Androgen receptor-dependent and independent functions of ARIP4

Androgen receptor (AR) is necessary for normal male phenotype development and essential for spermatogenesis. AR is a classical steroid receptor mediating actions of male sex steroids testosterone and 5-alpha-dihydrotestosterone. Numerous coregulators interact with the receptor and regulate AR activity on target genes. This study deals with the characterization of androgen receptor-interacting protein 4 (ARIP4). ARIP4 binds DNA, interacts with AR in vitro and in cultured yeast and mammalian cells, and modulates AR-dependent transactivation. ARIP4 is an active DNA-dependent ATPase, and this enzymatic activity is essential for the ability of ARIP4 to modulate AR function. On the basis of sequence homology in its ATPase domain, ARIP4 belongs to the SNF2 family of proteins involved in chromatin remodeling, DNA repair, and homologous recombination. Similar to its closest homologs ATRX and Rad54, ARIP4 does not seem to be a classical chromatin remodeling protein in that it does not appear to form large protein complexes in vivo or remodel mononucleosomes in vitro. However, ARIP4 is able to generate superhelical torsion on linear DNA fragments. ARIP4 is covalently modified by SUMO-1, and mutation of six potential SUMO attachment sites abolishes the ability of ARIP4 to bind DNA, hydrolyze ATP, and activate AR function. ARIP4 expression starts in early embryonic development. In mouse embryo ARIP4 is present mainly in the neural tube and limb buds. In adult mouse tissues ARIP4 expression is virtually ubiquitous. In mouse testis ARIP4 is expressed in the nuclei of Sertoli cells in a stage-dependent manner. ARIP4 is also present in the nuclei of Leydig cells, spermatogonia, pachytene and diplotene spermatocytes. Testicular expression pattern of ARIP4 does not differ significantly in wild-type, FSHRKO, and LuRKO mice. In the testis of hpg mice, ARIP4 is found mainly in interstitial cells and has very low, if any, expression in Sertoli and germ cells. Heterozygous Arip4+/ mice are fertile and appear normal; however, they are haploinsufficient with regard to androgen action in Sertoli cells. In contrast, Arip4 / embryos are not viable. They have significantly reduced body size at E9.5 and die by E11.5. Compared to wild-type littermates, Arip4 / embryos possess a higher percentage of apoptotic cells at E9.5 and E10.5. Fibroblasts derived from Arip4 / embryos cease growing after 2-3 passages and exhibit a significantly increased apoptosis and decreased proliferation rate than cells from wild-type embryos. Our findings demonstrate that ARIP4 plays an essential role in mouse embryonic development. In addition, testicular expression and AR coregulatory activity of ARIP4 suggest a role of ARIP4-AR interaction in the somatic cells of the testis.

Allostery and conformational free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and structure networks

The interdependence of the concept of allostery and enzymatic catalysis, and they being guided by conformational mobility is gaining increased prominence. However, to gain a molecular level understanding of llostery and hence of enzymatic catalysis, it is of utter importance that the networks of amino acids participating in allostery be deciphered. Our lab has been exploring the methods of network analysis combined with molecular dynamics simulations to understand allostery at molecular level. Earlier we had outlined methods to obtain communication paths and then to map the rigid/flexible regions of proteins through network parameters like the shortest correlated paths, cliques, and communities. In this article, we advance the methodology to estimate the conformational populations in terms of cliques/communities formed by interactions including the side-chains and then to compute the ligand-induced population shift. Finally, we obtain the free-energy landscape of the protein in equilibrium, characterizing the free-energy minima accessed by the protein complexes. We have chosen human tryptophanyl-tRNA synthetase (hTrpRS), a protein esponsible for charging tryptophan to its cognate tRNA during protein biosynthesis for this investigation. This is a multidomain protein exhibiting excellent allosteric communication. Our approach has provided valuable structural as well as functional insights into the protein. The methodology adopted here is highly generalized to illuminate the linkage between protein structure networks and conformational mobility involved in the allosteric mechanism in any protein with known structure.

