Journal: ACS Comb Sci / Year: 2018 Title: A General Small-Angle X-ray Scattering-Based Screening Protocol Validated for Protein-RNA Interactions. Authors: Po-Chia Chen / Pawel Masiewicz / Vladimir Rybin / Dmitri Svergun / Janosch Hennig / Abstract: We present a screening protocol utilizing small-angle X-ray scattering (SAXS) to obtain structural information on biomolecular interactions independent of prior knowledge, so as to complement ...We present a screening protocol utilizing small-angle X-ray scattering (SAXS) to obtain structural information on biomolecular interactions independent of prior knowledge, so as to complement affinity-based screening and provide leads for further exploration. This protocol categorizes ligand titrations by computing pairwise agreement between curves, and separately estimates affinities by quantifying complex formation as a departure from the linear sum properties of solution SAXS. The protocol is validated by sparse sequence search around the native poly uridine RNA motifs of the two-RRM domain Sex-lethal protein (Sxl). The screening of 35 RNA motifs between 4 to 10 nucleotides reveals a strong variation of resulting complexes, revealed to be preference-switching between 1:1 and 2:2 binding stoichiometries upon addition of structural modeling. Validation of select sequences in isothermal calorimetry and NMR titration retrieves domain-specific roles and function of a guanine anchor. These findings reinforce the suitability of SAXS as a complement in lead identification.
Instrument name: PETRA III P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 3 mm
Detector
Name: Pilatus 2M
Scan
Title: Wild-type Protein sex-lethal / Measurement date: Oct 16, 2016 / Storage temperature: 10 °C / Cell temperature: 25 °C / Exposure time: 0.045 sec. / Number of frames: 20 / Unit: 1/nm /
Min
Max
Q
0.0201
3.78
Distance distribution function P(R)
Sofotware P(R): GNOM 4.5a / Number of points: 433 /
Min
Max
Q
0.3052
3
P(R) point
1
433
R
0
6.868
Result
Type of curve: single_conc
Experimental
Standard
Standard error
Porod
MW
16.07 kDa
16.075 kDa
3.21
15.3 kDa
Volume
-
-
-
26.02 nm3
P(R)
P(R) error
Guinier
Guinier error
Forward scattering, I0
1186
8.6
1190.6
6.6
Radius of gyration, Rg
1.99 nm
0.02
1.97 nm
0.1
Min
Max
D
-
6.87
Guinier point
29
308
+
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