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第三届数字制造与自动化国际会议

作者： Zhao Li Zhang Tianchi Zhang Jing College of Computer Science and Technology Harbin Engineering University Department of computer science and Information Engineering Harbin Normal University

The flexibility in protein docking is a major challenge in bioinformatic research.. protein docking problem is essentially an optimization problem. In this review we describe the methods of existing flexible protein-protein docking ,focusing on the optimization algorithms . We divide the different methods into categories for presenting clearly.

关键词： flexible docking optimization algorithms protein-protein docking

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Molecular basis of cross-interactions between Aβ and Tau protofibrils probed by molecular simulations

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Chinese Journal of Chemical Engineering 2023年第3期55卷 173-180页

作者： Fufeng Liu Luying Jiang Jingcheng Sang Fuping Lu Li Li State Key Laboratory of Food Nutrition and Safety Key Laboratory of Industrial Fermentation Microbiology of Ministry of EducationTianjin Key Laboratory of Industrial MicrobiologyCollege of BiotechnologyTianjin University of Science&TechnologyTianjin 300457China College of Marine and Environmental Science Tianjin University of Science&TechnologyTianjin 300457China

Amyloid β-protein(Aβ) and Tau, two common pathogenic proteins associated with Alzheimer’s disease(AD), cross-interact, and thus co-assemble into hybrid aggregates. However, molecular mechanism of the cross-interactions remains unclear. To explore the issue, docking and molecular dynamics(MD) simulations were coupled to study the cross-interactions between Aβ pentamer and Tau pentamer. Four stable hybrid decamer conformations including double layer, single layer, block, and part-in were obtained by protein-protein docking software HADDOCK 2.2. Then, MD simulations were used to explore the molecular mechanism of cross-interactions between Aβ pentamer and Tau pentamer. The results of MD simulations showed that the part-in structure was the most stable among all the above four representative ones. The binding energy between Aβ and Tau was about-759.77 kJ·mol-1in the part-in structure. Moreover, the part-in conformation would undergo conformational transition, which would improve its hydrophobicity and make the structure more compact. This work offers a structural understanding of cross-interactions between Aβ and Tau linked to AD.

关键词： Alzheimer’s disease Amyloidβ-protein Tau Cross-interactions protein-protein docking Molecular dynamics simulation

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Modes of parasite profilin recognition by Toll-like receptors in mice and humans

Modes of parasite profilin recognition by Toll-like receptor...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息...

作者： Shoudao Yuan Tianren Li Tiandi Wei Jing Gong Cancer Research Center School of MedicineShandong University State Key Laboratory of Microbial Technology School of Life ScienceShandong University

Background:Profilin is involved in motility and invasion of apicomplexan(protozoan) parasites and is used for invading host cells.In 2005,mouse Toll-like receptor(TLR) 11 was found to initiate an innate immune response inducing interleukin-12(IL-12) upon sensing Toxoplasma gondii profilins.However,the molecular mechanism of TLR11 binding profilins remains unknown.On the other hand,the TLR11 expression is suppressed in humans.Thus, whether other TLRs can recognize parasite profilins in human instead of TLR11 becomes a mystery. Methods:We first analyzed the structural features of the crystal structure of T.gondii profilin(PDB code:3NEC) and a homology model of mouse TLR11.Then,protein-protein docking and molecular dynamics simulation(MDS) methods were used to generate a TLR11- profilin complex model.Finally,a similarity search of the potential profilin-binding site based on structure features was performed across all human TLR models(TLR1-10). Results:Electrostatic analysis reveals that the entire surface of the T.gondii profilin is predominantly negatively charged,whereas TLR11 exhibits several positively charged patches.docking and MDS studies provided a model of TLR 11-profilin complex structure. The model shows that the potential profilin-binding site is a positively charged patch located at LRR1 to LRR7 on TLR11,which is rich in Ser,Thr,Cys and lactam amino acids.Very interestingly,a similar structure pattern just appeared on human TLR(exact TLR family number hidden due to unpublished data).Accordingly,we proposed a potential model of human TLR interacting with profilin. Conclusions:The profilin-binding site of mouse TLR11 processes a specified structural pattern.We suggest that human TLR that also has this pattern might recognize parasite profilin.If it is true,it will enlighten new therapeutic measures for human infectious diseases.

关键词： parasite profilin TLR protein-protein docking

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Molecular Modeling of Janus Kinase 2（JAK2） Pseudokinase-Kinase Complex Structure

Molecular Modeling of Janus Kinase 2（JAK2） Pseudokinase-Ki...

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第十一届全国计算（机）化学学术会议

作者：万小波黄牛 National Institute of Biological Sciences

＜正＞protein-protein interaction is essential in many cellular signaling transduction pathways. However,computational prediction of PPI structure is challenging.We developed a hierarchical protocol to improve the efficiency and accuracy of protein-protein docking by applying a "fast-compute" empirical docking method（RosettaDock） to explore the conformational space of the binding interfaces,followed by extensive refining and rescoring of the docked complex structures using more rigorous molecular mechanics methods.We have demonstrated that this protocol could be successfully applied to predict the CHBP-ubiquitin complex structure,which was subsequently validated by crystallization.Here,we further implemented an informatics method -Mutinf, in combination with our protein-protein docking protocol to model the pseudokinase-kinase complex structure of JAK2.Based on our model,we propose that JAK2 pseudokinase domain autoinhibits its kinase activity via blocking the movements ofαC helix and activation loop in kinase domain.The experimental validation of the predicted interfacial residues is undergoing,and the preliminary results will be discussed.

关键词： protein-protein docking molecular mechanics JAK2 MutInf

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