Affinity precipitation of an antibody by ligand-modified phospholipids

A new method for the selective precipitation of proteins is applied to the isolation and purification of an antibody. Ligand-modified phospholipids (LMPs) are solubilized by the nonionic ethoxylated alcohol detergent, resulting in small (50 to 100 A) micellar aggregates of LMPs and surfactant. When introduced into protein solutions containing an antibody for which the LMP has specific affinity, the ligand binds to the protein. Hydrophobic interactions between phospholipid tail groups bound to the protein molecules result in an insoluble precipitate. Polyclonal and monoclonal antibiotin antibody (pABA and mABA) are shown to be selectively precipitated using ratios of dimyristoylphosphatidylethanolamidobiotin (DMPE-B) to ABA ranging from 1:1 to 19:1. The kinetics and yield of the precipitation achieve a maximum at a ratio of DMPE-B to ABA of approximately 7:1. The kinetics and magnitude of the turbidity change are modeled using the Mie theory of light scattering coupled with the smoluchowski theory of aggregation. The kinetics are shown to be enhanced significantly by the addition of salt. In particular, the addition of 0.5 M ammonium sulfate salt increases the rate of precipitation by more than an order of magnitude. It is demonstrated that pABA can be recovered with total activity yields of 60% to 70% from mixtures containing nonspecific lgG antibodies in very high purity (>99%). (c) 1994 John Wiley & Sons, Inc.     

Type-specific separation of animal cells in aqueous two-phase systems using antibody conjugates with temperature-sensitive polymers.

A new type of aqueous two-phase system (ATPS) has been developed in which a temperature-sensitive polymer, poly-N-isopropylacrylamide [poly (NIPAM)] was used as a ligand carrier for the specific separation of animal cells. Monoclonal antibodies were modified with itaconic anhydride and copolymerized with N-isopropylacrylamide, and the ligand-conjugated carriers were added to the polyethylene glycol 8000-dextran T500 aqueous two-phase systems. The antibody-polymer conjugates were partitioned to the top phase in the absence or presence of 0.15 M NaCl. When ligand-conjugated carriers were used, more than 80% of the cells were specifically partitioned to the top phase in the presence of NaCl up to 0.1 M. The cells were partitioned almost completely to the bottom phase at 0.1 M NaCl or above, when no antibody-conjugate was added in the ATPS. As a model system, CD34-positive human acute myeloid leukemia cells (KG-1) were specifically separated from human T lymphoma cells (Jurkat) by applying anti-CD34 conjugated with poly-N-isopropylacrylamide in the aqueous two-phase system. By the temperature-induced precipitation of the polymer, about 90% of the antibody-polymer conjugates were recovered from the top phase, which gave approximately 75% cell separating efficiency in the next cycle of reuse.     

Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design

Improving the affinity of a high-affinity protein-protein interaction is a challenging problem that has practical applications in the development of therapeutic biomolecules. We used a combination of structure-based computational methods to optimize the binding affinity of an antibody fragment to the I-domain of the integrin VLA1. Despite the already high affinity of the antibody (Kd approximately 7 nM) and the moderate resolution (2.8 A) of the starting crystal structure, the affinity was increased by an order of magnitude primarily through a decrease in the dissociation rate. We determined the crystal structure of a high-affinity quadruple mutant complex at 2.2 A. The structure shows that the design makes the predicted contacts. Structural evidence and mutagenesis experiments that probe a hydrogen bond network illustrate the importance of satisfying hydrogen bonding requirements while seeking higher-affinity mutations. The large and diverse set of interface mutations allowed refinement of the mutant binding affinity prediction protocol and improvement of the single-mutant success rate. Our results indicate that structure-based computational design can be successfully applied to further improve the binding of high-affinity antibodies.     

Development of a novel and efficient cell culture flocculation process using a stimulus responsive polymer to streamline antibody purification processes

Recent advances in mammalian cell culture processes have significantly increased product titers, but have also resulted in substantial increases in cell density and cellular debris as well as process and product related impurities. As such, with improvements in titer, corresponding improvements in downstream processing are essential. In this study we have developed an alternative antibody harvest process that incorporates flocculation using a novel stimulus responsive polymer, benzylated poly(allylamine), followed by depth filtration. As tested on multiple antibodies, this process demonstrates high process yield, improved clearance of cells and cell debris, and efficient reduction of aggregates, host cell proteins (HCP) and DNA. A wide operating window was established for this novel flocculation process through design of experiments condition screening and optimization. Residual levels of impurities in the Protein A eluate were achieved that potentially meet requirements of drug substance and thus alleviate the burden for further impurities removal in subsequent chromatography steps. In addition, efficient clearance of residual polymer was demonstrated using a fluorescence tagged polymer in the presence of a stimulus reagent. The mechanism of HCP and aggregates removal during flocculation was also explored. This novel and efficient process can be easily integrated into current mAb purification platforms, and may overcome downstream processing challenges. Biotechnol. Bioeng. 2013;110: 2928–2937. © 2013 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.     

