Misfolding,’ this is a relative term. Researchers commonly consider whether particular
Misfolding,’ this is a relative term. Researchers commonly consider whether particular assemblies of A are `on-pathway’ or `off-pathway,’ but to what pathway do they refer? Typically, the pathway is fibril formation. From a strictly academic perspective, these considerations are meritorious. However, they contribute little to the quest of understanding and treating AD, and for the same reason that folding/misfolding is an irrelevant concept. A assembly comprises a conformational `space,’ not a pathway per se. This space comprises many pathways that result in equilibria among A monomers and higher-order structures. Fibril formation simply is one of many different `random walks’ [76] (stochastic events, although with different occurrence frequencies) that nascent A monomers may take. The therapeutically relevant question is: `what positions in A conformational space are occupied by neurotoxic structures?’Generic structureWhen myoglobin was shown to form amyloid fibrils in 50 mM sodium borate, pH 9.0, at 65 [77], conditions known to destabilize the protein’s native fold, the concept emerged that amyloid formation could be a default process through which many, if not all, proteins might proceed [78]. The result of this process, both structurally and immunologically, was the formation of a `generic’ amyloid structure [79]. Many, or even most, proteins may form amyloid, but the process is not generic per se [80]. The process is simply one pathway through assembly space that leads to a particularly low-energy state.c The actual amyloid conformers formed by different proteins are not `generic.’ They are structurally distinct, one from the other, because their primary structures are not identical. If we stipulate this fact, then we can discuss amyloid structural motifs, which are non-identical in structure but do share some structural characteristics. The most compelling example of this is the steric zipper [81]. X-ray crystallographic studies have shown how this steric zipper can constitute the cross- structure of amyloid fibrils and how side-chain and peptide backbone interactions stabilize the structure. The steric zipper is a structural motif, but it is not generic per se. At least eight different structural forms of the steric zipper exist [69].Generic oligomer epitopePolyclonal antibody reagents cannot reveal different epitopes existing in oligomers formed by different proteins. The different immunoglobulins comprising the antibody mixture will bind to different epitopes and the result will be a positive dot blot or Western blot for each of many different proteins. The deduction that a JNJ-26481585 price common epitope exists is illogical and fallacious. The explanation lies in antibody cross-reactivity. However, even if a monoclonal antibody, which by definition expresses a single idiotope, binds to oligomers formed by distinct proteins, this does not support the conjecture that a common `oligomer-specific’ epitope exists. The correct conclusion is that the antibody binds to the protein under study, nothing more. Competition assays and X-ray crystallographic analyses are necessary to determine the structure of the epitope. Such studies will elucidate the binding PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/27385778 modes of different oligomers and, for oligomers of different primary structure, will show the atomic basis for antibody affinity and cross-reactivity. These studies also can determine dissociation constants for each antigen:antibody complex. It is important to note, as I discussed immediately above.
