While studying several energy-converting enzymes simultaneously, we try to clarify the general mechanisms of bioenergetic coupling, namely to understand the interplay between redox transitions, ion translocation and chemical reactions.
Conformationally-controlled shifts of pK values.By such comparative approach, the conformationally-controlled pK shifting was identified as a new mechanism of enzyme catalysis. The hearth of this concept is that enzymes can go between isoenergetic conformations that differ strongly in the reactivity of their catalytic groups .
Relaxation controlled electron transfer reactions in proteins
As well, upon our studies, we have confronted the fact that the observable rate of ET was essentially determined by the rate of slow protein relaxation in response to the electrical charging of redox center(s). Together with Dr. Dmitry Cherepanov of the A.N.Frumkin Institute of Electrochemistry in Moscow, we defined such ET reactions as relaxation-controlled ones and developed a formalism to describe and analyze them. We showed that the relaxation control over ET in proteins is expected for the low-exothermic reactions and argued that the relaxationally controlled ET prevails in proteins because the vast majority of biological redox reactions are only slightly exothermic .
Scheme of a relaxationally controlled ET reaction. The figure is taken taken from 
Surface-to-surface electrochemical coupling mechanism
The elucidation of the nature of the electrostatic barrier between the membrane surface and the bulk water phase allowed us to redefine the interactions between the membrane energy-converting enzymes. Indeed, the height of the barrier for protons could be estimated as ~0.12 eV. While the proton exchange between the surface and the bulk aqueous phase is retarded by the interfacial barrier, the proton diffusion along the membrane, between neighboring enzymes, takes only microseconds. The proton spreading over the membrane is facilitated by the hydrogen-bonded networks at the surface. The membrane-buried layers of these networks can eventually serve as a storage/buffer for protons (proton sponges). As the proton equilibration between the surface and the bulk aqueous phase is slower than the lateral proton diffusion between the "sources" and "sinks", the proton activity at the membrane surface, as sensed by the energy transducing enzymes at steady state, might deviate from that measured in the adjoining water phase. This trait should increase the driving force for ATP synthesis, especially in the case of alkaliphilic bacteria [1,5].
4. Mulkidjanian, A.Y., K.S. Makarova, M.Y. Galperin and E.V. Koonin. 2007. Inventing the dynamo machine: On the origin of the F-type and V-type membrane ATPases from membrane RNA/protein translocases, Nature Reviews Microbiology, 5:892-899.(Full text, pdf)
8. Mulkidjanian,A.Y., D.A.Cherepanov, and M.A.Kozlova. 2005. Ubiquinone reduction in the photosynthetic reaction center of Rhodobacter sphaeroides: Interplay between electron transfer, proton binding and the flips of quinone ring. Biochem. Soc. Trans. 33:845-850. (Full text, pdf)
Mulkidjanian, A.Y. 2010. Activated Q-cycle as a common mechanism for cytochrome bc1 and cytochrome b6f complexes. Biochim. Biophys. Acta, in press, doi:10.1016/j.bbabio.2010.07.008. (Full text, pdf)
12. Kozlova, M.A., H.D. Juhnke, D.A. Cherepanov, C.R.D Lancaster, A.Y. Mulkidjanian. 2008. Proton transfer in the photosynthetic reaction center of Blastochloris viridis, FEBS Letters, 582, 238-242.(Full text, pdf)
13. Cherepanov, D.A., W. Junge, and A.Y. Mulkidjanian. 2004. Proton transfer dynamics at the membrane/water interface: Dependence on the fixed and mobile pH buffers, the geometry of membrane particles, and the interfacial potential barrier. Biophys. J. 86:665-680.(Full text, pdf)
14. Cherepanov, D.A., B.A. Feniouk, W. Junge, and A.Y. Mulkidjanian. 2003. Low dielectric permittivity of water at the membrane interface: effect on the energy coupling mechanism in biological membranes. Biophys. J. 85:1307-1316.(Full text, pdf)
15.Feniouk, BA, Cherepanov, DA, Junge, W, Mulkidjanian, AY. 2001. Coupling of proton flow to ATP synthesis in Rhodobacter capsulatus: FoF1-ATP synthase is absent from about half of chromatophores. Biochim. Biophys. Acta 1506, 189-203(Full text, pdf)
16. Cherepanov, D.A., and Mulkidjanian, A.Y. 2001. Proton transfer in Azotobacter vinelandii ferredoxin I: Entatic Lys84 operates as elastic counterbalance for the proton-carrying Asp15, Biochim. Biophys. Acta, 1505, 179-184. (Full text, pdf)
17. Cherepanov, D.A., Krishtalik. L.I., Mulkidjanian, A.Y., 2001. Photosynthetic electron transfer controlled by protein relaxation: Analysis by Langevin stochastic approach, Biophysical Journal, 80, 1033-1049.(Full text, pdf)
18. Cherepanov, D.A., S.I. Bibikov, M.V. Bibikova, D.A. Bloch, L.A. Drachev, O.A. Gopta, D. Oesterhelt, A.Y. Semenov, and A.Y. Mulkidjanian. 2000. Reduction and protonation of the bound QB ubiquinone in the photosynthetic reaction centers of Rb. sphaeroides: Kinetic model based on a comparison between wild type chromatophores and the mutants with arginine substituted by isoleucine at 207 and 217 sites in the L-subunit. Biochim.Biophys.Acta, 1459, 10-34.(Full text, pdf)
19. Gopta, O.A., D.A. Cherepanov, W. Junge, and A.Y. Mulkidjanian. 1999. Proton transfer from the bulk to the bound ubiquinone QB of the reaction center in chromatophores of Rhodobacter sphaeroides: Retarded conveyance by neutral water. Proc.Natl.Acad.Sci.U.S.A. 96:13159-13164.(Full text, pdf)
21. Cherepanov, D.A. and A.Y. Mulkidjanian. 1998. Effect of dielectric relaxation on the kinetics of electron transfer in photosynthetic reaction centers. In Photosynthesis: Mechanisms and Effects. G. Garab, editor. Kluwer Academic Publishers, Dordrecht. 795-798.
22. Mulkidjanian, A. and W. Junge. 1995. Electrogenic proton displacements in the cytochrome-bc1 complex of Rhodobacter capsulatus. p. 547-550, In: Photosynthesis: From Light to Biosphere, Vol. II., Kluver Academic Publishers, Dordrecht./p>
23. Mulkidjanian, A. Y., M. D. Mamedov, and L. A. Drachev. 1991. Slow electrogenic events in the cytochrome-bc1 complex of Rhodobacter sphaeroides: The electron transfer between cytochrome b hemes can be non-electrogenic. FEBS Letters 284:227-231.(Full text, pdf)
24. Mulkidjanian, A. Y., M. I. Verkhovsky, V. P. Shinkarev, V. D. Sled', N. P. Grishanova, and B. S. Kaurov. 1985. Study of photosynthetic electron transfer reactions by redox probes: Electron transport in non-sulphur purple bacteria. Biokhimiya 50:1786-1796.