Investigation of Highly Designable Dented Structures in HP Model with Hydrogen Bond Energy

Some highly designable protein structures have dented on the surface of their native structures, and are not full compactly folded. According to hydrophobic-polar （HP） model the most designable structures are full compactly folded. To investigate the designability of the dented structures, we introduce the hydrogen bond energy in the secondary structures by using the secondary-structure-favored HP model proposed by Ou-yang etc. The result shows that the average designability increases with the strength of the hydrogen bond. The designabilities of the structures with same dented shape increase exponentially with the number of secondary structure sites. The dented structures can have the highest designabilities for a certain value of hydrogen bond energy density.

RATE OF INTRA-MOLECULAR CONTACT FORMATION IN SHORT TWO-DIMENSIONAL COMPACT POLYMERS CHAINS

It is important to know the rate of intra-molecular contact formation in proteins in order to understand how proteins fold clearly. Here we investigate the rate of intra-molecular contact formation in short two-dimensional compact polymer chains by calculating the probability distribution p（r） of end-to-end distance r using the enumeration calculation method and HP model on two-dimensional square lattice. The probability distribution of end-to-end distance p（r） of short two-dimensional compact polymers chains may consist of two parts, i.e. p（r） = p1（r） ＋ p2（r）, where p1（r） and p2（r） are different for small r. The rate of contact formation decreases monotonically with the number of bonds N, and the rate approximately conforms to the scaling relation of k（N）∝ N^-α. Here the value of α increases with the contact radius a and it also depends on the percentage of H （hydrophobic） residues in the sequences of compact chains and the energy parameters of ^εНН、 ^εНН and ^εpp. Some comparisons of theoretical predictions with experimental results are also made. This investigation may help us to understand the protein folding.

Application of ACO algorithm in protein structure prediction

The hydrophobic-polar (HP) lattice model is an important simplified model for studying protein folding. In this paper, we present an improved ACO algorithm for the protein structure prediction. In the algorithm, the "lone"ethod is applied to deal with the infeasible structures, and the "oint mutation and reconstruction"ethod is applied in local search phase. The empirical results show that the presented method is feasible and effective to solve the problem of protein structure prediction, and notable improvements in CPU time are obtained.

A Branch and Bound Algorithm for the Protein Folding Problem in the HP Lattice Model

A branch and bound algorithm is proposed for the two-dimensional protein folding problem in the HP lattice model. In this algorithm, the benefit of each possible location of hydrophobic monomers is evaluated and only promising nodes are kept for further branching at each level. The proposed algorithm is compared with other well-known methods for 10 benchmark sequences with lengths ranging from 20 to 100 monomers. The results indicate that our method is a very efficient and promising tool for the protein folding problem.

Spatial patterns of a savanna palm tree Borassus aethiopum and its temporal variability

The spatial distributions and associations of plant species in a stand can provide essential information about their dynamics.However,since tree spatial distribution and association depend on factors that operate at different scales,disentangling the effects of environmental heterogeneity and plant-plant interactions requires the choice of a suitable null model for spatial analysis.We analyzed the spatial distributions of the same savanna palm tree populations that were studied,the underlying hypothesis being that these distributions have changed in 20 years.To remove the effect of large-scale environmental heterogeneity,the inhomogeneous L-function under the heterogeneous Poisson null model was used.We showed:(i)unlike 20 years ago,adults had a regular distribution instead of an aggregated distribution in the grass savanna;(i)although the spatial distribution of seedlings and juveniles was always aggregated,we observed a decrease in the size of the aggregates(intensities);ili)except for juveniles,no other stages were associated with nutrient-rich patches,which was also different 20 years ago;(iv)we did not observe any particular difference in structure between two study sites,only that female palm trees were spatially associated with entire-leafed seedlings in the reserve while they were spatially independent in the rural area.Our study supports the hypothesis that the spatial distributions have partially changed,and that the management of spatial heterogeneity has improved and given more precision in the results.