Modeling bond correlations in denatured proteins and polypeptides

Bond‐orientational correlations for finite‐length homopolypeptides and a selected group of denatured proteins are obtained by numerical simulations using a polypeptide model with a potential of mean force. These correlations characterize the stiffness of the polypeptide backbone and are generally described by either an exponential or a power‐law decay in the asymptotic limit. However, for finite length polypeptides and unfolded proteins the correlations significantly deviate from either single exponential or power‐law behavior. A heuristic model is developed to analyze the correlations of homopolypeptides, which depends on the chain length and the side‐chain properties. The model contains power‐law and multi‐exponential terms, the latter which could be interpreted as local persistence lengths. In the asymptotic limit, the model reduces to the expected power‐law behavior. Simulations of denatured proteins show that the power‐law behavior of the correlations is significantly suppressed and only the multi‐exponential term is needed to model the correlations. In addition, average persistence lengths (ranging from 2.0 to 2.5 nm) are obtained from the correlations by fitting single exponentials and shown to be in general agreement with experiments, which also assume single exponential decay. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 312–323, 2016.     

Is the fracto‐mechanoluminescence of ZnS:Mn phosphor dominated by charged dislocation mechanism or piezoelectrification mechanism?

Mathematical approaches made for both the charged dislocation model and piezoelectrically induced electron bombardment model of fracto‐mechanoluminescence (FML), the luminescence induced by fracture of solids, in ZnS:Mn phosphor indicate that the piezoelectrically induced electron bombardment model provides a dominating process for the FML of ZnS phosphors. The concentration of 3000 ppm Mn²⁺ is optimal for ML intensity of ZnS:Mn phosphor. The decay time of ML gives the relaxation time of the piston used to deform the sample and the time t_m of maximum of ML is controlled by both the relaxation time of the piston and decay time of charges on the newly created surfaces of crystals. As the product of the velocity of dislocations and pinning time of dislocations gives the mean free path of a moving dislocation. Both factors play an important role in the ML excitation of impurity doped II–VI semiconductors. The linear increase of total ML intensity I_T with the impact velocity indicates that the damage increases linearly with impact velocity of the load. Thus, the ML measurement can be used remotely to monitor the real‐time damage in the structures, and therefore, the ML of ZnS:Mn phosphor has also the potential for a structural health monitoring system. Copyright © 2015 John Wiley & Sons, Ltd.     

昆虫几丁质酶基因家族功能研究进展

昆虫几丁质酶的研究历史很长,研究内容也非常广泛;但仅局限于传统的方法研究某个昆虫单个基因的功能及应用。近年来,随着生物信息学和RNAi技术在生命科学研究工作中的广泛应用,在昆虫几丁质酶的研究方面也取得了较大进展。本文主要以生物信息学在几丁质酶家族基因鉴定和分类研究过程中的应用,以及利用RNAi技术分析几丁质酶不同家族成员在赤拟谷盗和褐飞虱两种昆虫生长发育中的功能比较分析,对全面认识昆虫几丁质酶基因家族功能和作用机理,并利用几丁质酶基因防治害虫奠定良好的基础。     

家蝇溶菌酶MDLZM2基因的克隆、序列分析及原核表达

对家蝇溶菌酶(Musca domestica lysozyme,MDLZM2)基因进行克隆、序列分析,构建原核表达载体并在大肠杆菌中表达。从Gen Bank家蝇基因组中筛选获得MDLZM2基因。以该基因的序列设计引物,进行PCR扩增,测序分析获得该基因完整编码序列。运用生物信息学方法对该基因及其编码蛋白的基本理化性质、信号肽、二级结构、三级结构和保守结构域等方面进行预测和分析。构建p EASY-E1-MDLZM2重组质粒,转化到大肠杆菌BL21(DE3)p Lys S Chemically Competent Cell中进行诱导表达及纯化。结果表明MDLZM2基因ORF全长552 bp,编码183个氨基酸,理论分子量21.2 k Da;等电点为6.13,具有Lysozyme家族的蛋白保守结构域。成功构建重组原核表达p EASY-E1-MDLZM2并诱导表达、纯化重组蛋白,为进一步研究该蛋白的生物学及免疫学活性奠定了基础。     

Chlorophyll a is the crucial redox sensor and transmembrane signal transmitter in the cytochrome b6f complex. Components and mechanisms of state transitions from the hydrophobic mismatch viewpoint

The cytochrome (cyt) b₆f complex is involved in the transmembrane redox signaling that triggers state transitions in cyanobacteria and chloroplasts. However, the components and molecular mechanisms are still unclear. In an attempt to solve this long-standing problem, we first focused on the unknown role of a single chlorophyll a (Chla) in cyt b₆f with a new approach based on Chla structural properties. Various b₆f X-ray crystal structures were analyzed to identify their differences, which correlate with differences in Chla molecular volume. We found that the distance of the Rieske [2Fe-2S] cluster to Chla correlates with the distance between a pair of residues at the Q_o-site and the distance between a pair of residues at the opposite membrane side. These correlations were accompanied by the rotation of a key peripheral residue and by changes in the hydrophobic thickness of cyt b₆f. Parallel analysis of cyt bc₁ crystal structures allowed us to conclude that Chla acts as the crucial redox sensor and transmembrane signal transmitter in b₆f for changes in the plastoquinone pool redox state. The hydrophobic mismatch induced by the changed hydrophobic thickness of cyt b₆f is the driving force for the structural reorganizations of the photosynthetic apparatus during induction and the progression of state transitions in cyanobacteria and chloroplasts. A mechanism for LHCII kinase activation in chloroplasts is also proposed. Our understanding of the dynamic structural changes in bc-complexes during turnover at the Q_o-site and state transitions is augmented by the time-sequence ordering of 56 bc crystal structures.     

Protein‐fold recognition using an improved single‐source K diverse shortest paths algorithm

Protein structure prediction, when construed as a fold recognition problem, is one of the most important applications of similarity search in bioinformatics. A new protein‐fold recognition method is reported which combines a single‐source K diverse shortest path (SSKDSP) algorithm with Enrichment of Network Topological Similarity (ENTS) algorithm to search a graphic feature space generated using sequence similarity and structural similarity metrics. A modified, more efficient SSKDSP algorithm is developed to improve the performance of graph searching. The new implementation of the SSKDSP algorithm empirically requires 82% less memory and 61% less time than the current implementation, allowing for the analysis of larger, denser graphs. Furthermore, the statistical significance of fold ranking generated from SSKDSP is assessed using ENTS. The reported ENTS‐SSKDSP algorithm outperforms original ENTS that uses random walk with restart for the graph search as well as other state‐of‐the‐art protein structure prediction algorithms HHSearch and Sparks‐X, as evaluated by a benchmark of 600 query proteins. The reported methods may easily be extended to other similarity search problems in bioinformatics and chemoinformatics. The SSKDSP software is available at http://compsci.hunter.cuny.edu/~leixie/sskdsp.html . Proteins 2016; 84:467–472. © 2016 Wiley Periodicals, Inc.