Folding of Protein L with Implications for Collapse in the Denatured State Ensemble

A fundamental question in protein folding is whether the coil to globule collapse transition occurs during the initial stages of folding (burst phase) or simultaneously with the protein folding transition. Single molecule fluorescence resonance energy transfer (FRET) and small-angle X-ray scattering (SAXS) experiments disagree on whether Protein L collapse transition occurs during the burst phase of folding. We study Protein L folding using a coarse-grained model and molecular dynamics simulations. The collapse transition in Protein L is found to be concomitant with the folding transition. In the burst phase of folding, we find that FRET experiments overestimate radius of gyration, R-g, of the protein due to the application of Gaussian polymer chain end-to-end distribution to extract R-g from the FRET efficiency. FRET experiments estimate approximate to 6 angstrom decrease in R-g when the actual decrease is approximate to 3 angstrom on guanidinium chloride denaturant dilution from 7.5 to 1 M, thereby suggesting pronounced compaction in the protein dimensions in the burst phase. The approximate to 3 angstrom decrease is close to the statistical uncertainties of the R-g data measured from SAXS experiments, which suggest no compaction, leading to a disagreement with the FRET experiments. The transition-state ensemble (TSE) structures in Protein L folding are globular and extensive in agreement with the Psi-analysis experiments. The results support the hypothesis that the TSE of single domain proteins depends on protein topology and is not stabilized by local interactions alone.

Kinetic and Size Control of Polystyrene and Polyacrylic Octadecyl Ester Lattices Via Polymerization in O/W Microemulsions

The kinetic studies of the acrylic octadecyl ester and styrene polymerization in microemulsion systems, (1) cetyl pyridine bromide (CPDB)/t-butanol/styrene/water; (2) CPDB/t-butanol/toluene + acrylic octadecyl ester (1:1, w/v)/ water; (3) cetyl pyridine bromide/styrene/formamide, were made by using dynamic laser light scattering techniques (DLS). The mechanisms of nucleation of latex particles were discussed. The most possible nucleation location of the styrene and acrylic octadecyl ester microlatex particles in aqueous microemulsion system is in aqueous phase via homogeneous nucleation. Meanwhile, parts of microlatex particles are possibly produced via swollen micelles (microemulsions) and monomer droplets nucleation. On the other hand, the most possible nucleation location of the styrene microlatex particles in nonaqueous microemulsion system is inside monomer droplets. The relationship between the amount of monomer and the size of microlatex was also investigated. It has been found that the size of microlatex particles could be controlled by changing the amount of monomer. (C) 2002 Elsevier Science B.V. All rights reserved.

配液结晶法制备溶菌酶蛋白质晶体的生长机理研究

采用配液结晶法制取了溶菌酶蛋白质晶体,使用动态光散射测量了溶液中聚集体的颗粒度几率分布;使用Zeiss显微镜测定了溶菌酶(110)晶面的生长速度.实验表明:随着蛋白质和NaCl浓度的增加,溶液中聚集体的颗粒尺寸也相应增加.随着反应时间的增加,溶菌酶分子在溶液中的聚集反应,逐渐达到平衡;在蛋白质和NaCl浓度较高时,溶菌酶晶体的(110)面生长较快,而在蛋白质和NaCl浓度较低时,该晶面生长较慢.基于二维成核生长机理,从晶体生长动力学理论方程出发,计算了二维成核的形成能a=4.01×10-8J?cm-2.

