Table 1.
Free Protein | Simulation Length | Portion of Simulation Selected for Analysis | # Snapshots for MM-PB(GB)SA/NMode Analysis |
---|---|---|---|
Wild type U1A (closed) | 5 ns | 2 − 5 ns | 150/150 |
F56A U1A (closed) | 5 ns | 3 − 5 ns | 100/100 |
F56L U1A (closed) | 5 ns | 2 − 5 ns | 150/150 |
F56W U1A (closed) | 5 ns | 2 − 5 ns | 150/150 |
Wild type U1A (open) | 5 ns | 3 − 5 ns | 100/100 |
F56A U1A (open) | 3 ns | 0.5 − 3 ns | 125/125 |
F56L U1A (open) | 3 ns | 0.5 − 3 ns | 125/125 |
F56W U1A (open) | 3 ns | 0.5 − 3 ns | 125/125 |
Free RNA |
|||
Stem loop 2 RNA | 32 ns | 8 − 32 ns | 1200/120 |
Protein-RNA Complex |
|||
Wild type U1A-RNA | 3 ns | 0.5 − 3 ns | 125/125 |
F56A U1A-RNA | 3 ns | 0.5 − 3 ns | 125/125 |
F56L U1A-RNA | 3 ns | 0.5 − 3 ns | 125/125 |
F56W U1A-RNA | 3 ns | 0.5 − 3 ns | 125/125 |