Kinetic vs. Thermodynamic Variables Governing Protein Tyrosyl Radical Migration and Reduction in Heme Binding Proteins

One point that comes out of these articles [Reeder et al., 2008: (http://www.ncbi.nlm.nih.gov/pubmed/18215735); Reeder et al., 2008b: (http://www.ncbi.nlm.nih.gov/pubmed/18215736)] and that I think is important is that, in view of the fact that protonated, protein-bound perferryl heme is thought to contribute heavily to the damaging effects of acellular myoglobin or hemoglobin and that the concentration of the most damaging, protonated ferryl heme species (which is likely to consist, primarily, of protein-bound perferryl heme with a tyrosyl radical, given that ferryl heme, as in compound II, apparently is protonated under normal circumstances, constitutively) was estimated to be one-10-millionth of the concentrations of the deprotonated species (Reeder et al., 2008b), protein-bound, protonated perferryl heme may be as much as ten million times as damaging as deprotonated perferryl (and ferryl) hemes are. More importantly, the "through-protein" radical transfer reactions and also the capacities of reductants, such as those that concentrate in lysosomes as lysosomotropic amines that exhibit net charges of -3 at pH 7.4 and of +1 at the lysosomal pH range of 4-5, to reduce perferryl heme appear to be governed more by thermodynamic variables than kinetic variables (Reeder et al., 2008b), meaning that the rates of reduction are slow and plateau at concentrations that are relatively low. That seems to me to be a key point that emerges from the articles, and Reeder et al. (2008b) are basically saying that the reductions, by some of these reductants, of tyrosyl radicals on myoglobin are slow and that pH (in this case, acidic pH), which is a thermodynamic variable [Mongan and Case, 2005: (http://www.ncbi.nlm.nih.gov/pubmed/15837173)] that can affect the redox potentials for redox reactions (see Schaefer and Buettner, 2001, cited in past postings), causes a fraction of myoglobin to exist as a species in which perferryl heme is protonated and a tyrosyl radical near to the heme binding site is deprotonated. In essence, some reductants seem to be able to gain "thermodynamically-privileged" access, as reductants, to this species, given that other reductants' charge distribution or intracellular localization may hinder, in pH-dependent manners, their capacities to serve as reductants of this particular fraction of protein-bound perferryl heme. The pH and other thermodynamic variables cause tyrosyl radicals to form and be reduced slowly by reductants, perhaps in a manner that's specific to the pH-dependence of the charge distribution on the reductant. These authors [Al-Ayash and Wilson, 1979: (http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1186415&blobtype=pdf)(http://www.ncbi.nlm.nih.gov/pubmed/35158)] suggested, similarly, that the failure of ascorbate to reduce an "alkaline isomer" of cytochrome c might have been explainable in terms of thermodynamic variables and not kinetic ones. The within-protein radical transfer reactions that govern the location of a protein radical, at any given time, also tend to be driven by thermodynamics and not kinetics. For example, the thermodynamic "product" of within-protein, radical transfer reactions in equine myoglobin, in one case, was a tyrosyl radical that was closer to the site at which the radical initiated (namely, heme), and the kinetic "transfer product" was an indolyl radical on a tryptophan residue that was farther from the initiation site than the tyrosyl radical was. That's not the scenario one would expect to see if the within-protein radical transfer migration were governed by kinetics. The protein tyrosyl radicals that have been identified in many heme binding proteins are long-lived, and this contrasts with the extremely short half-life of other protein tyrosyl radicals and of free tyrosyl radicals. Additionally, some reductants are inefficient reductants of free tyrosyl radicals because of kinetic factors that make those reactions unfavorable. Anyway, it's an interesting area. Another factor, other than charge distribution per se, could be the presence of amide groups that don't serve as ligands in organometallic "complexation" reactions but that have been shown to be sites at which prokaryotic serine proteases cleave the reductants [Winkelmann et al., 1999: (http://www.bashanfoundation.org/hartmann/hartmannirakense.pdf)(http://www.ncbi.nlm.nih.gov/pubmed/10581690); Zaya et al., 1998: (http://www.ncbi.nlm.nih.gov/pubmed/9734303)]. Given that some reductants are substrates of prokaryotic serine proteases, some of the protein reductions might be lysosomal-protease-specific in some way or involve the kinds of amide-aromatic or amide-tyrosyl-specific interactions that are known to be important in determining the tertiary and quaternary structures of proteins [Toth et al., 2001: (http://www.ncbi.nlm.nih.gov/pubmed/11340654); (http://scholar.google.com/scholar?hl=en&q=%22aromatic+amide%22+OR+%22amide+aromatic%22&as_sdt=2000&as_ylo=&as_vis=0); (http://scholar.google.com/scholar?hl=en&q=amide+aromatic+interactions&as_sdt=2000&as_ylo=&as_vis=0)]. Ayala et al. (2002) [Ayala et al., 2002: (http://pubs.acs.org/doi/abs/10.1021/ja0164327)] found evidence for a sequence-specific interaction between amide groups and tyrosyl radicals, etc., as one might expect, given that tyrosine is, obviously, a major aromatic amino acid (and given that histidine is an aromatic molecule at all pH values but is not classified as being an aromatic amino acid, given that it is basic, aromatic, and carries a net charge) and, along with histidine, tends to be present near to or as part of the heme binding sites of heme-binding proteins (or as an axial ligand of heme) [(http://scholar.google.com/scholar?hl=en&q=amide+interactions+aromatic+tyrosyl+OR+tyrosine&as_sdt=2000&as_ylo=&as_vis=0); (http://scholar.google.com/scholar?hl=en&q=amide+interactions+aromatic+histidyl+OR+histidine&as_sdt=2000&as_ylo=&as_vis=0)].