Guidelines for reducing porpoise mortality in tuna purse seining

More than a decade has passed since the passage of the Marine Mammal Protection Act of 1972. During that time the U.S. tuna purse seine neet reduced its incidental porpoise mortality rate more than 10-fold. This was made possible through the development of gear and techniques aimed at reducing the frequency of many low probability events that contribute to the kill. Porpoise are killed by becoming entangled or entrapped in folds and canopies of the net and suffocating. The configuration of the net, both before and during the backdown release procedure, is a major determinant of the number of porpoise killed. Speedboats can be used to tow on the corkllne to prevent net collapse and also to adjust the net configuration to reduce net canopies prior to backdown. Deepening a net can reduce the probability of porpoise being killed by prebackdown net collapse. The effects of environmental conditions and mechanical failures on net configuration can result in high porpoise mortality unless mitigated by skilled vessel maneuvers or prevented by the timely use of speedboats to adjust the net. The backdown procedure is the only means to effectively release captured porpoise from a purse seine. It is also the time during the set when most of the mortality occurs. The use of small mesh safety panels and aprons in the backdown areas of nets reduces porpoise entanglement, and Increases the probability of an effective release. The tie-down points on the net for preparing the backdown channel must be properly located in order to optimize porpoise release. A formula uses the stretched depth of the net to calculate one of these points, making it a simple matter to locate the other. Understanding the dynamics of the backdown procedure permits a thorough troubleshooting of performance, thus preventing the repetition of poorly executed backdowns and thereby reducing mortality. Porpoise that cannot be released must be rescued by hand. A rescuer in a rigidly inflated raft can rescue porpoise effectively at any time during a net set. Hand rescue can make the difference between above average kill and zero kill sets. In all circumstances, the skill and motivation of the captain and his crew are the final determinants in the prevention of incidental porpoise mortality in tuna seining. (PDF file contains 22 pages.)

Metal-Free Polymethyl Methacrylate (PMMA) Nanoparticles by Enamine "Click" Chemistry at Room Temperature

"Click" chemistry has become an efficient avenue to unimolecular polymeric nanoparticles through the self-crosslinking of individual polymer chains containing appropriate functional groups. Herein we report the synthesis of ultra-small (7 nm in size) polymethyl methacrylate (PMMA) nanoparticles (NPs) by the "metal-free" cross-linking of PMMA-precursor chains prepared by reversible addition-fragmentation chain transfer (RAFT) polymerization containing beta-ketoester functional groups. Intramolecular collapse was performed by the one-pot reaction of beta-ketoester moieties with alkyl diamines in tetrahydrofurane at r.t. (i.e., by enamine formation). The collapsing process was followed by size exclusion chromatography and by nuclear magnetic resonance spectroscopy. The size of the resulting PMMA-NPs was determined by dynamic light scattering. Enamine "click" chemistry increases the synthetic toolbox for the efficient synthesis of metal-free, ultra-small polymeric NPs.

Genetically engineered sensors of cell signaling

Measuring electrical activity in large numbers of cells with high spatial and temporal resolution is a fundamental problem for the study of neural development and information processing. To address this problem, we have constructed FlaSh: a novel, genetically-encoded probe that can be used to measure trans-membrane voltage in single cells. We fused a modified green fluorescent protein (GFP) into a voltage-sensitive potassium channel so that voltage dependent rearrangements in the potassium channel induce changes in the fluorescence of GFP. A voltage sensor encoded into DNA has the advantage that it may be introduced into an organism non-invasively and targeted to specific developmental stages, brain regions, cell types, and sub-cellular compartments.

We also describe modifications to FlaSh that shift its color, kinetics, and dynamic range. We used multiple green fluorescent proteins to produce variants of the FlaSh sensor that generate ratiometric signal output via fluorescence resonance energy transfer (FRET). Finally, we describe initial work toward FlaSh variants that are sensitive to G-protein coupled receptor (GPCR) activation. These sensors can be used to design functional assays for receptor activation in living cells.

Detection of constitutive heterodimerization of the integrin Mac-1 subunits by fluorescence resonance energy transfer in living cells

Macrophage differentiation antigen associated with complement three receptor function (Mac-1) belongs to beta(2) subfamily of integrins that mediate important cell-cell and cell-extracellular matrix interactions. Biochemical studies have indicated that Mac-1 is a constitutive heterodimer in vitro. Here, we detected the heterodimerization of Mac-1 subunits in living cells by means of two fluorescence resonance energy transfer (FRET) techniques (fluorescence microscopy and fluorescence spectroscopy) and our results demonstrated that there is constitutive heterodimerization of the Mac-1 subunits and this constitutive heterodimerization of the Mac-1 subunits is cell-type independent. Through FRET imaging, we found that heterodimers of Mac-1 mainly localized in plasma membrane, perinuclear, and Golgi area in living cells. Furthermore, through analysis of the estimated physical distances between cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) fused to Mac-1 subunits, we suggested that the conformation of Mac-1 subunits is not affected by the fusion of CFP or YFP and inferred that Mac-1 subunits take different conformation when expressed in Chinese hamster ovary (CHO) and human embryonic kidney (HEK) 293T cells, respectively. (c) 2006 Elsevier Inc. All rights reserved.

