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Shet SM, Bharadwaj P, Bisht M, Pereira MM, Thayallath SK, Lokesh V, Franklin G, Kotrappanavar NS, Mondal D. Presenting B-DNA as macromolecular crowding agent to improve efficacy of cytochrome c under various stresses. Int J Biol Macromol 2022; 215:184-191. [PMID: 35716795 DOI: 10.1016/j.ijbiomac.2022.06.093] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/05/2022] [Accepted: 06/12/2022] [Indexed: 11/05/2022]
Abstract
Existence of numerous biomolecules results in biological fluids to be extremely crowded. Thus, Macromolecular crowding is an essential phenomenon to sustain active conformation of proteins in biological systems. Herein, double helical deoxyribonucleic acid (B-DNA) is presented for the first time as a biomacromolecular crowding system for sustainable packaging of cytochrome c (Cyt C). The peroxidase activity of Cyt C was investigated in the presence of various concentrations of B-DNA (from salmon milt). At an optimized concentration of 0.125 mg/mL B-DNA, an 11-fold higher catalytic activity was found than in native Cyt C with improved stability. Molecular docking and spectroscopic analyses revealed that electrostatic and H-bonding are the main interactions between DNA and Cyt C that affect the structural stability and activity of the protein. Moreover, the catalytic activity and stability of the protein were further investigated in the presence of severe process conditions by UV-visible, circular dichroism, and Fourier-transform infrared spectroscopies. Molecularly crowded Cyt C showed significantly higher activity and stability under severe environments such as high temperature (110 °C), oxidative stress, high pH (pH 10) and biological (trypsin) and chemical denaturants (urea) compared to bare Cyt C. The observed results support the suitability of DNA-based macromolecular crowding media as a viable and effective stabilizer of proteins against multiple stresses.
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Affiliation(s)
- Sachin M Shet
- Centre for Nano and Material Sciences, Jain University, Bangalore 562112, India
| | - Pranav Bharadwaj
- Centre for Nano and Material Sciences, Jain University, Bangalore 562112, India
| | - Meena Bisht
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Matheus M Pereira
- Departamento de Química, CICECO, Universidade de Aveiro, Aveiro 3810-193, Portugal
| | | | - Veeresh Lokesh
- Institute of Plant Genetics (IPG), Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
| | - Gregory Franklin
- Institute of Plant Genetics (IPG), Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
| | | | - Dibyendu Mondal
- Centre for Nano and Material Sciences, Jain University, Bangalore 562112, India; Institute of Plant Genetics (IPG), Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland.
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2
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Naiyer A, Khan B, Hussain A, Islam A, Alajmi MF, Hassan MI, Sundd M, Ahmad F. Stability of uniformly labeled ( 13C and 15N) cytochrome c and its L94G mutant. Sci Rep 2021; 11:6804. [PMID: 33762670 PMCID: PMC7990917 DOI: 10.1038/s41598-021-86332-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/02/2021] [Indexed: 11/21/2022] Open
Abstract
Cytochrome c (cyt c) is widely used as a model protein to study (i) folding and stability aspects of the protein folding problem and (ii) structure-function relationship from the evolutionary point of view. Databases of cyts c now contain 285 cyt c sequences from different organisms. A sequence alignment of all these proteins with respect to horse cyt c led to several important conclusions. One of them is that Leu94 is always conserved in all 30 mammalian cyts c. It is known that mutation L94G of the wild type (WT) horse cyt c is destabilizing and mutant exists as molten globule under the native condition (buffer pH 6 and 25 °C). We have expressed and purified uniformly labeled (13C and 15N) and unlabeled WT horse cyt c and its L94G mutant. We report that labeling does not affect the thermodynamic stability of proteins. To support this conclusion, the secondary and tertiary structure of each protein in labeled and unlabeled forms was determined by conventional techniques (UV-Vis absorption and circular dichroism spectroscopy).
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Affiliation(s)
- Abdullah Naiyer
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Bushra Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, 11451, Kingdom of Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, 11451, Kingdom of Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Monica Sundd
- NMR-II Lab, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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Naiyer A, Khan B, Islam A, Hassan MI, Sundd M, Ahmad F. Heme-iron ligand (M80-Fe) in cytochrome c is destabilizing: combined in vitro and in silico approaches to monitor changes in structure, stability and dynamics of the protein on mutation. J Biomol Struct Dyn 2020; 40:4122-4139. [PMID: 34043488 DOI: 10.1080/07391102.2020.1853607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Structure, stability and dynamics properties of horse cytochrome c (cyt c) and its genetically engineered M80G mutant have been investigated. The nature of the Met80 axial ligation to heme iron is believed to be the major determinant of the oxidation-reduction reactions inside and outside the cell of a particular cytochrome. This ligation has played an important role in the studies of protein structure, stability and protein folding/unfolding. To understand this ligation better, Met80 of horse cyt c has been mutated to Gly that is unable to bind to the heme iron. We have examined the effect of the M80G mutation on the structure and stability of the WT (wild type) protein by using absorbance spectroscopy, far-UV, near-UV and Soret circular dichroism, fluorescence spectroscopy and differential scanning calorimetry. We have observed that mutation caused a partial loss of secondary and tertiary structure with slightly increased overall stability of the protein. We have also measured the dynamic behavior of WT cyt c and its M80G mutant in the oxidized form (Fe3+) using the essential dynamics (ED) method. A 400 ns MD simulations were run for WT cyt c and its mutant M80G in water using GROMOS96 force field. MD results revealed that the stability and flexibility increased in mutant M80G (Fe…S (Met80) bond removed). Essential dynamics analysis revealed that the first five eigenvectors were mainly involved in overall motions of WT cyt c and its M80G mutant but the amplitude of concerted motions decreased in M80G mutant relative to WT cyt c.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdullah Naiyer
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Bushra Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Monica Sundd