TSpred: a web server for the rational design of temperature-sensitive mutants

Temperature sensitive (Ts) mutants of proteins provide experimentalists with a powerful and reversible way of conditionally expressing genes. The technique has been widely used in determining the role of gene and gene products in several cellular processes. Traditionally, Ts mutants are generated by random mutagenesis and then selected though laborious large-scale screening. Our web server, TSpred (http://mspc.bii.a-star.edu.sg/TSpred/), now enables users to rationally design Ts mutants for their proteins of interest. TSpred uses hydrophobicity and hydrophobic moment, deduced from primary sequence and residue depth, inferred from 3D structures to predict/identify buried hydrophobic residues. Mutating these residues leads to the creation of Ts mutants. Our method has been experimentally validated in 36 positions in six different proteins. It is an attractive proposition for Ts mutant engineering as it proposes a small number of mutations and with high precision. The accompanying web server is simple and intuitive to use and can handle proteins and protein complexes of different sizes.

Chemical specificity and conformational flexibility in proteinase-inhibitor interaction: Scaffolds for promiscuous binding

One of the most important roles of proteins in cellular milieu is recognition of other biomolecules including other proteins. Protein protein complexes are involved in many essential cellular processes. Interfaces of protein protein complexes are traditionally known to be conserved in evolution and less flexible than other solvent interacting tertiary structural surface. But many examples are emerging where these features do not hold good. An understanding of inter-play between flexibility and sequence conservation is emerging, providing a fresh dimension to the paradigm of sequence structure function relationship. The functional manifestation of the inter-relation between sequence conservation and flexibility of interface is exemplified in this review using proteinase inhibitor protein complexes. (C) 2014 Elsevier Ltd. All rights reserved.

Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated.We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard–Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.

The Metabolic Core and Catalytic Switches Are Fundamental Elements in the Self-Regulation of the Systemic Metabolic Structure of Cells

19 p.

Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated. We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard-Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.

The Development of Biosensor with Imaging Ellipsometry

The concept of biosensor with imaging ellipsometry was proposed about ten years ago. It has become an automatic analysis technique for protein detection with merits of label-free, multi-protein analysis, and real-time analysis for protein interaction process, etc. Its principle, andrelated technique units, such as micro-array, micro-fluidic and bio-molecule interaction cell, sampling unit and calibration for quantitative detection as well as its applications in biomedicine field are presented here.

Optical properties of excited silicon and germanium at low temperatures

Part I of this thesis deals with 3 topics concerning the luminescence from bound multi-exciton complexes in Si. Part II presents a model for the decay of electron-hole droplets in pure and doped Ge.

Part I.

We present high resolution photoluminescence data for Si doped With Al, Ga, and In. We observe emission lines due to recombination of electron-hole pairs in bound excitons and satellite lines which have been interpreted in terms of complexes of several excitons bound to an impurity. The bound exciton luminescence in Si:Ga and Si:Al consists of three emission lines due to transitions from the ground state and two low lying excited states. In Si:Ga, we observe a second triplet of emission lines which precisely mirror the triplet due to the bound exciton. This second triplet is interpreted as due to decay of a two exciton complex into the bound exciton. The observation of the second complete triplet in Si:Ga conclusively demonstrates that more than one exciton will bind to an impurity. Similar results are found for Si:Al. The energy of the lines show that the second exciton is less tightly bound than the first in Si:Ga. Other lines are observed at lower energies. The assumption of ground state to ground-state transitions for the lower energy lines is shown to produce a complicated dependence of binding energy of the last exciton on the number of excitons in a complex. No line attributable to the decay of a two exciton complex is observed in Si:In.

We present measurements of the bound exciton lifetimes for the four common acceptors in Si and for the first two bound multi-exciton complexes in Si:Ga and Si:Al. These results are shown to be in agreement with a calculation by Osbourn and Smith of Auger transition rates for acceptor bound excitons in Si. Kinetics determine the relative populations of complexes of various sizes and work functions, at temperatures which do not allow them to thermalize with respect to one another. It is shown that kinetic limitations may make it impossible to form two-exciton complexes in Si:In from a gas of free excitons.

We present direct thermodynamic measurements of the work functions of bound multi-exciton complexes in Al, B, P and Li doped Si. We find that in general the work functions are smaller than previously believed. These data remove one obstacle to the bound multi-exciton complex picture which has been the need to explain the very large apparent work functions for the larger complexes obtained by assuming that some of the observed lines are ground-state to ground-state transitions. None of the measured work functions exceed that of the electron-hole liquid.

Part II.

A new model for the decay of electron-hole-droplets in Ge is presented. The model is based on the existence of a cloud of droplets within the crystal and incorporates exciton flow among the drops in the cloud and the diffusion of excitons away from the cloud. It is able to fit the experimental luminescence decays for pure Ge at different temperatures and pump powers while retaining physically reasonable parameters for the drops. It predicts the shrinkage of the cloud at higher temperatures which has been verified by spatially and temporally resolved infrared absorption experiments. The model also accounts for the nearly exponential decay of electron-hole-droplets in lightly doped Ge at higher temperatures.

