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The composition of ferric exogenous ligand-free His93Gly sperm whale myoglobin (H93G Mb) at neutral pH has been determined by examination of the spectral properties of the protein over the pH range from 3.0 to 10.5. An apparent pK_a value of ~6.6 has been observed for the conversion of a postulated six-coordinate bis-water-bound coordination structure at pH 5.0 to a five-coordinate hydroxide-bound form at pH 10.5. Starting from the exogenous ligand-free ferric H93G protein, ferric mono- and bis-thioether (tetrahydrothiophene, THT)-ligated adducts have been prepared and characterized by UV-visible (UV-vis) absorption and magnetic circular dichroism (MCD) spectroscopy. The mon-THT ferric H93G Mb species has hydroxide as the sixth ligand. The bis-THT derivative is a model for the low-spin ferric heme binding site of native bis-Met-ligated bacterioferritin or streptococcal heme-associated protein (Shp). A novel THT-bound ferryl H93G Mb moiety has been partially formed. The high-spin five-coordinate ferric H93G(selenolate) Mb complex has been prepared using benzeneselenol and characterized by UV-vis and MCD spectroscopy as a model for Se-Cys-ligated ferric cytochrome P450. The results described herein further demonstrate the versatility of the H93G cavity mutant for modeling the coordination structures of novel heme iron protein active sites.

Three manganese biscorrole dyads were synthesized, physicochemically characterized and investigated as to their electrochemistry and spectroelectrochemistry in nonaqueous media. Each dyad contained the same two corroles linked in a face-to-face arrangement via one of the three different linking groups, 9,9-dimethylxanthene, anthracene or diphenylether, the exact nature of which determined the distance and possible interaction between the two metallomacrocycles. The initial compounds contained Mn(III) in their air stable form and were shown to exhibit two major redox processes, one being a Mn(III)/Mn(IV) conversion and the other being either Mn(III)/Mn(II) or reduction at the conjugated macrocycle to give a Mn(III) corrole π-anion radical when the solvent was pyridine. The potentials and reversibility of each electron transfer reaction were shown to depend upon the solvent (pyridine, CH₂Cl₂, or PhCN), type of spacer separating the two macrocycles and/or the presence or absence of axial ligation. The site of each electron transfer was assigned on the basis of spectroscopic and electrochemical data and by comparison with reactions and properties of the monocorrole (Mes₂PhCor)Mn which was characterized in a previous publication and also examined in the current study under the same solution conditions as the newly investigated dyads. Some electrode reactions of the dyads were followed by coupled chemical reactions and these were also elucidated in the present study.

UV-vis absorption and emission studies on zinc and iron porphyrin complexes bearing H-bonding distal superstructures have been performed in two different organic solvents- tetrahydrofuran (THF) (coordinating) and dichloromethane (DCM) (non-coordinating). Quantum yields and lifetimes have been measured for these complexes which are in good agreement with the other reported metalloporphyrins. Binding affinities with anionic ligands such as N_3^-, CN^-, S^-2, F^- were monitored for these two complexes in aqueous media and the respective binding constant values were calculated. The Zn complex shows more selectivity towards cyanide while the Fe complex shows more selectivity towards azide.

Assembling an “integrated structural map of the human cell” at atomic resolution will require a complete set of all human protein structures available for interaction with other biomolecules - the human protein structure targetome - and a pipeline of automated tools that allow quantitative analysis of millions of protein-ligand interactions. Toward this goal, we here describe the creation of a curated database of experimentally determined human protein structures. Starting with the sequences of 20,422 human proteins, we selected the most representative structure for each protein (if available) from the protein database (PDB), ranking structures by coverage of sequence by structure, depth (the difference between the final and initial residue number of each chain), resolution, and experimental method used to determine the structure. To enable expansion into an entire human targetome, we docked small molecule ligands to our curated set of protein structures. Using design constraints derived from comparing structure assembly and ligand docking results obtained with challenging protein examples, we here propose to combine this curated database of experimental structures with AlphaFold predictions and multi-domain assembly using DEMO2 in the future. To demonstrate the utility of our curated database in identification of the human protein structure targetome, we used docking with AutoDock Vina and created tools for automated analysis of affinity and binding site locations of the thousands of protein-ligand prediction results. The resulting human targetome, which can be updated and expanded with an evolving curated database and increasing numbers of ligands, is a valuable addition to the growing toolkit of structural bioinformatics.