High-throughput methods for screening large populations of variant proteins are provided. The methods utilize large-scale arrays of microcapillaries, where each microcapillary comprises a solution containing a variant protein, an immobilized target molecule, and a reporter element. Immobilized target molecules may include any molecule of interest, including proteins, nucleic acids, carbohydrates, and other biomolecules. The association of a variant protein with a molecular target is assessed by measuring a signal from the reporter element. The contents of microcapillaries identified in the assays as containing variant proteins of interest can be isolated, and cells expressing the variant proteins of interest can be characterized. Also provided are systems for performing the disclosed screening methods.

The present disclosure discloses a method for identifying an optimized protein. The method involves constructing and targeting targeted libraries against a target antigen using a first set of selection conditions to select a pool of binders in each library, combining the selected libraries into one or more libraries; and selecting the combined library against the target antigen using a second set of selection conditions to identify at least one protein having an optimized functional profile. An exemplar protein that can be identified with this method is an antibody or a fragment thereof.

Provided herein is a protein including an epitope display motif, the motif having a sequence of amino acids that forms the following sequence of secondary structures: alpha.sub.1-X.sub.1-beta.sub.1-X.sub.2-beta.sub.2-X.sub.3-alpha.sub.2-X.sub.4-beta.sub.3-X.sub.5-beta.sub.4, wherein alpha is a sequence of amino acids that forms, or is capable of forming, an alpha helix, wherein beta is a sequence of amino acids that forms, or is capable of forming, a beta strand, and wherein X.sub.1, X.sub.2, X.sub.3, X.sub.4 and X.sub.5 each, independently, include a sequence of amino acids that forms an unstructured loop. Optionally, the unstructured loops can each, independently, include 2 to 10 amino acids.

The disclosure provides for mass spectrometry (MS)-cleavable haloacetamide cross-linkers, and uses thereof, including for proteome-wide analysis of protein-protein interactions.

A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.

Disclosed are proteinaceous coagulation factor XIIa (FXIIa) inhibitors and their use for treating or inhibiting the development of a condition in which inhibiting FXIIa stimulates or effects treatment or inhibition of the development of the condition. Suitable conditions include thromboembolism-associated conditions such as acute coronary syndrome, stroke, deep vein thrombosis and pulmonary embolism, a thrombosis, a thrombosis-associated hematologic disorder such as sickle cell disease or thrombophilia, and an inflammatory condition or a condition related to the kallikrein-kinin system such as hereditary angioedema, multiple sclerosis, rheumatoid arthritis or lupus. The proteinaceous FXIIa inhibitors are also useful for treating or inhibiting thrombus and/or embolus formation. In vitro methods for identifying a disulfide rich peptide which binds to a target substance are also disclosed.

Proto-antigen-presenting surfaces and related kits, methods, and uses are provided. The proto-antigen-presenting surface can comprise a plurality of primary activating molecular ligands comprising a major histocompatibility complex (MHC) molecule configured to bind to a T cell receptor (TCR) of a T cell and a plurality of co-activating molecular ligands each including a TCR co-activating molecule or an adjunct TCR activating molecule, wherein an exchange factor is bound to the MHC molecules. Exchange factors include, e.g., dipeptides such as GL, GF, GR, etc. Proto-antigen-presenting surfaces can be used to rapidly prepare antigen-presenting surfaces comprising one or more peptide antigens of interest by contacting the proto-antigen-presenting surface with one or more peptide antigens so as to displace the exchange factor. As such, the disclosure facilitates rapid evaluation of the immunogenicity of peptide antigens for activating T lymphocytes.

Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., clocking), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information. The kits may be used in high-throughput, multiplexed, and/or automated analysis, and are suitable for analysis of a proteome or subset thereof.

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.

Disclosed is a library consisting essentially of a plurality of antigen-binding molecules differing in sequence from each other, wherein an antigen-binding domain in each of the antigen-binding molecules comprises at least one amino acid residue that changes the antigen-binding activity of the antigen-binding molecule depending on ion concentration conditions. Also disclosed are a composition comprising a plurality of polynucleotide molecules each encoding the antigen-binding molecules, a composition comprising a plurality of vectors each comprising the polynucleotide molecules, a method for selecting the antigen-binding molecules, a method for isolating the polynucleotide molecules, a method for producing the antigen-binding molecules, and a pharmaceutical composition comprising any of the antigen-binding molecules.