Prediction of hydrodynamic parameters of Lumbricus terrestris hemoglobin from small-angle X-ray and electron microscopic structures

Abstract

The 3.5-MDa extracellular hemoglobin from Lumbricus terrestris is a giant heteromultimeric hexagonal bilayer complex. The consensus model of the complex as derived from small-angle X-ray scattering (SAXS) and a 3D reconstruction obtained from cryoelectron microscopy (EM) were used as bases for the prediction of hydrodynamic parameters (sedimentation coefficient, s, diffusion coefficient, D, and intrinsic viscosity, [η]) by the bead modeling approach implemented in Garcia de la Torre’s program HYDRO. Since the number of beads in the initial EM and SAXS models was too high, appropriate data reduction had to be performed. For this purpose, the original hexagonal structures were mapped into a hexagonal grid to maintain symmetry details. Thereby the initial models, consisting of up to 23,000 beads of equal size and unequal density, were transformed to reduced models of about 500 beads of unequal size but equal density. A comparison of the results obtained for the various models reveals good agreement between predicted and experimental hydrodynamic parameters s and D, provided the models refer to hydrated volumes. In an alternative modeling approach, low-resolution models were generated directly by applying the genetic algorithm (GA) implemented in the program DALAI_GA2 by Chacon et al. to the experimental SAXS curve of L. terrestris hemoglobin and, for the purpose of testing, to the SAXS curve calculated from the initial hydrated EM model. While the resulting GA models are of peculiar shape and certainly without physical relevance, they nevertheless provide perfect fits to the experimental scattering functions and good predictions for s and D.