Analysis of Ras:RasGEF interactions by phage display and static multi-angle light scattering

Molecular switches such as small GTPases of the Ras family cycle between inactive GDP-bound and active GTP-bound states. Their essential role in controlling development and cell homeostasis requires mechanisms which determine amplitude and timing of activation. This is achieved in part by the action of guanine nucleotide exchange factors, which function as highly controlled enzymes whose activity relies on spatial segregation and intra- and intermolecular regulation. Here, we describe two experimental methodologies that permit the identification and characterization of GTPase binding sites on activators by assaying complex formation within a broad range of affinities. In the first assay system, proteins presented on the surface of filamentous phage are used to probe affinity determinants of protein-protein interactions. In this application, a protein-displayed phage library is generated by random mutagenesis and a plate-based selection is performed to identify mutations that confer higher binding affinity to an immobilized target. The second method uses light scattering as a tool for measuring the molecular weight, stoichiometry, and polydispersity of protein complexes in solution. In this application, conventional gel filtration chromatography provides initial fractionation, and in-line light scattering measurements allow accurate determination of molar masses of the eluent. This technique also provides information about conformational homogeneity which can be used as a quality     

高效液相尺寸排阻色谱-多角度激光散射定量检测灭活禽流感病毒抗原中完整病毒颗粒

本研究旨在建立一种灭活禽流感病毒原料液中完整病毒颗粒准确定量的方法。针对直接采用高效液相尺寸排阻色谱法（high performance size exclusion chromatography,HPSEC）检测灭活禽流感病毒原液存在杂质干扰的问题,首先以H5N8型抗原为对象,分别考察了聚乙二醇（polyethylene glycol,PEG）沉淀和离子交换色谱法（ion exchange chromatography,IEC）进行预处理。在优化条件下,经DEAE FF阴离子交换层析纯化预处理,杂蛋白去除率为86.87%,病毒血凝回收率为100%。HPSEC分析预处理后的样品,8.5–10.0 min处色谱峰样品电泳检测显示主要为H5N8病毒蛋白,动态光散射分析平均粒径为127.7 nm,推测为完整病毒特征峰;在IEC预处理后的样品中加入抗体进行HPSEC检测,8.5-10.0 min处特征峰消失,显示IEC预处理有效去除了杂质干扰。通过将HPSEC与多角度激光散射技术（multi-angle laser scattering technique,MALLS）联用,可以准确获得样品中完整病毒颗粒的数量,且病毒颗粒数与色谱峰面积具有良好线性关系（R²=0.997）。建立的IEC预处理-HPSEC-MALLS检测方法应用于其他亚型（H7N9）、批次和浓度的病毒原液中完整病毒颗粒数的准确检测,均具有良好适用性,且重复性好,相对标准偏差（relative standard deviation,RSD）<5%,n=3。     

Facile purification of mono-PEGylated interleukin-1 receptor antagonist and its characterization with multi-angle laser light scattering

Recombinant human interleukin-1 receptor antagonist (rhIL-1ra) was chemically conjugated with succinimidyl carbonate monomethoxyl polyethylene glycols of 5 kDa (SC-PEG_5k) and 10 kDa (SC-PEG_10k) molecular weight. A facile purification of the conjugates was achieved by one-step cationic exchange chromatography. The purity of mono-PEGylated protein was greater than 95%. The purified conjugate was characterized by multi-angle laser light scattering (MALLS) for determining the apparent gyration radius (r_g) and hydrodynamic radius (r_h). MALLS results showed that the conjugation of PEG markedly enhanced r_g and r_h of parent protein (r_g: from 15.7 to 48.2 nm for the PEG_5k and 81.9 nm for the PEG_10k; r_h: from 4.2 to 58.4 nm for the PEG_5k and 102.3 nm for the PEG_10k). The PEGylated rhIL-1ra retained 44.6% of binding activities to the cell receptor for PEG_5k and 40.2% for PEG_10k, compared to the original protein.     