牛耳草Bose hygrometrica 离体叶脱水-复水过程的光合作用及基因表达

本文以复苏植物牛耳草Boea hygrometrica成熟植株的离体叶片为试材，对比非复苏植物烟叶唇苣苔Chirita heterotricha, 以光合作用在脱水－复水过程中的变化为切入点，从生理水平上探讨其脱水保护位点：应用mRNA差异显示技术，从分子水平上探讨其脱水保护机制。 光合放氧速率、快速荧光诱导动力学、慢速荧光诱导动力学、荧光发射光谱、荧光激发谱的结果表明，相对于烟叶唇柱苣苔，脱水对牛耳草净光合速率、PS II和PS I光化学活性、电子传递、光合磷酸化及CO_2固定的影响有一个共同的特点，即脱水时迅速降低，复水后恢复能力强。通过非变性绿胶的研究牛耳草叶片类囊体膜叶绿素－蛋白复合体在脱水－复水过程中保持高度稳定。色素含量分析表明牛耳草的叶绿素含量在脱水－复水过程中也相对稳定。这些特征可能是牛耳草叶片光合作用脱水保护机制的一部分。 SDS－PAGE和IEF电泳结果表明，牛耳草脱水复苏过程中蛋白质表达有差异，或增或减，并分别发现了一条（SDS－PAGE）和两条（IEF）在脱水过程中特异出现的蛋白质。 本文以银染法代替放射自显影用于mRNA差异显示，不但简化了实验步骤，缩短了实验周期，而且在不降低灵敏度的前提下避免了放射性危害，降低了实验成本。本文证明了mRNA差异银染显示法用于复苏植物牛耳草脱水－复水过程中基因表达变化的研究是可行的。 mRNA差异银染显示法揭示牛耳草耐脱水复苏机制涉及到基因表达的调控。脱水－复水过程中差异表达的基因有6种，其中脱水特异诱导表达的13个cDNA所相应的基因、脱水上调节的15个cDNA所相应的基因可能参与牛耳草叶片脱水保护机制，复水特异诱导的8个cDNA的所相应基因可能参与牛耳草复水后的修复机制。2个脱水特异诱导表达的cDNA片段进行了克隆和测序。

高等植物PSI ,PSII反应中心及天线系统色素蛋白复合体结构与功能的研究

一、实验证明了Cd H、Mg“在小麦类囊体膜上色素蛋白复合体的解聚和再聚合过程中，具有不同的作用。因此，二阶阳离子对激发能在光系统间的分配调节作用，可能不能仅仅用“静电现象”(Barber(1980))去解释。分析表明，在Ca2+作用下与PSII内周天线CP-47，GP-43多肽结合的L H C II和LHClb是来自间质膜区的PS I系统的。从PSI迁移到P S II的捕光色素蛋白，增加了PSII的捕光截面，从而促进了激发能有利于PsII分配。 二、Ca2*、Mg2+对小麦和菠菜类囊体膜光谱性质的影响有所差异。Ca2+对小麦类囊体膜光谱性质的影响还可以随着介质中Ca2+的消除而消除。同小麦类囊体膜相比，菠菜PSII以及LHCII更为集中在基粒区域，这可能是菠菜类囊体膜强Fv以及高F888／F735，F89H／F735比值的原因。因此，Ca2+，HgH对激发能在光系统间分配的调节作用是依赖于光系统间激发能及天线色素蛋白的分配状况的。 三、对菠菜叶中分离的PSII-RC: D1-D2-cyt b55g复合物进行的低温荧光发射光谱的研究表明，这一复合物可能具有F681和F684两种波长的低温荧光发射，但它们通常并不是同时存在，而是取决于Ca-670与Ca-680 Chla分子的相对含量的。PSII-RC内周无线GP-47，GP-43多肽的存在是D1-D2-cyt b559复合物低温荧光发射红移的原因;而D1一D2cyt b559复合物的不稳定性则与其低温荧光发射的蓝移现象有关。 从蕹菜叶中分离的Dl—D2-cyt b559复合物的F 381低温荧光发射也是由其相对含量较高的C．i-6 7 0 Chla分子的存在决定的。对蕹菜D 1一D 2-cyt b559复合物中的分析还表明，F 681的低温荧光发射直接来源于Di／D2复合物，而415nm处相对较强的吸收，则可能主要是与Pheo的存在有关的。 四、多肽分析与光谱分析的对照表明，CP-26内周天线多肽可能是PSII中F695低温荧光发射的真正来源。 五、实验分析了蔗糖密度离心分离的LHClI和PSI颗粒。结果排除了CP-27多肽（以及CP，一2 5，GP-47，CP -4 3多肽）具有F695低温荧光发射的可能，因此支持了CP-26多肽是PSII中F695低荧光发射来源的看法。对PsI颗粒的分析表明，P700的存在可能是与PSI-RC中较大的Sub-I亚基相联系的。 六、根据以上的研究结果，提出了PSI，PSII在类囊体膜上的结构模式，并对其内容进行了分析和讨论。

