Chinese Journal of Magnetic Resonance >

2023 , Vol. 40 >Issue 1: 22 - 29

DOI: https://doi.org/10.11938/cjmr20222985

Articles

Track the Conformational Change of Unlabeled Yeast Cytochrome c in Cell Homogenate Using NMR

  • Jianhua ZHAN ,
  • Qin HU ,
  • Qinjun ZHU ,
  • Bin JIANG ,
  • Xu ZHANG ,
  • Maili LIU
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  • 1. State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan (Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences), Wuhan 430071, China
    2. University of Chinese Academy of Sciences, Beijing 100049, China
    3. Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
    4. Optics Valley Laboratory, Wuhan 430074, China

Received date: 2022-03-21

  Online published: 2022-04-28

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Abstract

Cytochrome c (cyt c) is an important multifunctional protein. In mitochondria, it acts as a carrier for electron transporting. In cytoplasm, it may act as an apoptotic initiator to initiate the apoptotic process. Whether and how a complex cytoplasmic environment affects its conformation has not been confirmed yet. In this study, the conformational changes of wild type saccharomyces cerevisiae iso-1 cyt c in yeast cell homogenate were tracked by methyl-based nuclear magnetic resonance (NMR) technique. At least four different oxidative conformations and one reduced conformation of cyt c were identified in cell homogenate. And over time, the transitions among different conformations of cyt c were observed. The results indicate that the conformation of cyt c changes with environment, which may be closely related to resistance to oxidative stress.

Key words： nuclear magnetic resonance (NMR); conformational change; methyl; cytochrome c

Cite this article

Jianhua ZHAN , Qin HU , Qinjun ZHU , Bin JIANG , Xu ZHANG , Maili LIU . Track the Conformational Change of Unlabeled Yeast Cytochrome c in Cell Homogenate Using NMR[J]. Chinese Journal of Magnetic Resonance, 2023 , 40(1) : 22 -29 . DOI: 10.11938/cjmr20222985