Computational neural networks: Enhancing supervised learning algorithms via self-organization

A neural network processing scheme is proposed which utilizes a self-organizing Kohonen feature map as the front end to a feedforward classifier network. The results of a series of benchmarking studies based upon artificial statistical pattern recognition tasks indicate that the proposed architecture performs significantly better than conventional feedforward classifier networks when the decision regions are disjoint. This is attributed to the fact that the self-organization process allows internal units in the succeeding classifier network to be sensitive to a specific set of features in the input space at the outset of training.     

Self-association of long-acting insulin analogues studied by size exclusion chromatography coupled to multi-angle light scattering

Two structurally very different insulin analogues analysed here, belong to a class of analogues of which two have been reported to have a protracted action through self-assembly to high molar mass in subcutis. The process of self-association of insulin analogues Lys(B29) (N(ε)ω-carboxyheptadecanoyl) des(B30) human insulin and Lys(B29) (N(ε)-lithocholyl) des(B30) human insulin was investigated using size exclusion chromatography (SEC) in connection with multi-angle light-scattering. Self-assembly to high molar mass was obtained by exchanging the formulation containing phenolic preservatives with an isotonic eluent during SEC. It was shown that increasing amounts of zinc in the formulations of the two analogues increased the size of the self assemblies formed during gel filtration. The addition of 0.2 mM phenol to the elution buffer slowed down the self-association process of zinc containing formulations and shed light on the initial association process. The results indicated that a dihexamer is a possible building block during self-association of Lys(B29) (N(ε)ω-carboxyheptadecanoyl) des(B30) human insulin. Surprisingly, in the absence of zinc the two analogues behaved very differently. Lys(B29) (N(ε)ω-carboxyheptadecanoyl) des(B30) human insulin was in equilibrium between oligomers smaller than a hexamer, whereas Lys(B29) (N(ε)-lithocholyl) des(B30) human insulin self-associated and formed even larger complexes than in the presence of zinc.     

Aggregation of amphiphilic pullulan derivatives evidenced by on-line flow field flow fractionation/multi-angle laser light scattering

Size-exclusion chromatography (SEC) is a useful steric separation technique for the analysis of water-soluble polysaccharides in aqueous solution. However, in the case of amphiphilic derivatives, the usefulness is limited because of interactions between hydrophobic segments and the stationary phase. Alkyl-bearing pullulans differing from the extent and the length of alkyl groups were characterized using flow-field flow fractionation with on-line coupling multi-angle laser light scattering (F⁴/MALLS). Comparison of SEC and F⁴ is presented and the interest of F⁴ in the field of amphiphilic derivatives is demonstrated.     

Leukocyte differential analysis in multiple laboratory species by a laser multi-angle polarized light scattering separation method.

Leukocyte differential analysis was performed in various species, particularly laboratory animals, by the laser multi-angle polarized light scattering separation method. Venous blood specimens were drawn from the following subjects: healthy adult men and women ("humans"); cynomolgus monkeys ("monkeys"); common marmosets ("marmosets"); beagle dogs ("dogs"); miniature potbelly pigs ("swine"); Japanese white rabbits ("rabbits"); Hartley guinea pigs ("guinea pigs"); and Sprague-Dawley rats ("rats"). 90 degrees/10 degrees scatter plot: Basophils and mononuclear-polymorphonuclear cells were separated in all subjects, but individual 10 degrees and 90 degrees scatter plots overlapped in dogs and guinea pigs, respectively. 90 degrees depolarized /90 degrees scatter plot: Neutrophils and eosinophils were clearly separated in human, monkey, guinea pig, swine and rat subjects. The eosinophil cluster was not clearly plotted in marmoset, dog, or rabbit. 0 degree/10 degrees scatter plot: Regarding this plot for monocytes and lymphocytes, cells were plotted in the following order in all subjects: lymphocytes < basophils < or = monocytes in the 0 degree (size) scatter; and lymphocytes [symbol: see text] monocytes < or = basophils in the 10 degrees (complexity) scatter. Compared to other species, the rat scatter showed a tendency to overlapping plots in both the 0 degree and 10 degrees scatters in the monocyte and lymphocyte clusters. In both dog and guinea pig, the monocyte and neutrophil plots overlapped in the 0 degree and 10 degrees scatters. Basobox: In the human and rabbit subjects, the basophil cluster was plotted within the established basobox, but no clear cell cluster was plotted in the other subjects. As a result of comparing the percentage values for leukocytes in various species obtained by using the CD3500 apparatus versus the corresponding values obtained manually, good correspondence was found in the monkey, and eosinophils in the marmoset were lower with CD3500 than manually. In the rabbit, the mean measured value for basophils matched in the manual and CD3500 findings. In the guinea pig, the CD3500 values were lower than the manual values for lymphocytes, but higher for monocytes and neutrophils. The above findings suggest that the laser multi-angle polarized light scattering separation method is indeed capable of analyzing leukocytes from various species based on cell size and cell complexity, i.e., the presence or absence of nuclei, granules and cell enclosures.     

