The present disclosure provides modified antibodies which contain an antibody or antibody fragment (AB) modified with a masking moiety (MM). Such modified antibodies can be further coupled to a cleavable moiety (CM), resulting in activatable antibodies (AAs), wherein the CM is capable of being cleaved, reduced, photolysed, or otherwise modified. AAs can exhibit an activatable conformation such that the AB is more accessible to a target after, for example, removal of the MM by cleavage, reduction, or photolysis of the CM in the presence of an agent capable of cleaving, reducing, or photolysing the CM. The disclosure further provides methods of making and using such modified antibodies and activatable antibodies.

The present disclosure provides a method of identifying a peptide antigen, including: contacting an antibody-comprising composition to a peptide microarray having an array surface and a plurality of feature pairs disposed thereon. Each of the feature pairs includes a first feature of wild-type peptides having a defined sequence and a second feature of mutant peptides having the defined sequence with a single amino acid mutation. Each of the wild-type peptides and the mutant peptides has an array-coupled terminus coupled to the array surface and an opposing free terminus, and the position of the amino acid mutation in the mutant peptides is located closer to the array-coupled terminus of the mutant peptides than tire free terminus. The method further includes detecting binding of an antibody in the antibody-comprising composition to at least one of the feature pairs on the peptide microarray, and identifying feature pairs exhibiting differential binding.

Provided herein are methods, chemical library and simulation system for performing in situ patterned chemistry. Methods, systems and assays comprising the use of the synthesized chemical libraries, which increase explored protein space in a knowledge-based manner, are also provided for characterizing antibody-target interactions including: identifying target proteins of antibodies, characterizing antibody-binding regions in target proteins, identifying linear and structural epitopes in target proteins, and determining the propensity of antibody binding to target proteins.

Contemplated microfluidic devices and methods are drawn to protein arrays in which distinct and detergent-containing antigen preparations are deposited onto an optical contrast layer in a non-specific and non-covalent manner. Detection of binding a is carried out using a dye that precipitates or agglomerates to so form a visually detectable signal at a dynamic range of at least three orders of magnitude.

Methods for the quantification of influenza HA proteins and anti-influenza antibodies for the fields of vaccine-related protein quantification, potency determination, and efficacy evaluation are provided. According to the technology, quantification is achieved by providing capture agents attached to an array in a series of decreasing concentrations. Serial dilutions of a reference material also may be introduced. The reference material within each solution binds to the capture agents on the array and is labeled with a label agent capable of producing a detectable signal used to construct a calibration curve. A target material of unknown concentration is introduced to a separate identical array, and the target material binds to the capture agents and also is labeled by a label agent to produce a detectable signal. The calibration curve based on the reference material is then utilized to determine the concentration of the target material without the need to perform replicate experiments.

A device for studying protein conformation transformation can include a macroscopic substrate, and chaperonin proteins bound to the substrate, each chaperonin protein being capable of binding to a protein of interest during or after undergoing protein conformation transformation. The device may also include the proteins of interest bound to the substrate, where the substrate is included in a label-free assay system. A method of studying protein conformation transformation can include: providing a macroscopic substrate bound with the chaperonin protein and immersing the chaperonin protein in a study composition having the protein of interest, or include providing a macroscopic substrate bound with the protein of interest; and immersing the protein in a study composition having the chaperonin. Such a method can be done with and without a potential stabilizer in order to determine whether the potential stabilizer stabilizes the protein of interest.

Synthetic nanostructures, proteins that are useful, for example, in making synthetic nanostructures, and methods for designing such synthetic nanostructures are disclosed herein.

Polypeptides with desirable biophysical properties such as solubility, stability, high expression, monomericity, binding specificity or non-aggregation, including monomeric human V.sub.Hs and V.sub.Ls, are identified using a high throughput method for screening polypeptides, comprising the steps of obtaining a phage display library, allowing infection of a bacterial lawn by the library phage, and identifying phage which form larger than average plaques on the bacterial lawn. Sequences of monomeric human V.sub.Hs and V.sub.Ls are identified, which may be useful for immunotherapy or as diagnostic agents. Multimer complexes of human V.sub.Hs and V.sub.Ls are also identified. The V.sub.Hs and V.sub.Ls identified may be used to create further libraries for identifying additional polypeptides. Further, the V.sub.Hs and V.sub.Ls may be subjected to DNA shuffling to select for improved biophysical properties.

The inventors have found that the interaction between HP1 and INCENP can serve as an indicator for chromosome instability and established a method for evaluating chromosome instability of cancer cells. The evaluation system can be used for screening of anticancer agent with a new-concept of targeting chromosome instability of cancer cells. The inventors further prepared an antibody for specifically recognizing phosphorylation of serine at position 92 of HP1, by which the action of Aurora B can be evaluated. The interaction between HP1 and INCENP can be readily evaluated by the antibody.

The invention relates to methods for conducting solid-phase binding assays. One example is an assay method having improved analyte specificity where specificity is limited by the presence of non-specific binding interactions.