Binding domain mapping
The present disclosure relates to compositions and methodology for revealing binding sites between proteins, proteins and nucleic acids, or proteins and small molecules. The disclosure provides rapid and direct positive identification and sequencing of the contact region between such molecules, and can be applied to individual interacting pairs, as well as large-scale or global interactions.
1. An aryl hydrocarbon containing organic compound less than 30 Angstroms in total length taken from at least one of the following structure formulas listed below, or salts or solvates thereof, complexed or bound to a portion of a unfolded protein polypeptide chain of at least 3 amino acids where the amino acid in position 1 (P1) from the amino terminus is any amino acid, position 2 (P2) is K or R and the amino acid in position 3 (P3) is not P,
Polymethine compounds
wherein RI represents H, halo, CO 2 H, NO 2 , SH, NR 4 R 6 , C1-6 alkyl, C1-6 alkoxy, cyano, carbonyl, pyrrolidinyl, pyrrolyl, pyrazolyl, imidazolyl, or triazolyl;
R 5 , R 6 represent H or C1-4 alkyl;
E 1 represents benzene ring or ring Q;
A represents CH or N;
D represents S, NH, N—C1-3 alkyl, O, or CH 2 ;
R 2 represents H, C1-4 alkyl, halo-C1-4 alkyl, OH, or cyano;
n represents an integer of 1-4;
E=benzene ring or ring Q′;
X represents CH or N;
Y represents S, NH, N—C1-3 alkyl, O, or CH 2 ;
R 3 =H, halo, CO 2 H, NO 2 , SH, NR 5 R 6 , C1-6 alkyl, C1-6 alkoxy, cyano, carbonyl, pyrrolidinyl, pyrrolyl, pyrazolyl, imidazolyl, or triazolyl;
Triarylmethane compounds
wherein X and Y represent H, NR 1 R 2 , sulfo, halo, CO 2 H, NO 2 , SH, C1-6 alkyl, or C1-6 alkoxy;
Z represents NR 1 R 2 , sulfo, O, CO 2 H, NO 2 , C1-6 alkyl, or C1-6 alkoxy;
R 1 , R 2 represent H, C1-6 alkyl, or sulfophenyl;
E 1 , E 2 , E 3 , E 4 , E 5 , E 6 represent H, sulfo, C1-6 alkyl, halo, CO 2 H, NO 2 , or SH;
Aryl azo compounds
wherein E 1 , E2, E 3 represent H, halo, sulfo, C1-6 alkyl, or C1-6 alkyl aryl;
R1 represents ring Q or ring Q′;
D represents H or NR 2 R 3 ;
R 2 , R 3 represent C1-6 alkyl or C1-6 alkyl aryl;
E represents H, OH, or C1-6 alkyloxy;
Xanthenes
wherein E 1 , E 2 , E 3 , E 4 represent H, NO 2 , OH, Halo, or C1-6 alkyl;
E 5 , E 6 represent H or Carbon in position 3 and oxygen in position 1 in group Q; or
Thiazine
wherein E 1 represents N, O, or S;
E 2 , E 3 represent H or C in aryl;
E 4 represents O, N, or NR 1 R 2 ;
R 1 , R 2 represent C1-6 alkyl;
E 5 represents N, O, or S;
E 6 represents H, NH, or NC1-6 alkyl.
2. The aryl hydrocarbon containing organic compound complexed or bound to the portion of the unfolded protein polypeptide chain of claim 1 , wherein the organic compound has the following structure formula:
Polymethine compounds
wherein R 1 represents H, halo, CO 2 H, NO 2 , SH, NR 5 R 6 , C1-6 alkyl, C1-6 alkoxy, cyano, carbonyl, pyrrolidinyl, pyrrolyl, pyrazolyl, imidazolyl, or triazolyl;
R 5 , R 6 represent H or C1-4 alkyl;
E 1 represents benzene ring or ring Q;
A represents CH or N;
D represents S, NH, N—C1-3 alkyl, O, or CH 2 ;
R 2 represents H, C1-4 alkyl, halo-C1-4 alkyl, OH, or cyano;
n represents an integer of 1-4;
E=benzene ring or ring Q′;
X represents CH or N;
Y represents S, NH, N—C1-3 alkyl, O, or CH 2 ;
R 3 =H, halo, CO 2 H, NO 2 , SH, NR 5 R 6 , C1-6 alkyl, C1-6 alkoxy, cyano, carbonyl, pyrrolidinyl, pyrrolyl, pyrazolyl, imidazolyl, or triazolyl.
3. The aryl hydrocarbon containing organic compound complexed or bound to the portion of the unfolded protein polypeptide chain of claim 1 , wherein the organic compound has the following structure formula:
Triarylmethane compounds
wherein X and Y represent H, NR 1 R 2 , sulfo, halo, CO 2 H, NO 2 , SH, C1-6 alkyl, or C1-6 alkoxy;
Z represents NR 1 R 2 , sulfo, CO 2 H, NO 2 , C1-6 alkyl, or C1-6 alkoxy;
R 1 , R 2 represent H, C1-6 alkyl, or sulfophenyl;
E 1 , E 2 , E 3 , E 4 , E 5 , E 6 represent H, sulfo, C1-6 alkyl, halo, CO 2 H, NO 2 , or SH.
4. The aryl hydrocarbon containing organic compound complexed or bound to the portion of the unfolded protein polypeptide chain of claim 1 , wherein the organic compound has the following structure formula:
Aryl azo compounds
wherein E 1 , E 2 , E 3 represent H, halo, sulfo, C1-6 alkyl, or C1-6 alkyl aryl;
R1 represents ring Q or ring Q′;
D represents H or NR 2 R 3 ;
R 2 , R 3 represent C1-6 alkyl or C1-6 alkyl aryl;
E represents H, OH, or C1-6 alkyloxy.
5. The aryl hydrocarbon containing organic compound complexed or bound to the portion of the unfolded protein polypeptide chain of claim 1 , wherein the organic compound has the following structure formula:
Xanthenes
wherein E 1 , E 2 , E 3 , E 4 represent H, NO 2 , OH, Halo, or C1-6 alkyl,
E 5 , E 6 represent H or Carbon in position 3 and oxygen in position 1 in group Q.
6. The aryl hydrocarbon containing organic compound complexed or bound to the portion of the unfolded protein polypeptide chain of claim 1 , wherein the organic compound has the following structure formula:
Thiazine
wherein E 1 represents N, O, or S;
E 2 , E 3 represent H or C in aryl;
E 4 represents O, N, or NR 1 R 2 ;
R 1 , R 2 represent C1-6 alkyl;
E 5 represents N, O, or S;
E 6 represents H, NH, or NC1-6 alkyl.