Folding of chains
with random and edited sequences
Oxana Galzitskaya, 142292,
Pushchino, Moscow Region, Russia Institute
of Protein Research Russian Academy of Sciences
We found that exist a range of "optimal" temperatures
and solvent
strengths where the native fold is achieved by the MC process
much
faster than by exaustive sorting of all the chain folds. The
"optimal"
(for folding kinetics) conditions are essentially equal for
different
random and "edited" sequences (for the latter, the
native fold energy
is separated by a considerable gap from the energies of other
low-energy folds; for random sequences, this gap is negligible).
The
native folds of "edited" chains are thermodynamically
stable at
conditions optimal for fast folding, while the native fold of
random
chains is unstable at these conditions. All the chains are
capable of
fast achievement of their lowest-energy ("native")
folds. However,
when the native folds are thermodynamically stable, they are
formed
slowly by random sequences and rapidly only by the
"edited" ones. This
is observed in computer simulation for both
"protein-like" and
"rna-like" models. We have obtained a characteristic
first passage
time dependence on the chain length using Monte Carlo simulations
for
a simple model of formation of RNA secondary structure. Our
results
are compatible with the dependence t=AL^b where t is a number of
MC
steps typical for achievement of energy minimum, L is the chain
length, and A, B are some constants. Such dependences have been
obtained for random sequences (for them, b is obove 5) as well as
for
the sequences edited as to stabilize their native folds (for
them, b
is below 3).
|