Detection of constitutive homomeric associations of the integrins Mac-1 subunits by fluorescence resonance energy transfer in living cells

Integrins alpha(M)beta(2) plays important role on leukocytes, such as adhesion, migration, phagocytosis, and apoptosis. It was hypothesized that homomeric associations of integrin subunits provide a driving force for integrins activation, and simultaneously inducing the formation of integrins clusters. However, experimental reports on homomeric associations between integrin subunits are still controversial. Here, we proved the homomeric associations of the isolated Mac-1 subunits in living cells using three-channel fluorescence resonance energy transfer (FRET) microscopy and FRET spectra methods. We found that the extent of homomeric associations between beta(2) subunits is higher than alpha(M) subunits. Furthermore, FRET imaging indicated that the extent of homomeric associations of the Mac-1 subunits is higher along the plasma membrane than in the cytoplasm. Finally, we suggested that homomeric associations of the transmernbrane domains or/and cytoplasmic domains may provide the driving force for the formation of constitutive homomeric associations between alpha(M) or beta(2) subunits. (c) 2006 Elsevier Inc. All rights reserved.

(Report of the) Institute of Marine Biology and Oceanography, Fourah Bay College, University of Sierra Leone

Details are given of the Institute and its activities, in particular the research projects being undertaken. These include studies on the marine molluscs of Sierra Leone, the cockle fishery, a preliminary investigation on the fouling organisms affecting the raft-cultured oyster populations, larval oyster ecology in relation to oyster culture, preliminary studies on the reproductive cycle of the mangrove oyster (Crassostrea tulipa), and catch composition of fishes taken by beach-seines at Lumley (Freetown). Records of the west African manatee (Trichechus senegalensis) are noted.

Preparação de nanopartículas funcionalizadas do tipo casca-núcleo à base de poliestireno e poli(acrilato de butila) para processamento baroplástico

Copolímeros casca-núcleo de poli(acrilato de butila) (núcleo) e poliestireno (casca) foram sintetizados por meio de polimerização em emulsão, conduzida em duas etapas. A adição de ácido itacônico como monômero funcional na polimerização do núcleo foi realizada para verificar seu efeito sobre suas propriedades mecânicas e de processamento. Os copolímeros foram caracterizados por espalhamento dinâmico de luz (DLS), microscopia eletrônica de transmissão (MET), cromatografia de exclusão por tamanho (SEC), espectrometria na região do infravermelho (FTIR) e calorimetria diferencial por varredura (DSC). A incorporação do monômero funcional foi confirmada por DSC e quantificada por titulação. A proporção de poli(acrilato de butila) e poliestireno influenciou diretamente o processamento e as propriedades mecânicas do polímero. Os copolímeros com teores de poliestireno acima de 50% foram processados por compressão e extrusão a temperatura ambiente, apresentando comportamento baroplástico. A presença do monômero funcional não alterou o processamento do polímero e melhorou significativamente sua resistência à tração, aumentando sua tenacidade

Preparação e caracterização de microesferas poliméricas à base de poli(ácido metacrílico-co-divinilbenzeno) obtidas por polimerização por precipitação

Neste trabalho foi feito um estudo sobre a preparação e caracterização de microesferas poliméricas à base de poli(ácido metacrílico-co-divinilbenzeno) por polimerização por precipitação. As partículas foram sintetizadas e analisadas em diferentes condições de reação. Partículas esféricas políméricas foram sintetizadas na faixa de 1,66 - 8,41 m, assim como partículas no estado de microgel. As partículas foram caracterizadas pelas técnicas de espalhamento de luz dinâmica (DLS), análise termogravimétrica (TGA), espectroscopia na região do infravermelho (FTIR), adsorção de nitrogênio pelos métodos BET (Brunauer, Emmett e Teller) e BJH (Barret, Joyner e Halenda), microscopia ótica, microscopia eletrônica de varredura, e testes de razão de inchamento. A análise das partículas foi feita para verificar a influência da mudança na composição de comonômeros, grau de reticulação, relação de monômeros totais/diluentes em massa/volume (g/100 mL), e quanto à relação volumétrica de diluentes. Verificou-se que houve um aumento no tamanho das partículas e da resistência térmica com a diminuição da fração molar de MAA (ácido metacrílico). Na preparação de partículas com fração molar de 50% de MAA, e relação volumétrica acetonitrila/tolueno de 75/25, quanto maior a relação de monômeros totais/diluentes (g/100 mL), maior o tamanho e o rendimento das partículas. Com a mudança da relação volumétrica de diluentes, houve mudança nas características de porosidade, tamanho das partículas, e grau de inchamento das partículas, sendo que na relação volumétrica acetonitrila/tolueno de 50/50, houve formação de microgel

