Dynamical Aspects of Biomacromolecular Multi-resolution Modelling Using the UltraScan Solution Modeler (US-SOMO) Suite

Abstract

Notwithstanding the continuous technological advancements in the current high-resolution methods (X-ray crystallography/NMR), an exhaustive list of every relevant biological structure and of its complexes with every partner remains a far fetched goal. Furthermore, dynamical aspects, from local or large scale flexibility, to conformational changes following interactions/binding, to supramolecular structures formation, are not easily amenable to high-resolution analysis. A host of intermediate-resolution techniques are, however, available to complement the higher resolution data, like cryo-electron microscopy and electron tomography, while small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) are in addition capable to monitor the evolution of structural changes in solution. Since the above-mentioned techniques can provide 3D envelopes at ~10–20 A resolution, a typical task involves placing the atomic structures of the components inside the envelope or to optimize their arrangement to fit experimental scattering data. Single-valued parameters provided by low-resolution techniques, such as the radius of gyration R g , the translational diffusion coefficient D t , the sedimentation coefficient s, the Stokes radius R s , the rotational correlation time τ c , and the intrinsic viscosity (η), can be also utilized to screen/confirm potential spatial arrangements of modules/domains, or to monitor their overall conformational changes. The UltraScan SOlution MOdeler (US-SOMO) suite of computer programs was developed for the computation of the solution properties of biomacromolecules starting from their atomic resolution structures, and their comparison with experimental data. In this brief review, its use with respect to dynamical aspects in multi-resolution modeling, including conformational variation and flexibility issues, is discussed.