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131 results on '"Chen, Wei-zu"'

14. Identification of key residues for protein conformational transition using elastic network model.

Author

Su, Ji Guo, Jin Xu, Xian, Hua Li, Chun, Chen, Wei Zu, and Wang, Cun Xin

Subjects
PROTEIN conformation, ELASTICITY, MATHEMATICAL models, THERMODYNAMICS, QUANTUM perturbations, HEAT shock proteins, PROTEIN binding, DNA polymerases
Abstract

Proteins usually undergo conformational transitions between structurally disparate states to fulfill their functions. The large-scale allosteric conformational transitions are believed to involve some key residues that mediate the conformational movements between different regions of the protein. In the present work, a thermodynamic method based on the elastic network model is proposed to predict the key residues involved in protein conformational transitions. In our method, the key functional sites are identified as the residues whose perturbations largely influence the free energy difference between the protein states before and after transition. Two proteins, nucleotide binding domain of the heat shock protein 70 and human/rat DNA polymerase β, are used as case studies to identify the critical residues responsible for their open-closed conformational transitions. The results show that the functionally important residues mainly locate at the following regions for these two proteins: (1) the bridging point at the interface between the subdomains that control the opening and closure of the binding cleft; (2) the hinge region between different subdomains, which mediates the cooperative motions between the corresponding subdomains; and (3) the substrate binding sites. The similarity in the positions of the key residues for these two proteins may indicate a common mechanism in their conformational transitions. [ABSTRACT FROM AUTHOR]

Published
2011
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15. Inhibition of CK2 Activity by TCDD via binding to ATP-competitive binding site of catalytic subunit: Insight from computational studies

Author

Cannistraro Salvatore, Wang Cun-xin, XU Xian-jin, Zeng Yi, Chen Wei-zu, and Bizzarri Anna-rita

Subjects
biology, Chemistry, Stereochemistry, Protein subunit, General Chemistry, Aryl hydrocarbon receptor, Molecular mechanics, In vitro, Docking (molecular), In vivo, biology.protein, heterocyclic compounds, Binding site, Casein kinase 2
Abstract

Alternative mechanisms of toxic effects induced by 2,3,7,8-tetrachlorodibenzo-p-dioxin(TCDD), instead of the binding to aryl hydrocarbon receptor(AhR), have been taken into consideration. It has been recently shown that TCDD reduces rapidly the activity of CK2(casein kinase II) both in vivo and in vitro. It is found that TCDD has high molecular similarities to the known inhibitors of CK2 catalytic subunit(CK2α). This suggests that TCDD could also be an ATP-competitive inhibitor of CK2α. In this work, docking TCDD to CK2 was carried out based on the two structures of CK2α from maize and human, respectively. The binding free energies of the predicted CK2α-TCDD complexes estimated by the molecular mechanics/Poisson-Boltzmann surface area(MM/PBSA) method are from −85.1 kJ/mol to −114.3 kJ/mol for maize and are from −96.1 kJ/mol to −118.2 kJ/mol for human, which are comparable to those estimated for the known inhibitor and also ATP with CK2α. The energetic analysis also reveals that the van der Waals interaction is the dominant contribution to the binding free energy. These results are also useful for designing new drugs for a target of overexpressing CK2 in cancers.

Published
2013

17. Progress in the Scoring Functions of Protein-Protein Docking

Author

Gong Xin-Qi, Wang Cunxin, Chang Shan, Li Chunhua, Chen Wei-zu, and Yang Feng

Subjects
Lead Finder, Engineering, business.industry, Protein protein, computer.software_genre, Machine learning, Scoring functions for docking, Protein–ligand docking, Docking (molecular), Complementarity (molecular biology), Artificial intelligence, Data mining, Physical and Theoretical Chemistry, business, computer, Electrostatic interaction
Abstract

Molecular docking technology is an effective approach for prediction of intermolecular interactions and recognition. The design of a scoring function for selecting near-native structures is very important for successful prediction of complex structures. In this article, the main computational methods for scoring items in protein-protein docking, such as geometric complementarity, contact area, van der Waalsʹ interaction, electrostatic interaction, and statistical pair propensity potential, are reviewed. Including our work, we introduce commonly used scoring schemes and some strategies in screening decoys based on the information for protein binding sites. The characteristic scoring functions in the commonly used docking programs are compared and summarized. The major problems in the existing scoring function in protein-protein docking are discussed along with prospect for future research.

Published
2012

18. Conformational Change of HIV-1 Viral DNA after Binding with Integrase

Author

Chen Wei-zu, HU Jian-Ping, KE Guo-Tao, Wang Cunxin, and Chang Shan

Subjects
Conformational change, biology, Chemistry, Human immunodeficiency virus (HIV), medicine, biology.protein, Physical and Theoretical Chemistry, Dna viral, medicine.disease_cause, Virology, Integrase
Published
2008

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