- NMR-II Lab, National Institute of Immunology, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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Khan SH, Prakash A, Pandey P, Lynn AM, Islam A, Hassan MI, Ahmad F. Protein folding: Molecular dynamics simulations and in vitro studies for probing mechanism of urea- and guanidinium chloride-induced unfolding of horse cytochrome-c. Int J Biol Macromol 2019; 122:695-704. [DOI: 10.1016/j.ijbiomac.2018.10.186] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/27/2018] [Accepted: 10/27/2018] [Indexed: 11/26/2022]
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Tomášková N, Varhač R, Lysáková V, Musatov A, Sedlák E. Peroxidase activity of cytochrome c in its compact state depends on dynamics of the heme region. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1073-1083. [DOI: 10.1016/j.bbapap.2018.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/06/2018] [Accepted: 09/10/2018] [Indexed: 10/28/2022]
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Quanten T, De Mayaer T, Shestakova P, Parac-Vogt TN. Selectivity and Reactivity of Zr IV and Ce IV Substituted Keggin Type Polyoxometalates Toward Cytochrome c in Surfactant Solutions. Front Chem 2018; 6:372. [PMID: 30211153 PMCID: PMC6121075 DOI: 10.3389/fchem.2018.00372] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/02/2018] [Indexed: 12/15/2022] Open
Abstract
In this paper we investigate the effect of three different types of surfactants, on the hydrolysis of Cytochrome c (Cyt c), a predominantly α helical protein containing a heme group, promoted by [Ce(α PW11O39)2]10- (CeK) and [Zr(α PW11O39)2]10- (ZrK) polyoxometalates. In the presence of SDS, Zw3 12, or CHAPS surfactants, which are commonly used for solubilizing hydrophobic proteins, the specificity of CeK or ZrK toward hydrolysis of Cyt c does not change. However, the hydrolysis rate of Cyt c by CeK was increased in the presence of SDS, but decreased in the presence of CHAPS, and was nearly inhibited in the presence of Zw3 12. The Circular dichroism and Tryptophan fluorescence spectroscopy have shown that the structural changes in Cyt c caused by surfactants are similar to those caused by POMs, hence the same specificity in the absence or presence of surfactants was observed. The results also indicate that for Cyt c hydrolysis to occur, large unfolding of the protein is needed in order to accommodate the POMs. While SDS readily unfolds Cyt c, the protein remains largely folded in the presence of CHAPS and Zw3 12. Addition of POMs to Cyt c solutions in CHAPS results in unfolding of the structure allowing the interaction with POMs to occur and results in protein hydrolysis. Zw3 12, however, locks Cyt c in a conformation that resists unfolding upon addition of POM, and therefore results in nearly complete inhibition of protein hydrolysis.
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Affiliation(s)
- Thomas Quanten
- Laboratory of Bio-Inorganic Chemistry, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Tessa De Mayaer
- Laboratory of Bio-Inorganic Chemistry, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Pavletta Shestakova
- NMR Centre, Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Tatjana N Parac-Vogt
- Laboratory of Bio-Inorganic Chemistry, Department of Chemistry, KU Leuven, Leuven, Belgium
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Khan SH, Islam A, Hassan MI, Sharma S, Singh TP, Ahmad F. Effect of conservative mutations (L94V and L94I) on the structure and stability of horse cytochrome c. Arch Biochem Biophys 2017; 633:40-49. [DOI: 10.1016/j.abb.2017.08.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/07/2017] [Accepted: 08/25/2017] [Indexed: 02/07/2023]
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8
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Structural and thermodynamic characterisation of L94F mutant of horse cytochrome c. Int J Biol Macromol 2016; 92:202-212. [DOI: 10.1016/j.ijbiomac.2016.06.096] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/24/2016] [Accepted: 06/30/2016] [Indexed: 12/11/2022]
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9
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Idrees D, Prakash A, Haque MA, Islam A, Hassan MI, Ahmad F. GdnHCl-induced unfolding intermediate in the mitochondrial carbonic anhydrase VA. Int J Biol Macromol 2016; 91:1151-60. [DOI: 10.1016/j.ijbiomac.2016.06.080] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/24/2016] [Accepted: 06/26/2016] [Indexed: 10/21/2022]
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10
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Varhač R, Sedláková D, Stupák M, Sedlák E. Non-two-state thermal denaturation of ferricytochrome c at neutral and slightly acidic pH values. Biophys Chem 2015; 203-204:41-50. [DOI: 10.1016/j.bpc.2015.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 05/08/2015] [Accepted: 05/11/2015] [Indexed: 12/19/2022]
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11
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Gómez-Mingot M, Montiel V, Banks CE, Iniesta J. Screen-printed graphite macroelectrodes for the direct electron transfer of cytochrome c: a deeper study of the effect of pH on the conformational states, immobilization and peroxidase activity. Analyst 2015; 139:1442-8. [PMID: 24492631 DOI: 10.1039/c3an02137h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The direct electron transfer of cytochrome c has been studied at screen-printed graphite macroelectrodes without recourse to mediators or the need for any electrode pre-treatment as is commonly employed within the literature. A wide range of pH values from 2.0 to 11.0 have been explored upon the electrochemical response of cytochrome c and different voltammetric signatures have been observed. The direct electron transfer of the alkaline transition of cytochrome c was found impeded within alkaline media leading to either an irreversible redox process or even no voltammetric responses. In acidic aqueous media the electrochemical process is observed to undergo a mixed diffusion and adsorption controlled process rather than a purely diffusional process of the native conformation as observed at pH 7.0. Interestingly, at pH 3.5 a new conformational state is revealed in cooperation with the native conformation. The immobilization of the protein was satisfactorily obtained using a simple method by cycling the protein at specific solution pH values allowing amperometric responses to be obtained and gives rise to useful pseudo-peroxidase activity for sensing H2O2. Apparent Michaelis-Menten constant values (Km) were calculated via the Lineweaver-Burk method with deduced values of 25 ± 4, 98 ± 12 and 230 ± 30 mM, respectively for pH values of 2.0, 3.0 and 7.0. Such work is important for those utilising cytochrome c in bio-electrochemical and related applications.
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Affiliation(s)
- Maria Gómez-Mingot
- Physical Chemistry Department and Institute of Electrochemistry, University of Alicante, 03690 San Vicente del Raspeig, Alicante, Spain.
