A MINIMAL OFF-LATTICE MODEL FOR ALPHA-HELICAL PROTEINS
Frank Potthast
A minimal off-lattice model for $\alpha$-helical proteins is presented.
It is based on hydrophobicity forces and sequence independent local
interactions. The latter are chosen so as to favor the formation of
$\alpha$-helical structure. They model chirality and $\alpha$-helical
hydrogen bonding. The global structures resulting from the competition
between these forces are studied by means of an efficient Monte Carlo
method. The model is tested on two sequences of length N=21 and 33
which are intended to form 2- and 3-helix bundles, respectively.
The local structure of our model proteins is compared to that of
real $\alpha$-helical proteins, and is found to be very similar.
The two sequences display the desired numbers of helices in the folded
phase. Only a few different relative orientations of the helices are
thermodynamically allowed. Our ability to investigate the thermodynamics
relies heavily upon the efficiency of the used algorithm, simulated
tempering; in this Monte Carlo approach, the temperature becomes
a fluctuating variable, enabling the crossing of free-energy barriers.
LU TP 98-13
Submitted to Journal of Computational Biology