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CHIN.PHYS.LETT. Vol. 18, No. 3 (2001) 449 Comp osition Preference of Amino Acids in Mo del-Proteins  WANG Jian-Yong(  ), WANG Jun(
), WANG Wei(  ) National Lab oratory of Solid State Microstructure and Departmen t of Physics, Nanjing University, Nanjing 210093 (Received 14 August 2000) The folding b ehaviour is in vestigated of some sequences of 36 monomers with dierent prop ortions of hydrophobic residues in a three-dimensional lattice based on the Miyazawa{Jernigen in teraction matrix. It is found that the sequences with go o d folding prop erties are those with an optimal n umb er of hydrophobic residues, neither to o many nor to o few. The reason for the deterioration of folding prop erties of sequences out of this range has also b een analysed. PA CS: 87. 15. Cc, 87. 15. Aa, 87. 14. Ee As the basic `alphab et of proteins, the comp osi- residues make the landscap e rather rugged since there tion of amino acid residues is one of the imp ortant in- may b e many non-native contacts b etween the H-typ e gredients in proteins. [1;2] Naturally, proteins are com- residues, which makes the transition from one mini- p osed of 20 kinds of residue, and the ratio of various mum to another diÆcult (see Fig. 1). Therefore, there residues is sometimes regarded as the zeroth struc- should b e a suitable prop ortion of the H-typ e residues ture of proteins. According to their dierent aÆnities which optimizes the mobility of the system on the en- to water, protein residues are classied into two typ es: e