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12
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Haque MA, Ubaid-ullah S, Zaidi S, Hassan MI, Islam A, Batra JK, Ahmad F. Characterization of pre-molten globule state of yeast iso-1-cytochrome c and its deletants at pH 6.0 and 25 °C. Int J Biol Macromol 2015; 72:1406-18. [DOI: 10.1016/j.ijbiomac.2014.10.053] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 10/21/2014] [Accepted: 10/29/2014] [Indexed: 10/24/2022]
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13
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Cherney MM, Junior CC, Bergquist BB, Bowler BE. Dynamics of the His79-heme alkaline transition of yeast iso-1-cytochrome c probed by conformationally gated electron transfer with Co(II)bis(terpyridine). J Am Chem Soc 2013; 135:12772-82. [PMID: 23899348 PMCID: PMC3856690 DOI: 10.1021/ja405725f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Alkaline conformers of cytochrome c may be involved in both its electron transport and apoptotic functions. We use cobalt(II)bis(terpyridine), Co(terpy)2(2+), as a reagent for conformationally gated electron-transfer (gated ET) experiments to study the alkaline conformational transition of K79H variants of yeast iso-1-cytochrome c expressed in Escherichia coli , WT*K79H, with alanine at position 72 and Saccharomyces cerevisiae , yK79H, with trimethyllysine (Tml) at position 72. Co(terpy)2(2+) is well-suited to the 100 ms to 1 s time scale of the His79-mediated alkaline conformational transition of these variants. Reduction of the His79-heme alkaline conformer by Co(terpy)2(2+) occurs primarily by gated ET, which involves conversion to the native state followed by reduction, with a small fraction of the His79-heme alkaline conformer directly reduced by Co(terpy)2(2+). The gated ET experiments show that the mechanism of formation of the His79-heme alkaline conformer involves only two ionizable groups. In previous work, we showed that the mechanism of the His73-mediated alkaline conformational transition requires three ionizable groups. Thus, the mechanism of heme crevice opening depends upon the position of the ligand mediating the process. The microscopic rate constants provided by gated ET studies show that mutation of Tml72 (yK79H variant) in the heme crevice loop to Ala72 (WT*K79H variant) affects the dynamics of heme crevice opening through a small destabilization of both the native conformer and the transition state relative to the His79-heme alkaline conformer. Previous pH jump data had indicated that the Tml72→Ala mutation primarily stabilized the transition state for the His79-mediated alkaline conformational transition.
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Affiliation(s)
| | - Carolyn C. Junior
- Department of Chemistry & Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812
| | - Bryan B. Bergquist
- Department of Chemistry & Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812
| | - Bruce E. Bowler
- Department of Chemistry & Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812
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Castellini E, Bortolotti CA, Di Rocco G, Bernini F, Ranieri A. Enhancing Biocatalysis: The Case of Unfolded Cytochrome cImmobilized on Kaolinite. ChemCatChem 2013. [DOI: 10.1002/cctc.201200876] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Cherney MM, Junior CC, Bowler BE. Mutation of trimethyllysine 72 to alanine enhances His79-heme-mediated dynamics of iso-1-cytochrome c. Biochemistry 2013; 52:837-46. [PMID: 23311346 DOI: 10.1021/bi301599g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Trimethyllysine 72 (Tml72) of yeast iso-1-cytochrome c lies across the surface of the heme crevice loop (Ω-loop D, residues 70-85) like a brace. Lys72 is oriented similarly in horse cytochrome c (Cytc). To determine whether this residue affects the dynamics of opening the heme crevice loop, we have studied the effect of a Tml72 to Ala substitution on the formation of the His79-heme alkaline conformer near neutral pH using a variant of iso-1-Cytc including K72A and K79H mutations. Guanidine hydrochloride denaturation shows that the Tml72 to Ala substitution within error does not affect the global stability of the protein. The effect of the Tml72 to Ala substitution on the thermodynamics of the His79-heme alkaline transition is also small. However, pH-jump kinetic studies of the His79-heme alkaline transition show that both the forward and backward rates of conformational change are increased by the Tml72 to Ala substitution. The barrier for opening the heme crevice is reduced by 0.5 kcal/mol and for closing the heme crevice by 0.3 kcal/mol. The ability of Tml72 to modulate the heme crevice dynamics may indicate a crucial role in regulating function, such as in the peroxidase activity seen in the early stages of apoptosis.
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Affiliation(s)
- Melisa M Cherney
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, United States
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Zaragoza A, Teruel JA, Aranda FJ, Marqués A, Espuny MJ, Manresa Á, Ortiz A. Interaction of a Rhodococcus sp. trehalose lipid biosurfactant with model proteins: thermodynamic and structural changes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:1381-90. [PMID: 22172005 DOI: 10.1021/la203879t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
One major application of surfactants is to prevent aggregation during various processes of protein manipulation. In this work, a bacterial trehalose lipid (TL) with biosurfactant activity, secreted by Rhodococcus sp., has been identified and purified. The interactions of this glycolipid with selected model proteins have been studied by using differential scanning calorimetry (DSC), Fourier-transform infrared (FTIR) spectroscopy, isothermal titration calorimetry (ITC), and fluorescence spectroscopy. Bovine serum albumin (BSA) and cytochrome c (Cyt-c) have been chosen because of their quite different secondary structures: BSA contains essentially no β-sheets and an average 66% α-helix, whereas Cyt-c possesses up to 25% β-sheets and up to 45% α-helical structure. Differential scanning calorimetry shows that addition of TL to BSA at concentrations below the critical micelle concentration (cmc) shifts the thermal unfolding temperature to higher values. FTIR indicates that TL does not alter the secondary structure of native BSA, but the presence of TL protects the protein toward thermal denaturation, mainly by avoiding formation of β-aggregates. Studies on the intrinsic Trp fluorescence of BSA show that addition of TL to the native protein results in conformational changes. BSA unfolding upon thermal denaturation in the absence of TL makes the Trp residues less accessible to the quencher, as shown by a decrease in the value of Stern-Volmer dynamic quenching constant, whereas denaturation in the presence of the biosurfactant prevents unfolding, in agreement with FTIR results. In the case of Cyt-c, interaction with TL gives rise to a new thermal denaturation transition, as observed by DSC, at temperatures below that of the native protein, therefore facilitating thermal unfolding. Binding of TL to native BSA and Cyt-c, as determined by ITC, suggests a rather nonspecific interaction of the biosurfactant with both proteins. FTIR indicates that TL slightly modifies the secondary structure of native Cyt-c, but protein denaturation in the presence of TL results in a higher proportion of β-aggregates than in its absence (20% vs 3.9%). The study of Trp fluorescence upon TL addition to Cyt-c results in a completely opposite scenario to that described above for BSA. In this case, addition of TL considerably increases the value of the dynamic quenching constant, both in native and denatured protein; that is, the interaction with the glycolipid induces conformational changes which facilitate the exposure of Trp residues to the quencher. Considering the structures of both proteins, it could be derived that the characteristics of TL interactions, either promoting or avoiding thermal unfolding, are highly dependent on the protein secondary structure. Our results also suggest the rather unspecific nature of these interactions. These might well involve protein hydrophobic domains which, being buried into the protein native structures, become exposed upon thermal unfolding.
