Prediction of hydrodynamic and other solution properties of rigid proteins from atomic- and residue-level models

Abstract

Here we extend the ability to predict hydrodynamic coefficients and other solution properties of rigid macromolecular structures from atomic-level structures, implemented in the computer program HYDROPRO, to models with lower, residue-level resolution. Whereas in the former case there is one bead per nonhydrogen atom, the latter contains one bead per amino acid (or nucleotide) residue, thus allowing calculations when atomic resolution is not available or coarse-grained models are preferred. We parameterized the effective hydrodynamic radius of the elements in the atomic- and residue-level models using a very large set of experimental data for translational and rotational coefficients (intrinsic viscosity and radius of gyration) for >50 proteins. We also extended the calculations to very large proteins and macromolecular complexes, such as the whole 70S ribosome. We show that with proper parameterization, the two levels of resolution yield similar and rather good agreement with experimental data. The new version of HYDROPRO, in addition to considering various computational and modeling schemes, is far more efficient computationally and can be handled with the use of a graphical interface.

Figure 1

Values of 100Δ_X and 100Δ as a function of the radius of elements in the PHM, a, calculated for small and medium-sized proteins, with the WHOLE set of experimental data. (a) Atomic-level PHM, HYDROPRO shell calculation. (b) Residue-level PHM, HYDROPRO shell calculation. (c) Residue-level PHM, HYDRO bead-model calculation.

Figure 2

Representation of the values calculated by HYDROPRO shell-model from the Cα coordinates (y axis) versus experimental values (x axis) of the four equivalent radii employed in this work, for the WHOLE set of proteins as well as the large proteins and macromolecular complexes.