fully unfolded conditions indicate that a state M that is structurally analogous to M-CO is populated even in the absence of CO. The binding energy of the CO ligand lowers the free energy of this high-energy state to such an extent that it accumulates even under mildly denaturing equilibrium conditions. The thermodynamic and kinetic parameters obtained in this study provide a fully self-consistent description of the linked unfolding/CO binding equilibria of reduced cytochrome c.
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17
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Karmodiya K, Surolia N. A unique and differential effect of denaturants on cofactor mediated activation of Plasmodium falciparum β-ketoacyl-ACP reductase. Proteins 2007; 70:528-38. [PMID: 17879351 DOI: 10.1002/prot.21530] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The urea and guanidinium chloride (GdmCl) induced unfolding of FabG, a beta-ketoacyl-ACP reductase of Plasmodium falciparum, was examined in detail using intrinsic fluorescence of FabG, UV-circular dichroism (CD), spectrophotometric enzyme activity measurements, glutaraldehyde cross-linking, and size exclusion chromatography. The equilibrium unfolding of FabG by urea is a multistep process as compared with a two-state process by GdmCl. FabG is fully unfolded at 6.0M urea and 4.0M GdmCl. Approximately 90% of the enzyme activity could be recovered on dialyzing the denaturants, showing that denaturation by both urea and GdmCl is reversible. We found two states in the reversible unfolding process of FabG in presence of NADPH; one is an activity-enhanced state and the other, an inactive state in case of equilibrium unfolding with urea. On the contrary, in presence of NADPH, there is no stabilization of FabG in case of equilibrium unfolding with GdmCl. We hypothesize that the hydrogen-bonding network may be reorganized by the denaturant in the activity-enhanced state formed in presence of 1.0M urea, by interrupting the association between dimer-dimer interface and help in accommodating the larger substrate in the substrate binding tunnel thus, increasing the activity. Furthermore, binding of the active site organizer, NADPH leads to compaction of the FabG in presence of urea, as evident by acrylamide quenching. We have shown here for the first time, the detailed inactivation kinetics of FabG, which have not been evaluated in the past from any of the FabG family of enzymes from any of the other sources. These findings provide impetus for exploring the influences of ligands on the structure-activity relationship of Plasmodium beta-ketoacyl-ACP reductase.
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Affiliation(s)
- Krishanpal Karmodiya
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
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18
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Droghetti E, Oellerich S, Hildebrandt P, Smulevich G. Heme coordination states of unfolded ferrous cytochrome C. Biophys J 2006; 91:3022-31. [PMID: 16877519 PMCID: PMC1578467 DOI: 10.1529/biophysj.105.079749] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structural changes of ferrous Cyt-c that are induced by binding to SDS micelles, phospholipid vesicles, DeTAB, and GuHCl as well as by high temperatures and changes in the pH have been studied by RR and UV-Vis absorption spectroscopies. Four species have been identified in which the native methionine-80 ligand is removed from the heme iron. This coordination site is either occupied by a histidine (His-33 or His-26) to form a 6cLS configuration, which is the prevailing species in GuHCl at pH 7.0 and ambient temperature, or remains vacant to yield a 5cHS configuration. The three identified 5cHS species differ with respect to the hydrogen-bond interactions of the proximal histidine ligand (His-18) and include a nonhydrogen-bonded, a hydrogen-bonded, and a deprotonated imidazole ring. These structural motifs have been found irrespective of the unfolding conditions used. An unambiguous spectroscopic distinction of these 5cHS species is possible on the basis of the Fe-N(imidazole) stretching vibrations, the RR bands in the region between 1300 and 1650 cm(-1), and the electronic transitions in the Soret- and Q-band regions. In acid and neutral solutions, the species with a hydrogen-bonded and a nonhydrogen-bonded His-18 prevail, whereas in alkaline solutions a configuration with a deprotonated His-18 ligand is also observed. Upon lowering the pH or increasing the temperature in GuHCl solutions, the structure on the proximal side of the heme is perturbed, resulting in a loss of the hydrogen-bond interactions of the His-18 ligand. Conversely, the hydrogen-bonded His-18 of ferrous Cyt-c is stabilized by electrostatic interactions which increase in strength from phospholipid vesicles to SDS micelles. The results here suggest that unfolding of Cyt-c is initiated by the rupture of the Fe-Met-80 bond and structural reorganizations on the distal side of the heme pocket, whereas the proximal part is only affected in a later stage of the denaturation process.
