The knowledge of subnuclear localization in eukaryotic cells is indispensable for under-standing the biological function of nucleus, genome regulation and drug discovery. In this study, a new feature representation wa...The knowledge of subnuclear localization in eukaryotic cells is indispensable for under-standing the biological function of nucleus, genome regulation and drug discovery. In this study, a new feature representation was pro-posed by combining position specific scoring matrix (PSSM) and auto covariance (AC). The AC variables describe the neighboring effect between two amino acids, so that they incorpo-rate the sequence-order information;PSSM de-scribes the information of biological evolution of proteins. Based on this new descriptor, a support vector machine (SVM) classifier was built to predict subnuclear localization. To evaluate the power of our predictor, the benchmark dataset that contains 714 proteins localized in nine subnuclear compartments was utilized. The total jackknife cross validation ac-curacy of our method is 76.5%, that is higher than those of the Nuc-PLoc (67.4%), the OET- KNN (55.6%), AAC based SVM (48.9%) and ProtLoc (36.6%). The prediction software used in this article and the details of the SVM parameters are freely available at http://chemlab.scu.edu.cn/ predict_SubNL/index.htm and the dataset used in our study is from Shen and Chou’s work by downloading at http://chou.med.harvard.edu/ bioinf/Nuc-PLoc/Data.htm.展开更多
Proteins adsorption at solid surfaces are of paramount important for many natural processes. However, the role of specific water in influencing the adsorption process has not been well understood. We used molecular dy...Proteins adsorption at solid surfaces are of paramount important for many natural processes. However, the role of specific water in influencing the adsorption process has not been well understood. We used molecular dynamics simulation to study the adsorption of BPTI on Au surface in three water environments （dielectric constant model, partial and full solvation models）. The result shows that a fast and strong adsorption can occur in the dielectric environment, which leads to significant structure changes, as confirmed by great deviation from the crystal structure, largely spreading along the Au surface, rapid lose in all secondary structures and the great number of atoms in contact with the surface. Compared to the dielectric model, slower adsorption and fewer changes in the calculated properties above are observed in the partial solvation system since the specific water layer weakens the adsorption effects. However, in the partial solvation system, the adsorption of polar Au surface causes a significant decrease in the specific hydration around the protein, which still results in large structure changes similar to the dielectric system, but with much less adsorption extent. Enough water molecules in the full solvation system could allow the protein to rotate, and to large extent preserve the protein native structure, thus leading to the slowest and weakest adsorption. On the whole, the effects of non-specific and specific solvation on the protein structure and adsorption dynamics are significantly different, highlighting the importance of the specific water molecule in the protein adsorption.展开更多
文摘The knowledge of subnuclear localization in eukaryotic cells is indispensable for under-standing the biological function of nucleus, genome regulation and drug discovery. In this study, a new feature representation was pro-posed by combining position specific scoring matrix (PSSM) and auto covariance (AC). The AC variables describe the neighboring effect between two amino acids, so that they incorpo-rate the sequence-order information;PSSM de-scribes the information of biological evolution of proteins. Based on this new descriptor, a support vector machine (SVM) classifier was built to predict subnuclear localization. To evaluate the power of our predictor, the benchmark dataset that contains 714 proteins localized in nine subnuclear compartments was utilized. The total jackknife cross validation ac-curacy of our method is 76.5%, that is higher than those of the Nuc-PLoc (67.4%), the OET- KNN (55.6%), AAC based SVM (48.9%) and ProtLoc (36.6%). The prediction software used in this article and the details of the SVM parameters are freely available at http://chemlab.scu.edu.cn/ predict_SubNL/index.htm and the dataset used in our study is from Shen and Chou’s work by downloading at http://chou.med.harvard.edu/ bioinf/Nuc-PLoc/Data.htm.
文摘Proteins adsorption at solid surfaces are of paramount important for many natural processes. However, the role of specific water in influencing the adsorption process has not been well understood. We used molecular dynamics simulation to study the adsorption of BPTI on Au surface in three water environments （dielectric constant model, partial and full solvation models）. The result shows that a fast and strong adsorption can occur in the dielectric environment, which leads to significant structure changes, as confirmed by great deviation from the crystal structure, largely spreading along the Au surface, rapid lose in all secondary structures and the great number of atoms in contact with the surface. Compared to the dielectric model, slower adsorption and fewer changes in the calculated properties above are observed in the partial solvation system since the specific water layer weakens the adsorption effects. However, in the partial solvation system, the adsorption of polar Au surface causes a significant decrease in the specific hydration around the protein, which still results in large structure changes similar to the dielectric system, but with much less adsorption extent. Enough water molecules in the full solvation system could allow the protein to rotate, and to large extent preserve the protein native structure, thus leading to the slowest and weakest adsorption. On the whole, the effects of non-specific and specific solvation on the protein structure and adsorption dynamics are significantly different, highlighting the importance of the specific water molecule in the protein adsorption.
