Patent Document ID: 9069700
Application ID: 13692859
Patent Status: 1

Claim One:
1. A method of obtaining structures for active, inactive, and intermediate active forms of rhodopsin for identifying or designing ligands that bind to the intermediate rhodopsin forms comprising: (a) obtaining three-dimensional structural coordinates for the crystal structure of rhodopsin in the ground state; (b) pivoting transmembrane helix 3 (TM3) about the Cα carbon of Cys110 such that Cys140 is at a set distance from transmembrane 6 (TM6), while keeping the distance of TM3 to transmembrane helix 2 (TM2) at 5 Å or more, wherein the set distance from TM6 is selected from the group consisting of: 4.3 Å to form activated metarhodopsin I intermediate of rhodopsin, 6.8 Å to form activated metarhodopsin Ib intermediate of rhodopsin, and 9.0 Å to form activated metarhodopsin I 380 intermediate of rhodopsin; (c) pivoting transmembrane helix 4 (TM4) about Gly174 such that Glu150 is at a set distance from transmembrane helix 5 (TM5), wherein the set distance from TM5 is selected from the group consisting of: 7.4 Å to form activated metarhodopsin I intermediate of rhodopsin, 12.1 Å to form activated metarhodopsin Ib intermediate of rhodopsin, and 17.1 Å to form activated metarhodopsin I 380 intermediate of rhodopsin, and wherein the combination of steps (b) and (c) enlarges the ligand binding site by an interaction between Glu134, Arg135, and Try136 on the cytoplasmic side of TM3 and Glu247 on the cytoplasmic side of transmembrane 6 (TM6); (d) optimizing the structural model of step (c) at 300K by molecular dynamics and energy minimization such that the Cα carbons of the amino acids are fixed, wherein amino acid residues have the same numbering as in bovine rhodopsin, and wherein transmembrane helixes 1, 2, and 7 are not subjected to a conformational change; (e) optionally further comprising, to form activated metarhodopsin II intermediate of rhodopsin from metarhodopsin I, metarhodopsin Ib, or metarhodopsin I 380 intermediate of rhodopsin: (i) rotating TM6 clockwise by an angle 100 degrees as viewed from the intracellular side; and (ii) decreasing the distance between the residues of TM6 and the residues of TM3 to a minimal distance that does not cause steric interference; (iii) twisting TM5 about Asn200 to avoid steric interference resulting from said rotation of TM6; (iv) translating TM4 by 4.1 Å to place it between TM3 and TM5, thereby placing the Cα-carbon of Cys140 12.7 Å from the Cα-carbon of Ala246 on TM6 and 4.8 Å from Glu150 on TM4, and placing Leu226 on TM5 10.5 Å from Alu246 on TM6; (v) moving TM5 and TM4 to a distance that does not cause steric interference with TM6; and (vi) optimizing the structural model of step (v) at 300K by molecular dynamics and energy minimization such that the Cα carbons of the amino acids are fixed, wherein amino acid residues have the same numbering as in bovine rhodopsin, and wherein transmembrane helixes 1, 2, and 7 are not subjected to a conformational change; and (f) binding a previously identified or designed ligand to the activated metarhodopsin I, metarhodopsin Ib, metarhodopsin I 380 , or metarhodopsin II intermediate of rhodopsin to form a complex of the ligand and the activated intermediate of rhodopsin.