Table 1.
List of simulations
| Simulation name | Source PDBa | #Hfq | #RNA | #Crc | Number of simulations × length (μs) |
|---|---|---|---|---|---|
| Quaternary complex simulations | |||||
| 2Hfq_2Crc_2RNA | 6o1k | 2 | 2 | 2 | 1 × 5, 2 × 1 |
| 2Hfq_3Crc_2RNA | 6o1l | 2 | 2 | 3 | 2 × 1 |
| 2Hfq_4Crc_2RNA | 6o1m | 2 | 2 | 4 | 1 × 5, 1 × 1 |
| 2Hfq_4Crc_2RNA_AA-synb | 6o1m | 2 | 2 | 4 | 2 × 5, 1 × 1 |
| Hfq_Crc1_RNAc | 6o1k | 1 | 1 | 1 | 2 × 2 |
| Hfq_Crc2_RNAc | 6o1k | 1 | 1 | 1 | 2 × 2 |
| Hfq_2Crc_RNA | 6o1k | 1 | 1 | 2 | 2 × 1 |
| 2Hfq_4Crc_2RNA_noHBfixd | 6o1m | 2 | 2 | 4 | 1 × 1 |
| Quaternary complex simulations–modified systems | |||||
| 2Hfq_2Crc_2RNA_G18Ce | 6o1k | 2 | 2 | 2 | 2 × 1 |
| 2Hfq_2Crc_2RNA_circe | 6o1k | 2 | 2 | 2 | 2 × 1 |
| 2Hfq_2Crc_2RNA_exte | 6o1k | 2 | 2 | 2 | 2 × 1 |
| Other simulations | |||||
| Hfq_RNA | 6o1k | 1 | 1 | 0 | 1 × 15, 2 × 1 |
| Hfq_RNA_allGRf | 6o1k | 1 | 1 | 0 | 1 × 10, 2 × 2 |
| Hfq_RNA_I30Ae | 6o1k | 1 | 1 | 0 | 2 × 1 |
| Hfq_RNA_pol-Ag | 3gib | 1 | 1 | 0 | 1 × 2 |
| 2Crc | 6o1k | 0 | 0 | 2 | 2 × 1 |
| 2Crc_4jg3 | 4jg3 | 0 | 0 | 2 | 2 × 1 |
| 4Crc | 6o1m | 0 | 0 | 4 | 1 × 2 |
| Hfq_RNA_noHBfixd | 6o1k | 1 | 1 | 0 | 2 × 2 |
| Hfq_RNA_2×HBfixh | 6o1k | 1 | 1 | 0 | 1 × 2 |
Crc, catabolite repression control; PDB, Protein Data Bank.
PDB ID of the experimental structure which was utilized as the initial structure. In some simulations, only selected parts of the experimental structure were used (see Selection of initial structures and Fig. S1).
All bases of the “A” nucleotides within the ARN repeats were modified to be in syn conformation before the simulation start.
Crc1 and Crc2 refer to the Crc proteins that bind near and away from G18, respectively (Fig. S1).
Simulations were done without the HBfix (see System building and simulation protocol and Supporting information).
In “G18C”, “circ”, “ext”, or “I30A” simulations, the G18 nucleotide of the RNA was replaced with C18, the RNA chain was circularized by covalently connecting the 5′- and 3′-nucleotides via a newly modeled phosphate, the RNA was extended from its 3′-end by adding nucleotides U19 and G20, or I30 was mutated into alanine, respectively.
All the “R” nucleotides within the ARN repeats were modified to be guanosines.
A circular polyadenine RNA octadecamer was bound to Hfq.
HBfix with 2 kcal/mol penalty was utilized (see System building and simulation protocol and Supporting information).