A fundamental open problem in biophysics is how the folded structure of the main chain (MC) of a protein is determined by the physics of the interactions between the side chains (SCs). All-atom molecular dynamics simulations of a model protein (Trp-cage) revealed that strong correlations between the motions of the SCs and the MC occur transiently at 380 K in unfolded segments of the protein and during the simulations of the whole amino-acid sequence at 450 K. The high correlation between the SC and MC fluctuations is a fundamental property of the unfolded state and is also relevant to unstructured proteins as intrinsically disordered proteins (IDPs), for which new reaction coordinates are introduced. The presented findings may open a new door as to how functions of IDPs are related to conformations, which play a crucial role in neurodegenerative diseases.
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| http://dx.doi.org/10.1021/acs.jpclett.5b00055 | DOI Listing |
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