Protein Folding

Venkatesh Murthy venkmurthy at worldnet.att.net
Wed Jan 28 19:23:42 EST 1998


Alan J. Robinson wrote in message <61238.robin073 at tc.umn.edu>...
>Real proteins are obviously more complex than this in several
>different ways, so that the values of phi and psi observed in practice
>don't always fall within the regions shown on the plot, and certainly
>don't constrain the folding process itself in any direct way (though
>obviosuly constrained by steric considerations too.)


While Ramachandran outliers are observed in protein crystal structures,
typically their numbers are smaller in higher resolution structures
suggesting that, except in very rare cases, all amino acids must conform to
the Ramachandran plot.

This makes sense when you consider that the Ramachandran plot is primarily
dependent (including favorable terms has very little effect overall) on the
repulsive portion of the van der Waals potential.  Two atoms simply cannot
occupy the same space -- the electronic repulsions in dissallowed regions is
much stronger than favorable forces at work in proteins.  Simply put, except
in exceptionally rare cases, Ramachandran outliers are more indicative of
model errors than anything else.

Also, Ramachandran did not use a computer model to generate the plot.  The
plot was calculated (and intuited) by hand.  Finally, the plot is for a
dipeptide, not a polypeptide.


Venkatesh Murthy
-------
MD/PhD Candidate
Department of Biophysics & Biophysical Chemistry
Johns Hopkins University School of Medicine





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