Calculation of Hydrodynamic Properties of Globular Proteins from Their Atomic-Level Structure

Abstract

The solution properties, including hydrodynamic quantities and the radius of gyration, of globular proteins are calculated from their detailed, atomic-level structure, using bead-modeling methodologies described in our previous article (, Biophys. J. 76:3044-3057). We review how this goal has been pursued by other authors in the past. Our procedure starts from a list of atomic coordinates, from which we build a primary hydrodynamic model by replacing nonhydrogen atoms with spherical elements of some fixed radius. The resulting particle, consisting of overlapping spheres, is in turn represented by a shell model treated as described in our previous work. We have applied this procedure to a set of 13 proteins. For each protein, the atomic element radius is adjusted, to fit all of the hydrodynamic properties, taking values close to 3 A, with deviations that fall within the error of experimental data. Some differences are found in the atomic element radius found for each protein, which can be explained in terms of protein hydration. A computational shortcut makes the procedure feasible, even in personal computers. All of the model-building and calculations are carried out with a HYDROPRO public-domain computer program.

Aggregation of a multidomain protein: A coagulation mechanism governs aggregation of a model IgG1 antibody under weak thermal stress

“…The hydrodynamic radius of the Rituximab monomer was fixed at R h,m ¼ 5.6 nm, a value measured in a 1 mg/mL Rituximab solution at ambient temperatures. This hydrodynamic size is in accordance with the value predicted by using the Hydropro software 53 on the crystal structure of an intact IgG1 mAb (PDB ID 1hzh). 54 Refractive index, refractive index increment, and viscosity…”

Domain structure of human complement C4b extends with increasing NaCl concentration: implications for its regulatory mechanism

“…The 100 best-fit atomistic models from each of the 137 and 250 mM NaCl analyses are available in Supplementary Material. Sedimentation coefficients s 20,w for the C4b crystal structure and best-fit scattering models were calculated directly from the atomic coordinates using the HYDROPRO shell-modelling program [35]. The default value of 0.31 nm for the atomic element radius for all atoms was used to represent the hydration shell.…”

Crystal Structure of Pyridoxal Biosynthesis Lyase PdxS from Pyrococcus horikoshii

“…MWGF1000-1KT). The Stokes radii of apoferritin, β-amylase, alcohol dehydrogenase, albumin, and carbonic anhydrase were calculated from the crystal structure (PDB IDs: 2W0O, 1FA2, 2HCY, 3V03, 1V9E, respectively) using HYDROPRO program (Garcia De La Torre et al, 2000).…”