. Author manuscript; available in PMC: 2011 Jan 1.

Published in final edited form as: J Chem Theory Comput. 2010 Jan 1;2010(6):910–929.

Table 1.

Survey of performed simulations. The sequence of the simulated molecules was unified to match the sequence used in the NMR study (see Materials and Methods and Supporting Information).

Organism	Simulated segment (original experimental numbering)	Simulation name	Resolution (Å) and pdb code	Length of simulation (ns)	RMSD ⁺(Å)	Force field
Standard MD simulations with net-neutralizing Na⁺ atmosphere

E.c.	996–1004, 1151– 1159	MD_Ec_99	3.5, 2AW4	350^*	4.4±1. 2	Parm99
E.c.	996–1004, 1151– 1159	MD_Ec_bsc0	3.5, 2AW4	100	2.3±0. 4	Bsc0
H.m.	1093–1101,1255– 1263	MD_Hm_99	2.4,1S72	250^**	3.5±1. 0	Parm99
H.m.	1093–1101,1255– 1263	MD_Hm_bsc0	2.4, 1S72	100	2.7±0. 5	Bsc0
D.r.	1007–1015, 1162– 1170	MD_Dr_99	3.1, 1NKW	200	4.8±0. 7	Parm99
D.r.	1007–1015, 1162– 1170	MD_Dr_bsc0	3.1, 1NKW	100	4.3±0. 8	Bsc0
T.t.	996–1004, 1151– 1159	MD_Tt_99	2.8, 2J01	200^**	2.4±0. 7	Parm99
T.t.	996–1004, 1151– 1159	MD_Tt_bsc0	2.8, 2J01	100	2.3±0. 5	Bsc0
E.c.	996–1004, 1151– 1159	MD_A5U^%	3.5, 2AW4	100	2.4±0. 5	Parm99
E.c.	996–1004, 1151– 1159	MD_A14U^&	3.5, 2AW4	100	2.2±0. 3	Parm99
H.m.	1093–1101,1255– 1263	MD_A14G_U4 C^@	2.4, 1S72	50	1.9±0. 4	Parm99
E.c.	996–1004, 1151– 1159	MD_nosalt^#	3.5, 2AW4	150	4.3±1. 0	Parm99
E.c.	996–1004, 1151– 1159	MD_400K^$	3.5, 2AW4	20	6.7±3. 2	Parm99
E.c.	996–1004, 1151– 1159	MD_400K^$$	3.5, 2AW4	20	5.1±2. 7	Parm99
E.c.	996–1004, 1151– 1159	MD_LES_Ec^~	3.5, 2AW4	80	4.2±1. 7	Parm99
N/A	1–18	MD_NMR_99	N/A, 2H49	200	1.6±0. 3	Parm99
N/A	1–18	MD_NMR_bsc 0	N/A, 2H49	100	1.2±0. 2	Bsc0
N/A	1–18	MD_NMR_rest r^##	N/A, 2H49	200	1.7±0. 3	Parm99
E.c.	1885–1893, 1849– 1857	MD_H68	3.5, 2AW4	100	3.9±0. 5	Parm99

Standard MD simulations in excess of KCl

E.c.	996–1004, 1151– 1159	MD_Ec_K1^x	3.5, 2AW4	100	2.1±0. 5	Parm99
E.c.	996–1004, 1151– 1159	MD_Ec_K2 ^x	3.5, 2AW4	100	2.0±0. 3	Bsc0
E.c.	996–1004, 1151– 1159	MD_Ec_K3^xx	3.5, 2AW4	100	2.9±0. 4	Parm99
N/A	1–18	MD_NMR_K ^x	N/A, 2H49	100	1.5±0. 3	Parm99

LES simulations

E.c.	996–1004, 1151– 1159	LES_Ec	3.5, 2AW4	60	6.7±2. 2	Parm99
D.r.	1007–1015, 1162– 1170	LES_Dr	3.1, 1NKW	40	5.9±1. 3	Parm99
T.t.	996–1004, 1151– 1159	LES_Tt	2.8, 2J01	40	6.4±1. 3	Parm99
H.m.	1093–1101,1255– 1263	LES_Hm	2.4, 1S72	40	6.4±2. 0	Parm99

⁺

RMSD values are calculated along the trajectory for the individual snapshots with respect to the starting structure.

Due to disruption of the structure we considered only 0–300 ns trajectory portion in the analyses.

^**

Due to disruption of the structure we considered only 0–150 ns in the analyses.

Simulation run with A5U mutation.

Simulation run with A14U mutation.

Simulation run with A14G and U4C mutations.

Simulation run under no-salt condition.

Simulation run at 400K (NVT).

^$$

simulation run at 400K (NPT).

Standard MD simulation that started from the NMR-like conformation observed in the LES_Ec simulation.

^##

Simulation run with restraint, which enforced direct A(N1)-U(O2´) H-bond of the cWS A/U base pair (instead of the water-mediated one) for 10 ns.

Simulation run with Dang’s parameters for K⁺ and Cl⁻ (see Materials and Methods).

^xx

Simulation run with Joung and Cheatham’s parameters for K⁺ and Cl⁻ (see Materials and Methods).