Do theoretical physicists care about the protein-folding problem?
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The prediction of the biologically active native conformation of a protein is
one of the fundamental challenges of structural biology. This problem remains
yet unsolved mainly due to three factors: the partial knowledge of the
effective free energy function that governs the folding process, the enormous
size of the conformational space of a protein and, finally, the relatively
small differences of energy between conformations, in particular, between the
native one and the ones that make up the unfolded state.
Herein, we recall the importance of taking into account, in a detailed
manner, the many interactions involved in the protein folding problem (such as
steric volume exclusion, Ramachandran forces, hydrogen bonds, weakly polar
interactions, coulombic energy or hydrophobic attraction) and we propose a
strategy to effectively construct a free energy function that, including the
effects of the solvent, could be numerically tractable. It must be pointed out
that, since the internal free energy function that is mainly described does not
include the constraints of the native conformation, it could only help to reach
the 'molten globule' state. We also discuss about the limits and the lacks from
which suffer the simple models that we, physicists, love so much.