Methods and reagents for analyzing protein-protein interfaces

A conjugate comprising a presenter protein binding moiety conjugated to a target protein,

• (i) wherein the presenter protein binding moiety is a cyclophilin binding moiety comprising the structure of Formula III or IV:
• wherein Z3, Z4, Z5, and Z6 are each, independently, hydroxyl, optionally substituted C1-C6 alkyl, optionally substituted C1-C6 heteroalkyl, or Z3 and Z4 or Z5 and Z6 combine to form, with the atoms to which they are attached, an optionally substituted 10 to 40 member macrocycle;
• at least one of Z3, Z4, Z5, Z6, or R5 comprises a point of attachment to a cross-linking group;
• e is 0, 1, 2, 3, or 4;
• R5 is optionally substituted C1-C6 alkyl, optionally substituted C2-C6 alkenyl, optionally substituted C2-C6 alkynyl, optionally substituted C1-C6 heteroalkyl, optionally substituted C2-C6 heteroalkenyl, optionally substituted C2-C6 heteroalkynyl, optionally substituted C3-C10 carbocyclyl, optionally substituted C6-C10 aryl, optionally substituted C6-C10 aryl C1-C6 alkyl, optionally substituted C2-C9 heterocyclyl, or optionally substituted C2-C9 heterocyclyl C1-C6 alkyl;
• R6 is optionally substituted C1-C6 alkyl;
• each R7 is, independently, hydroxyl, cyano, optionally substituted amino, halogen, thiol, optionally substituted C1-C6 alkyl, optionally substituted C2-C6 alkenyl, optionally substituted C2-C6 alkynyl, optionally substituted C1-C6 heteroalkyl, optionally substituted C2-C6 heteroalkenyl, optionally substituted C2-C6 heteroalkynyl, optionally substituted C3-C10 carbocyclyl, optionally substituted C6-C10 aryl, optionally substituted C6-C10 aryl C1-C6 alkyl, optionally substituted C2-C9 heterocyclyl, or optionally substituted C2-C9 heterocyclyl C1-C6 alkyl;
• and
• R8 is hydrogen, optionally substituted C1-C6 alkyl, optionally substituted C2-C6 alkenyl, optionally substituted C2-C6 alkynyl, optionally substituted aryl, C3-C7 carbocyclyl, optionally substituted C6-C10 aryl C1-C6alkyl, and optionally substituted C3-C7 carbocyclyl C1-C6 alkyl;
• or
• (ii) wherein the presenter protein binding moiety is an FKBP binding moiety comprising the structure of Formula IIa:
• wherein Z1 and Z2 are each, independently, optionally substituted C1-C6 alkyl, optionally substituted C1-C6 heteroalkyl, or Z1 and Z2 combine to form, with the atoms to which they are attached, an optionally substituted 10 to 40 member macrocycle;
• at least one of Z1 or Z2 comprises a point of attachment to a cross-linking group;
• X2 is absent, CH2, O, S, SO, SO2, or NR4;
• and
• each R4 is, independently, hydrogen, optionally substituted C1-C6 alkyl, optionally substituted C2-C6 alkenyl, optionally substituted C2-C6 alkynyl, optionally substituted aryl, C3—C carbocyclyl, optionally substituted C6-C10 aryl C1-C6 alkyl, and optionally substituted C3-C7 carbocyclyl C1-C6 alkyl,
• wherein the cross-linking group of the presenter protein binding moiety forms a covalent bond with the target protein.