Caracterização e utilização do resíduo de palha de milho para obtenção de nanocelulose

Esta Dissertação discorre sobre a pesquisa de caracterização de palha de milho e a sua utilização como matéria prima para a obtenção de nanocelulose. Segundo o IBGE, este resíduo agrícola foi produzido no Brasil, no ano de 2013, em cerca de seis milhões de toneladas. As amostras deste resíduo lignocelulósico utilizadas neste trabalho foram coletadas na forma cotidiana de descarte mais frequentemente encontrada em supermercados e feiras livres. Procedeu-se, então, ao beneficiamento mecânico, beneficiamento químico (mercerização e branqueamento) e hidrólise ácida dessas amostras, o que produziu os seguintes materiais: palha de milho beneficiada mecanicamente, palha de milho beneficiada quimicamente e nanocelulose. Cada um destes materiais foi caracterizado, conforme o tipo, por menos ou mais dos seguintes ensaios: determinação de densidade, determinação de umidade, determinação do teor de cinzas, resistência à tração, determinação do teor de extraíveis, determinação do teor de holocelulose, determinação do teor de hemicelulose, determinação do teor de alfacelulose, determinação do teor de lignina, análise termogravimétrica (TGA), espectroscopia por infravermelho por transformada de Fourier (FTIR), índice de cristalinidade por difração de raios-x (CrI), medição do tamanho de partícula por espalhamento de luz dinâmico (DLS), morfologia por microscopia eletrônica de varredura (SEM) e determinação do rendimento dos produtos de hidrólise. Nesta pesquisa também se estudou, empregando a técnica de planejamento de experimento fatorial com ponto central, a influência dos fatores razão fibra/ácido e tempo da reação na obtenção da nanocelulose, conseguida com êxito em todos os experimentos executados com a palha de milho que foi branqueada de forma efetiva neste trabalho

Efficient Synthesis of Single-Chain Polymer Nanoparticles via Amide Formation

Single-chain technology (SCT) allows the transformation of individual polymer chains to folded/collapsed unimolecular soft nanoparticles. In this work we contribute to the enlargement of the SCT toolbox by demonstrating the efficient synthesis of single-chain polymer nanoparticles (SCNPs) via intrachain amide formation. In particular, we exploit cross-linking between active methylene groups and isocyanate moieties as powerful "click" chemistry driving force for SCNP construction. By employing poly(methyl methacrylate)- (PMMA-) based copolymers bearing beta-ketoester units distributed randomly along the copolymer chains and bifunctional isocyanate cross-linkers, SCNPs were successfully synthesized at r.t. under appropriate reaction conditions. Characterization of the resulting SCNPs was carried out by means of a combination of techniques including size exclusion chromatography (SEC), infrared (IR) spectroscopy, proton nuclear magnetic resonance (H-1 NMR) spectroscopy, dynamic light scattering (DLS), and elemental analysis (EA).