Monoclonal antibody purification using cationic polyelectrolytes: an alternative to column chromatography

The potential of cationic polyelectrolytes to precipitate host cell and process related impurities was investigated, to replace one or more chromatography steps in monoclonal antibody purification. The impact of antibody isoelectric point, solution properties (pH and ionic strength), and polyelectrolyte properties (structure, molecular weight and pK(a)) on the degree of precipitation was studied. At neutral pH, increasing solution ionic strength impeded the ionic interaction between the polyelectrolyte and impurities, reducing impurity precipitation. Increasing polyelectrolyte molecular weight and pK(a) enabled precipitation of impurities at higher ionic strength. PoIy(arginine) was selected as the preferred polyelectrolyte in unconditioned cell culture fluid. PoIy(arginine) precipitation achieved consistent host cell protein clearance and antibody recovery for multiple antibodies across a wider range of polyelectrolyte concentrations. Poly(arginine) precipitation was evaluated as a flocculant and as a functional replacement for anion exchange chromatography in an antibody purification process. Upstream treatment of cell culture fluid with poly(arginine) resulted in flocculation of solids (cells and cell debris), and antibody recovery and impurity clearance (host cell proteins, DNA and insulin) comparable to the downstream anion exchange chromatography step.     

Rapid separation of solasodine glycosides by an immunoaffinity column using anti-solamargine monoclonal antibody

Immunoaffinity column using anti-solamargine monoclonal antibody for separation of solasodine glycosides was established. This method was specific for solasodine glycosides which was detected by thin layer chromatography and the western blotting. Total solasodine glycosides have been separated directly from the crude extract of Solanum khasianum fruit by the newly established immunoaffinity column. This revised version was published online in August 2006 with corrections to the Cover Date.     

Monitoring the conformational changes of an intrinsically disordered peptide using a quartz crystal microbalance

Intrinsically disordered peptides (IDPs) have recently garnered much interest because of their role in biological processes such as molecular recognition and their ability to undergo stimulus-responsive conformational changes. The block V repeat-in-toxin motif of the Bordetella pertussis adenylate cyclase is an example of an IDP that undergoes a transition from a disordered state to an ordered beta roll conformation in the presence of calcium ions. In solution, a C-terminal capping domain is necessary for this transition to occur. To further explore the conformational behavior and folding requirements of this IDP, we have cysteine modified three previously characterized constructs, allowing for attachment to the gold surface of a quartz crystal microbalance (QCM). We demonstrate that, while immobilized, the C-terminally capped peptide exhibits similar calcium-binding properties to what have been observed in solution. In addition, immobilization on the solid surface appears to enable calcium-responsiveness in the uncapped peptides, in contrast to the behavior observed in solution. This work demonstrates the power of QCM as a tool to study the conformational changes of IDPs immobilized on surfaces and has implications for a range of potential applications where IDPs may be engineered and used including protein purification, biosensors, and other bionanotechnology applications.     

Affinity maturation of antiHER2 monoclonal antibody MIL5 using an epitope-specific synthetic phage library by computational design

Increased affinities mainly equal to improved biological efficacy in many cases. By now, display methods including phage library are widely exploited to obtain higher affinity antibodies. Traditional library methods mainly focus on complementary determining region mutagenesis, in which extensive screening of variant combinations as well as large library capacity is required to find higher affinity clones. In this study, based on the modeling 3D complex structure of antigen (HER2)–antibody (MIL5) complex, the key residues of contact surface were predicted and identified to guide the synthetic phage library design. Then, epitope-specific site-directed mutagenesis phage library comprised of MIL5_scFv mutants was constructed, from which a higher affinity single chain antibody (M5scFv_ph) was screened out. Following experimental results showed that the novel antibody M5scFv_ph retained superimposed epitope to the parent antibody MIL5_scFv, and possessed similar tumor growth inhibitory activity in vivo on ovarian carcinoma xenografts.     