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Affiliation(s)
- Ana Zaragoza
- Departamento de Bioquímica y Biología Molecular-A, Facultad de Veterinaria, Universidad de Murcia , E-30100 Murcia, Spain
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Monari S, Ranieri A, Bortolotti CA, Peressini S, Tavagnacco C, Borsari M. Unfolding of cytochrome c immobilized on self-assembled monolayers. An electrochemical study. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.06.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Khan MKA, Rahaman H, Ahmad F. Conformation and thermodynamic stability of pre-molten and molten globule states of mammalian cytochromes-c. Metallomics 2011; 3:327-38. [DOI: 10.1039/c0mt00078g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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19
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Nuffer JH, Siegel RW. Nanostructure-biomolecule interactions: implications for tissue regeneration and nanomedicine. Tissue Eng Part A 2010; 16:423-30. [PMID: 19827941 DOI: 10.1089/ten.tea.2009.0294] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Great strides are being made worldwide in our ability to synthesize and assemble nanoscale building blocks to create advanced materials with novel properties and functionalities. The novel properties of nanostructures are derived from their confined sizes and their very large surface-to-volume ratios. Nanostructured surfaces have also been shown to elicit more favorable and selective biomolecule and cellular responses than surfaces at coarser length scales. In the case of nanoscale ceramics and osteoblasts, for example, the benefit results from protein (vitronectin) unfolding at the nanostructured surface. These nanoscale attributes are enabling a variety of nanostructures to form the bases for a new field--nanomedicine. A fundamental issue in much of nanomedicine, and especially tissue regeneration, is to understand and to eventually control nanostructure-biomolecule interactions. To elucidate the fundamental bases for changes of protein conformation and function on nanostructured surfaces, and hence select responses including those of stem cells, a number of model experiments have been carried out. The results of these studies are presented and discussed in the context of the fundamental driving forces for protein conformation changes associated with nanostructures, their relationship to modified cell responses and tissue engineering, and our present knowledge regarding nanostructure properties.
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Affiliation(s)
- Joseph H Nuffer
- Rensselaer Nanotechnology Center, Rensselaer Polytechnic Institute, Troy, New York 12180, USA.
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20
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The impact of urea-induced unfolding on the redox process of immobilised cytochrome c. J Biol Inorg Chem 2010; 15:1233-42. [DOI: 10.1007/s00775-010-0681-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 06/02/2010] [Indexed: 11/25/2022]
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21
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Shang W, Nuffer JH, Muñiz-Papandrea VA, Colón W, Siegel RW, Dordick JS. Cytochrome C on silica nanoparticles: influence of nanoparticle size on protein structure, stability, and activity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2009; 5:470-6. [PMID: 19189325 DOI: 10.1002/smll.200800995] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The structure, thermodynamic and kinetic stability, and activity of cytochrome c (cyt c) on silica nanoparticles (SNPs) of different sizes have been studied. Adsorption of cyt c onto larger SNPs results in both greater disruption of the cyt c global structure and more significant changes of the local heme microenvironment than upon adsorption onto smaller SNPs. The disruption of the heme microenvironment leads to a more solvent-accessible protein active site, as suggested by Soret circular dichroism spectroscopy and through an increase in peroxidase activity as a function of increased SNP size. Similarly, the stability of cyt c decreases more dramatically upon adsorption onto larger SNPs. These results are consistent with changes in protein-nanoparticle interactions that depend on the size or surface curvature of the supporting nanostructure. This study provides further fundamental insights into the effects of nanoscale surfaces on adsorbed protein structure and function.
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Affiliation(s)
- Wen Shang
- Department of Materials Science and Engineering, Rensselaer Nanotechnology Center, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
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22
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Monari S, Ranieri A, Di Rocco G, van der Zwan G, Peressini S, Tavagnacco C, Millo D, Borsari M. Redox thermodynamics of cytochromes c subjected to urea induced unfolding. J APPL ELECTROCHEM 2009. [DOI: 10.1007/s10800-009-9804-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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How does reorganization energy change upon protein unfolding? Monitoring the structural perturbations in the heme cavity of cytochrome c. Biophys Chem 2008; 134:225-31. [DOI: 10.1016/j.bpc.2008.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Revised: 02/17/2008] [Accepted: 02/17/2008] [Indexed: 11/21/2022]
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24
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Jang DS, Lee HJ, Lee B, Hong BH, Cha HJ, Yoon J, Lim K, Yoon YJ, Kim J, Ree M, Lee HC, Choi KY. Detection of an intermediate during the unfolding process of the dimeric ketosteroid isomerase. FEBS Lett 2006; 580:4166-71. [PMID: 16828747 DOI: 10.1016/j.febslet.2006.06.069] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2006] [Revised: 06/15/2006] [Accepted: 06/23/2006] [Indexed: 10/24/2022]
Abstract
Failure to detect the intermediate in spite of its existence often leads to the conclusion that two-state transition in the unfolding process of the protein can be justified. In contrast to the previous equilibrium unfolding experiment fitted to a two-state model by circular dichroism and fluorescence spectroscopies, an equilibrium unfolding intermediate of a dimeric ketosteroid isomerase (KSI) could be detected by small angle X-ray scattering (SAXS) and analytical ultracentrifugation. The sizes of KSI were determined to be 18.7A in 0M urea, 17.3A in 5.2M urea, and 25.1A in 7M urea by SAXS. The size of KSI in 5.2M urea was significantly decreased compared with those in 0M and 7M urea, suggesting the existence of a compact intermediate. Sedimentation velocity as obtained by ultracentrifugation confirmed that KSI in 5.2M urea is distinctly different from native and fully-unfolded forms. The sizes measured by pulse field gradient nuclear magnetic resonance (NMR) spectroscopy were consistent with those obtained by SAXS. Discrepancy of equilibrium unfolding studies between size measurement methods and optical spectroscopies might be due to the failure in detecting the intermediate by optical spectroscopic methods. Further characterization of the intermediate using (1)H NMR spectroscopy and Kratky plot supported the existence of a partially-folded form of KSI which is distinct from those of native and fully-unfolded KSIs. Taken together, our results suggest that the formation of a compact intermediate should precede the association of monomers prior to the dimerization process during the folding of KSI.
