Immobilized monolithic enzyme reactors for application in proteomics and pharmaceutics

Scaled-Down Thermal Profiling and Coaggregation Analysis of the Proteome for Drug Target and Protein Interaction Analysis

Thermal proteome profiling (TPP), an experimental technique combining the cellular thermal shift assay (CETSA) with quantitative protein mass spectrometry (MS), identifies interactions of drugs and chemicals with endogenous proteins. Thermal proximity coaggregation (TPCA) profiling extended TPP to study the intracellular dynamics of protein complexes. In TPP and TPCA, samples are subjected to multiple denaturing temperatures, each requiring over 100 μg of proteins, which restricts their applications for rare cells and precious clinical samples. We developed a workflow termed STASIS (scaled-down thermal profiling and coaggregation analysis with SISPROT) that scales down the required protein to as low as 1 μg per temperature. This is achieved by heating and centrifugation using the same PCR tube, processing samples with the SISPROT technology (simple and integrated spintip-based proteomics technology), and tip-based manual fractionation of TMT-labeled peptides. We evaluate the STASIS workflow with starting protein quantities of 10, 5, and 1 μg per temperature prior to heating, identifying between 4000 and 5000 proteins with 6 h of acquisition time. Importantly, we observed a high correlation in the Tm of proteins with minimal difference in TPCA performance for predicting protein complexes. Moreover, STASIS could identify the targets of methotrexate and panobinostat with high precision with 1 μg of proteins per temperature. In conclusion, STASIS is a robust cost-effective technique for target deconvolution and extended TPCA to rare primary cells and precious clinical samples for the analysis of protein complexes.

Thiol-ene Monolithic Pepsin Microreactor with a 3D-Printed Interface for Efficient UPLC-MS Peptide Mapping Analyses

To improve the sample handling, and reduce cost and preparation time, of peptide mapping LC-MS workflows in protein analytical research, we here investigate the possibility of replacing conventional enzymatic digestion methods with a polymer microfluidic chip based enzyme reactor. Off-stoichiometric thiol-ene is utilized as both bulk material and as a monolithic stationary phase for immobilization of the proteolytic enzyme pepsin. The digestion efficiency of the, thiol-ene based, immobilized enzyme reactor (IMER) is compared to that of a conventional, agarose packed bed, pepsin IMER column commonly used in LC-MS based protein analyses. The chip IMER is found to rival the conventional column in terms of digestion efficiency at comparable residence time and, using a 3D-printed interface, be directly interfaceable with LC-MS.

Papain-functionalized gold nanoparticles as heterogeneous biocatalyst for bioanalysis and biopharmaceuticals analysis

Surface-modified gold nanoparticles (GNPs) were synthesized via layer-by-layer process with alternating cationic polyallylamine and anionic poly(acrylic acid) polyelectrolyte layers leading to a highly hydrophilic biocompatible shell supporting colloidal stability. Afterwards, papain was covalently immobilized on the modified GNPs via amide coupling between the amino groups on papain and the terminal carboxylic groups of the modified GNPs by using N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide and N-hydroxysulfosuccinimide sodium as coupling agents. The resultant papain-functionalized gold nanoparticles were characterized by surface plasmon resonance, dynamic light scattering and zeta potential measurements. The new technology resonant mass measurement was applied for determining the average number of papain molecules immobilized per GNP by measurement of the single nanoparticle buoyant mass in the range of femtograms. The activity of the immobilized enzyme was estimated by determination of the kinetic parameters (K_m, V_max and k_cat) with the standard chromogenic substrate N_α-benzoyl-dl-arginine-4-nitroanilide hydrochloride. It was found that K_m of immobilized and free enzyme are in the same order of magnitude. On contrary, turnover numbers k_cat were significantly higher for GNP-conjugated papain. Further, the gold nanobiocatalyst was applied for digestion of polyclonal human immunoglobulin G to yield protein fragments. The resultant fragment mixture was further analyzed by high-performance liquid chromatography-microelectrospray ionization-quadrupole-time-of-flight mass spectrometry, which demonstrated the applicability of the bioreactor based on papain functionalized GNPs. The immobilized papain not only has higher catalytic activity and better stability, but also can be easily isolated from the reaction medium by straightforward centrifugation steps for reuse.

Preparation of monolithic affinity media for nano-liquid chromatography applications

In this protocol, a strategy is described for preparing affinity media with monolithic materials as stationary phase, which is exemplified for the biotin-avidin interaction pair. The capillary columns prepared in this manner are compatible with nano-liquid chromatographic conditions. Our protocol is easily adapted to the preparation of specific affinity media with different functionalities and as such provides a platform for a multitude of applications.

Bioconjugation of trypsin onto gold nanoparticles: effect of surface chemistry on bioactivity

The systematic study of activity, long-time stability and auto-digestion of trypsin immobilized onto gold nanoparticles (GNPs) is described in this paper and compared to trypsin in-solution. Thereby, the influence of GNP's size and immobilization chemistry by various linkers differing in lipophilicity/hydrophilicity and spacer lengths was investigated with regard to the bioactivity of the conjugated enzyme. GNPs with different sizes were prepared by reduction and simultaneous stabilization with trisodium citrate and characterized by UV/vis spectra, dynamic light scattering (DLS), ζ-potential measurements and transmission electron microscopy (TEM). GNPs were derivatized by self-assembling of bifunctional thiol reagents on the nanoparticle (NP) surface via dative thiol-gold bond yielding a carboxylic acid functionalized surface. Trypsin was either attached directly via hydrophobic and ionic interactions onto the citrate stabilized GNPs or immobilized via EDC/NHS bioconjugation onto the carboxylic functionalized GNPs, respectively. The amount of bound trypsin was quantified by measuring the absorbance at 280 nm. The activity of bound enzyme and its Michaelis Menten kinetic parameter K(m) and v(max) were measured by the standard chromogenic substrate N(α)-Benzoyl-DL-arginine 4-nitroanilide hydrochloride (BApNA). Finally, digestion of a standard protein mixture with the trypsin-conjugated NPs followed by analysis with LC-ESI-MS and successful MASCOT search demonstrated the applicability of the new heterogenous nano-structured biocatalyst. It could be shown that the amount of immobilized trypsin and its activity can be increased by a factor of 6 using a long hydrophilic spacer with simultaneous reduced auto-digestion and reduced digestion time. The applicability of the new trypsin bioreactor was proven by digestion of casein and identification of α- as well as κ-casein by subsequent MASCOT search.