A Novel Branch-and-Bound Algorithm for the Protein Folding Problem in the 3D HP Model.

The protein folding problem (PFP) is an important issue in bioinformatics and biochemical physics. One of the most widely studied models of protein folding is the hydrophobic-polar (HP) model introduced by Dill. The PFP in the three-dimensional (3D) lattice HP model has been shown to be NP-complete; the proposed algorithms for solving the problem can therefore only find near-optimal energy structures for most long benchmark sequences within acceptable time periods. In this paper, we propose a novel algorithm based on the branch-and-bound approach to solve the PFP in the 3D lattice HP model. For 10 48-monomer benchmark sequences, our proposed algorithm finds the lowest energies so far within comparable computation times than previous methods.

Preparation and copper ions adsorption properties of thiosemicarbazide chitosan from squid pens.

Chitosan was prepared by alkaline N-deacetylation of ß-chitin from squid pens. Thiosemicarbazide group was introduced to chitosan via formaldehyde-derived linkages, and thiosemicarbazide chitosan (TSFCS) with different degrees of substitution (DS) was synthesized. The DS values of TSFCS calculated by elemental analysis were 0.19, 0.36 and 0.63. The structure of the TSFCS was confirmed by elemental analysis, FTIR, XRD, TGA and SEM. The adsorption capacity of Cu(II) ions by TSFCS showed good correlation with the DS and pH (pH range 2.2-5.8). The maximum Cu(II) ions adsorption capacity of all three TSFCS samples reached 134.0mgg-1 at pH 3.6, but chitosan showed no adsorption at this pH. The adsorption equilibrium process of Cu(II) ions onto TSFCS was better described by the Langmuir model than the Freundlich isotherm model. Cu(II) ions adsorbed by TSFCS could be released using 0.01M Na2EDTA and the adsorption capacity could retain above 80% after five adsorption-desorption cycles. TSFCS exhibited good potential for heavy metal removal because of its high adsorption capacity at the low pH.