Automated linkage of proteins and payloads producing monodisperse conjugates

Controlled protein functionalization holds great promise for a wide variety of applications. However, despite intensive research, the stoichiometry of the functionalization reaction remains difficult to control due to the inherent stochasticity of the conjugation process. Classical approaches that exploit peculiar structural features of specific protein substrates, or introduce reactive handles via mutagenesis, are by essence limited in scope or require substantial protein reengineering. We herein present equimolar native chemical tagging (ENACT), which precisely controls the stoichiometry of inherently random conjugation reactions by combining iterative low-conversion chemical modification, process automation, and bioorthogonal trans-tagging. We discuss the broad applicability of this conjugation process to a variety of protein substrates and payloads.

Controlled protein functionalization holds great promise for a wide variety of applications.

Applications of protein conjugates are limitless, including imaging, diagnostics, drug delivery, and sensing.^1–4 In many of these applications, it is crucial that the conjugates are homogeneous.⁵ The site-selectivity of the conjugation process and the number of functional labels per biomolecule, known as the degree of conjugation (DoC), are crucial parameters that define the composition of the obtained products and are often the limiting factors to achieving adequate performance of the conjugates. For instance, immuno-PCR, an extremely sensitive detection technique, requires rigorous control of the average number of oligonucleotide labels per biomolecule (its DoC) in order to achieve high sensitivity.⁶ In optical imaging, the performance of many super-resolution microscopy techniques is directly defined by the DoC of fluorescent tags.⁷ For therapeutics, an even more striking example is provided by antibody–drug conjugates, which are prescribed for the treatment of an increasing range of cancer indications.⁸ A growing body of evidence from clinical trials indicates that bioconjugation parameters, DoC and DoC distribution, directly influence the therapeutic index of these targeted agents and hence must be tightly controlled.⁹Standard bioconjugation techniques, which rely on nucleophile–electrophile reactions, result in a broad distribution of different DoC species (Fig. 1a), which have different biophysical parameters, and consequently different functional properties.¹⁰Open in a separate windowFig. 1Schematic representation of the types of protein conjugates.To address this key issue and achieve better DoC selectivity, a number of site-specific conjugation approaches have been developed (Fig. 1b). These techniques rely on protein engineering for the introduction of specific motifs (e.g., free cysteines,¹¹ selenocysteines,¹² non-natural amino acids,^13,14 peptide tags recognized by specific enzymes^15,16) with distinct reactivity compared to the reactivity of the amino acids present in the native protein. These motifs are used to simultaneously control the DoC (via chemo-selective reactions) and the site of payload attachment. Both parameters are known to influence the biological and biophysical parameters of the conjugates,¹¹ but so far there has been no way of evaluating their impact separately.The influence of DoC is more straightforward, with a lower DoC allowing the minimization of the influence of payload conjugation on the properties of the protein substrate. The lowest DoC that can be achieved for an individual conjugate is 1 (corresponding to one payload attached per biomolecule). It is noteworthy that DoC 1 is often difficult to achieve through site-specific conjugation techniques due to the symmetry of many protein substrates (e.g., antibodies). Site selection is a more intricate process, which usually relies on a systematic screening of conjugation sites for some specific criteria, such as stability or reactivity.¹⁷Herein, we introduce a method of accessing an entirely new class of protein conjugates with multiple conjugation sites but strictly homogenous DoCs (Fig. 1c). To achieve this, we combined (a) iterative low conversion chemical modification, (b) process automation, and (c) bioorthogonal trans-tagging in one workflow.The method has been exemplified for protein substrates, but it is applicable to virtually any native bio-macromolecule and payload. Importantly, this method allows for the first time the disentangling of the effects of homogeneous DoC and site-specificity on conjugate properties, which is especially intriguing in the light of recent publications revealing the complexity of the interplay between payload conjugation sites and DoC for in vivo efficacy of therapeutic bioconjugates.¹⁸ Finally, it is noteworthy that this method can be readily combined with an emerging class of site-selective bioconjugation reagents to produce site-specific DoC 1 conjugates, thus further expanding their potential for biotechnology applications.¹⁹     

A sharp exponential inequality for Lorentz-Sobolev spaces on bounded domains

This paper generalizes an inequality of Moser from the case that is in the Lebesgue space to certain subspaces, namely the Lorentz spaces , where . The conclusion is that is integrable, where . This is a higher degree of integrability than in the Moser inequality when . A formula for is given and it is also shown that no larger value of works.

