Novel strategy for the selection of human recombinant Fab fragments to membrane proteins from a phage-display library

Nanodiscs allow phage display selection for ligands to non-linear epitopes on membrane proteins

In this work, we exploited a method that uses polytopic membrane proteins as targets for phage display selections. Membrane proteins represent the largest class of drug targets and drug discovery is mostly based on the identification of ligands binding to target molecules. The screening of a phage display library for ligands against membrane proteins is typically hindered by the requirement of these proteins for a membrane environment, which is necessary to retain correct folding and epitope formation. Especially in proteins with multiple transmembrane domains, epitopes often are non-linear and consist of a combination of loops between transmembrane stretches of the proteins. Here, we have used bacteriorhodopsin (bR) as a model of polytopic membrane protein, assembled into nanoscale phospholipid bilayers, so called nanodiscs, to screen a phage display library for potential ligands. Nanodiscs provide a native-like environment to membrane proteins and thus selection of ligands can take place in a near physiological state. Screening a 12-mer phage display peptide library against bR nanodiscs led to the isolation of phage clones binding specifically to bR. We were further able to identify the binding site of selected phage clones proving that the clones bind to extramembranous, non-linear epitopes of bR. Thus, nanodiscs provide a suitable and general tool that allows screening of a phage display library against membrane proteins in a near native environment.

Synthetic antibodies: concepts, potential and practical considerations

The last 100 years of enquiry into the fundamental basis of humoral immunity has resulted in the identification of antibodies as key molecular sentinels responsible for the in vivo surveillance, neutralization and clearance of foreign substances. Intense efforts aimed at understanding and exploiting their exquisite molecular specificity have positioned antibodies as a cornerstone supporting basic research, diagnostics and therapeutic applications [1]. More recently, efforts have aimed to circumvent the limitations of developing antibodies in animals by developing wholly in vitro techniques for designing antibodies of tailored specificity. This has been realized with the advent of synthetic antibody libraries that possess diversity outside the scope of natural immune repertoires and are thus capable of yielding specificities not otherwise attainable. This review examines the convergence of technologies that have contributed to the development of combinatorial phage-displayed antibody libraries. It further explores the practical concepts that underlie phage display, antibody diversity and the methods used in the generation of and selection from phage-displayed synthetic antibody libraries, highlighting specific applications in which design approaches gave rise to specificities that could not easily be obtained with libraries based upon natural immune repertories.

Screening of Combinatorial Libraries for Substrate Preference by Mass Spectrometry

We present a rapid screening method for monitoring enzyme specificity using both combinatorial chemistry and mass spectrometry where, as an example, the substrate specificity of peptidylglycine alpha-amidating enzyme was determined and compared against a conventional quantitative technique. Whereas alternative methods for library screening are generally limited to certain enzymes and can present difficulties in the synthesis or derivatization of potential substrates, the approach we call chirality-based isotope labeling for a library of substrates (CHILLS) does not fall short to such limitations, since we exploit the inherent stereospecificity of enzymes to determine preferred substrates. Additionally, the CHILLS method generates accurate results, as compared to typical screening procedures that require tedious method development, because the synthesized library contains a structurally similar internal standard for each individual library component in order to quantitate the progress of enzymatic reactions.