Residue networks are constructed by defining the residues as the vertices and atom contacts between them as the edges. The residue network of a protein complex is divided into two types of networks, i.e. the hydrophobic and the hydrophilic residue networks. By analyzing the network parameters, it is found that the correct binding complex conformations are of both higher sum of the interface degree values and lower characteristic path length than those incorrect ones. These features reflect that the correct bind-ing complex conformations have better geometric and/or residue type complementarity, and the correct binding modes are very important for preserving the characteristic path lengths of native protein complexes. In addition, two scoring terms are proposed based on the network parameters, in which the characteristics of the entire complex shape and residue type complementarity are taken into account. These network-based scoring terms have also been used in conjunction with other scoring terms, and the new multi-term scoring HPNCscore is devised in this work. It can improve the discrimination of the combined scoring function of RosettaDock more than 12%. This work might enhance our knowledge of the mechanisms of protein-protein interactions and recognition.
Shan ChangXinQi GongXiong JiaoChunHua LiWeiZu ChenCunXin Wang
A holistic protein-protein molecular docking approach,HoDock,was established,composed of such steps as binding site prediction,initial complex structure sampling,refined complex structure sampling,structure clustering,scoring and final structure selection.This article explains the detailed steps and applications for CAPRI Target 39.The CAPRI result showed that three predicted binding site residues,A191HIS,B512ARG and B531ARG,were correct,and there were five submitted structures with a high fraction of correct receptor-ligand interface residues,indicating that this docking approach may improve prediction accuracy for protein-protein complex structures.
GONG XinQiLIU BinCHANG ShanLI ChunHuaCHEN WeiZuWANG CunXin
The "relative entropy" has been used as a minimization function to predict the tertiary structure of a protein backbone, and good results have been obtained. However, in our previous work, the ensemble average of the contact potential was estimated by an approximate calculation. In order to improve the theoretical integrity of the relative-entropy-based method, a new theoretical calculation method of the ensemble average of the contact potential was presented in this work, which is based on the thermodynamic perturbation theory. Tests of the improved algorithm were performed on twelve small proteins. The root mean square deviations of the predicted versus the native structures from Protein Data Bank range from 0.40 to 0.60 nm. Compared with the previous approximate values, the average prediction accuracy is improved by 0.04 nm.
Based on the crystal structure of the vitamin B12 transporter protein of Escherichia coli(BtuCD) a system consisting of the BtuCD transmembrane domain(BtuC) and the palmitoyloleoyl phosphatidylcholine(POPC) lipid bilayer was constructed in silica,and a more-than-57-nanosecond molecular dynamics(MD) simulation was performed on it to reveal the intrinsic functional motions of BtuC.The results showed that a stable protein-lipid bilayer was obtained and the POPC lipid bilayer was able to adjust its thickness to match the embedded BtuC which underwent relatively complicated motions.These results may help to understand the mechanism of transmembrane substrate transport at the atomic level.
SUN TingGuang1,2,LIU Ming1,CHEN WeiZu1 & WANG CunXin1 1College of Life Science and Bioengineering,Beijing University of Technology,Beijing 100124,China
