# Heads and tails: Energetic and structural bases of binding and electron transfer performance of cofactors at the Q(A) site of the reaction center protein from Rhodobacter sphaeroides

#### Abstract

Factors controlling cofactor binding and electron transfer function at the primary quinone, Q$\sb{\rm A}$ site in isolated reaction center protein from Rhodobacter sphaeroides are determined from effects of quinone cofactor head group and tail structure alterations on: (1) Q$\sb{\rm A}$ site binding free energy in water ($\rm\Delta G\sbsp{\rm B,W}{\circ}$) and hexane ($\rm\Delta G\sbsp{\rm B,H}{\circ}$), (2) cofactor electrochemical potential in the site relative to dimethylformamide solution, and (3) temperature and reaction free energy dependences of the electron transfer rate constants for Q$\sb{\rm A}$ reduction by bacteriopheophytin (k$\sb1$) and charge recombination with the oxidized bacteriochlorophyll dimer (k$\sb{\rm b}$). A thermodynamic cycle formalism is developed to resolve intrinsic ligand-protein interaction and aqueous solvation contributions to binding. Relative to hexane, the aqueous solvation contribution to $\rm\Delta G\sbsp{\rm B,W}{\circ}$ is specified by 0.8$\rm\Delta G\sbsp{\rm tr}{\circ}$, where $\rm\Delta G\sbsp{\rm tr}{\circ}$ is the quinone solvent transfer free energy (range: -0.5 to -6.8 Kcal/mole). Effects of systematic variation of the native isoprene tail structure on $\rm\Delta G\sbsp{\rm B,H}{\circ}$ and $\rm\Delta G\sbsp{\rm B,W}{\circ}$ at the Q$\sb{\rm A}$ and secondary, Q$\sb{\rm B}$ sites reveals: (1) a defined tail binding domain spanning the first three isoprene units, and (2) a strong binding specificity for the isoprene relative to saturated alkyl structures ($>$4.1 Kcal/mole). Tail structure does not significantly influence electron transfer rates (variation of k$\sb1$ and k$\sb{\rm b}$ $<$5 fold). Comparison of Q$\sb{\rm A}$ site $\rm\Delta G\sbsp{\rm B,H}{\circ}$ values of quinone and analog head groups in which one or both carbonyl groups are removed shows that one carbonyl oxygen atom dominates hydrogen bond contact with the protein ($\rm\Delta H$ = -3.5 Kcal/mole). In contrast, both oxygen atoms participate in the semiquinone-site interaction, as shown by a 166 mV loss of in situ cofactor redox couple stability relative to DMF associated with single removal. The rationally-selected exotic cofactors tetrafluoro- and trinitro-fluorenone, and m-dinitrobenzene display k$\sb1$ and k$\sb{\rm b}$ dependences on temperature (7 to 295 K) and reaction free energy ($\rm\Delta G\sbsp{\rm et}{\circ}$) that are comparable with quinones. These results indicate that: (1) structural elements of the native quinone-Q$\sb{\rm A}$ site interaction are not essential for electron transfer function, and (2) the values of k$\sb1$ and k$\sb{\rm b}$ appear to be determined at the Q$\sb{\rm A}$ site primarily through the contribution of the in situ electrochemical free energy of the cofactor to $\rm\Delta G\sbsp{\rm et}{\circ}$.

#### Subject Area

Biochemistry|Biophysics

#### Recommended Citation

Warncke, Kurt, "Heads and tails: Energetic and structural bases of binding and electron transfer performance of cofactors at the Q(A) site of the reaction center protein from Rhodobacter sphaeroides" (1990). Dissertations available from ProQuest. AAI9026666.
https://repository.upenn.edu/dissertations/AAI9026666

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