HP-sequence design for lattice proteins - an exact enumeration study on diamond as well as square lattice

摘要

We present an exact enumeration algorithm for identifying the {\it native}configuration - a maximally compact self avoiding walk configuration that isalso the minimum energy configuration for a given set of contact-energyschemes; the process is implicitly sequence-dependent. In particular, we showthat the 25-step native configuration on a diamond lattice consists of twosheet-like structures and is the same for all the contact-energy schemes,${(-1,0,0);(-7,-3,0); (-7,-3,-1); (-7,-3,1)}$; on a square lattice also, the24-step native configuration is independent of the energy schemes considered.However, the designing sequence for the diamond lattice walk depends on theenergy schemes used whereas that for the square lattice walk does not. We havecalculated the temperature-dependent specific heat for these designed sequencesand the four energy schemes using the exact density of states. These data showthat the energy scheme $(-7,-3,-1)$ is preferable to the other three for bothdiamond and square lattice because the associated sequences give rise to asharp low-temperature peak. We have also presented data for shorter (23-, 21-and 17-step) walks on a diamond lattice to show that this algorithm helpsidentify a unique minimum energy configuration by suitably taking care of theground-state degeneracy. Interestingly, all these shorter target configurationsalso show sheet-like secondary structures.