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Affiliation(s)
- Do Soo Jang
- National Research Laboratory of Protein Folding and Engineering, Division of Molecular Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
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25
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Latypov RF, Cheng H, Roder NA, Zhang J, Roder H. Structural Characterization of an Equilibrium Unfolding Intermediate in Cytochrome c. J Mol Biol 2006; 357:1009-25. [PMID: 16473367 DOI: 10.1016/j.jmb.2006.01.055] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Revised: 01/11/2006] [Accepted: 01/15/2006] [Indexed: 10/25/2022]
Abstract
Although the denaturant-induced unfolding transition of cytochrome c was initially thought to be a cooperative process, recent spectroscopic studies have shown deviations from two-state behavior consistent with accumulation of an equilibrium intermediate. However, little is known about the structural and thermodynamic properties of this state, and whether it is stabilized by the presence of non-native heme ligands. We monitored the reversible denaturant-induced unfolding equilibrium of oxidized horse cytochrome c using various spectroscopic probes, including fluorescence, near and far-UV CD, heme absorbance bands in the Soret, visible and near-IR regions of the spectrum, as well as 2D NMR. Global fitting techniques were used for a quantitative interpretation of the results in terms of a three-state model, which enabled us to determine the intrinsic spectroscopic properties of the intermediate. A well-populated intermediate was observed in equilibrium experiments at pH 5 using either guanidine-HCl or urea as a denaturant, both for wild-type cytochrome c as well as an H33N mutant chosen to prevent formation of non-native His-heme ligation. For a more detailed structural characterization of the intermediate, we used 2D 1H-15N correlation spectroscopy to follow the changes in peak intensity for individual backbone amide groups. The equilibrium state observed in our optical and NMR studies contains many native-like structural features, including a well-structured alpha-helical sub-domain, a short Trp59-heme distance and solvent-shielded heme environment, but lacks the native Met80 sulfur-iron linkage and shows major perturbations in side-chain packing and other tertiary interactions. These structural properties are reminiscent of the A-state of cytochrome c, a compact denatured form found under acidic high-salt conditions, as well as a kinetic intermediate populated at a late stage of folding. The denaturant-induced intermediate also resembles alkaline forms of cytochrome c with altered heme ligation, suggesting that disruption of the native methionine ligand favors accumulation of structurally analogous states both in the presence and absence of non-native ligands.
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Affiliation(s)
- Ramil F Latypov
- Basic Science Division, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
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26
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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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27
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Rodriguez-Cruz SE, Khoury JT, Parks JH. Protein fluorescence measurements within electrospray droplets. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2001; 12:716-725. [PMID: 11401162 DOI: 10.1016/s1044-0305(01)00241-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The conformation of cytochrome c molecules within electrospray droplets is investigated by monitoring the laser induced fluorescence of its single tryptophan residue (Trp-59). By increasing the alcohol concentration of the electrosprayed solutions, protein denaturation is induced, giving rise to significant changes in the intensity of the detected fluorescence. Comparison with analogous denaturation experiments in solution provides information about the relative protein conformations and differences between the bulk-solution and droplet environments. Both electrospray-plume and bulk-solution fluorescence measurements using low methanol concentration solutions indicate the presence of folded protein structures. At high methanol content, fluorescence measurements are consistent with the presence of partly denatured or unfolded conformations. At intermediate methanol content, differences are observed between the extent of denaturation in solution and that within the droplets, suggesting electrosprayed proteins have more compact structures than those detected in bulk measurements using solutions of similar composition. This infers that some fraction of the proteins within the droplets have refolded relative to their bulk-solution conformation. Protein denaturation experiments using the low vapor pressure solvent 1-propanol indicate that differences between the droplet and solution measurements are not due to solvent evaporation effects. It is suggested that different droplet conformations are more likely the result of protein diffusion to the droplet surface and effects of the droplet/air interface. To our knowledge, these are the first reported measurements of protein fluorescence within electrospray droplets.
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28
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Russell BS, Melenkivitz R, Bren KL. NMR investigation of ferricytochrome c unfolding: detection of an equilibrium unfolding intermediate and residual structure in the denatured state. Proc Natl Acad Sci U S A 2000; 97:8312-7. [PMID: 10880578 PMCID: PMC26944 DOI: 10.1073/pnas.150239397] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Horse ferricytochrome c (cyt c) undergoes exchange of one of its axial heme ligands (Met-80) for one or more non-native ligands under denaturing conditions. We have used (1)H NMR spectroscopy to detect two conformations of paramagnetic cyt c with non-native heme ligation through a range of urea concentrations. One non-native form is an equilibrium unfolding intermediate observed under partially denaturing conditions and is attributed to replacement of Met-80 with one or more Lys side chains. The second non-native form, in which the native Met ligand is replaced by a His, is observed under strongly denaturing conditions. Thermodynamic analysis of these data indicates a relatively small DeltaG (17 kJ/mol) for the transition from native to the Lys-ligated intermediate and a significantly larger DeltaG (47 kJ/mol) for the transition from native to the His-ligated species. Although CD and fluorescence data indicate that the equilibrium unfolding of cyt c is a two-state process, these NMR results implicate an intermediate with His-Lys ligation.
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Affiliation(s)
- B S Russell
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216, USA
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29
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Santucci R, Fiorucci L, Sinibaldi F, Polizio F, Desideri A, Ascoli F. The heme-containing N-fragment (residues 1-56) of cytochrome c is a bis-histidine functional system. Arch Biochem Biophys 2000; 379:331-6. [PMID: 10898952 DOI: 10.1006/abbi.2000.1885] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structural and redox properties of a heme-containing fragment (1-56 residues) of cytochrome c have been investigated by spectroscopic (circular dichroism, electronic absorption, and EPR) and voltammetric techniques. The results indicate that the N-fragment lacks ordered secondary structure and has two histidines axially bound to the heme-iron (the native His18 and a misligated His26 or His33). Despite the absence of ordered secondary structure, the peptide chain shields the heme group from solvent, as shown by (i) the pK(a) of protonation of the nonnative histidine ligand (5.18 +/- 0.05), lower than that of the bis-histidine guanidine-unfolded cytochrome c (5.58 +/- 0.05), and (ii) the redox potential, E(o) = 0 +/- 5 mV versus NHE, close to that of bis-histidine cytochrome c mutants but less negative than that of bis-histidine complexes of microperoxidase with short peptides. The electroactive N-fragment may be taken as a "minichrome c" model, with interesting potential for application to biosensor technology; further, the system provides useful information for a deeper understanding of cytochrome c folding and structural/functional organization.
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Affiliation(s)
- R Santucci
- Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università di Roma "Tor Vergata,", Rome, Italy.