脂筏极化参与活性氧介导的白杄花粉管顶端生长

质膜上存在一种富含甾醇物质的液相有序膜脂微区，被称作脂筏 (lipid rafts或lipid microdomains)。这种小的膜微区可以通过在质膜上的侧向移动，聚集形成较大的片状结构，而与微区相关联的蛋白可以通过脂筏的这种聚合作用而凝聚分布于特定的亚细胞结构上。脂筏区域在真菌和动物质膜上具极性分布，并参与细胞的极性形态建成和运动。最近，通过生物化学研究证实，脂筏也存在于植物细胞，然而迄今为止，脂筏与植物细胞极性生长相关联的直接功能证据尚未见报道。 NADPH氧化酶 (NOX，在植物中又称为 Rboh) 产生的活性氧 (Reactive oxygen species, ROS) 可能是调控植物细胞（包括花粉管、根毛和墨角藻合子等）极性生长的通用信号机制。花粉管作为研究细胞极性控制的一种理想模式系统，已被许多信号转导调控研究所采用。在本研究中，我们使用一种能螯合甾醇类物质的多烯类抗生素filipin破坏脂筏结构，以探讨脂筏极化对ROS介导的白杄花粉管极性生长的作用。 我们首次在白杄 (Picea meyeri) 花粉管上应用一种全新的苯乙烯基染料di-4-ANEPPDHQ，成功地在活体细胞上观察到脂筏在花粉管生长顶端的极性分布模式。通过脂筏和甾醇在质膜上的相似定位清楚表明：在花粉管极性生长过程中，存在富含甾醇类物质的质膜微区在花粉管生长顶端的极化现象。 氮蓝四唑（NBT）的还原和二氯二氢荧光素（H2DCF）的氧化均显示，在活跃生长的花粉管顶端区域存在一个以顶端为基底的陡峭ROS梯度，从而进一步验证了ROS在细胞极性生长过程中的信号作用。此外，我们还发现在生长花粉管的亚顶端位置有另一类性质的活性氧组分存在，该ROS组分与线粒体的能量代谢相关。研究结果首次揭示，在快速生长的花粉管中同时存在两类性质不同的ROS组分。 ROS是一种寿命很短而且容易扩散的分子，NADPH氧化酶产生的ROS信号在细胞伸长位点的准确定位是调控极性生长的必要条件。免疫共定位实验显示，NOX成簇极化分布于花粉管的生长顶端。使用filipin进行甾醇的螯合会破坏膜的异质性，干扰NOX簇在生长顶端的定位，减少了顶端的ROS形成，消弱了胞质Ca2+ 浓度梯度，进而抑制了花粉管的顶端生长。 在纯化质膜的基础上，我们使用Triton去垢剂处理结合Optiprep密度梯度离心，分离纯化了抗去垢剂抽提的质膜微区 (Detergent-resistant microdomains, DRMs)。通过免疫印迹分析证实，NADPH氧化酶部分地存在于DRMs中。非变性胶活性实验证明，该酶需要脂筏定位来保持酶活性。因此我们认为，在正常的细胞极性生长中，脂筏招募并运载NADPH氧化酶到花粉管的生长顶端，并为NOX及其活性亚基的有效互作提供了适宜的微环境，由此保证了NOX蛋白产生ROS的较高酶活性，进而维持花粉管的极性顶端生长。 总之，甾醇螯合对白杄花粉管生长影响的研究，为脂筏极化在花粉管极性生长中的作用提供了证据。基于以上生物化学和细胞生物学的结果，我们针对花粉管中富含甾醇的脂筏微区和NOX功能之间的联系，提出了一种假说模式：(1) 植物细胞质膜上的脂筏为信号分子ROS在特定位点的聚集提供了物理载体；(2) 脂筏的完整性和甾醇依赖性对NOX的定位和活性是必要的，并为花粉管细胞极性产生和维持所必需。上述研究结果表明，脂筏在花粉管顶端的极化，以及作为关键生长因子的NOX在质膜脂筏中的定位，对花粉管的高度极性生长具有重要作用。

Coupled foundation-superstructure analysis and influence of building stiffness on foundation response

This paper proposes a simple method to include superstructure stiffness in foundation analyses. The method involves extracting a small "condensed structural matrix" from finite element models of the superstructure, which can then be incorporated into pile group or piled raft analyses using common approaches such as elastic continuum or load transfer methods. The matrix condensation method directly couples structural and geotechnical analyses, and eliminates the need for iterative analyses between structural and geotechnical engineers. Effectiveness of the approach is illustrated through analyses of several buildings designed with a typical floor plan but with varying heights. The parametric study illustrates that superstructure stiffness can have a significant influence on foundation settlement estimates, and the stiffening effects are dominated by the lower stories of the superstructure. The proposed method aims to bridge the gap between structural and geotechnical analyses. Also, being a computationally simple and accurate approach, it is applicable to parametric or optimization studies that would otherwise involve large amounts of analyses. © 2010 ASCE.