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Affiliation(s)
- Enrica Droghetti
- Dipartimento di Chimica, Università di Firenze, Sesto Fiorentino FI, Italy
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19
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Wu L, Wang R. Carbon Monoxide: Endogenous Production, Physiological Functions, and Pharmacological Applications. Pharmacol Rev 2005; 57:585-630. [PMID: 16382109 DOI: 10.1124/pr.57.4.3] [Citation(s) in RCA: 648] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Over the last decade, studies have unraveled many aspects of endogenous production and physiological functions of carbon monoxide (CO). The majority of endogenous CO is produced in a reaction catalyzed by the enzyme heme oxygenase (HO). Inducible HO (HO-1) and constitutive HO (HO-2) are mostly recognized for their roles in the oxidation of heme and production of CO and biliverdin, whereas the biological function of the third HO isoform, HO-3, is still unclear. The tissue type-specific distribution of these HO isoforms is largely linked to the specific biological actions of CO on different systems. CO functions as a signaling molecule in the neuronal system, involving the regulation of neurotransmitters and neuropeptide release, learning and memory, and odor response adaptation and many other neuronal activities. The vasorelaxant property and cardiac protection effect of CO have been documented. A plethora of studies have also shown the importance of the roles of CO in the immune, respiratory, reproductive, gastrointestinal, kidney, and liver systems. Our understanding of the cellular and molecular mechanisms that regulate the production and mediate the physiological actions of CO has greatly advanced. Many diseases, including neurodegenerations, hypertension, heart failure, and inflammation, have been linked to the abnormality in CO metabolism and function. Enhancement of endogenous CO production and direct delivery of exogenous CO have found their applications in many health research fields and clinical settings. Future studies will further clarify the gasotransmitter role of CO, provide insight into the pathogenic mechanisms of many CO abnormality-related diseases, and pave the way for innovative preventive and therapeutic strategies based on the physiologic effects of CO.
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Affiliation(s)
- Lingyun Wu
- Department of Biology, Lakehead University, 955 Oliver Rd., Thunder Bay, Ontario, Canada P7B 5E1
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20
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DiCarlo CM, Compton DL, Evans KO, Laszlo JA. Bioelectrocatalysis in ionic liquids. Examining specific cation and anion effects on electrode-immobilized cytochrome c. Bioelectrochemistry 2005; 68:134-43. [PMID: 16009598 DOI: 10.1016/j.bioelechem.2005.01.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2004] [Revised: 12/28/2004] [Accepted: 01/11/2005] [Indexed: 11/21/2022]
Abstract
Cytochrome c immobilized on alkylthiol self-assembled monolayers exhibits a characteristic Fe(II)/Fe(III) redox signal that is lost when exposed to ionic liquids composed of a butylimidazolium cation combined with either hexafluorophosphate or bis(trifluoromethylsulfonyl)imide anion. In this study it was shown that exposure to the aqueous solubilized ionic liquid components, butyl-, hexyl-, and octyl-imidazolium cations and hexafluorophosphate, tetrafluoroborate, and bis(trifluoromethylsulfonyl)imide anions, resulted in partial electrochemical signal loss. Absorbance and fluorescence measurements showed that signal loss due to the cationic ionic liquid component followed a different mechanism than that of the anionic component. Although a portion of the signal was recoverable, irreversible signal loss also occurred in both cases. The source of the irreversible component is suggested to be the loss of protein secondary structure through complexation between the ionic liquid components and the protein surface residues. The reversible electrochemical signal loss is likely due to interfacial interactions imposed between the electrode and the cytochrome heme group. The influence of the amount of exposed surface residues was explored with a simplified model protein, microperoxidase-11.
