Homology Modelling of Large Protein Complexes taking into account Electron Density Maps

Until now complex phenomena in proteins such as cooperativity and allosteric control, which originate from signal transduction within protein complexes, are poorly understood on a structural level. Although for cooperativity a lot of functional data and a well established theory exist, only little structural data are available to interpret them. The reason for this is that cooperativity and allosteric control are typically found in large protein complexes, whose structure is difficult to determine due to their size. Two established methods exist for structure determination of large protein complexes: X-ray structure determination and cryo-EM (electron microscopy) reconstruction. In principle X-ray structure determination can provide atomic detail. However with the technical abilities available today typically structures with resolutions of about 6 Å are obtained for very big protein complexes which is largely due to the quality of the crystals. Structures solved by cryo-EM reconstruction also mostly have resolutions of about 6 Å. To obtain pseudoatomic models of large protein complexes, which allow interpretation on a molecular level, structures of subunits are fitted into medium resolution (i.e. 6-10 Å) electron density maps. If possible the structures of the subunits are solved by X-ray structure determination or NMR with atomic resolution. If this does not work out homology models are calculated from sequence data and known similar structures. To obtain the structure of protein complexes the monomers are fitted into the electron density map by rigid body a fit. However, due to the rigid body fit it is almost inevitable that the resulting structure of the complex contains overlapping and tense parts, which need to by optimized in a subsequent step. Well established program packages (MODELLER, CHIMERA, CCP4, DIREX) are available for homology modeling as well as for the rigid body fit of (pseudo-)atomic structures into electron density maps and a subsequent flexible fit. For very big protein complexes these programs unfortunately are of only of limited use, since they have been developed and tested primarily for small and monomeric proteins The aim of this project is to develop a program package for very big protein complexes, which is especially suited for homology modelling and fit into electron density maps of this special set of proteins. Problems, which could occur in development of this program package, will be solved by improved algorithms, new parametrization and novel techniques for software.