Screening the physical properties of novel Pseudomonas exopolysaccharides by HPSEC with multi-angle light scattering and viscosity detection

The physical properties of three novel acidic exopolysaccharides obtained from P. marginalis types A, B and C, one from P. ‘gingen’, one from P. andropogenis and one from P. fluorescens have been partially characterized. These EPSs were chromatographed on three serially placed SE Shodex OH pak columns covering a molar mass range for pullulans from about 4 × 10⁷ to 1 × 10³. The mobile phase was 0.05 M NaNO₃. Physical measurements were performed on about 30 mg of sample for each EPS. The weight average molar mass of these EPSs ranged from about 0.71 to 2.85 × 10⁶, the weight average intrinsic viscosity from 7.15 to 35.3 dl/ g and the radius of gyration from 62 to 123nm. The polydispersities of these EPSs ranged from 1.01 to 1.37. The large molar mass, size and viscosities of these EPSs may indicate that they have potential for use as thickeners, stabilizers, emulsifiers, and gelling agents in the food and non-food industries.     

Determination of the second virial coefficient of bovine serum albumin under varying pH and ionic strength by composition-gradient multi-angle static light scattering

Composition-gradient multi-angle static light scattering (CG-MALS) is an emerging technique for the determination of intermolecular interactions via the second virial coefficient B₂₂. With CG-MALS, detailed studies of the second virial coefficient can be carried out more accurately and effectively than with traditional methods. In addition, automated mixing, delivery and measurement enable high speed, continuous, fluctuation-free sample delivery and accurate results. Using CG-MALS we measure the second virial coefficient of bovine serum albumin (BSA) in aqueous solutions at various values of pH and ionic strength of a univalent salt (NaCl). The systematic variation of the second virial coefficient as a function of pH and NaCl strength reveals the net charge change and the isoelectric point of BSA under different solution conditions. The magnitude of the second virial coefficient decreases to 1.13 x 10⁻⁵ ml*mol/g² near the isoelectric point of pH 4.6 and 25 mM NaCl. These results illuminate the role of fundamental long-range electrostatic and van der Waals forces in protein-protein interactions, specifically their dependence on pH and ionic strength. Electronic supplementary material The online version of this article (doi:10.1007/s10867-014-9367-7) contains supplementary material, which is available to authorized users.     