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Affiliation(s)
- Cory M DiCarlo
- New Crops and Processing Technology Research Unit, United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, IL 61604 USA
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21
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Santoni E, Scatragli S, Sinibaldi F, Fiorucci L, Santucci R, Smulevich G. A model for the misfolded bis-His intermediate of cytochrome c: the 1-56 N-fragment. J Inorg Biochem 2005; 98:1067-77. [PMID: 15149817 DOI: 10.1016/j.jinorgbio.2004.02.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2003] [Revised: 02/09/2004] [Accepted: 02/19/2004] [Indexed: 10/26/2022]
Abstract
We have characterized the ferric and ferrous forms of the heme-containing (1-56 residues) N-fragment of horse heart cytochrome c (cyt c) at different pH values and low ionic strength by UV-visible absorption and resonance Raman (RR) scattering. The results are compared with native cyt c in the same experimental conditions as this may provide a deeper insight into the cyt c unfolding-folding process. Folding of cyt c leads to a state having the heme iron coordinated to a histidine (His18) and a methionine (Met80) as axial ligands. At neutral pH the N-fragment (which lacks Met80) shows absorption and RR spectra that are consistent with the presence of a bis-His low spin heme, like several non-native forms of the parental protein. In particular, the optical spectra are identical to those of cyt c in the presence of a high concentration of denaturants; this renders the N-fragment a suitable model to study the heme pocket microenvironment of the misfolded (His-His) intermediate formed during folding of cyt c. Acid pH affects the ligation state in both cyt c and the N-fragment. Data obtained as a function of pH allow a correlation between the structural properties in the heme pocket of the N-fragment and those of non-native forms of cyt c. The results underline that the (57-104 residues) segment under native-like conditions imparts structural stability to the protein by impeding solvent access into the heme pocket.
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Affiliation(s)
- Elisa Santoni
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Florence, Italy
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22
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Kumar R, Prabhu NP, Yadaiah M, Bhuyan AK. Protein stiffening and entropic stabilization in the subdenaturing limit of guanidine hydrochloride. Biophys J 2004; 87:2656-62. [PMID: 15454460 PMCID: PMC1304684 DOI: 10.1529/biophysj.104.044701] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2004] [Accepted: 07/07/2004] [Indexed: 11/18/2022] Open
Abstract
Subdenaturing concentrations of guanidine hydrochloride (GdnHCl) stabilize proteins. For ferrocytochrome c the stabilization is detected at subglobal level with no measured change in global stability. These deductions are made by comparing observed rates of thermally driven ferrocytochrome cHCO reactions with global unfolding rates of ferrocytochrome c measured by stopped flow and NMR hydrogen exchange in the presence of a wide range of GdnHCl concentrations at pH 7, 22 degrees C.
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Affiliation(s)
- Rajesh Kumar
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India
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23
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Prabhu NP, Kumar R, Bhuyan AK. Folding barrier in horse cytochrome c: support for a classical folding pathway. J Mol Biol 2004; 337:195-208. [PMID: 15001362 DOI: 10.1016/j.jmb.2004.01.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2003] [Revised: 01/07/2004] [Accepted: 01/07/2004] [Indexed: 11/23/2022]
Abstract
Native-state structures and conformations of ferrocytochrome c, nitrosylcytochrome c, and carbonmonoxycytochrome c are very similar. They are, however, immensely different from each other in terms of thermodynamic stability. The dramatic destabilization of ferrocytochrome c to the extent of 12 kcal mol(-1) produces no effect on the folding rate, and this is so in spite of the fact that all three test-tube variants fold in an apparent two-state manner. For all three proteins the folding barrier is early in time, sizable in energy, and is of the same magnitude (approximately 6.5 kcal mol(-1)). These results raise some challenges to the "new view" of protein folding. An early transition state, the search for which consumes most of the observed folding time, is suggested.
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Affiliation(s)
- N Prakash Prabhu
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
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Miksovská J, Larsen RW. Photothermal studies of pH induced unfolding of apomyoglobin. JOURNAL OF PROTEIN CHEMISTRY 2003; 22:387-394. [PMID: 13678303 DOI: 10.1023/a:1025398325578] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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.
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Affiliation(s)
- Jaroslava Miksovská
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, USA
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