The Reversible Opening of Water Channels in Cytochrome c Modulates the Heme Iron Reduction Potential

Abstract

Dynamic protein-solvent interactions are fundamental for life processes, but their investigation is still experimentally very demanding. Molecular dynamics simulations up to hundreds of nanoseconds can bring to light unexpected events even for extensively studied biomolecules. This paper reports a combined computational/experimental approach that reveals the reversible opening of two distinct fluctuating cavities in Saccharomyces cerevisiae iso-1-cytochrome c. Both channels allow water access to the heme center. By means of a mixed quantum mechanics/molecular dynamics (QM/MD) theoretical approach, the perturbed matrix method (PMM), that allows to reach long simulation times, changes in the reduction potential of the heme Fe(3+)/Fe(2+) couple induced by the opening of each cavity are calculated. Shifts of the reduction potential upon changes in the hydration of the heme propionates are observed. These variations are relatively small but significant and could therefore represent a tool developed by cytochrome c for the solvent driven, fine-tuning of its redox functionality.

Surface Packing Determines the Redox Potential Shift of Cytochrome c Adsorbed on Gold

“…The atomic partial charges for the oxidized heme and the missing parameters describing axial and covalent links between the protein and the heme are taken from the literature. 32 The GolP force field, 34 that includes image charge effects, 35 is adopted for the polarizable Au(111) surface and to describe the interaction of YCC with the gold surface. Note that GolP parameters that describe the Lennard Jones interaction between the gold and the protein atoms were optimized for the OPLS/AA force field while here the protein is parametrized with the gromos96 force field.…”

“…are the same previously used for YCC in water. 32 The first 10 ns and 80 ns are not used for the calculation of the reduction potential of the monomeric and dimeric systems, respectively. It is worth to remark that the dimeric system conformation is not directly extracted from a crystallographic structure but is manipulated in order to achieve the desired orientation between the monomers and toward the surface (see the discussion above).…”

“…46 More details on the quantum chemical calculations (including considerations on the choice of the size of the QC) can be found in the Supporting Information of Ref. 32 …”

“…The calculated redox potentials are summarized in Table 1. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 V, +300±14 mV vs SHE) 32 The comparison between the calculated and the experimental absolute potentials is thus also meaningful and their agreement is good (see Table 1). The results calculated here reproduce the experimental finding of a relevant effect of the electrode coverage on the redox potential of YCC bound to gold.…”

Progress and challenges in simulating and understanding electron transfer in proteins

“…The simulation protocol was applied to evaluate the reduction potential of the Fe(III)/Fe(II) couple. They found the opening of a protein cavity in cytochrome c permits water molecules to enter the cavity, in turn shifting the redox potential of the heme by 50 mV [78]. This mechanism allows the redox potential to be finely tuned for biological function.…”