Genetic classification of populations using supervised learning

There are many instances in genetics in which we wish to determine whether two candidate populations are distinguishable on the basis of their genetic structure. Examples include populations which are geographically separated, case-control studies and quality control (when participants in a study have been genotyped at different laboratories). This latter application is of particular importance in the era of large scale genome wide association studies, when collections of individuals genotyped at different locations are being merged to provide increased power. The traditional method for detecting structure within a population is some form of exploratory technique such as principal components analysis. Such methods, which do not utilise our prior knowledge of the membership of the candidate populations. are termed unsupervised. Supervised methods, on the other hand are able to utilise this prior knowledge when it is available.In this paper we demonstrate that in such cases modern supervised approaches are a more appropriate tool for detecting genetic differences between populations. We apply two such methods, (neural networks and support vector machines) to the classification of three populations (two from Scotland and one from Bulgaria). The sensitivity exhibited by both these methods is considerably higher than that attained by principal components analysis and in fact comfortably exceeds a recently conjectured theoretical limit on the sensitivity of unsupervised methods. In particular, our methods can distinguish between the two Scottish populations, where principal components analysis cannot. We suggest, on the basis of our results that a supervised learning approach should be the method of choice when classifying individuals into pre-defined populations, particularly in quality control for large scale genome wide association studies.     

Determination of size distribution and encapsulation efficiency of liposome-encapsulated hemoglobin blood substitutes using asymmetric flow field-flow fractionation coupled with multi-angle static light scattering

In this study, we investigated the size distribution, encapsulation efficiency, and oxygen affinity of liposome-encapsulated tetrameric hemoglobin (LEHb) dispersions and correlated the data with the variation in extruder membrane pore size, ionic strength of the extrusion buffer, and hemoglobin (Hb) concentration. Asymmetric flow field-flow fractionation (AFFF) in series with multi-angle static light scattering (MASLS) was used to study the LEHb size distribution. We also introduced a novel method to measure the encapsulation efficiency using a differential interferometric refractive index (DIR) detector coupled to the AFFF-MASLS system. This technique was nondestructive toward the sample and easy to implement. LEHbs were prepared by extrusion using a lipid combination of dimyristoyl-phosphatidylcholine, cholesterol, and dimyristoyl-phosphatidylglycerol in a 10:9:1 molar ratio. Five initial Hb concentrations (50, 100, 150, 200, and 300 mg Hb per mL of buffer) extruded through five different membrane pore diameters (400, 200, 100, 80, and 50 nm) were studied. Phosphate buffered saline (PBS) and phosphate buffer (PB) both at pH 7.3 were used as extrusion buffers. Despite the variation, extrusion through 400-nm pore diameter membranes produced LEHbs smaller than the pore size, extrusion through 200-nm membranes produced LEHbs with diameters close to the pore diameter, and extrusion through 100-, 80-, and 50-nm membranes produced LEHbs larger than the pore sizes. We found that the choice of extrusion buffer had the greatest effect on the LEHb size distribution compared to either Hb concentration or extruder membrane pore size. Extrusion in PBS produced larger LEHbs and more monodisperse LEHb dispersions. However, LEHbs extruded in PB generally had higher Hb encapsulation efficiencies and lower methemoglobin (metHb) levels. The choice of extrusion buffer also affected how the encapsulation efficiency correlated with Hb concentration, extruder pore size, and the metHb level. The most optimum encapsulation efficiency and amount of Hb entrapped were achieved at the highest Hb concentration and the largest pore size for both extrusion buffers (62.38% and 187.14 mg Hb/mL of LEHb dispersion extruded in PBS, and 69.98% and 209.94 mg Hb/mL of LEHb dispersion extruded in PB). All LEHbs displayed good oxygen-carrying properties as indicated by their P(50) and cooperativity coefficients. LEHbs extruded in PB had an average P(50) of 23.04 mmHg and an average Hill number of 2.29, and those extruded in PBS had average values of 27.25 mmHg and 2.49. These oxygen-binding properties indicate that LEHbs possess strong potential as artificial blood substitutes. In addition, the metHb levels in PB-LEHb dispersions are significantly low even in the absence of antioxidants such as N-acetyl-L-cysteine.     

