Comparative modeling of giant annelid hemoglobins

Abstract

The information provided by small-angle X-ray scattering, electron microscopy and hydrodynamics for the giant hemoglobins from different annelid species (Lumbricus terrestris, Macrobdella decora,Eudistylia vancouverii) has been compared. The results reveal that these hemoglobins exhibit slight differences in their fine structure, particularly with respect to the presence of a cavity in the central part of the proteins. Results have been obtained by application of several advanced modeling strategies. The low-resolution shape and internal structure of the hemoglobins under analysis were restored ab initio from experimental small-angle scattering data by means of the program DAMMIN using simulated annealing. To improve the results, however, the strict ab initio modeling approach had to be replaced with a procedure which exploited additionally the knowledge of symmetry and anisometry of the proteins. Moreover, 3D reconstructions from electron microscopy were advantageously used as templates for the analysis of scattering data by DAMMIN. For all the models obtained, hydrodynamic data (s, D) were predicted by use of the program HYDRO and compared to literature data. In all cases satisfactory agreement between observed and predicted values could be achieved. The results led to consensus models for the various hemoglobins.

Acknowledgements. The authors are much obliged to F. de Haas and J.-C. Taveau for providing the 3D reconstructions of the annelid hemoglobins analyzed, and to D.I. Svergun, J. Garcia de la Torre, and R.A Sayle for use of the programs DAMMIN and GNOM, HYDRO, and RASMOL, respectively. A.K. is thankful to the Austrian Academy of Sciences for supporting the project.