Friction Effects On Folded Proteins

Werner Kuhn is not a well known name but those who do know of him would probably associate him with chemistry, physical chemistry in particular. I, however, consider him to be a physicist who simply used this focus to examine chemicals and the mechanics of polymers in particular. He developed the theory of modelling polymer chain as a series of N number of Kuhn segments and then applying statistical approaches to that of the action of the molecule as a whole. He also worked on various parts of particle statistics in order to model the viscosity of any polymer solution. His prediction was that as the length of the polymer increased the growth of the solvent friction (caused by the solution) would overwhelm that of internal friction (friction of the polymer against itself) until the internal friction became completely irrelevant. This is not the case.

Even with polymers of considerable length, the speed of the folding and the time taken for functional groups to align is affected noticeably by internal forces. Possibly the greatest hindrance to the analysis of this discrepancy is that there is no real consensus as to what internal friction really is and what causes it. The computational models created are effective at matching the experimental data but are inherently flawed as they fail to take into account basic concepts such as the polymers twisting. When will these models cease to give accurate predictions? In order to find some answers researchers have used a series of theoretical analysis techniques to examine simple peptide polymers at first, and then moving up to more complex chains.

For the simple peptides dividing a 66 unit long chain into six, eleven segment long peptide fragments was enough for atomistic analysis. For longer chains the more advanced course grain models were used which took into account the elasticity, geometry and potential energy of the polypeptide. Finally an rotational isomeric state model was also applied to examine the rational capability of the molecule based on the angle subtended between each segment. It was found that measurements of the internal friction can give important details about what timescales the polymers motion will take place over such as uncoiling after being put under stress. It is unfortunately still unknown what property of the chain determines this time scale (in other words we still don’t know what’s causing the friction). Hopefully a satisfactory theory can be presented soon.

Paper links: Theoretical and computational validation of the Kuhn barrier friction mechanism in unfolded proteins

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