Calculation of the hydrodynamic radius of H-NS species

The 3D structures of different forms of H-NS namely, ^mCheH-NS dimer, ^mCheH-NSΔs2 dimer and ^mCheH-NS multimers were built using PyMol and Swiss Model (59) based on PDB entries 3NR7, 2L93 and 5FHV WinHYDROPRO 1.0 (GUI) was used to calculate the hydrodynamic radius using the translational diffusion coefficient (Dt) for each structure modeled (60). HYDROPRO uses the coordinates from the PDB file at the atomic as well as residue level. The program also needs simple supplementary data such as temperature, molecular weight and the type of calculation. The type of calculation was set to the atomic level with the AER value of 2.9 Å, as recommended by the developers when using atomic level shell calculation. The solution viscosity was set to 0.01, adapted for non-viscous aqueous buffers (60). The protein molecular weight was calculated using the protein sequence by ProtParam (61). Based on this input, WinHydroPro produced the value for the radius of gyration (R_g), but not the hydrodynamic radius. We calculated the hydrodynamic radius with the help of translational diffusion coefficient provided by the WinHydroPro output. The translational diffusion coefficient (Dt) is expressed as Dt = kT/f (where f is the friction coefficient, k is the Boltzmann constant and T is temperature (in K). The formula to calculate the hydrodynamic radius using the diffusion coefficient can be expressed by R_H = kT/6*π*η*Dt (where π = 3.14, k = Boltzman constant (1.38064852 × 10⁻²³ m² kg s⁻² K⁻¹), temperature = 293 K and η = 0.01 Pa s (viscosity)) (3). The values of R_H were calculated for all the models using the above equation.