     

Synthesis of Organic-Inorganic Hybrid Particles by Sol-Gel Chemistry

The synthesis of ORganically MOdified SILica (ORMOSIL) particles has been carried out using both the hydrolytic and non-hydrolytic sol-gel routes. The hybrid (nano)composites are organically modified with an alkyl or aryl group covalently bonded to silicon. Hybrids have been synthesised in an aqueous sol-gel process by a modified Stöber route, producing spherical nanoparticles with diameters in the range 50–300 nm. The size of the particles can be controlled by control of certain reaction parameters. Smaller ormosil nanoparticles can be synthesised by a base-catalysed emulsion polymerisation route, by varying the type and concentration of surfactant and precursor feed rate. In this case, particles in the size range 3.5–10 nm can be obtained. Hybrids have been synthesised from hyperbranched polyesters by encapsulation in a silica matrix using the hydrolytic sol-gel route. Optimisation of the reaction conditions allows the hybrids to be produced as isolated sub-micron spherical particles. Ormosil particles have also been synthesised using the non-hydrolytic sol-gel route, which may lead to products of different morphologies because of the different polarity of the reaction medium. Different reaction conditions were studied in order to optimise the size and shape of the particles, including choice of solvent, use of surfactants and addition of polystyrene. Dimethylsulfoxide acts as a novel oxygen donor for the catalyst-free formation of colourless silsesquioxanes.     

Design of surface active soluble peptide molecules at the air/water interface

Surface active molecules collect at interfaces and have the potential to be used for water evaporation reduction. The objective of this work is to design surface active soluble peptides that collect at the air/water interface using molecular simulations. Rotational isomeric state Monte Carlo (RISMC) sampling together with a solvation model that we recently invented, the AAD solvation model [Gu, C.; Lustig, S.; Trout, B. J. Phys. Chem. B 2006, 110 (3), 1476-1484] was applied to calculate the adsorption free energy of the peptide molecule at the air/water interface. The results were validated by both molecular dynamics simulations with an explicit solvent model and surface tension measurements on synthesized peptides. It was demonstrated that this approach is able to give a reasonable prediction of surface activity with an approximately 50% hit rate in terms of designed surface active molecules actually being surface active. The relationship between the chemical composition and the surface morphology is also discussed.     

The Interaction between Quasilinear Elastodynamics and the Navier-Stokes Equations

The interaction between a viscous fluid and an elastic solid is modeled by a system of parabolic and hyperbolic equations, coupled to one another along the moving material interface through the continuity of the velocity and traction vectors. We prove the existence and uniqueness (locally in time) of strong solutions in Sobolev spaces for quasilinear elastodynamics coupled to the incompressible Navier-Stokes equations. Unlike our approach in [5] for the case of linear elastodynamics, we cannot employ a fixed-point argument on the nonlinear system itself, and are instead forced to regularize it by a particular parabolic artificial viscosity term. We proceed to show that with this specific regularization, we obtain a time interval of existence which is independent of the artificial viscosity; together with a priori estimates, we identify the global solution (in both phases), as well as the interface motion, as a weak limit in strong norms of our sequence of regularized problems.     

Hardy and BMO spaces associated to divergence form elliptic operators

Consider a second order divergence form elliptic operator L with complex bounded measurable coefficients. In general, operators based on L, such as the Riesz transform or square function, may lie beyond the scope of the Calderón–Zygmund theory. They need not be bounded in the classical Hardy, BMO and even some L ^p spaces. In this work we develop a theory of Hardy and BMO spaces associated to L, which includes, in particular, a molecular decomposition, maximal and square function characterizations, duality of Hardy and BMO spaces, and a John–Nirenberg inequality. S. Hofmann was supported by the National Science Foundation.     

Luciferase-transfected colon adenocarcinoma cell line (DLD-1) for use in Orthotopic Xenotransplantation studies

ABSTRACT: BACKGROUND: Renilla Luciferase reporter gene (rLuc) GL4.82 and GL4.13 promoter are key player in transfection, but precise knowledge of its targets in colon cancer remains limited. The aim of this study was to characterize the best transfection technique to produce a stable transfected colon DLD1 (colorectal adenocarcinoma cell line), therefore imaging based approaches were employed. RESULTS: DLD1 cells were transfected with a Plasmid (SV40-RLuc) carrying Renilla luciferase under the control of the SV-40 promoter, by using two different transfection techniques. Cells expressing the required DNA were isolated after antibiotic (Puramycin) selection. Clones of DLD-1/SV40-RLuc were produced using two different techniques (96 well plates and Petri dish) and their florescence intensity was recorded using IVIS machine (Calliper Life Sciences, Hopkinton, USA). Both techniques were characterized with the help of serial dilution technique. Results from this study substantiated that electroporation is the best. As expected, clones varied in their specific luciferase activity along with the dilutions. With the increase in cell concentration increase in intensity of florescence was recorded. CONCLUSIONS: Based on the results we are confident that this transfected cell line DLD-1/SV40-RLuc (colorectal adenocarcinoma cell line) is the best for further Orthotopic Xenotransplantation Studies and in-vivo experiments as well. Investigation shows that DLD1/SV-rLuc cells have gained little bit resistance against both drugs therefore further study is suggested to know the reasons.     

Permutations Generated by Stacks and Deques

Lower and upper bounds are given for the the number of permutations of length n generated by two stacks in series, two stacks in parallel, and a general deque.