Determination of multi-component protein structures in solution using global orientation and shape restraints

摘要

Determining architectures of multi-component proteins or protein complexes in solution is a challenging problem. Here we report a methodology that simultaneously uses residual dipolar couplings (RDC) and the small-angle X-ray scattering (SAXS) restraints to mutually orient subunits and define the global shape of multi-component proteins and protein complexes. Our methodology is implemented in an efficient algorithm and demonstrated using five examples. First, we demonstrate the general approach with simulated data for the HIV-1 protease, a globular homodimeric protein. Second, we use experimental data to determine the structures of the two-domain proteins L11 and γD-crystallin, in which the linkers between the domains are relatively rigid. Finally, complexes with Kd values in the high micro- to millimolar range (weakly associating proteins) such as a homodimeric GB1 variant and with Kd valus in the nano-molar range (tightly bound) such as the heterodimeric complex of the ILK ankyrin repeat domain (ARD) and PINCH LIM1 domain, respectively, are evaluated. Furthermore, the proteins or protein complexes that were determined using this method exhibit better solution structures than those obtained by either NMR or X-ray crystallography alone as judged based on the pair-distance distribution functions (PDDF) calculated from experimental SAXS data and back-calculated from the structures