Epitope characterization of an anti‐PD‐L1 antibody using orthogonal approaches

The binding of programmed death ligand 1 protein (PD‐L1) to its receptor programmed death protein 1 (PD‐1) mediates immunoevasion in cancer and chronic viral infections, presenting an important target for therapeutic intervention. Several monoclonal antibodies targeting the PD‐L1/PD‐1 signaling axis are undergoing clinical trials; however, the epitopes of these antibodies have not been described. We have combined orthogonal approaches to localize and characterize the epitope of a monoclonal antibody directed against PD‐L1 at good resolution and with high confidence. Limited proteolysis and mass spectrometry were applied to reveal that the epitope resides in the first immunoglobulin domain of PD‐L1. Hydrogen–deuterium exchange mass spectrometry (HDX‐MS) was used to identify a conformational epitope comprised of discontinuous strands that fold to form a beta sheet in the native structure. This beta sheet presents an epitope surface that significantly overlaps with the PD‐1 binding interface, consistent with a desired PD‐1 competitive mechanism of action for the antibody. Surface plasmon resonance screening of mutant PD‐L1 variants confirmed that the region identified by HDX‐MS is critical for the antibody interaction and further defined specific residues contributing to the binding energy. Taken together, the results are consistent with the observed inhibitory activity of the antibody on PD‐L1‐mediated immune evasion. This is the first report of an epitope for any antibody targeting PD‐L1 and demonstrates the power of combining orthogonal epitope mapping techniques. Copyright © 2015 John Wiley & Sons, Ltd.     

Evaluation of swimming performance for fish passage of longnose dace Rhinichthys cataractae using an experimental flume

The swimming performance of longnose dace Rhinichthys cataractae, the most widely distributed minnow (Cyprinidae) in North America, was assessed in relation to potential passage barriers. The study estimated passage success, maximum ascent distances and maximum sprint speed in an open‐channel flume over a range of water velocities and temperatures (10·7, 15·3 and 19·3° C). Rhinichthys cataractae had high passage success (95%) in a 9·2 m flume section at mean test velocities of 39 and 64 cm s^–1, but success rate dropped to 66% at 78 cm s^–1. Only 20% of fish were able to ascend a 2·7 m section with a mean velocity of 122 cm s^–1. Rhinichthys cataractae actively selected low‐velocity pathways located along the bottom and corners of the flume at all test velocities and adopted position‐holding behaviour at higher water velocities. Mean volitional sprint speed was 174 cm s^–1 when fish volitionally sprinted in areas of high water velocities. Swimming performance generally increased with water temperature and fish length. Based on these results, fishways with mean velocities <64 cm s^–1 should allow passage of most R. cataractae. Water velocities >100 cm s^–1 within structures should be limited to short distance (<1 m) and structures with velocities ≥158 cm s^–1 would probably represent movement barriers. Study results highlighted the advantages of evaluating a multitude of swimming performance metrics in an open‐channel flume, which can simulate the hydraulic features of fishways and allow for behavioural observations that can facilitate the design of effective passage structures.     

Ecogeographical variation of body size in the newt Triturus carnifex: comparing the hypotheses using an information‐theoretic approach

Aim Ecogeographical variation of body size in vertebrates (e.g. Bergmann's rule) has long been recognized. However, the patterns and causes of intra‐specific ecogeographical variation of body size in ectotherms, and in amphibians in particular, are strongly debated. We identified the relationship between bioclimatic variables and body size predicted a priori by alternative hypotheses (heat balance, endurance, seasonality, starvation resistance, water availability, primary productivity, parental investment) proposed to explain ecogeographical patterns of body size in ectotherms, and we evaluated the relative support of these hypotheses in explaining variation in body size of the Italian crested newt, Triturus carnifex. Location Twenty‐three populations covering the whole range of T. carnifex (Austria, Croatia, Italy and Slovenia). Methods We obtained data on body size (snout–vent length, SVL) of 2639 adult newts from direct measurements and the literature; we obtained high‐resolution environmental data for the sampled localities. We used an information‐theoretic approach to evaluate the support of the data for the different hypotheses. We also integrated information on population genetics in our models. Results We observed strong geographical variation of body size. The best Akaike information criterion (AIC) models showed that populations with larger body size are associated with cold climates and secondarily with high primary productivity. Furthermore, sexual dimorphism increases in cold climates, as the increase in body size was stronger for females. When taking into account population genetics, we did not find support for relationships with the other variables. Main conclusion Our results are consistent with three hypotheses proposed to explain ecogeographical variation in amphibians: heat balance, increased parental investment of females and productivity. Information theory provides the framework for comparing hypotheses rather than looking for patterns. We suggest that evaluating the support for mechanisms can provide better insights than simply assessing whether ecogeographical variation is in agreement with some ‘rule’.     

Climate change effects on plant biomass alter dominance patterns and community evenness in an experimental old‐field ecosystem

Atmospheric and climatic change can alter plant biomass production and plant community composition. However, we know little about how climate change‐induced alterations in biomass production affect plant species composition. To better understand how climate change will alter both individual plant species and community biomass, we manipulated atmospheric [CO₂], air temperature, and precipitation in a constructed old‐field ecosystem. Specifically, we compared the responses of dominant and subdominant species to our climatic treatments, and explored how changes in plant dominance patterns alter community evenness over 2 years. Our study resulted in four major findings: (1) all treatments, elevated [CO₂], warming, and increased precipitation increased plant community biomass and the effects were additive rather than interactive, (2) plant species differed in their response to the treatments, resulting in shifts in the proportional biomass of individual species, which altered the plant community composition; however, the plant community response was largely driven by the positive precipitation response of Lespedeza, the most dominant species in the community, (3) precipitation explained most of the variation in plant community composition among treatments, and (4) changes in precipitation caused a shift in the dominant species proportional biomass that resulted in lower community evenness in the wet relative to dry treatments. Interestingly, compositional and evenness responses of the subdominant community to the treatments did not always follow the responses of the whole plant community. Our data suggest that changes in plant dominance patterns and community evenness are an important part of community responses to climatic change, and generally, that such compositional shifts can alter ecosystem biomass production and nutrient inputs.     

