TABLE 1.
Comparison of RNA binding to ProQ, ProQNTD, and FinO proteins
| 32P-RNA | Kd (nM) (max. fraction bound %) | ||
|---|---|---|---|
| ProQ | ProQNTD | FinO | |
| malM-3′ | 27 ± 12 (91%) | 5.8 ± 0.7 (80%) | >200 (15%) |
| FinP | 79 ± 18 (85%) | 19 ± 6 (44%) | 110 ± 16 (76%) |
| malM-FinP | 78 ± 22 (91%) | >200 (23%) | 86 ± 17 (82%) |
| FinP-malM | 25 ± 6.7 (79%) | 5.3 ± 1.5 (62%) | 280 ± 110 (57%) |
| malM-A-GU6 | n.m. | 1.9 ± 0.59 (56%) | 150 ± 40 (59%) |
| malM-A-GAU5 | 160 ± 30 (64%)a | >200 (21%) | 130 ± 18 (73%) |
| FinP-U-UAU4 | n.m. | 6.2 ± 3.1 (78%) | 200 ± 73 (60%) |
| FinP-U-U6 | 37 ± 5.4 (75%)a | 9.4 ± 4.5 (82%) | 170 ± 45 (68%) |
| cspE81-3′ | 37 ± 7.1 (91%)a | 2.4 ± 0.27 (85%) | >200 (10%) |
| cspE81-FinP | n.m. | 4.9 ± 0.32 (61%) | 88 ± 39 (74%) |
| cspE81-FinP-stem | 130 ± 34 (85%)a | >200 (37%) | 56 ± 16 (72%) |
| RepX | >1000 (29%)a | >200 (6%) | 61 ± 23 (86%) |
| RepX-malM | n.m. | 3.2 ± 1.6 (62%) | 150 ± 67 (77%) |
| malM-RepX | 61 ± 29 (67%)a | >200 (8%) | 180 ± 93 (55%) |
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The Kd values were obtained by fitting the quadratic equation into binding data. The average Kd values with standard deviations were calculated from at least three independent experiments. When the fraction bound at the highest protein concentration used was lower than 40%, the Kd value was estimated as higher than 200 nM for FinO and ProQNTD, or higher than 1000 nM for ProQ. (n.m.) Not measured.
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aThe Kd values are calculated based on the data provided in Supplemental Figure S9.
