Dk. Klimov et D. Thirumalai, LINKING RATES OF FOLDING IN LATTICE MODELS OF PROTEINS WITH UNDERLYING THERMODYNAMIC CHARACTERISTICS, The Journal of chemical physics, 109(10), 1998, pp. 4119-4125
We investigate the sequence-dependent properties of proteins that dete
rmine the dual requirements of stability of the native stare and its k
inetic accessibility using simple cubic lattice models. Three interact
ion schemes are used to describe the potentials between nearest neighb
or nonbonded beads. We show that, under the simulation conditions when
the native basin of attraction (NBA) is the most stable, there is an
excellent correlation between folding times tau(F) and the dimensionle
ss parameter sigma(T) = (T-theta-T-F)/T-theta, where T-theta is the co
llapse temperature and T-F is the folding transition temperature. Ther
e is also a significant correlation between tau(F) and another dimensi
onless quantity Z = (E-N-E-ms)/delta, where E-N is the energy of the n
ative state, E-ms is the average energy of the ensemble of misfolded s
tructures, and delta is the dispersion in the contact energies. In con
trast, there is no significant correlation between tau(F) and the Z-sc
ore gap Delta(Z) = E-N - E-ms. An approximate relationship between sig
ma(T) and the Z-score is derived, which explains the superior correlat
ion seen between tau(F) and sigma(T). For two state folders tau(F) is
linked to the free energy difference (not simply energy gap, however i
t is defined) between the unfolded states and the NEA. (C) 1998 Americ
an institute of Physics. [S0021-9606(98)51134-8].