Catalytic center of cytochrome c oxidase: Effects of protein environment on pKa values of CuB histidine ligands

Dragan M. Popović, Ivana S. Đorđević


Molecular mechanism by which the electron transfer (ET) is coupled to proton pumping in cytochrome oxidase is one of main unsolved problems in biochemistry. Particularly, the nature and position of the proton-loading site is under dispute. The CuB complex has three ligated histidines, whereas only His290 and His291 are ionizable sites with the equal pKas in aqueous solution, but apparently quite different ones within the enzyme. Earlier, it was proposed a model of proton pumping with the central role of His290. Recent calculations indicate that His291 ligand of CuB center might play the role of the pumping element, since its protonation state depends on the oxidation state of the binuclear complex (BNC). The present electrostatic study is applied to assess the role of the protein environment on acidity of the two histidines. Their pKa values and effects of different energy terms are evaluated to discover the nature of their diverse behavior in the enzyme. Here, a new set of pKas for the non-standard model compounds within the BNC is applied. The enhanced results are compared with results of previous studies in the light of the plausible proton pumping mecha­nism. The obtained microscopic and apparent pKa values in the oxidized state of BNC are virtually the same, indicating that deprotonated form of His291 accounts for the large pKa increase of His290, since the both titratable sites on CuB center cannot simultaneously be in the charged state. The present results support the underlined His291 pumping model.


Bioenergetics; binuclear complex; bovine; histidine ligands; linear Poisson-Boltzmann equation; pKa calculations; reaction and protein field

Full Text:

PDF (902 kB)


M. Wikström, K. Krab, V. Sharma, Chem. Rev. 118 (2018) 2469 (

J. P. Shapleigh, J. P. Hosler, M. M. J. Tecklenburg, Y. Kim, G. T. Babcock, R. B. Gennis, S. Ferguson-Miller, Proc. Natl. Acad. Sci. USA 89 (1992) 4786 (

J. P. Hosler, S. Ferguson-Miller, D. A. Mills, Annu. Rev. Biochem. 75 (2006) 165 (

L. Qin, J. Liu, D. A. Mills, D. A. Proshlyakov, C. Hiser, S. Ferguson-Miller, Biochemistry 48 (2009) 5121 (

A. A. Konstantinov, S. Siletsky, D. Mitchell, A. Kaulen, R. B. Gennis, Proc. Natl. Acad. Sci. USA 94 (1997) 9085 (

A. K. L. Dürr, J. Koepke, P. Hellwig, H. Müller, H. Angerer, G. Peng, E. Olkhova, O. M. H. Richter, B. Ludwig, H. Michel, J. Mol. Biol. 384 (2008) 865 (

S. Yoshikawa, K. Shinzawa-Itoh, R. Nakashima, R. Yaono, E. Yamashita, N. Inoue, M. Yao, M. J. Fei, C. P. Libeu, T. Mizushima, H. Yamaguchi, T. Tomizaki, T. Tsukihara, Science 280 (1998) 1723 (

A. M. Svensson-Ek, J. Abramson, G. Larsson, S. Tornroth, P. Brzezinski, S. Iwata, J. Mol. Biol. 321 (2002) 329 (

T. Tsukihara, K. Shimokata, Y. Katayama, H. Shimada, K. Muramoto, H. Aoyama, M. Mochizuki, K. Shinzawa-Itoh, E. Yamashita, M. Yao, Y. Ishimura, S. Yoshikawa, Proc. Natl. Acad. Sci. USA 100 (2003) 15304 (

N. Yano, K. Muramoto, A. Shimada, S. Takemura, J. Baba, H. Fujisawa, M. Mochizuki, K. Shinzawa-Itoh, E. Yamashita, T. Tsukihara, S. Yoshikawa, J. Biol. Chem. 291 (2016) 23882 (