PSII色素蛋白复合物的脂质体重组及反应中心的功能研究

光系统II（PSII）是存在于类囊体膜中的多亚基色素蛋白复合物，是吸收光能、催化光诱导水裂解释放氧气、质子和电子的重要机构。它在体内的基本单位是由外周天线蛋白（LHCII）与PSII核心复合物结合形成的PSII-LHCII超分子复合物，这一结构保证了LHCII吸收的能量能够快速有效的传递到PSII反应中心（RC），进行原初光化学反应。 本论文分为两部分：1、利用捕光色素蛋白复合物（LHCII）与PSII核心复合物在以DGDG、PG、SQDG三种类囊体膜脂形成的脂质体中重组的方法，研究了LHCII与PSII在脂膜上结构与功能的相互作用;2、通过研究光破坏和色素置换对PSII RC的影响，探讨了RC中不同色素的功能。主要结果如下： 1、LHCII与PSII核心复合物的蛋白脂质体研究： 将OECC（粗提核心复合物）、pdOE（纯化核心复合物）、LHCII（大量天线）制剂分别与脂质体重组并研究了其光谱性质。LHCII在与脂质体重组前表现出典型的聚集态光谱特征，重组后吸收和荧光发射峰发生明显蓝移;LHCII、OECC和pdOE三种蛋白脂质体与重组前的样品相比荧光发射强度增加;表明脂环境影响了色素蛋白复合物的聚集状态以及色素和蛋白之间的相互作用。 OECC和pdOE分别与LHCII在脂质体中重组，得到两种重组蛋白（LHCII-OECC和LHCII-pdOE）脂质体，用冰冻蚀刻电镜技术和低温荧光光谱的方法研究其结构和功能特征。LHCII和核心复合物（OECC或pdOE）结合形成PSII-LHCII重组颗粒，并在脂质体中均匀排布，阻止了LHCII晶格状结构的形成。重组蛋白脂质体的吸收光谱既有LHCII的吸收特征，又有核心复合物的特征吸收峰，但低温荧光光谱的主要发射峰是核心复合物的特征峰（684 nm-685 nm），而不是LHCII的特征峰（680 nm）;而且激发不同色素得到的荧光发射光谱基本一致，这些结果证明LHCII吸收的能量传递到了核心复合物中，在重组蛋白脂质体中不同色素蛋白复合物在结构和功能上都实现了相互偶联。 通过对OECC或pdOE与LHCII重组形成的蛋白脂质体放氧或DCPIP光还原活性的检测研究了PSII光化学活性特征。LHCII和核心复合物（OECC或pdOE）的重组蛋白脂质体与单独核心脂质体相比，在强光和弱光下光化学活性都明显提高。这从另一个角度证明了核心复合物与LHCII的功能偶联，LHCII的结合使捕光截面积增大，从而使PSII光化学活性增加。 用77K飞秒时间分辨荧光光谱分析了几种蛋白脂质体的能量传递和捕获情况。LHCII、OECC和pdOE三种蛋白脂质体的主要荧光衰减组分分别是670 ps（发射峰在680 nm）、650 ps（发射峰在690 nm）和570 ps（发射峰在685 nm）。LHCII-OECC和LHCII-pdOE脂质体的主要衰减组分分别是940 ps（发射峰在690 nm）和840 ps（发射峰在685 nm），并且出现了一个在核心复合物脂质体和LHCII脂质体中没有的40 ps组分，可以推测，这是LHCII和核心复合物之间达到平衡的时间组分，比激发态衰减的平均寿命要快得多，因此支持了PSII的trap-limited激发能衰减动力学模型。此外，可以看到天线的增大使Chl a荧光衰减的寿命延长，这一特性可能与PSII的光保护机制有关。 LHCII和OECC、LHCII和pdOE在脂质体中都成功的实现了重组，而且在结构和功能上没有明显差异;表明小天线以及23 kDa、17 kDa蛋白可能不是LHCII和核心复合物结合及能量传递所必需的。 2、受体侧光破坏和色素置换对PSII RC的影响： 在800 μmol.m-2 .s-1光照和无外加电子受体、供体的情况下，研究了PSII RC色素的受体侧光破坏情况。Chl a、Pheo和β-Car的光漂白几乎同时发生，其中在680 nm吸收的色素破坏最为显著，670 nm吸收的外周Chl比其他色素更加稳定。荧光发射强度呈先升高后降低的趋势，最大发射峰位逐渐蓝移，表明色素之间的能量传递受到破坏。用β-Car的主要吸收波长488 nm和514.5 nm激发得到两组谱带峰位和强度不同的拉曼光谱，表明在PSII RC中存在两个光谱性质不同的β-Car。光破坏过程中两组谱带的位置和带宽都没有明显变化，表明β-Car的光保护机制不涉及自身构象的变化。 将PSII RC与Cu-Chl a进行色素置换，得到了与Cu-Chl重组的RC（Cu-Chl-RC），含有0.5 Cu-Chl/2Pheo。与对照RC（按同样方式与Chl a置换的RC）和天然RC相比，Cu-Chl含量增加而Chl含量减少，660 nm的吸收增加而670 nm吸收降低，因此推测是外周Chl被替换。色素置换过程对RC的多肽组分及大部分的P680活性没有影响，CD光谱的变化也很小，表明产生CD信号的色素和蛋白环境也没有受到明显影响。但是Cu-Chl-RC的荧光发射强度明显降低，最大发射峰蓝移且峰形发生变化，Cu-Chl可能在重组RC中作为激发态的淬灭剂，阻碍了色素之间的能量传递。