References

[1] SAREWICZ M, OSYCZKA A. Electronic connection between the quinone and cytochrome c redox pools and its role in regulation of mitochondrial electron transport and redox signaling[J]. Physiol Rev, 2015, 95(1): 219-243.
[2] BAISTROCCHI P, BANCI L, BERTINI I, et al. Three-dimensional solution structure of Saccharomyces cerevisiae reduced iso-1-cytochrome c[J]. Biochemistry, 1996, 35(43): 13788-13796.
[3] BANCI L, BERTINI I, BREN K L, et al. Solution structure of oxidized saccharomyces cerevisiae iso-1-cytochrome c[J]. Biochemistry, 1997, 36(29): 8992-9001.
[4] FANG Z P, SUN P, WANG Q W, et al. Conformational change of wild type cytochrome c characterized by NMR spectroscopy at natural isotropic abundance[J]. Chinese J Magn Reson, 2019, 36 (4): 481-489.
[4] 方仲佩, 孙鹏, 王倩文, 等. 天然同位素丰度野生型酵母细胞色素c构象变化的核磁共振检测[J]. 波谱学杂志, 2019, 36 (4): 481-489.
[5] BROWN G C, BORUTAITE V. Regulation of apoptosis by the redox state of cytochrome c[J]. BBA-Bioenergetics, 2008, 1777(7-8): 877-881.
[6] MADEO F, HERKER E, WISSING S, et al. Apoptosis in yeast[J]. Curr Opin Microbiol, 2004, 7(6): 655-660.
[7] OW Y P, GREEN D R, HAO Z Y, et al. Cytochrome c: functions beyond respiration[J]. Nat Rev Mol Cell Biol, 2008, 9(7): 532-542.
[8] RIPPLE M O, ABAJIAN M, SPRINGETT R. Cytochrome c is rapidly reduced in the cytosol after mitochondrial outer membrane permeabilization[J]. Apoptosis, 2010, 15(5): 563-573.
[9] BORUTAITE V, BROWN G C. Mitochondrial regulation of caspase activation by cytochrome oxidase and tetramethylphenylenediamine via cytosolic cytochrome c redox state[J]. J Biol Chem, 2007, 282(43): 31124-31130.
[10] MENDEZ D L, AKEY I V, AKEY C W, et al. Oxidized or reduced cytochrome c and axial ligand variants all form the apoptosome in vitro[J]. Biochemistry, 2017, 56(22): 2766-2769.
[11] MUENZNER J, TOFFEY J R, HONG Y N, et al. Becoming a peroxidase: Cardiolipin-induced unfolding of cytochrome c[J]. J Phys Chem B, 2013, 117(42): 12878-12886.
[12] VEITCH N C. Horseradish peroxidase: a modern view of a classic enzyme[J]. Phytochemistry, 2004, 65(3): 249-259.
[13] HANNIBAL L, TOMASINA F, CAPDEVILA D A, et al. Alternative conformations of cytochrome c: Structure, function, and detection[J]. Biochemistry, 2016, 55(3): 407-428.
[14] YIN V, SHAW G S, KONERMANN L. Cytochrome c as a peroxidase: Activation of the precatalytic native state by H2O2-induced covalent modifications[J]. J Am Chem Soc, 2017, 139(44): 15701-15709.
[15] MORENO-BELTRAN B, GUERRA-CASTELLANO A, DIAZ-QUINTANA A, et al. Structural basis of mitochondrial dysfunction in response to cytochrome c phosphorylation at tyrosine 48[J]. Proc Natl Acad Sci U S A, 2017, 114(15): E3041-E3050.
[16] BANCI L, BERTINI I, REDDIG T, et al. Monitoring the conformational flexibility of cytochrome c at low ionic strength by 1H-NMR spectroscopy[J]. Eur J Biochem, 2010, 256(2): 271-278.
[17] KOU X H, LIU Y X, LIU X H, et al. Visualizing the pre-active conformation of response regulator PhoBNF20D in its apo state[J]. Chinese J Magn Reson, 2019, 36(2): 164-171.
[17] 寇新慧, 刘乙祥, 刘兴弘, 等. 探测应答调控蛋白PhoBNF20D自由态中存在的Pre-Active构象[J]. 波谱学杂志, 2019, 36(2): 164-171.
[18] CROWLEY P B, CHOW E, PAPKOVSKAIA T. Protein interactions in the Escherichia coli cytosol: an impediment to in-cell NMR spectroscopy[J]. ChemBioChem, 2011, 12(7): 1043-1048.
[19] NYGAARD R, ZOU Y, DROR R O, et al. The dynamic process of beta(2)-adrenergic receptor activation[J]. Cell, 2013, 152(3): 532-542.
[20] KERFAH R, PLEVIN M J, SOUNIER R, et al. Methyl-specific isotopic labeling: a molecular tool box for solution NMR studies of large proteins[J]. Current Opinion in Structural Biology, 2015, 32: 113-122.
[21] KLUCK R M, ELLERBY L M, ELLERBY H M, et al. Determinants of cytochrome c pro-apoptotic activity - the role of lysine 72 trimethylation[J]. J Biol Chem, 2000, 275(21): 16127-16133.
[22] SUN P, WANG Q W, YUAN B, et al. Monitoring alkaline transitions of yeast iso-1 cytochrome c at natural isotopic abundance using trimethyllysine as a native NMR probe[J]. Chem Commun, 2018, 54(89): 12630-12633.
[23] SZABO C M, SANDERS L K, LE H C, et al. Expression of doubly labeled Saccharomyces cerevisiae iso-1 ferricytochrome c and H-1,C-13 and N-15 chemical shift assignments by multidimensional NMR[J]. Febs Letters, 2000, 482(1-2): 25-30.
[24] NAIYER A, KHAN B, HUSSAIN A, et al. Stability of uniformly labeled (13C and 15N) cytochrome c and its L94G mutant[J]. Sci Rep, 2021, 11(1): 6804.
[25] HAMPTON M B, ZHIVOTOVSKY B, SLATER A F G, et al. Importance of the redox state of cytochrome c during caspase activation in cytosolic extracts[J]. Biochem J, 1998, 329: 95-99.
[26] COLON W, WAKEM L P, SHERMAN F, et al. Identification of the predominant non-native histidine ligand in unfolded cytochrome c[J]. Biochemistry, 1997, 36(41): 12535-12541.
[27] NELSON C J, BOWLER B E. pH dependence of formation of a partially unfolded state of a Lys 73→His variant of iso-1-cytochrome c:? Implications for the alkaline conformational transition of cytochrome c[J]. Biochemistry, 2000, 39(44): 13584-13594.
[28] YIN V, MIAN S H, KONERMANN L. Lysine carbonylation is a previously unrecognized contributor to peroxidase activation of cytochrome c by chloramine-T[J]. Chem Sci, 2019, 10(8): 2349-2359.
[29] DAI D F, CHIAO Y A, MARCINEK D J, et al. Mitochondrial oxidative stress in aging and healthspan[J]. Longevity & Healthspan, 2014, 3: 6.
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