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30
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Arai M, Kuwajima K. Role of the molten globule state in protein folding. ADVANCES IN PROTEIN CHEMISTRY 2000; 53:209-82. [PMID: 10751946 DOI: 10.1016/s0065-3233(00)53005-8] [Citation(s) in RCA: 355] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- M Arai
- Department of Physics, School of Science, University of Tokyo, Japan
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31
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Gebicka L, Gebicki JL. Kinetic studies on the interaction of ferricytochrome c with anionic surfactants. JOURNAL OF PROTEIN CHEMISTRY 1999; 18:165-72. [PMID: 10333289 DOI: 10.1023/a:1020619804635] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The kinetics of absorbance and fluorescence changes of cytochrome c as induced by an aqueous solution of the anionic surfactant sodium dodecyl sulfate (SDS) or sodium bis(2-ethylhexyl)sulfosuccinate (AOT) are studied. The results are compared with far-UV circular dichroism (CD) spectra. Both surfactants cause similar alterations in the secondary structure of cytochrome c, while their influence on the heme environment of cytochrome c is different. In the presence of AOT below and above critical micellar concentration a conversion of the low-spin native cytochrome c to a denatured low-spin protein not having methionine ligand takes place. In the presence of SDS micelles conversion of the native protein to a denatured mixed-spin form occurs. The changes in the heme group induced by both surfactants occur independently of the alterations in tertiary structure.
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Affiliation(s)
- L Gebicka
- Institute of Applied Radiation Chemistry, Technical University of Lódź, Poland.
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32
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33
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Zhang B, Zhu Y, Dong S, Wang E. Scanning tunnelling microscopy observation of cytochrome-c denaturation induced by bromopyrogal red on highly oriented pyrolytic graphite. Int J Biol Macromol 1997; 21:251-61. [PMID: 9352371 DOI: 10.1016/s0141-8130(97)00073-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The denaturation of cytochrome-c (cyt-c) induced by bromopyrogal red (BPR) was studied by scanning tunnelling microscopy (STM) on the electrochemically pretreated highly oriented pyrolytic graphite (HOPG) surface. STM images reveal that denatured cyt-c molecules exist in variable states including aggregates, globular compact, partially unfolded and combined with BPR molecule. The apparently low image contrast of denatured cyt-c observed in this experiment comparing to that of native cyt-c molecules, and the relative low image contrast of the unfolded part comparing with the compact globular part, are ascribed to the unfavourable tunnelling paths for the conformational variations of denatured cyt-c molecules.
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Affiliation(s)
- B Zhang
- Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, People's Republic of China
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34
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Hamachi I, Fujita A, Kunitake T. Protein Engineering Using Molecular Assembly: Functional Conversion of Cytochrome c via Noncovalent Interactions. J Am Chem Soc 1997. [DOI: 10.1021/ja9711775] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Itaru Hamachi
- Contribution from the Department of Chemistry & Biochemistry (Molecular Science Engineering), Kyushu University, Hakozaki, Fukuoka 812-81, Japan
| | - Akio Fujita
- Contribution from the Department of Chemistry & Biochemistry (Molecular Science Engineering), Kyushu University, Hakozaki, Fukuoka 812-81, Japan
| | - Toyoki Kunitake
- Contribution from the Department of Chemistry & Biochemistry (Molecular Science Engineering), Kyushu University, Hakozaki, Fukuoka 812-81, Japan
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35
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Zhu Y, Dong S. Electrochemical identification of intermediate forms of urea denaturation of horse heart cytochrome c. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/0302-4598(96)05080-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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36
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Cai C, Ju H, Chen H. The effects of temperature and electrolyte on the redox potential of cytochrome c at a chemically modified microband gold electrode. Electrochim Acta 1995. [DOI: 10.1016/0013-4686(95)00023-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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37
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Ahmad Z, Ahmad F. Physico-chemical characterization of products of unfolding of cytochrome c by calcium chloride. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1207:223-30. [PMID: 8075155 DOI: 10.1016/0167-4838(94)00045-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Cytochrome c (cyt c) denaturation by calcium chloride (CaCl2) and guanidine hydrochloride (GdnHCl) denaturation in presence of low fixed concentrations of CaCl2 has been carried out by UV/Vis spectrophotometry at pH 7.0 and 25 degrees C. The unfolding process was followed by measuring changes in difference molar extinction coefficient around 400 nm and delta epsilon 290. The products of denaturation were further characterized by intrinsic viscosity ([eta]) measurements. It has been observed that the reversible unfolding of cyt c by CaCl2 occurs in two distinct stages or involves three species (or states) namely N<-->X<-->D. Characterization of the native state, N intermediate state, X and the end product, D suggests that (i) During N<-->X only heme is exposed and no secondary structure unfolding occurs so that X state remains as compact as the native state. (ii) Stage X<-->D shows the melting of secondary structure. (iii) The end product corresponds to a random coil. and (iv) Thermodynamic characterization of the end product shows that heme plays an important role in the stability of the protein and removal of heme will lead to the unfolding of cyt c. Mixed denaturation shows a highly cooperative reversible transition between the native and denatured conformation. Analysis of the mixed results shows that (1) Gdn+ does not have any binding site (s) on the native cyt c, (2) there is one binding site for Ca2+ which stabilizes the protein, and (3) the binding constant, ks, is 5 M-1 for Ca2+.
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Affiliation(s)
- Z Ahmad
- Centre for Biosciences, Jamia Millia Islamia, New Delhi, India
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38
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Abstract
We report the measurement of the adiabatic compressibility beta for "molten globule" states of cytochrome b562 and cytochrome c. Precise density and sound velocity measurements allow determination of beta in aqueous solution. Surprisingly, the molten globule apocytochrome b562 shows a beta comparable to the native holocytochrome b562. We estimated the maximum difference in the hydration contribution to the compressibility of apocytochrome b562 relative to holocytochrome b562 to be only -2.6 x 10(-11) Pa-1. Our results suggest that the intrinsic compressibility and the overall volume fluctuations in the molten globule state differ only slightly from those in the native protein. With cytochrome c we investigated the changes in beta for the transitions from the native to the acid molten globule and expanded premolten globule states. The molten globule at pH 2.2 was found to be somewhat "softer" than the native protein at neutral pH. In contrast, a decrease in beta of the premolten globule indicates an increased penetration of water into the macromolecule. In both of these intermediates the differences in adiabatic compressibility relative to the native state are small in comparison to the range of adiabatic compressibility observed for different native globular proteins.
