An automated data processing and analysis pipeline for transmembrane proteins in detergent solutions

D. Molodenskiy; H. Mertens; D. Svergun

For a spherical (ellipticity, e = 1) detergent torus with the height (a) and cross-sectional axes (minor = b/e, major = b•e) equal to the length of a detergent tail (Tanford tail ), the geometrical parameters are set as: a = b = t = Tanford tail (28) (Figure 4) , where t is the thickness of the hydrophilic detergent head group. Although the hydrophobic tail of a detergent is typically slightly longer than its hydrophilic head, this assumption appears to be a reasonable first approximation for the further refinement. AMPP employs the MEMPROT minimization procedure, refining the starting parameters within a limited range, estimated empirically based on several tests conducted on different MPs. The a, b and t parameters are searched in the ± 1/3(Tanford tail ) range, while ellipticity and rotation parameters are kept fixed in order to speed up the computations. The hydrophobic radius of the model is taken as a + t = 2•Tanford tail , which is in a good agreement with the statistical mean value of transmembrane thickness D Transmemb ≈ 30 ±3 Å, obtained from the OPM database (36) (https://opm.phar.umich.edu/types/1). The maximum value of D Transmemb is checked during the modelling such that it does not exceed 45 Å.