Table 2.

Summary of pathways observed in RAMD simulations of the leucine transporter. Setups correspond to those listed in Table 1. Pathway clusters are identified as intracellular (I) or extracellular (E), followed by a number denoting a specific pathway. After analysis, each pathway was assigned to one of two recurring pathways observed: along TMs 6b/8 or along TMs 1a/6b. Observation of sodium movement (Na1 in all cases) with leucine is indicated, as well as how many paths belong to the cluster. Observed residues interacting via hydrogen bonding for each pathway cluster are listed. Note that the residue list omits binding pocket residues (as described in Yamashita et al.:¹² N21, A22, L25, G26, V104, Y108, F252, F253, S256, F259, S355, I359) for clarity. A complete list can be found in supporting information.

Setup	Path	TMs	Na?	# Times	Residues
R1	E1	–	No	7	6T254
	I1	6b/8	Yes	14	il1T77, 6T254, 6G260, 6A261, 6T264, 8A358, 12L500
	I2	1a/6b	No	14	1R5, 6T254, 6G260, 6T264, 6S267, 6Y268, 8A358, 8Q361
R2	I1	1a/6b	Yes	8	2E62, 2W63, 6T254, 6L255, 7D274
	I2	1a/6b	No	9	2W63, 6T254, 6L255, 7Q273
R3	I1	6b/8	Yes	31	1G24, 1N27, il1G73, il1H74, 6T254, 6A261, 6T264, 6Y265, 6Y268
R4	I1	1a/6b	Yes	9	6T254, 6T264
	I2	1a/6b	No	23	il1G73, il1G75, il1T76, 6T254, 6T264, 6Y265, 8E368
R5	I1	1a/6b	Yes	24	2W63, 6T254, 6R270, 6T264, 6Y265, 8E360
	I2	1a/6b	No	18	6T254, 6R270, 7Q273