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Affiliation(s)
- B Nölting
- Department of Biochemistry, University of Illinois, Urbana 61801
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39
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Zhang Z, Smith DL. Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation. Protein Sci 1993; 2:522-31. [PMID: 8390883 PMCID: PMC2142359 DOI: 10.1002/pro.5560020404] [Citation(s) in RCA: 788] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A new method based on protein fragmentation and directly coupled microbore high-performance liquid chromatography-fast atom bombardment mass spectrometry (HPLC-FABMS) is described for determining the rates at which peptide amide hydrogens in proteins undergo isotopic exchange. Horse heart cytochrome c was incubated in D2O as a function of time and temperature to effect isotopic exchange, transferred into slow exchange conditions (pH 2-3, 0 degrees C), and fragmented with pepsin. The number of peptide amide deuterons present in the proteolytic peptides was deduced from their molecular weights, which were determined following analysis of the digest by HPLC-FABMS. The present results demonstrate that the exchange rates of amide hydrogens in cytochrome c range from very rapid (k > 140 h-1) to very slow (k < 0.002 h-1). The deuterium content of specific segments of the protein was determined as a function of incubation temperature and used to indicate participation of these segments in conformational changes associated with heating of cytochrome c. For the present HPLC-FABMS system, approximately 5 nmol of protein were used for each determination. Results of this investigation indicate that the combination of protein fragmentation and HPLC-FABMS is relatively free of constraints associated with other analytical methods used for this purpose and may be a general method for determining hydrogen exchange rates in specific segments of proteins.
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Affiliation(s)
- Z Zhang
- Department of Medicinal Chemistry and Pharmacognosy, Purdue University, West Lafayette, Indiana 47907
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40
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Logovinsky V, Kaposi AD, Vanderkooi JM. Native and denatured Zn cytochrome c studied by fluorescence line narrowing spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1161:149-60. [PMID: 8381668 DOI: 10.1016/0167-4838(93)90208-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Fluorescence Line Narrowing (FLN) spectroscopy was employed to compare the environment around the porphyrin in folded and unfolded Zn-substituted cytochrome c (Zn cyt c). Parameters of the resolved spectra, including the inhomogeneous energy-distribution function, vibrational energy levels, and phonon coupling, were compared for guanidine-denatured Zn cyt c and native Zn cyt c. The spectra of denatured Zn cyt c showed increased broad background and decreased peak resolution when compared to the native protein, indicating that denaturation results in increased phonon coupling. The energy-distribution function for the unfolded protein was fitted to a single Gaussian centered at 17,230 cm-1 with a width of approx. 360 cm-1, which proved to be blue shifted and much wider than that for native Zn cyt c (approx. 65 cm-1). Vibrational frequencies of the ground-state for Zn cyt c were identified and shown to change upon denaturation. Temperature-dependence of the FLN spectra of native Zn cyt c was analyzed and found to have step-like broadening between 40 K and 50 K. Such discontinuous spectral broadening behavior suggests that a discrete conformational change occurs in the protein at these temperatures.
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Affiliation(s)
- V Logovinsky
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia 19104
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41
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Daido T, Akaike T. Electrochemistry of cytochrome c: influence of coulombic attraction with indium tin oxide electrode. J Electroanal Chem (Lausanne) 1993. [DOI: 10.1016/0022-0728(93)80048-m] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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42
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Myer YP, Saturno AF. Horse heart ferricytochrome c: conformation and heme configuration of high ionic strength acidic forms. JOURNAL OF PROTEIN CHEMISTRY 1991; 10:481-94. [PMID: 1665977 DOI: 10.1007/bf01025476] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The absorption, circular dichroism, and resonance Raman spectra of horse heart ferricytochrome c in the presence of 0.2 M KCl, 0.1 M NaClO4, and 0.2 M KNO3, in the pH region 7 to 0.5, have been investigated to determine the nature and the course of the processes involved. As in the absence of salts (Myer, Y., and Saturno, A. F. (1990) J. Protein Chem, 9, 379-387), the change from neutral to low acidic pH's in the presence of salts is a three-step process: state IIIs----state IIIS,a----state IIS----state IS, with pKa's of 3.5 +/- 0.2, 2.2 +/- 0.2, and 1.1 +/- 0.2, and with two, one, and one number of protons, respectively. The addition of salts at neutral pH's has little or no effect on the protein conformation and the heme-iron configuration (i.e., they remain the same, low-spin hexacoordinated heme iron with a Met-80-Fe-His-18 axial coordination), but such addition does cause a slight tightening of the heme crevice and the enlargement of the porphyrin core. State IIIS,a is a folded state with about the same degree of folding and with a similar spin state and coordination configuration of iron, but the heme crevice is loosened and the porphyrin core is smaller. Both states IIS and IS are also essentially folded forms, but with a smaller degree of protein secondary structure. State IIS has a high-spin hexacoordinated heme iron with a water molecular and a protonated and/or hydrogen-bonded imidazole of his-18 as the two axial ligates; and state IS has a high-spin pentacoordinated heme iron, which is about 0.49 A out of the porphyrin plane, with a protonated and/or hydrogen-bonded imidazole nitrogen as the only axial ligate. The addition of anions causes the stabilization of the protein secondary structures and the state IIIa----state II transition. The mode of effectiveness of anions appears to be nonspecific (i.e., because of electrostatic shielding and/or disruption of salt bridges).
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Affiliation(s)
- Y P Myer
- Department of Chemistry, State University of New York, Albany 12222
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43
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Myer YP, Saturno AF. Horse heart ferricytochrome c: conformation and heme configuration of low ionic strength acidic forms. JOURNAL OF PROTEIN CHEMISTRY 1990; 9:379-87. [PMID: 2177335 DOI: 10.1007/bf01024613] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Resonance Raman, absorption and circular dichroism spectroscopic studies of the stable forms of horse heart ferricytochrome c in the pH range 6-0.8 and at the lowest possible ionic strengths, in water, and at 30 degrees C are reported. The neutral pH form, state III, changes to the acidic pH form, state I, through a three-step process: state III in equilibrium with IIIa in equilibrium with state II in equilibrium with state I, with pKa's of 3.6 +/- 0.3, 2.7 +/- 0.2, and 1.2 +/- 0.2, depending on the monitoring probe, respectively. State IIIa ferricytochrome c is like state III (i.e., with the Met-80-sulfur-iron linkage and a closed heme crevice) but with a higher degree of folding and a slightly larger porphyrin core. State II ferricytochrome c is an unfolded form with an open heme crevice and no Met-80-sulfur-iron linkage. The heme iron is high-spin, and hexacoordinated with weak ligand-field groups, water, and nitrogen of the protonated/hydrogen-bonded imidazole of the His-18 residue at the axial positions. The state I form also lacks the Met-80-sulfur-iron linkage and has an open heme crevice like the state II form; however, it is less unfolded and has a high-spin pentacoordinated heme iron, with the nitrogen of the imidazole of His-18 as the axial ligate, which is out of the porphyrin plane by about 0.45 A.
