The present invention relates to, among other things, probes, compositions, methods, and kits for simultaneous, multiplexed detection and quantification of protein and/or nucleic acid expression in a user-defined region of a tissue, user-defined cell, and/or user-defined subcellular structure within a cell.

Provided are methods of detecting and quantitatively measuring protein-protein interactions between proteins present on the surface of different cells using a sensitive antibody-based assay. Antibodies specific for each target protein are either directly labeled, or are detected by labeled secondary antibodies. The antibodies are labeled with detectable tags that are releasable when the target proteins are within proximity to each other. Also provided are methods for facilitating diagnosis, prognosis, and treatment of cancer using this assay to detect protein-protein interactions between target proteins of interest. Methods of screening test agents that impact the protein-protein interaction are also provided.

Methods of identifying target binding molecules by target guided synthesis are provided. The methods include providing two or more fragments capable of reacting to form the target binding molecule and mixing the fragments with the target. The methods can be used to identify target binding molecules that bind targets such as proteins or nucleic acids, including those that bind shallow binding pockets on the surface of such targets. The methods are applied to the Bcl-XL and Mcl-1 proteins from the Bcl-2 family of proteins. Using thio acid and sulfonyl azide fragments capable of reacting through sulfo-click chemistry, new acyl sulfonamides are identified that bind one or both of the Bcl-XL and Mcl-1 proteins. Pharmaceutical formulations of these target binding molecules are also provided.

The disclosure relates to a virus-like particle in which a protein complex is entrapped, ensuring the formation of the protein complex under physiological conditions, while protecting the protein complex during purification and identification. The disclosure further relates to the use of such virus-like particle for the isolation and identification of protein complexes.

The present invention provides a reporter for a protein fragment complementation assay characterized in that the reporter is a fused protein comprising a first fragment, a second fragment and a protein kinase sequence section, wherein the first fragment and the second fragment are derived from different sections of the same split protein, and wherein the protein kinase sequence section intervenes between the first fragment and the second fragment and wherein the kinase sequence section comprises a kinase domain sequence and one or more regulatory sequence(s). Further the invention provides polynucleotides and cells encoding for the reporter as well as methods of conducting a protein fragment complementation assay with the reporter according to the invention.

The invention provides methods, compositions, and kits for the characterisation and analysis of proteins. Methods are provided for determining, on a protein, a binding site for a binding partner, the methods comprising: contacting a protein with a plurality of monomers, and polymerising the monomers to create a protein:polymer complex; digesting the protein in the complex to produce a peptide:polymer complex; isolating the peptide:polymer complex; and sequencing the peptide, wherein the peptide corresponds to a binding site for a binding partner.

The invention relates to a method for selecting a glycopolypeptide that binds to a target protein, the method including the steps of providing a pool of glycopolypeptides fused via puromycin linker to an encoding mRNA-cDNA duplex; combining the pool with a target protein to form a mixture; incubating the mixture for a period of time sufficient to allow any target protein to bind to one or more of the glycopolypeptides, thereby forming glycopolypeptide-target protein complexes; and isolating from the mixture the glycopolypeptide-target protein complexes, thereby identifying a plurality of selected glycopolypeptides.

Disclosed are methods and systems for determining concentrations of a target molecule and a variant thereof in a sample. The sample can comprise or be suspected to comprise a target molecule and at least one variant thereof and is exposed to one or more recognition elements that bind to the target molecule and/or the at least one variant. A signal is detected that is associated with the binding of the target molecule and/or a signal is detected that is associated with the binding of the at least one variant to the one or more recognition elements. The concentration of the target molecule and/or the at least one variant thereof is determined based on the signals. The system can comprise a receiver adapted to receive a sample comprising or suspected to comprise a target molecule and the at least one variant thereof, the receiver comprising one or more recognition elements that bind to one or more epitopes in the target molecule and/or the at least one variant thereof.

A peptide that binds specifically to neuropilin-1 (NRP1) without binding to neuropilin-2 (NRP2) is provided. A fusion protein, a fusion antibody, small-molecule drug, a nanoparticle, or a liposome, which comprises the peptide, and a pharmaceutical composition for treating or preventing cancer or angiogenesis-related diseases, and a composition for diagnosing cancer or angiogenesis-related diseases are provided. A polynucleotide encoding the peptide that binds specifically to NRP1 and a method for screening the peptide that binds specifically to NRP1 are provided. An antibody heavy-chain constant region Fc-fused peptide binding specifically to NRP1 has the property of binding specifically to NRP1, and thus when it is administered in vivo, it accumulates selectively in tumor tissue, and widens the intercellular space between tumor-associated endothelial cells to promote its extravasation and increases its tumor tissue penetration.

Methods and systems for high-throughput Identification of receptor: ligand interactions are provided. Throughout this application various publications are referred to in parentheses. Full citations for these references may be found at the end of the specification. The disclosures of these publications, and all patents, patent application publications and books referred to herein, are hereby incorporated by reference in their entirety into the subject application to more fully describe the art to which the subject invention pertains.