Proteins searching for their target on DNA by one-dimensional diffusion: overcoming the “speed-stability” paradox

The sequence dependence of DNA-protein interactions that allows proteins to find the correct reaction site also slows down the 1D diffusion of the protein along the DNA molecule, leading to the so-called “speed-stability paradox,” wherein fast diffusion along the DNA molecule is seemingly incompatible with stable targeting of the reaction site. Here, we develop diffusion-reaction models that use discrete and continuous Gaussian random 1D diffusion landscapes with or without a high-energy cut-off, and two-state models with a transition to and from a “searching” mode in which the protein diffuses rapidly without recognizing the target. We show the conditions under which such considerations lead to a predicted speed-up of the targeting process, and under which the presence of a “searching” mode in a two-state model is nearly equivalent to the existence of a high-energy cut-off in a one-state model. We also determine the conditions under which the search is either diffusion-limited or reaction-limited, and develop quantitative expressions for the rate of successful targeting as a function of the site-specific reaction rate, the roughness of the DNA-protein interaction potential, and the presence of a “searching” mode. In general, we find that a rough landscape is compatible with a fast search if the highest energy barriers can be avoided by “hopping” or by the protein transitioning to a lower-energy “searching” mode. We validate these predictions with the results of Brownian dynamics, kinetic Metropolis, and kinetic Monte Carlo simulations of the diffusion and targeting process, and apply these concepts to the case of T7 RNA polymerase searching for its target site on T7 DNA.     

Characterization of novel microsatellite markers from the Yesso scallop Mizuhopecten yessoensis

Twelve polymorphic and informative microsatellite markers were isolated and characterized for the Yesso scallop, Mizuhopecten yessoensis. We characterized these loci by genotyping 48 individuals; the number of alleles ranged from two to eight, and the values of observed heterozygosity and expected heterozygosity varied from 0 to 0.8333 and from 0.2546 to 0.8231, respectively. No significant linkage disequilibrium between pairs of loci was found and three loci showed significant heterozygote deficiency from the Hardy–Weinberg equilibrium. These markers are potential for studies of the population structure, individual or hybrid identification of the species.     

川硬皮肿腿蜂染色体制备方法探讨

对川硬皮肿腿蜂Scleroderma sichuanensis Xiao(Hymenoptera:bethylidae Sclerderma)染色体制备方法进行了探讨,结果表明;以川硬皮肿腿蜂雌成虫卵巢为材料,经0.01%秋水仙素水溶液处理10min,蒸馏水低渗5min,用甲醇、冰醋酸(3∶1)固定液固定15min,Giemsa染液染色30min,可以获得形态良好、分散适中、着色清晰的染色体.     

甘肃鼢鼠骨骼13种微量元素测定

对甘肃鼢鼠(Myospalax cansus)骨骼中Fe、Cu、Zn、Mn、Cr、Ni、Co、Mo、Cd、As、Pb、F、Al等13种微量元素进行了测定。结果表明,甘肃鼢鼠全骨中13种元素含量依次为Al>Fe>Zn>F>Mn>Cu>Pb>As>Cr>Co>Ni>Mo>Cd;同一元素在不同骨骼分布不均,头骨最丰富,除Zn、Mn外,同一元素在不同部位骨骼的含量存在显著差异;13种微量元素之间的相关性,Zn-Pb、Mn-Cd、As-Pb3组呈显著负相关(0.01相似文献   

凤尾蕨内生真菌的研究Ⅱ——1株产芦丁内生真菌初步研究

报道了从凤尾蕨属井栏边草(Pteris multifida)根状茎中分离出一内生真菌——菌株JJF006,对其形态特征进行了初步研究,并用TLC对该菌株培养物进行了分析。初步结果表明:该真菌液体培养基中含有芦丁成分。     

生物传感芯片质谱及其在蛋白质组研究中的应用

目前蛋白质组研究技术在已有的研究基础上取得了长足进展 ,包括固相 ｐＨ梯度双向凝胶电泳、生物质谱技术、蛋白质双向电泳图谱的数字化和各种分析技术、蛋白质间相互作用分析的方法如酵母双杂交系统、噬菌体展示、表面等离子共振等。但均各有其利弊。目前质谱是进行蛋白质组成分鉴定的支撑技术 ,但是它在蛋白质间相互作用分析及结构与功能的关系分析方面显得无能为力 ,而生物分子相互作用分析技术 (Ｂｉｏｍｏｌｅｃｕｌａｒｉｎｔｅｒａｃｔｉｏｎａｎａｌｙｓｉｓ ,ＢＩＡ)是进行蛋白质相互作用分析的较好技术 ,将两者结合起来在蛋白质组…     

中国学术期刊网络出版总库节点文献新疆驴脑组织尼帕病毒N基因片段的检测

目的检测新疆伊犁草原地区放养新疆驴的脑组织样本中尼帕病毒（Nipah Virus,NiV）核蛋白（N）基因片段,调查该地区放养新疆驴NiV感染流行状况。方法采用一步法实时荧光定量逆转录聚合酶链反应（one-step Real-Time FQ RT-PCR）对采自新疆伊犁地区草原放养且未接种NiV疫苗的65例新疆驴脑组织进行NiVN基因片段检测。结果新疆驴脑组织标本中未检出NiV N基因片段。结论目前尚无证据表明我国新疆伊犁地区新疆驴中存在NiV感染,提示该地区短时间内爆发该病毒感染可能性较小。     

KcsA通道对Na+、K+及Rb+离子选择性的统计热力学研究

钾离了的通透率至少比钠离子的通透率大10000倍,这个问题至今没有很好地解决,为了存分子水平阐释钾离子通道的选择性机制,以KcsA钾通道X射线衍射结构为基础,采用密度泛函理论计算了不同离子在离子通道中的位能．计算结果表明,Rb^ 离子具有与K^ 离子相类似的位能曲线,但是其在通透过程遇到的位垒要比K^ 离子的位垒高,因而所对应的通透率也就小十钾离子的通透率,而钠离子的的通透率仅仅足钾离子通透率的0．0067％．文中所涉及的系统仪仅包含269个原子,而用分子动力学虽然也可以得到相近的结果,但是它的系统火小为41000个原子．     

来源于Rhinocladiella mackenziei的玉米赤霉烯酮水解酶的表达纯化与酶学性质

【背景】玉米赤霉烯酮(Zearalenone,ZEN)是污染最广泛的霉菌毒素之一,对饲料行业和畜牧业造成了巨大的经济损失。目前研究最为广泛的玉米赤霉烯酮降解酶ZHD101因其热稳定性较差,无法满足工业应用上的要求。【目的】为实现玉米赤霉烯酮降解酶在工业上的应用,寻找酶学性质更突出的ZEN降解酶。【方法】基于对Gen Bank数据库的挖掘,发现一个来源于麦氏喙枝孢霉(Rhinocladiella mackenziei CBS 650.93)的Rmzhd基因,构建p ET-46-Rmzhd质粒。利用大肠杆菌表达体系和亲和层析、离子交换纯化体系对蛋白进行表达和纯化,通过高效液相凝胶色谱分析酶学性质。【结果】发现一个新的ZEN水解酶Rm ZHD,RmZHD在pH 8.6和45°C条件下的活性最高,而且具有较高的耐热性。结构分析表明,较高的盐桥数目和溶剂暴露脯氨酸含量可能是造成其高耐热性的原因。【结论】本研究为促进玉米赤霉烯酮降解酶在工业上的应用打下基础。