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Affiliation(s)
- Y P Myer
- Department of Chemistry, State University of New York, Albany 12222
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Santucci R, Giartosio A, Ascoli F. Structural transitions of carboxymethylated cytochrome c: calorimetric and circular dichroic studies. Arch Biochem Biophys 1989; 275:496-504. [PMID: 2556966 DOI: 10.1016/0003-9861(89)90396-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Circular dichroism and differential scanning calorimetry studies on the unfolding-refolding process of native and carboxymethylated cytochrome c, induced either by temperature or chemical agents, have been performed. The results have shown that the modified protein has a decreased conformational stability with respect to the native state, in agreement with a structure less compact, but still highly folded, which behaves as a thermodynamically stable "intermediate" between native and fully unfolded cytochrome c.
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Affiliation(s)
- R Santucci
- Department of Biochemical Sciences, University La Sapienza, Rome, Italy
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Location of heme axial ligands in the cytochrome d terminal oxidase complex of Escherichia coli determined by site-directed mutagenesis. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)83145-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Kuwajima K. The molten globule state as a clue for understanding the folding and cooperativity of globular-protein structure. Proteins 1989; 6:87-103. [PMID: 2695928 DOI: 10.1002/prot.340060202] [Citation(s) in RCA: 1121] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- K Kuwajima
- Department of Polymer Science, Faculty of Science, Hokkaido University, Japan
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Tollin G, Brown K, De Francesco R, Edmondson DE. Flavodoxin-cytochrome c interactions: circular dichroism and nuclear magnetic resonance studies. Biochemistry 1987; 26:5042-8. [PMID: 2822104 DOI: 10.1021/bi00390a024] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Circular dichroism and 1H and 31P nuclear magnetic resonance spectroscopy have been used to investigate complex formation between cytochrome c and the flavodoxins from Azotobacter vinelandii and Clostridium pasteurianum. Such complexes are known to be involved in the mechanism of electron transfer between these two redox proteins. A large increase in ellipticity in the Soret band of the cytochrome heme was observed upon formation of the Clostridium flavodoxin complex, whereas much smaller changes were found for the complexes with either Azotobacter flavodoxin or an 8 alpha-imidazolyl-FMN-substituted Clostridium flavodoxin analogue. Similarly, the magnitudes of the perturbations of the contact-shifted heme proton resonances obtained upon complexation of cytochrome c by Azotobacter flavodoxin were much smaller than those previously shown for Clostridium flavodoxin [Hazzard, J. T., & Tollin, G. (1985) Biochem. Biophys. Res. Commun. 130, 1281-1286]. 31P nuclear magnetic resonance measurements were also consistent with differences in the interactions between the components in the complexes of the two flavodoxins with cytochrome c. It is suggested that these spectral changes are due to a loosening or opening of the heme crevice upon Clostridium flavodoxin binding, which allows closer contact between the heme and flavin prosthetic groups and results in a faster rate of electron transfer. The implications of these observations for biological oxidation-reduction processes are considered.
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Affiliation(s)
- G Tollin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
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Santucci R, Brunori M, Ascoli F. Unfolding and flexibility in hemoproteins shown in the case of carboxymethylated cytochrome c. BIOCHIMICA ET BIOPHYSICA ACTA 1987; 914:185-9. [PMID: 3038191 DOI: 10.1016/0167-4838(87)90062-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A circular dichroism study of carboxymethylated cytochrome c has been performed to obtain further information on the structural basis responsible for the observed changes in ligand binding and redox properties of the modified cytochrome c. The results give additional evidence of local structural changes occurring in the heme environment upon rupture of the (Met-80)-heme iron bond in the modified protein. This produces no alterations of the overall molecular conformation, but results in drastic changes in redox potential. In addition, analysis of the reversible conformational transitions induced by urea in the native and the modified proteins supports the idea that the modified derivative can be considered as an 'intermediate state' between the native and the fully unfolded protein.
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Mathews AJ, Brittain T. Some electron-transfer reactions involving carbodi-imide-modified cytochrome c. Biochem J 1987; 243:379-84. [PMID: 2820377 PMCID: PMC1147865 DOI: 10.1042/bj2430379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The reaction kinetics of native and carbodi-imide-modified tuna and horse heart cytochromes c with both a strong (dithionite) and a relatively weak (ascorbate) reducing agent were studied over a wide range of conditions. In their reactions with dithionite both the native and modified cytochromes exhibit single exponential time courses. The effects of dithionite concentration and ionic strength on the rate of the reduction are complex and can best be explained in terms of the model proposed by Lambeth & Palmer [(1973) J. Biol. Chem. 248, 6095-6103]. According to this model, at low ionic strength the native proteins are reduced almost exclusively by S2O4(2-) whereas the modified proteins showed reactivity towards both S2O4(2-) and SO2.-. These findings are interpreted in terms of the different charge characteristics of the carbodi-imide-modified proteins relative to the native proteins. The findings that the modified proteins react with ascorbate in a biphasic manner are explained as arising from ascorbate binding to a reducible form of the protein, before electron transfer, with an equilibrium between the ascorbate-reducible form of the protein and a non-reducible form. Estimates were obtained for both the ascorbate equilibrium binding constant and the rate constant for the internal electron transfer for both the native and modified horse and tuna proteins. The effect of pH on the reactions indicates that the active reductant in all cases is ascorbate2-. The studies of ascorbate reactivity yield important information concerning the proposed correlation between ascorbate reducibility and the presence of a 695 nm-absorption band, and the study of dithionite reactivity illustrates the effect of protein charge and solution ionic strength on the relative contributions made by the species SO2.- and S2O4(2-) to the reduction of ferricytochrome c.
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Rodrigues CG, Farchione F, Wedd AG, Bond AM. Relationship of two electroactive forms of horse heart cytochrome c at gold and glassy carbon electrodes in water and methanol. ACTA ACUST UNITED AC 1987. [DOI: 10.1016/0022-0728(87)87020-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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