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).

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