Hi,
I
have seen many forms for coevolution but one which tries to explain protein
conformational changes using protein sequence coevolution is unremarkable. This
article is
published in MBE and can raise interest of many. Author says in very beginning
that they observed coevolving residues in flexible region of protein, which
itself doesn't make much sense to me as coevolution is mostly complemented by
co-conservation but let see how they try to explain it.
For
estimating the conformational changes between two forms of similar protein they
have used MMTSB tool set, which can be interesting for measuring many
parameters in protein structures. Have a look here. For correlation three
different measures were computed, CN and SA, CN and FIR, CN and Ca RMSD, where
CN stands for coupling number, SA for solvent accessibility and FIR for
fractional changes.
An
illustration is shown here for CN calculations,
Validation
of the method on two the structures is shown below:
Surprisingly
enough, they have CN residues in loops which are rarely conserved and how can
we explain that coevolution we are looking at is not merely random changes due
to less conservation in coupling residues.
Result
and discussion session confer the importance of CN in protein motion and
significance was shown. If I haven't mentioned so far then Coevolution score
was calculated by using McLachlan-based substitution matrix.
Here
is last figure explained in the paper,
That's
all and let see if I can also reproduce similar results using higher order of
coevolution calculations.
Vi
sis,
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