Provided herein are methods and compositions relating to G protein-coupled receptor (GPCR) libraries having nucleic acids encoding for a scaffold comprising a GPCR binding domain. Libraries described herein include variegated libraries comprising nucleic acids each encoding for a predetermined variant of at least one predetermined reference nucleic acid sequence. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.

The invention pertains to a natural-variant combinatorial library of fibronectin Type 3 domain (Fn3) polypeptides useful in screening for the presence of one or more polypeptides having a selected binding or enzymatic activity. The library polypeptides include (a) regions A, AB, B, C, CD, D, E, EF, F, and G having wildtype amino acid sequences of a selected native fibronectin Type 3 polypeptide or polypeptides, and (b) loop regions AB, CD, and EF having selected lengths (Bottom Loops). The Fn3 may also have loop regions BC, DE, and FG having wildtype amino acid sequences, having selected lengths, or mutagenized amino acid sequences (Top Loops).

Provided are a tRNA obtained by modifying a tRNA for tryptophan of Mycoplasma pneumoniae, the tRNA including a UUA as an anticodon to pair with a UAA codon, and an application of the tRNA.

The present invention provides compositions including peptide display scaffolds that present at least one candidate peptide and at least one detectable moiety in at least one of the N-terminal and C-terminal candidate peptide presenting domains that when expressed in a cell are accessible at a surface of the cell outermembrane. In addition, the present invention also provides kits and methods for screening a library of cells presenting the candidate peptides in peptide display scaffolds to identify a ligand for an enzyme.

The present invention provides a fibronectin type III (Fn3) molecule, wherein the Fn3 contains a stabilizing mutation. The present invention also provides Fn3 polypeptide monobodies, nucleic acid molecules encoding monobodies, and variegated nucleic acid libraries encoding such monobodies. Also provided are methods of preparing a Fn3 polypeptide monobody, and kits to perform the methods.

The present invention provides a method for preparing a modular scaffold that can bind to a target antigen and a method for engineering a bispecific functional agent consisting of an existing polypeptide binder fused at its C-terminus with said modular scaffold.

The present invention relates to polypeptides that are resistant to degradation in the gastrointestinal tract and that bind to a target (i.e. a target ligand). In particular, it provides a mutant Kunitz-type soybean trypsin inhibitor (SBTI) family polypeptide comprising two or more amino acid mutations compared to the corresponding unmutated (e.g. wild-type) SBTI family polypeptide, wherein the mutant SBTI family polypeptide comprises: (i) one or more amino acid mutations in a first domain corresponding to positions 22-25 of SEQ ID NO: 1; and (ii) one or more amino acid mutations in a second domain corresponding to positions 47-50 of SEQ ID NO: 1, wherein the mutant SBTI family polypeptide: (a) binds selectively to a ligand that does not bind to the corresponding unmutated (e.g. wild-type) SBTI family polypeptide; and (b) is resistant to cleavage by pepsin.

Provided herein are methods and compositions relating to prostaglandin D2 receptor 2 (DP2 or CRTH2R) libraries having nucleic acids encoding for a scaffold comprising a CRTH2R binding domain. CRTH2R libraries described herein encode for immunoglobulins including antibodies and single domain antibodies. Libraries described herein include variegated libraries comprising nucleic acids each encoding for a predetermined variant of at least one predetermined reference nucleic acid sequence. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.

Activatable binding polypeptides (ABPs), which contain a target binding moiety (TBM), a masking moiety (MM), and a cleavable moiety (CM) are provided. Activatable antibody compositions, which contain a TBM containing an antigen binding domain (ABD), a MM and a CM are provided. Furthermore, ABPs which contain a first TBM, a second TBM and a CM are provided. The ABPs exhibit an activatable conformation such that at least one of the TBMs is less accessible to target when uncleaved than after cleavage of the CM in the presence of a cleaving agent capable of cleaving the CM. Further provided are libraries of candidate ABPs, methods of screening to identify such ABPs, and methods of use. Further provided are ABPs having TBMs that bind VEGF, CTLA-4, or VCAM, ABPs having a first TBM that binds VEGF and a second TBM that binds FGF, as well as compositions and methods of use.

Disclosed herein are expression vectors which display a passenger polypeptide on the outer surface of a biological entity. As disclosed herein the displayed passenger polypeptide is capable of interacting or binding with a given ligand. Also disclosed are methods of making and using the expression vectors. N/C terminal fusion expression vectors and methods of making and using are also disclosed.