Protein docking using surface matching and supervised machine learning

Computational prediction of protein complex structures through docking offers a means to gain a mechanistic understanding of protein interactions that mediate biological processes. This is particularly important as the number of experimentally determined structures of isolated proteins exceeds the number of structures of complexes. A comprehensive docking procedure is described in which efficient sampling of conformations is achieved by matching surface normal vectors, fast filtering for shape complementarity, clustering by RMSD, and scoring the docked conformations using a supervised machine learning approach. Contacting residue pair frequencies, residue propensities, evolutionary conservation, and shape complementarity score for each docking conformation are used as input data to a Random Forest classifier. The performance of the Random Forest approach for selecting correctly docked conformations was assessed by cross-validation using a nonredundant benchmark set of X-ray structures for 93 heterodimer and 733 homodimer complexes. The single highest rank docking solution was the correct (near-native) structure for slightly more than one third of the complexes. Furthermore, the fraction of highly ranked correct structures was significantly higher than the overall fraction of correct structures, for almost all complexes. A detailed analysis of the difficult to predict complexes revealed that the majority of the homodimer cases were explained by incorrect oligomeric state annotation. Evolutionary conservation and shape complementarity score as well as both underrepresented and overrepresented residue types and residue pairs were found to make the largest contributions to the overall prediction accuracy. Finally, the method was also applied to docking unbound subunit structures from a previously published benchmark set.     

Quantification of major classes of Xenopus phospholipids by high performance liquid chromatography with evaporative light scattering detection

Lipid signaling has become a major research area of cell biology and there is a need for methods that accurately and easily measure substrates and products of lipases involved in cell signaling. In this report, we provide new methodology for separation of more than 10 lipids in one chromatographic run by high pressure liquid chromatography (HPLC) and detection with an evaporative light scattering detector (ELSD). There is no significant loss of sphingomyelin and no large baseline change, no peak obscures another, and acidic phospholipids are cleanly separated. We have optimized the procedure for a two-pump HPLC, an inexpensive silica column without the use of a column heater jacket and for low grade nitrogen. An application of the procedure separates lipids from Xenopus laevis cells. These cells are commonly used in the study of various lipid signaling paths in cell division, fertilization, and after expression of exogenous membrane receptors.     

Liposome fractionation and size analysis by asymmetrical flow field-flow fractionation/multi-angle light scattering: influence of ionic strength and osmotic pressure of the carrier liquid

Asymmetrical flow field-flow fractionation (AsFlFFF)/multi-angle light scattering (MALS) was employed for studying filter-extruded liposomes in carrier solutions with different ionic strength and osmolarity. By dilution of preformed liposome suspensions with different media, only the ionic strength in the external free aqueous phase was changed. Under such conditions the liposomes were found to elute at almost identical elution times, which is in contrast to earlier studies. This may be explained by two opposing effects: (a) modulation of inter-particulate and particle-wall-repulsion effects and (b) osmotic stress-induced changes in vesicle size. The latter effect was demonstrated when analysing liposomes upon dilution in media of constant ionic strength, but varying osmotic pressure (with or without 150 mmol L^?1 sucrose supplement). The osmotic stress-induced change in liposome size was found to be size dependent. Larger liposomes appeared to both shrink and swell when exposed to hyper- or hypoosmotic media, respectively. Smaller liposomes appeared to shrink but not to swell. The potential causes of this effect are discussed.     

