Residue conservation information for generating near-native structures in protein-protein docking

MOTIVATION: Protein-protein docking algorithms typically generate large numbers of possible complex structures with only a few of them resembling the native structure. Recently (Duan et al., Protein Sci, 14:316-218, 2005), it was observed that the surface density of conserved residue positions is high at the interface regions of interacting protein surfaces, except for antibody-antigen complexes, where a lesser number of conserved positions than average is observed at the interface regions. Using this observation, we identified putative interacting regions on the surface of interacting partners and significantly improved docking results by assigning top ranks to near-native complex structures. In this paper, we combine the residue conservation information with a widely used shape complementarity algorithm to generate candidate complex structures with a higher percentage of near-native structures (hits). What is new in this work is that the conservation information is used early in the generation stage and not only in the ranking stage of the docking algorithm. This results in a significantly larger number of generated hits and an improved predictive ability in identifying the native structure of protein-protein complexes. RESULTS: We report on results from 48 well-characterized protein complexes, which have enough residue conservation information from the same 59 benchmark complexes used in our previous work. We compute conservation indices of residue positions on the surfaces of interacting proteins using available homologous sequences from UNIPROT and calculate the solvent accessible surface area. We combine this information with shape-complementarity scores to generate candidate protein-protein complex structures. When compared with pure shape-complementarity algorithms, performed by FTDock, our method results in significantly more hits, with the improvement being over 100% in many instances. We demonstrate that residue conservation information is useful not only in refinement and scoring of docking solutions, but also helpful in enrichment of near-native-structures during the generation of candidate geometries of complex structures.     

Optimal Formation Reconfiguration Control of Multiple UCAVs Using Improved Particle Swarm Optimization

Optimal formation reconfiguration control of multiple Uninhabited Combat Air Vehicles （UCAVs） is a complicated global optimum problem. Particle Swarm Optimization （PSO） is a population based stochastic optimization technique inspired by social behaviour of bird flocking or fish schooling. PSO can achieve better results in a faster, cheaper way compared with other bio-inspired computational methods, and there are few parameters to adjust in PSO. In this paper, we propose an improved PSO model for solving the optimal formation reconfiguration control problem for multiple UCAVs. Firstly, the Control Parameterization and Time Diseretization （CPTD） method is designed in detail. Then, the mutation strategy and a special mutation-escape operator are adopted in the improved PSO model to make particles explore the search space more efficiently. The proposed strategy can produce a large speed value dynamically according to the variation of the speed, which makes the algorithm explore the local and global minima thoroughly at the same time. Series experimental results demonstrate the feasibility and effectiveness of the proposed method in solving the optimal formation reconfiguration control problem for multiple UCAVs.     

Peptide models of four possible insulin folding intermediates with two disulfides

The single-chain insulin (PIP) can spontaneously fold into native structure through preferred kinetic intermediates. During refolding, pairing of the first disulfide A20-B19 is highly specific, whereas pairing of the second disulfide is likely random because two two-disulfide intermediates have been trapped. To get more details of pairing property of the second disulfide, four model peptides of possible folding intermediates with two disulfides were prepared by protein engineering, and their properties were analyzed. The four model peptides were named [A20-B19, A7-B7]PIP, [A20-B19, A6-B7]PIP, [A20-B19, A6-A11]PIP, and [A20-B19, A7-A11]PIP according to their remaining disulfides. The four model peptides all adopt partially folded structure with moderate conformational differences. In redox buffer, the disulfides of the model peptides are more easily reduced than those of the wild-type PIP. During in vitro refolding, the reduced model peptides share similar relative folding rates but different folding yields: The refolding efficiency of the reduced [A20-B19, A7-A11]PIP is about threefold lower than that of the other three peptides. The present results indicate that the folding intermediates corresponding to the present model peptides all adopt partially folded conformation, and can be formed during PIP refolding, but the chance of forming the intermediate with disulfide [A20-B19, A7-A11] is much lower than that of forming the other three intermediates.     

温度对超高浓度酒精生料发酵体系的影响

通过对超高底物浓度生料发酵中温度的影响研究发现,采用温度梯度的方法可大幅提高酵母的生产效率。以高粱为例,采用35%绝对干物浓度,在新型生料水解酶的配合下,通过合适的逐级降温培养方式,使用普通酒精干酵母,在90h内发酵醪液酒精浓度可达20%(V/V)以上。     

融合基因umcel5N-CBM的构建、表达及融合酶性质分析

BM,并实现了融合基因在大肠杆菌BL21(DE3)pLysS中的表达.研究结果表明,融合酶Umcel5N-CBM与结晶纤维素(avicel)以及滤纸粉末的结合能力比原始酶Umcel5N提高了约一倍,但未显示出降解结晶纤维素的新活性,说明在结晶纤维素的降解过程中,纤维素酶的催化功能域起到关键作用.     

重组α-银环蛇毒素的纯化及活性分析

以表达重组α-银环蛇毒素的高效表达菌株BL21(PDZ04)为材料,研究重组α-银环蛇毒素(α-bungarotoxin,α-BgTx)的分离纯化。采取亲和色谱和离子交换色谱的方法都得到了重组α-银环蛇毒素的纯品。参考文献报道的方法从天然的银环蛇毒干粉中分离纯化得到了天然α-银环蛇毒素的纯品。然后以天然α-银环蛇毒素为对照来检测重组α-银环蛇毒素的抗原性和毒性。ELISA结果显示其具有与天然α-银环蛇毒素相似的抗原性,以小鼠为动物模型,纯化的重组α-银环蛇毒素与天然α-银环蛇毒素相比,其腹腔注射的LD50也基本一致,约为0.22μg/g。结果表明利用基因工程的方法生产蛇神经毒素是可行的。     

Variation in the significant environmental factors affecting larval abundance of four major Chinese carp species: fish spawning response to the Three Gorges Dam

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