Bayesian correlated clustering to integrate multiple datasets.

MOTIVATION: The integration of multiple datasets remains a key challenge in systems biology and genomic medicine. Modern high-throughput technologies generate a broad array of different data types, providing distinct-but often complementary-information. We present a Bayesian method for the unsupervised integrative modelling of multiple datasets, which we refer to as MDI (Multiple Dataset Integration). MDI can integrate information from a wide range of different datasets and data types simultaneously (including the ability to model time series data explicitly using Gaussian processes). Each dataset is modelled using a Dirichlet-multinomial allocation (DMA) mixture model, with dependencies between these models captured through parameters that describe the agreement among the datasets. RESULTS: Using a set of six artificially constructed time series datasets, we show that MDI is able to integrate a significant number of datasets simultaneously, and that it successfully captures the underlying structural similarity between the datasets. We also analyse a variety of real Saccharomyces cerevisiae datasets. In the two-dataset case, we show that MDI's performance is comparable with the present state-of-the-art. We then move beyond the capabilities of current approaches and integrate gene expression, chromatin immunoprecipitation-chip and protein-protein interaction data, to identify a set of protein complexes for which genes are co-regulated during the cell cycle. Comparisons to other unsupervised data integration techniques-as well as to non-integrative approaches-demonstrate that MDI is competitive, while also providing information that would be difficult or impossible to extract using other methods.

Atomic force microscopic study of low temperature induced disassembly of RecA-dsDNA filaments

The assembly and disassembly of RecA-DNA nucleoprotein filaments on double-stranded DNA (dsDNA) or single-stranded DNA (ssDNA) are important steps for homologous recombination and DNA repair. The assembly and disassembly of the nucleoprotein filaments are sensitive to the reaction conditions. In this work, we investigated different morphologies of the formed nucleoprotein filaments at low temperature under different solution conditions by atomic force microscopy (AFM). We found that low temperature and long keeping time could induce the incomplete disassembly of the formed nucleoprotein filaments.

Atomic force microscope investigation of large-circle DNA molecules

A circular bacterial artificial chromosome of 148.9 kbp on human chromosome 3 has been extended and fixed on bare mica substrates using a developed fluid capillary flow method in evaporating liquid drops. Extended circular DNA molecules were imaged with an atomic force microscope (AFM) under ambient conditions. The measured total lengths of the whole DNA molecules were in agreement with sequencing analysis data with an error range of +/-3.6%. This work is important groundwork for probing single nucleotide polymorphisms in the human genome, mapping genomic DNA, manipulating biomolecular nanotechnology, and studying the interaction of DNA-protein complexes investigated by AFM.