应用高效体积排阻色谱偶联多角度激光散射鉴定猪圆环病毒2型灭活疫苗及病毒样颗粒疫苗抗原

本文旨在建立基于高效体积排阻色谱(high-performance size-exclusion chromatography,HPSEC)偶联多角度激光散射仪(multi-angle laser light scattering,MALLS)的猪圆环病毒2型(porcine circovirus type 2,PCV2)疫苗抗原检测方法。以纯化的PCV2灭活病毒及病毒样颗粒(virus-like particles,VLP)为参照,对4家生产企业的2种PCV2灭活病毒疫苗(a、b)及VLP疫苗(c、d)破乳后进行HPSEC-MALLS检测及分子量分析;结合PCV2抗原检测卡、Western blotting和透射电子显微镜(transmission electron microscope,TEM),鉴定了特征色谱峰;考察了方法的重复性和检测线性。结果表明,两家企业生产的PCV2灭活病毒疫苗破乳液水相经HPSEC分离,在保留时间约13.3 min处出现抗原特征峰;MALLS计算该色谱峰分子量分别为2.61×10⁶(±4.34%) Da和2.40×10⁶(±2.51%) Da。两种VLP疫苗也在13.3 min处出现抗原特征峰,分子量分别为2.09×10⁶(±2.94%) Da和2.88×10⁶(±11.85%) Da,接近PCV2的理论分子量;同时在保留时间约11.4 min处也出现色谱峰,经检测分子量为4.37×10⁶(±0.42%) Da,TEM表征显示为VLP二聚体。取疫苗d和PCV2 VLP纯品进行重复检测,抗原色谱峰面积的RSD(n=3)均小于1.5%,重复性好;将PCV2 VLP纯品梯度稀释检测,VLP及其多聚体的色谱峰面积与浓度均呈良好的线性关系,R²分别为0.999及0.997,能够满足定量及多聚体含量分析。该方法有望成为一种准确、高效的PCV2疫苗的体外评价方法,用于质量评价与提升。     

Modeling polyp activity of Paragorgia arborea using supervised learning

While the distribution patterns of cold-water corals, such as Paragorgia arborea, have received increasing attention in recent studies, little is known about their in situ activity patterns. In this paper, we examine polyp activity in P. arborea using machine learning techniques to analyze high-resolution time series data and photographs obtained from an autonomous lander cluster deployed in the Stjernsund, Norway. An interactive illustration of the models derived in this paper is provided online as supplementary material.We find that the best predictor of the degree of extension of the coral polyps is current direction with a lag of three hours. Other variables that are not directly associated with water currents, such as temperature and salinity, offer much less information concerning polyp activity. Interestingly, the degree of polyp extension can be predicted more reliably by sampling the laminar flows in the water column above the measurement site than by sampling the more turbulent flows in the direct vicinity of the corals.Our results show that the activity patterns of the P. arborea polyps are governed by the strong tidal current regime of the Stjernsund. It appears that P. arborea does not react to shorter changes in the ambient current regime but instead adjusts its behavior in accordance with the large-scale pattern of the tidal cycle itself in order to optimize nutrient uptake.     

Molecular characterization of recombinant Hepatitis B surface antigen from Chinese hamster ovary and Hansenula polymorpha cells by high-performance size exclusion chromatography and multi-angle laser light scattering

The molecular weight and size of recombinant Hepatitis B surface antigen (HBsAg) derived from Chinese hamster ovary (CHO) and the Hansenula polymorph have been characterized by high-performance size exclusion chromatography with multi-angle laser light scattering (HPSEC-MALLS). The average molecular weight of CHO-derived HBsAg particle (CHO-rHBsAg) (4921 kDa) was higher than that of H. polymorpha yeast strain (Hans-rHBsAg) (3010 kDa). The size of CHO-rHBsAg (22.1 nm) is nearly the same as that of native HBsAg compared to 18.1 nm for Hans-rHBsAg. The average monomer numbers were found to be 155 for CHO-rHBsAg and 86 for Hans-rHBsAg, respectively. The data obtained support the assumption that the higher immunogenicity of CHO-derived HBsAg is related to its more favorable macromolecular assembly structure.     

Molecular weight of scleroglucan and other extracellular microbial polysaccharides by size-exclusion chromatography and low angle laser light scattering

High-performance aqueous size-exclusion chromatography coupled to a low angle laser light scattering detector has been applied to the analysis of scleroglucan and various other extracellular microbial polysaccharides. Emphasis has been focused on three main findings. (1) The molecular weight of these macromolecules is not very sensitive to changes in fermentation conditions. This is specially true in the case of scleroglucan and related (1 → 3)-β- -glucans including schizophyllan, which all exhibited a constant weight-average molecular weight of 5·7×10⁶±5%. (2) In contrast to plant polysaccharides, polydispersity is very low, usually near unity. (3) The molecular weight levels off quickly during biosynthesis since the molecular weight is constant from the middle of fermentation, if not before.