Elucidation of Novel Structural Scaffold in Rohu TLR2 and Its Binding Site Analysis with Peptidoglycan, Lipoteichoic Acid and Zymosan Ligands, and Downstream MyD88 Adaptor Protein

Table 5

Molecular interaction of rohu TLR2-ECD with ligands.

(a) Docking analysis of TLR2-ECD with PGN, LTA, and zymosan by AutoDock 4.0

Grid centre and ligand	Interacting residues	Binding energy kcal/mol	No. of H-bonds^a
PGN-I (B5)	Tyr366, Thr395, Asn397, Ser399, Tyr421, Asn423, Ser425, His426, Asn446, Ser448, Ser449, Asp467, Glu470, Thr497	−4.29	6
PGN-I (B6)	Ser259, Ser285, Tyr286, His312, Thr313, Arg342, Ser344, Tyr366	−4.33	6
PGN-DAP (B5)	Asp368, Leu369, Ser370, Gln371, Asn397, Ser399, Gln400, Tyr421, Asp423, Ser425, His426, Asn446, Ser448, Ser449, Asp467, Ser469, Glu470, Thr489	−3.19	11
PGN-DAP (B6)	Thr246, Glu254, Gly255, Lys258, Leu276, Thr277, Met279, Asp280, Gly281, Ser282, Ser283, Leu284, Ser304, Tyr305, Thr306, His307, Tyr308, Glu309	−3.38	7
LTA sites	Glu323, Phe324, Phe325, Glu326, Met330, Met331, Phe335, Thr349, Val350, Phe351, Val352, Ile353, Pro354, Pro355, Ile356, Leu360, Asn372, Leu373, Leu374, Pro381	−1.92	1
Zymosan	Leu473, Thr474, Val475, Phe476, Asn477, Thr495, Leu496, Pro497, His498, Gly499, Glu500, Leu501, Ser520, Ser521, Asp522, Arg525	−7.55	13

aHydrogen bonds.

(b) Docking analysis of TLR2-ECD with PGN, LTA, and zymosan by FlexX 2.1

Ligands	Interacting residues	Binding energy kcal/mol	No. of H-Bonds^a
PGN-I	Asn397, Ser399, Gln400, Asn401, His426, Ser428, Lys451, Glu470	−18.85	18
PGN-II	Ser428, Phe429, Val430, Ser448, Lys451, Arg453, Lys454, Asp472, Ser469, Gln470	−12.80	14
PGN-DAP	Gln400, Asn401, His426, Ser428, Ser449, Lys451	−15.47	15
LTA	Asn318, Leu319, Asp320, Ile321, Phe324, Asn347, Gly348, Thr349, Val350, Gln371	−6.92	13
Zymosan	Arg492, Leu493, Met494, Leu496, Arg516, Met517, Ser520, Asp522	−13.81	10

aHydrogen bonds.

(c) Docking analysis of TLR2-ECD with PGN, LTA, and zymosan by GOLD 4.1

Ligands	Interacting residues	GOLD fitness score	No. of H-Bonds^a
PGN-I (B5)	Ile394, Asn397, Ser399, Gln400, Tyr421, Asp423, Ser425, His426, Asn446, Ser448, Ser449, Asp467, Ser469, Glu470, Thr489, Gly490, Glu511, Arg512	42.38	17
PGN-II (B5)	Tyr366, Asp368, Ser370, Gln371, Asn397, Ser399, Gln400, Tyr421, Ser425, Asn446, Ser448, Val465, Asp467, Ser469, Glu470, Thr489, Gly490, Arg512	44.01	20
PGN-DAP (B5)	Asn446, Ser448, Ser449, Asp467, Ser469, Glu470, Ile487, Thr489, Gly490, Gln511, Arg512	40.55	13
PGN-II (B6)	Thr246, Glu247, Pro248, Phe249, Lys250, Thr252, Thr277, Asp280, Ser304, Tyr305, Thr306, His307, Tyr308,	23.00	8
LTA	Leu319, Asp320, Ile321, Phe324, Phe327, Met330, Met331, Phe335, Gly348, Thr349, Val350, Phe351, Glu380, Pro381	44.65	4
Zymosan	Arg492, Leu493, Met494, Thr495, Leu496, Ala514, Leu515, Arg516, Met517, Phe518, Asn519, Ser520, Ser521, Asp522, Arg525	39.71	8

aHydrogen bonds.