Phenylalanine residues were placed at the center of each helical region ( a positions 15 and 53) to separate the two heme-binding sites, and a pair of Arg were placed at d positions 5 and 63 to modulate the redox potential of the heme in the H8,H60-binding site. By analogy to H10H24, His were placed in four heptad a positions (positions 8, 22, 46, and 60) in HLH–FdM for the purposes of binding hemes. The helices are comprised of minor variations of four coiled-coil heptad repeats of 4 ( 3). The peptide HLH–FdM, Ac-L KKLREEH LKLLEEF KKLLEEH LKLCE GGCIACGACGGGG ELWKL HEELLKK FEELLKL HEERLKK L-CONH 2, is designed to contain two helical regions of ≈27 amino acids, each joined by the FdM sequence that serves to terminate the α helices and to ligate a cluster in a rudimentary turn. Using helices consistent with the prototype heme–peptide maquette H10H24, a tetra-helix bundle that binds one to four hemes ( 9), we designed a –heme maquette, HLH–FdM. RESULTS Design of FdM.Īs indicated above, the natural sequence FdM was designed to lend itself to integration into larger structures as a basis for the construction of more sophisticated multicofactor maquettes. The doubly integrated spectral area was plotted against potential, and the data were fit to the Nernst equation with n = 1.0 (fixed), as shown in the Inset to Fig. Each spectrum is presented as the difference between an oxidized reference spectrum (−200 mV) and the reduced spectrum. After equilibration at each potential, a 300-μl sample was removed and frozen in liquid nitrogen, and the EPR spectrum was recorded. Electrode-solution mediation was facilitated by the following mediators at a 10-μM concentration: neutral red, 2-hydroxy-1,4-naphthoquinone, safranine T, and phenosafranine. Titrations were performed in 50 mM Hepes (pH 8.0) and 100 mM KCl. Ambient redox potentials (measured against the standard hydrogen electrode) were adjusted by addition of aliquots (<1 μl) of sodium dithionite or potassium ferricyanide. Solution Molecular Mass Determination.Ĭhemical redox titrations were performed in a cuvette within an inert atmosphere glove box with platinum working and calomel reference electrodes ( 33). The peptides were homogeneous and of the correct composition as assayed by analytical HPLC and laser desorption mass spectrometry. Crude peptides were precipitated and triturated with cold ether, dissolved in water (0.1% trifluoroacetic acid), lyophilized, and purified to homogeneity by reversed phase C 18 HPLC using aqueous–acetonitrile gradients containing 0.1% (vol/vol) trifluoroacetic acid. The peptides were cleaved from the resins and simultaneously deprotected using 90:8:2 trifluoroacetic acid/ethanedithiol/water for 2 h. The N terminus of the HLH-FdM was acetylated. The side chain protecting groups used were as follows: histidine (tert-butoxycarbonyl) lysine (tert-butoxycarbonyl) glutamic acid (OBu t) cysteine (trityl) arginine (Pmc). The peptides were synthesized on a continuous flow MilliGen model 9050 solid phase synthesizer using standard fluorenylmethoxycarbonyl/Bu t protection strategy. Additionally, the development of modular protein domains that can be spliced together to form multicofactor peptides offers a systematic approach to the design of more elaborate self-assembling biological structures. However, maquettes offer a tractable system in which to study the assembly of these biological cofactors in aqueous media to determine their delicate interplay with the surrounding heterogeneous chiral protein matrix, a major principle in the acquisition of biological specificity and activity. The interaction of iron–sulfur clusters with thiolate ligands in organic solvents has been studied extensively, and, in fact, preassembled clusters have been incorporated into cysteine-containing peptides in dimethyl sulfoxide/water (80:20) ( 15). The challenge evident in the synthesis of ferredoxin maquettes is to design a peptide that not only self-assembles iron and sulfur ions but also guides the formation of a single cluster architecture. As widespread and biochemically diverse as the heme proteins, the ferredoxins and related iron sulfur proteins differ from heme proteins in that they display a multitude of cluster nuclearities and coordination geometries ( 14).
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