Further characterization of the rabies virus glycoproteins produced by virus-infected and G cDNA-transfected cells using a monoclonal antibody, #1-30-44, which recognizes an acid-sensitive epitope

Expression of rabies virus glycoprotein (G) by G cDNA-transfected mammalian cells resulted in the production of only a fusion-negative form. Low pH-dependent fusion activity, however, was seen when the expression was done under control of the T7 promoter with the help of recombinant vaccinia virus (RVV-T7) that provided T7 RNA polymerase. Fusion-inactive G proteins were transported to the cell surface as being detected by a conformational epitope-specific monoclonal antibody (mAb; #1-46-12). The fusion-inactive G proteins were recognized by most of our 13 conformation-specific mAbs, except for one mAb, #1-30-44, that recognized the low pH-sensitive conformational epitope. When the G gene expression was done with the help of RVV-T7, although most G proteins remained in the epitope-negative form, a small fraction of G gene products were 1-30-44 epitope-positive, and cell fusion activity could be seen when cells were exposed to low pH conditions. From these results, we conclude that acquisition of low pH-dependent fusion activity is closely related to structural maturation of the G protein to form the low pH-sensitive 1-30-44 epitope. Such maturation seems to be dependent on certain rabies virus-induced cellular conditions or functions, which might also be provided in part by the vaccinia virus infection. We further assume that expression of G cDNA alone mostly results in the production of mis-folded and/or differently folded forms of G protein, and only a small fraction is correctly folded even under RVV-T7-mediated expression conditions.     

百年尺度地球系统模式模拟的陆地生态系统碳通量对CO2浓度升高和气候变化的响应

利用了加拿大地球系统模式CanE SM2(Canadian Earth System Model of the CCCma)的结果,针对百年尺度大气CO_2浓度升高和气候变化如何影响陆地生态系统碳通量这一问题,分析了1850—1989年间陆地生态系统碳通量趋势对二者响应,以及与关键气候系统变量的关系。结果表明,140年间,当仅仅考虑CO_2浓度升高影响时,陆地生态系统净初级生产力(NPP)增加了117.1 gC m~(-2)a~(-1),土壤呼吸(Rh)增加了98.4 gC m~(-2)a~(-1),净生态系统生产力(NEP)平均增加了18.7 gC m~(-2)a~(-1)。相同情景下,全球陆地生态系统的NPP呈显著增加的线性趋势(约为0.30 PgC/a~2),Rh同样呈显著增加线性趋势(约为0.25 PgC/a~2)。仅仅考虑气候变化单独影响时,NPP平均减少了19.3 gC/m~2,土壤呼吸减少了8.5 gC/m~2,NEP减少了10.8 gC/m~2。在此情景下,整个陆地生态系统的NPP线性变化趋势约为-0.07 PgC/a~2(P0.05),Rh线性变化趋势约为-0.04 PgC/a~2(P0.05)。综合二者的影响,前者是决定陆地生态系统碳通量变化幅度和空间分布的最重要影响因子,其影响明显大于气候变化。值得注意的是,CanE SM2并没有考虑氮素的限制作用,所以CO_2浓度升高对植被的助长作用可能被高估。此外,气候变化的贡献也不容忽视,特别是在亚马逊流域,由于当温度升高、降水和土壤湿度减少,NPP和Rh均呈显著减少趋势。     

Detection and characterisation of catechol 2,3-dioxygenase in an indigenous soil <Emphasis Type="Italic">Pseudomonad</Emphasis> by MALDI-TOF MS using a column separation

The key enzyme catalyzing the second step in the phenol degradation meta-cleavage pathway (C23O) has been purified to homogeneity from a new bacterial strain, which belongs to genus Pseudomonas. The species was growing on phenol as carbon source. The C23O was detected and identified by absorption spectroscopy. The protein was isolated using sucrose density centrifugation and anion exchange chromatography. The purified protein showed a molecular mass of 32 kDa to sodium dodecyl sulfate polyacrylamid gel electrophoresis and an isoelectric point of 5 estimated by analytical isoelectrical focusing. Matrix-assisted laser desorption ionization-time of flight mass spectrometry and peptide mapping was attempted for the identification of the isolated protein and proteins involved in the metabolic pathway.