Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc. are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including...Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc. are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including the membrane protein);theoretical mathematical and physical computational approaches can also allow us to obtain a description of the protein 3D structure at a submicroscopic level for some unstable, noncrystalline and insoluble proteins. X-ray crystallography finds the X-ray final structure of a protein, which usually need refinements using theoretical protocols in order to produce a better structure. This means theoretical methods are also important in determinations of protein structures. Optimization is always needed in the computer-aided drug design, structure-based drug design, molecular dynamics, and quantum and molecular mechanics. This paper introduces some optimization algorithms used in these research fields and presents a new theoretical computational method—an improved LBFGS Quasi-Newtonian mathematical optimization method—to produce 3D structures of prion AGAAAAGA amyloid fibrils (which are unstable, noncrystalline and insoluble), from the potential energy minimization point of view. Because the NMR or X-ray structure of the hydrophobic region AGAAAAGA of prion proteins has not yet been determined, the model constructed by this paper can be used as a reference for experimental studies on this region, and may be useful in furthering the goals of medicinal chemistry in this field.展开更多
The Aurora proteins are critical regulators of major mitotic events and attractive targets for anticancer therapy. 3D-QSAR studies based on molecular docking were performed on a dataset of 40 4-aminoquinazolines compo...The Aurora proteins are critical regulators of major mitotic events and attractive targets for anticancer therapy. 3D-QSAR studies based on molecular docking were performed on a dataset of 40 4-aminoquinazolines compounds. The CoMSIA model produced significantly better results than CoMFA model, with q2=0.652 and r2=0.991. The contours analysis provides useful information about the structural requirements for 4-aminoquinazolines for inhib- iting Aurora B. Scaffold hopping method was used to generate new structures based on the maximum common sub- structure of the training and test set compounds. The ADMET property, binding affinity and inhibitory activity of the new designed compounds were predicted, respectively. Finally 16 compounds were identified as the novel in- hibitors for Aurora B kinase.展开更多
As an aquatic fish,the spotted halibut Verasper variegatus is highly susceptible to bacterial and virus infections.Tumor necrosis factor-alpha(TNF-α)as a cytokine could control the inflammatory responses.The function...As an aquatic fish,the spotted halibut Verasper variegatus is highly susceptible to bacterial and virus infections.Tumor necrosis factor-alpha(TNF-α)as a cytokine could control the inflammatory responses.The functions of TNF-αin many species have been widely studied,particularly in mammals.However,little is known about the TNF-αfunctions in V.variegatus.We first cloned and sequenced the TNF-αgene in V.variegatus(VvTNF-α).The two conserved cysteine residues,transmembrane sequence,Thr-Leu motif,and TNF family signature,as well as the TA-rich motifs of its proteins related to inflammatory responses had high similarity to those of the other teleost and mammalian TNF-α.The phylogenetic analysis showed that VvTNF-αwas consistent with TNF-αgenes of other vertebrates.The VvTNF-αtranscripts were extensively distributed in the peripheral blood leukocytes(PBLs),spleen,and gill,indicating that the VvTNF-αhad a role in immune function.Furthermore,treatment with pathogen-associated molecular patterns(PAMPs)could induce a rapid and significant increase of VvTNF-αin the PBLs,which reveals that VvTNF-αdoes participate in the host immune responses against bacterial and viral pathogens.We found that VvTNF-αhad an interesting expression pattern during metamorphosis,showing that the flatfish TNF-αmay have some novel functions during specific developmental stages.In addition,the 3 D structure prediction of VvTNF-αprovided an indication of how it is likely to interact with other proteins.Therefore,VvTNF-αhas multiple functions,and provides valuable information to explore novel functions of TNF-α.展开更多
文摘Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc. are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including the membrane protein);theoretical mathematical and physical computational approaches can also allow us to obtain a description of the protein 3D structure at a submicroscopic level for some unstable, noncrystalline and insoluble proteins. X-ray crystallography finds the X-ray final structure of a protein, which usually need refinements using theoretical protocols in order to produce a better structure. This means theoretical methods are also important in determinations of protein structures. Optimization is always needed in the computer-aided drug design, structure-based drug design, molecular dynamics, and quantum and molecular mechanics. This paper introduces some optimization algorithms used in these research fields and presents a new theoretical computational method—an improved LBFGS Quasi-Newtonian mathematical optimization method—to produce 3D structures of prion AGAAAAGA amyloid fibrils (which are unstable, noncrystalline and insoluble), from the potential energy minimization point of view. Because the NMR or X-ray structure of the hydrophobic region AGAAAAGA of prion proteins has not yet been determined, the model constructed by this paper can be used as a reference for experimental studies on this region, and may be useful in furthering the goals of medicinal chemistry in this field.
基金Project supported by the National Major Science and Technology Project of China （Nos. 2008ZX09401-001, 2009ZX09501-003）, the Specialized Research Fund for the Doctoral Program of Higher Education （No. 20090096110003）, the National Natural Science Foundation for the Youth （No. 30801437）.
文摘The Aurora proteins are critical regulators of major mitotic events and attractive targets for anticancer therapy. 3D-QSAR studies based on molecular docking were performed on a dataset of 40 4-aminoquinazolines compounds. The CoMSIA model produced significantly better results than CoMFA model, with q2=0.652 and r2=0.991. The contours analysis provides useful information about the structural requirements for 4-aminoquinazolines for inhib- iting Aurora B. Scaffold hopping method was used to generate new structures based on the maximum common sub- structure of the training and test set compounds. The ADMET property, binding affinity and inhibitory activity of the new designed compounds were predicted, respectively. Finally 16 compounds were identified as the novel in- hibitors for Aurora B kinase.
基金Supported by the National High Technology Research and Development Program of China(863 Program)(No.31101891)the Hitech Research and Development Program of China(No.2012AA10A408)
文摘As an aquatic fish,the spotted halibut Verasper variegatus is highly susceptible to bacterial and virus infections.Tumor necrosis factor-alpha(TNF-α)as a cytokine could control the inflammatory responses.The functions of TNF-αin many species have been widely studied,particularly in mammals.However,little is known about the TNF-αfunctions in V.variegatus.We first cloned and sequenced the TNF-αgene in V.variegatus(VvTNF-α).The two conserved cysteine residues,transmembrane sequence,Thr-Leu motif,and TNF family signature,as well as the TA-rich motifs of its proteins related to inflammatory responses had high similarity to those of the other teleost and mammalian TNF-α.The phylogenetic analysis showed that VvTNF-αwas consistent with TNF-αgenes of other vertebrates.The VvTNF-αtranscripts were extensively distributed in the peripheral blood leukocytes(PBLs),spleen,and gill,indicating that the VvTNF-αhad a role in immune function.Furthermore,treatment with pathogen-associated molecular patterns(PAMPs)could induce a rapid and significant increase of VvTNF-αin the PBLs,which reveals that VvTNF-αdoes participate in the host immune responses against bacterial and viral pathogens.We found that VvTNF-αhad an interesting expression pattern during metamorphosis,showing that the flatfish TNF-αmay have some novel functions during specific developmental stages.In addition,the 3 D structure prediction of VvTNF-αprovided an indication of how it is likely to interact with other proteins.Therefore,VvTNF-αhas multiple functions,and provides valuable information to explore novel functions of TNF-α.
