Evidence of native-like substructure(s) in polypeptide chains of carbonic anhydrase deposited into insoluble aggregates during thermal unfolding

'Nunchuck' proteins: Short flexible linkers resist proteolysis by facilitating motions in flanking domains to inhibit the approach of proteases

Peptides linking well-folded and non-interacting domains in fusion proteins can undergo proteolytic degradation. This leads to physical separation of the domains that were originally sought to be joined. In order to identify characteristics that determine linker degradation propensity, we selected a pair of thermostable, proteolytically-resistant domains, and joined them using five different linkers. We then assessed linker degradation propensities through size-exclusion chromatography, and denaturing and non-denaturing electrophoresis. The domains used were Coh2, an all-beta cohesin from C. thermocellum CipA, and BSX, a beta/alpha barrel xylanase from Bacillus sp. NG-27, while the linkers used were Rigid (3 repeats of N-EAAAK-C), Flexible (two repeats of N-SGGGG-C), Nat-full (42 residues of a Coh2-adjacent linker from CipA), Nat-half (a 21 residues-long derivative of Nat-full) and Nat-quarter (a 9 residues-long derivative of Nat-full). Both with proteolysis effected by proteases present in the environment, and with an exogenously-added protease (Subtilisin A), we found that Flexible underwent little or no degradation, whereas linkers of comparable length like Nat-quarter or Rigid underwent extensive degradation, as did longer linkers like Nat-Half and Nat-Full. Our analyses disfavor the likelihood of the sequence of Flexible being naturally resistant to proteolysis, and instead favor the explanation that the flexibility of Flexible facilitates movements of Coh2 relative to BSX which then serve to sterically prevent the approach of proteases. Thus, the construct incorporating Flexible appears to behave like a 'nunchuck' in which rods/spheres flanking a chain collide with approaching swords that are capable of severing the chain, to prevent severance.

Metal-catalyzed proteolysis, conformational antigenicity, photosensitized oxidation, and electrical dysfunction explain the pathogenicity of protein aggregates

It is widely accepted that protein aggregates tend to be pathologic, although little is known about why they are pathologic. Here, we summarize published findings about protein aggregates which have implications for pathology, but which have not yet been covered in any review or hypothesis on the subject, to the best of our knowledge. These findings suggest that protein aggregates can: (i) act as proteases, using exposed surface serines, (ii) function as immunogens, using novel conformational epitopes, (iii) behave as photosensitization-aids, using a novel peptide-based fluorescence, and (iv) act as electrical conductors, using electrons tunneling through hydrogen-bonded networks of peptide bonds. The potential pathological consequences of each finding are speculated upon.