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A protein is a sequence of the 20 (common) amino acids.
This is the so-called primary sequence of the protein.
For some proteins the primary sequence determines the
folded three dimensional structure of the protein,
its tertiary structure.
In priciple it should be possible to predict the tertiary structure
from the primary sequence, but we do not know how to do this in general.
As an intermediate step, the secondary structure of a protein
is sometimes considered. This is the collection
of relatively "local" parts of the the 3-D structure of the protein.
Typically these may be classified as
{helix, turn, other}, although finer classifications are also used.
If secondary structure could be reliably predicted
predicting tertiary structure would be reduced to packing
dozens of secondary structures from packing
hundreds or thousands of amino acids, if . . . !
The picture is further complicated by the fact that some proteins
require other proteins, chaperonins, to assist them to fold, and
may be in a local, rather than a global energy minimum, when finally folded.
And a protein cannot truly be considered in isolation or at rest --
its vibrational energy and
the energy due to interactions with other molecules,
notably water, may be of the same order of magnitude as the
energy due to the protein's fold itself.
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