Substitution Matrices of Residue Triplets Derived from Protein Blocks.

In protein sequence alignment, residue similarity is usually evaluated by substitution matrix, which scores all possible exchanges of one amino acid with another. Several matrices are widely used in sequence alignment, including PAM matrices derived from homologous sequence and BLOSUM matrices derived from aligned segments of BLOCKS. However, most matrices have not addressed the high-order residue-residue interactions that are vital to the bioproperties of protein.With consideration for the inherent correlation in residue triplet, we present a new scoring scheme for sequence alignment. Protein sequence is treated as overlapping and successive 3-residue segments. Two edge residues of a triplet are clustered into hydrophobic or polar categories, respectively. Protein sequence is then rewritten into triplet sequence with 2 · 20 · 2 = 80 alphabets. Using a traditional approach, we construct a new scoring scheme named TLESUMhp (TripLEt SUbstitution Matrices with hydropobic and polar information) for pairwise substitution of triplets, which characterizes the similarity of residue triplets. The applications of this matrix led to marked improvements in multiple sequence alignment and in searching structurally alike residue segments. The reason for the occurrence of the ‘‘twilight zone,’’ i.e., structure explosion of lowidentity sequences, is also discussed.

Impact Parameter Dependence of Double Neutron/Proton Ratio of Nucleon Emissions in Isotopic Reaction Systems

Within the transport model IBUU04, we investigate the double neutron/proton ratio of free nucleons taken from two reaction systems using two Sn isotopes at the beam energy of 50MeV/nucleon and with the impact parameters 2 fm, 4 fm and 8 fm, respectively. It is found that the double neutron/proton ratio from peripheral collisions is more sensitive to the density dependence of the symmetry energy than those from mid-central and central collisions.