Dresden 2003 – scientific programme

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DY: Dynamik und Statistische Physik

DY 46: Poster

DY 46.55: Poster

Thursday, March 27, 2003, 15:30–18:00, P1

Exact Statistical Analysis of Native Ground States of Lattice Proteins — •Reinhard Schiemann, Michael Bachmann, and Wolfhard Janke — Institut für Theoretische Physik, Universität Leipzig, Augustusplatz 10/11, 04109 Leipzig

In order to investigate relations between lattice protein sequences and conformations forming native ground states, we use the quite simple HP model [1], where only two prototype amino acids enter, one of them being hydrophobic (H) and the other polar (P). In the most simple case, assuming that the polar residues screen the hydrophobic ones from an aqueous environment, the energy is only decreased when two hydrophobic residues are in contact, i.e. when they are neighbours on the lattice but nonadjacent on the chain. Additionally, we also considered an attractive interaction of HP contacts [2].

Within this simple model, we performed an exact enumeration in sequence and conformational spaces on a square and a cubic lattice in order to find all native ground states for HP sequences of up to 16 monomers. In a statistical analysis of these ground states we determined their hydrophobicity, moments of inertia and two-point correlation functions of monomers in the HP sequences. The results we obtained from our analysis can be used as a cross-check and speed-up of Monte Carlo algorithms which will allow investigations of longer sequences.
[1] K.F. Lau and K.A. Dill, Macromolecules 22, 3986 (1989).
[2] C. Tang, Physica A288, 31 (2000).