H. Michel, Proc. Natl. Acad. Sci. USA 95 (1998) 12819 (

T. K. Das, C. M. Gomes, M. Teixeira, D. L. Rousseau, Proc. Natl. Acad. Sci. USA 96 (1999) 9591 (ttps://

M. Wikström, Biochim. Biophys. Acta. 1458 (2000) 188 (

D. M. Popovic, A. A. Stuchebrukhov, J. Am. Chem. Soc. 126 (2004) 1858 (

K. Faxen, G. Gilderson, P. Ädelroth, P. Brzezinski, Nature 437 (2005) 286 (

Y. Song, E. Michonova-Alexova, M. R. Gunner, Biochemistry 45 (2006) 7959 (

M. A. Sharpe, S. Ferguson-Miller, J. Bioenerg. Biomembr. 40 (2008) 541 (

J. A. Fee, D. A. Case, L. Noodleman, J. Am. Chem. Soc. 130 (2008) 15002 (

S. A. Siletsky, A. A. Konstantinov, Biochim. Biophys. Acta 1817 (2012) 476 (

I. Belevich, D. A. Bloch, N. Belevich, M. Wikström, M. I. Verkhovsky, Proc. Natl. Acad. Sci. USA, 104 (2007) 2685 (

S. Han, S. Takahashi, D. L. Rousseau, J. Biol. Chem. 275 (2000) 1910 (

M. Wikström, Biochim. Biophys. Acta 1655 (2004) 241 (

P. Brzezinski, R. B. Gennis, J. Bioenerg. Biomembr. 40 (2008) 521 (

C. M. Soares, A. M. Baptista, M. M. Pereira, M. Teixeira, J. Biol. Inorg. Chem 9 (2004) 124 (

D. M. Popovic, I. V. Leontyev, D. G. Beech, A. A. Stuchebrukhov, Proteins Struct. Funct. Bioinform., 78 (2010) 2691 (

D. M. Popovic, Amino Acids 45 (2013) 1073 (

W.-G. Han Du, A. W. Götz, L. Noodleman, Inorg. Chem. 57 (2018) 1048 (

D. M. Popovic, A. A. Stuchebrukhov, FEBS Letters 566 (2004) 126 (

D. M. Popovic, A. A. Stuchebrukhov, J. Phys. Chem. B 109 (2005) 1999 (

D. M. Popovic, J. Quenneville, A. A. Stuchebrukhov, J. Phys. Chem. B 109 (2005) 3616 (

J. Quenneville, D. M. Popovic, A. A. Stuchebrukhov, Biochim. Biophys. Acta, 1757 (2006) 1035 (

D. M. Popovic, A. A. Stuchebrukhov, Biochim. Biophys. Acta 1817 (2012) 506 (

D. M. Popovic, A. A. Stuchebrukhov, Photochem. Photobiol. Sci. 5 (2006) 611 (

D. Bashford, K. Gerwert, J. Mol. Biol. 224 (1992) 473 (

D. Bashford, Scientific Computing in Object-Oriented Parallel Environments, Springer, Berlin, Germany, 1997, p. 233 (

M. R. Gunner, B. Honig, Proc. Natl. Acad. Sci. USA, 88 (1991) 9151 (

A.-S. Yang, M. R. Gunner, R. Sompogna, B. Honig, Prot. Struct. Funct. Genet. 15 (1993) 252 (

D. Bashford, D. A. Case, C. Dalvit, L. Tennant, P. E. Wright, Biochemistry 32 (1993) 8045 (

P. Beroza, D. R. Fredkin, J. Comput. Chem. 17 (1996) 1229 (¬1096-987X(19960730)17:10<1229::AID-JCC4>3.0.CO;2-Q)

J. Antosiewicz, J. M. Briggs, A. H. Elcock, M. K. Gilson, J. A. McCammon, J. Comput. Chem. 17 (1996) 1633 (<1633::AID-JCC5>3.0.CO;2-M)

J. Li, M. R. Nelson, C. Y. Peng, D. Bashford, L.Noodleman, J. Phys. Chem. A, 102 (1998) 6311 (

A. Warshel, A. Papazyan, Curr. Op. Struct. Biol. 8 (1998) 211 (

P. J. Martel, C. M. Soares, A. M. Baptista, M. Fuxreiter, G. Naray-Szabo, R. O. Louro, M. A. Carrondo, J. Biol. Inorg. Chem. 4 (1999) 73 (

D. M. Popovic, A. Zmiric, S. D. Zaric, E. W. Knapp, J. Am. Chem. Soc. 124 (2002) 3775 (

J. Quenneville, D. M. Popovic, A. A. Stuchebrukhov, J. Phys. Chem. B 108 (2004) 18383 (

D. M. Popovic, S. D. Zaric, B. Rabenstein, E. W. Knapp, J. Am. Chem. Soc. 123 (2001) 6040 (

V. Couch, D. Popovic, A. A. Stuchebrukhov, Biophys. J. 101 (2011) 431 (

D. S. Cerutti, N. A. Baker, J. A. McCammon, J. Chem. Phys. 127 (2007) 155101 (

D. V. Makhov, D. M. Popovic, A. A. Stuchebrukhov, J. Phys. Chem. B. 110 (2006) 12162 (


Copyright (c) 2020 Journal of the Serbian Chemical Society

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

5 Year Impact Factor 1.023
138 of 177 journals)