Mimicking nature: Phosphopeptide enrichment using combinatorial libraries of affinity ligands

Biomimetic Affinity Ligands for Protein Purification

The development of sophisticated molecular modeling software and new bioinformatic tools, as well as the emergence of data banks containing detailed information about a huge number of proteins, enabled the de novo intelligent design of synthetic affinity ligands. Such synthetic compounds can be tailored to mimic natural biological recognition motifs or to interact with key surface-exposed residues on target proteins, and are designated as "biomimetic ligands". A well-established methodology for generating biomimetic or synthetic affinity ligands integrates rational design with combinatorial solid-phase synthesis and screening, using the triazine scaffold and analogs of amino acid side chains to create molecular diversity.Triazine-based synthetic ligands are nontoxic, low-cost, and highly stable compounds that can replace advantageously natural biological ligands in the purification of proteins by affinity-based methodologies.

Affinity Tags in Protein Purification and Peptide Enrichment: An Overview

The reversible interaction between an affinity ligand and a complementary receptor has been widely explored in purification systems for several biomolecules. The development of tailored affinity ligands highly specific toward particular target biomolecules is one of the options in affinity purification systems. However, both genetic and chemical modifications in proteins and peptides widen the application of affinity ligand-tag receptors pairs toward universal capture and purification strategies. In particular, this chapter will focus on two case studies highly relevant for biotechnology and biomedical areas, namely the affinity tags and receptors employed on the production of recombinant fusion proteins, and the chemical modification of phosphate groups on proteins and peptides and the subsequent specific capture and enrichment, a mandatory step before further proteomic analysis.

β-Hairpins as peptidomimetics of human phosphoprotein-binding domains

Phosphoprotein-binding domains interact with cognate phosphorylated targets ruling several biological processes. The impairment of such interactions is often associated with disease development, namely cancer. The breast cancer susceptibility gene 1 (BRCA1) C-terminal (BRCT) domain is involved in the control of complex signaling networks of the DNA damage response. The capture and identification of BRCT-binding proteins and peptides may be used for the development of new diagnostic tools for diseases with abnormal phosphorylation profiles. Here we show that designed cyclic β-hairpin structures can be used as peptidomimetics of the BRCT domain, with high selectivity in binding to a target phosphorylated peptide. The amino acid residues and spatial constraints involved in the interaction between a phosphorylated peptide (GK14-P) and the BRCT domain were identified and crafted onto a 14-mer β-hairpin template in silico. Several cyclic peptides models were designed and their binding towards the target peptide and other phosphorylated peptides evaluated through virtual screening. Selected cyclic peptides were then synthesized, purified and characterized. The high affinity and selectivity of the lead cyclic peptide towards the target phosphopeptide was confirmed, and the possibility to capture it using affinity chromatography demonstrated. This work paves the way for the development of cyclic β-hairpin peptidomimetics as a novel class of affinity reagents for the highly selective identification and capture of target molecules.

Antibody purification via affinity membrane chromatography method utilizing nucleotide binding site targeting with a small molecule

Here, we present an affinity membrane chromatography technique for purification of monoclonal and polyclonal antibodies from cell culture media of hybridomas and ascites fluids. The m-NBST method utilizes the nucleotide-binding site (NBS) that is located on the Fab variable domain of immunoglobulins to enable capturing of antibody molecules on a membrane affinity column via a small molecule, tryptamine, which has a moderate binding affinity to the NBS. Regenerated cellulose membrane was selected as a matrix due to multiple advantages over traditionally used resin-based affinity systems. Rituximab was used for proof of concept experiments. Antibody purification was accomplished by first capture of injected samples while running equilibration buffer (50 mM sodium phosphate pH 7.0), followed by elution achieved by running a gradient of mild elution buffer (3 M NaCl in 50 mM phosphate pH 7.0). The results indicate that the m-NBST column efficiency for Rituximab was >98%, with a purity level of >98%. The quality and the capacity of this small molecule membrane affinity purification method is further evaluated for a number of parameters such as: injection concentrations, volumes, wash/bind time, elution gradient, antibody/protein-contaminant combinations, effects of injection buffer, post-purification antigen binding activity of antibodies, and column reusability and stability.

Designer Histone Complexes: Controlling Protein-DNA Interactions with Protein Charge as an "All-or-None" Digital Switch

An artificial histone is synthesized that functions as a DNA-protein digital switch, where DNA binding is all or none, controlled by a sharp threshold of protein charge. A non-DNA-binding protein, glucose oxidase (GOx), was chemically modified by attaching an increasing number of triethylenetetramine (TETA) side chains to its glutamate/aspartate groups to obtain a small library of covalently modified GOx(n) derivatives. The parameter n denotes the net charge on the protein at pH 7, which was increased from -62 (pristine GOx) to +75 by attaching an increasing number of TETA residues to the protein. All GOx(n) derivatives retained their secondary structure to a good extent, as monitored by UV circular dichroism (CD) spectroscopy, and they also retained oxidase activities to a significant extent. The interaction of the GOx(n) with calf thymus DNA was examined by isothermal titration calorimetry (ITC). Pristine GOx of -62 charge at pH 7 in 10 mM Tris-HCl and 50 mM NaCl buffer had no affinity for the negatively charged DNA helix, and GOx(n) with n < +30 had no affinity for DNA either. However, binding has been turned on abruptly when n ≥ +30 with binding constants (K_b) ranging from (1.5 ± 0.7) × 10⁷ to (7.3 ± 2.8) × 10⁷ M^-1 for n values of +30 and +75, respectively, and this type of "all-or-none" binding based on protein charge is intriguing. Furthermore, thermodynamic analysis of the titration data revealed that binding is entirely entropy-driven with ΔS ranging from 0.09 ± 0.007 to 0.19 ± 0.008 kcal/mol K with enthalpic penalties of 17.0 ± 2.3 and 46.1 ± 2.1 kcal/mol, respectively. The binding had intrinsic propensities (ΔG) ranging from -9.8 ± 0.14 to -10.7 ± 0.25 kcal/mol, independent of n. DNA binding distorted protein-DNA secondary structure, as evidenced by CD spectroscopy, but oxidase activity of GOx(n)/DNA complexes has been unaffected. This is the very first example of an artificial histone (GOx(n)) where the protein charge functioned as a DNA-binding switch; protein charge is in turn under complete chemical control while preserving the biological activity of the protein. The new insight gained here could be useful in the design of novel "on-off" protein switches.