The present disclosure provides methods and reagents useful for analyzing protein-protein interfaces such as interfaces between a presenter protein (e.g., a member of the FKBP family, a member of the cyclophilin family, or PIN1) and a target protein. In some embodiments, the target and/or presenter proteins are intracellular proteins. In some embodiments, the target and/or presenter proteins are mammalian proteins.

The present disclosure relates to a class of engineered polypeptides and provides a polypeptide comprising the sequence EX.sub.2X.sub.3X.sub.4AX.sub.6X.sub.7EIX.sub.10 X.sub.11LPNLX.sub.16X.sub.17X.sub.18QX.sub.20 X.sub.21AFIX.sub.25X.sub.26LX.sub.28X.sub.29X.sub.30 PX.sub.32QSX.sub.35X.sub.36LLX.sub.39E AKKLX.sub.45X.sub.46X.sub.47Q (SEQ ID NO: 55). The present disclosure also relates to populations of polypeptide variants based on a common scaffold, each polypeptide in the population comprising the amino acid sequence EX.sub.2X.sub.3X.sub.4AX.sub.6X.sub.7EIX.sub.10 X.sub.11LPNLX.sub.16X.sub.17X.sub.18QX.sub.20 X.sub.21AFIX.sub.25X.sub.26LX.sub.28X.sub.29X.sub.30 PX.sub.32QSX.sub.35X.sub.36LLX.sub.39E AKKLX.sub.45X.sub.46X.sub.47Q (SEQ ID NO: 55), and methods for selecting a desired polypeptide having an affinity for a predetermined target from said population.

This disclosure relates to a method of generating conditionally active biologic proteins from wild type proteins, in particular therapeutic proteins, which are reversibly or irreversibly inactivated at the wild type normal physiological conditions. For example, evolved proteins are virtually inactive at body temperature, but are active at lower temperatures.

Protein scaffolds and scaffold libraries based on a fibronectin type III (FN3) repeat with an alternative binding surface design, isolated nucleic acids encoding the protein scaffolds, vectors, host cells, and methods of making thereof are useful in the generation of therapeutic molecules and treatment and diagnosis of diseases and disorders.

Provided are dyes and compositions which are useful in a number of applications, such as the detection and monitoring protein aggregation, kinetic studies of protein aggregation, neurofibrillary plaques analysis, evaluation of protein formulation stability, and analysis of molecular chaperone activity.

A novel assay for determining a molecular process using a fluorescent protein exchange assay, and a composition for use thereof, are provided. The assay provides first and second signalling proteins and an exchange protein, wherein the exchange protein interacts with the first signalling protein to form a complex, then introducing the second signalling protein, wherein in response to the molecular process, the exchange protein dissociates from the first protein and associates with the second protein. The change in signal in response to the exchange of the proteins is measured to indicate a molecular process.

The invention provides a peptide obtainable from C. albicans as well as variants and fragments thereof, and labelled forms of these. The peptide is immunogenic and specific binding partners for the peptide and labelled forms of these specific binding partners form a further aspect of the invention. The peptide is a fragment of the ECE1 protein and has been found to be both immunogenic and act as a pore-forming toxin. A range of therapeutic and diagnostic applications for the peptide and the specific binding partners for it form further aspects of the invention. In addition, the peptide may be used in screens for identifying compounds having useful anti-fungal activity.

The invention provides fibronectin type III (Fn3)-based binding molecules that bind to a specific target antigen. The invention further provides bispecific Fn3-based binding molecules that bind to two or more targets simultaneously. The Fn3-based binding molecules of the invention can also be linked together to form multispecific Fn3-based binding molecules, and/or can be conjugated to a non-Fn3 moiety, such as, Human Serum Albumin (HSA), for improved half life and stability. The invention also provides methods for generating, screening and using Fn3-based binding molecules in a variety of therapeutic and diagnostic applications.

A method of analyzing protein-protein interactions includes binding the first proteins to the substrate where the first proteins are tagged with the first markers which bind specifically to the biomolecules immobilized on the substrate or the first proteins bind specifically to the biomolecules immobilized on the substrate; incubating the substrate bound first proteins with cell lysate containing the second proteins which are tagged with second markers; analyzing the interactions between the first proteins and the second proteins in the cell lysate, and obtaining the first analytic value representing the kinetic picture of the interactions; incubating the substrate bound first proteins with cell lysate mixture of a cell lysate consisting of the second markers-tagged second proteins and another cell lysate comprising other proteins including unlabelled second proteins and obtaining the second analytic value; comparing and analyzing the first and the second analytic values.

In some embodiments, the present disclosure pertains to method of screening a biological sample for a plurality of diseases. In some embodiments, such a method comprises obtaining a biological sample from a subject in need thereof. In some embodiments, the biological sample comprises a plurality of biomarkers. In some embodiments, each of the plurality of biomarkers is specific for at least one disease. In some embodiments, the method comprises contacting the biological sample with a display library of peptides. In some embodiments, each peptide in the library may have a unique amino acid sequence. In some embodiments, each of the peptides is physically linked to a nucleic acid sequence that identifies of encodes the peptide. In some embodiments, at least one of the peptides is capable of binding to at least one of the biomarkers in the biological sample. In some embodiments, the method comprises separating the bound peptide particles from the unbound peptide particle. In some embodiments, the method comprises eluting the bound peptide particles from the bound state. In some embodiments, the method comprises determining the identity of the nucleic acid sequences physically linked to the bound peptide particles. In some embodiments, the method comprises comparing the sequences thus obtained to a database of sequences representing a plurality of biomarkers of diseases.