Biological solution scattering: recent achievements and future challenges

Abstract

In the post-genomic age it is apparent that as structures of larger macromolecules and their complexes are investigated, structure-function investigations are often confronted with the necessity to apply a portfolio of tools for biochemical and biophysical characterization. A survey of the published literature over the last decade reveals that publications in the area of structural biology employing neutron or X-ray scattering as one of their techniques tripled since 1995. Yet, taken as a whole, the contribution from smallangle scattering (SAS) to research papers dealing with structural analyses is still only of the order of 1% in 2005 (for comparison, less than 0.5% in 1995). Nevertheless, the last few years saw stimulating biological applications and analysis procedures which emphasize the growing potential of SAS applications for the structural studies of macromolecules in solution. The usage of SAS largely consists of low-resolution reconstructions of molecules with partial or without presumption of structural details, consistency analysis of high-resolution crystallographic structures and their corresponding low-resolution models determined in the solution state, and rigid-body refinement of multi-subunit assemblies including complexes and full-length multidomain proteins. Complementary structural information obtained from SAS in conjunction with data acquired by protein crystallography, NMR, molecular dynamics or computational docking provides a means to link low-and high-resolution models essential for the elucidation of biomolecular organization, interactions and function. The capabilities as well as limitations of determining low-resolution structures of multidomain proteins, macromolecular complexes and assemblies are highlighted in three examples. The first example is the characterization of the conformation of the PDZ region of SAP97, a multidomain protein involved in the regulation and localization of membrane receptor molecules. The second example is the characterization of the structural features of the TIM10 complex, an escort molecule for mitochondrial inner-membrane proteins, and the third example is the description of the shape and pH-induced conformational transition of a full-length bacterial potassium channel. The latter two in particular benefited from neutron scattering with contrast variation by using H-D labelling of the macromolecular complex or the solvent, respectively.

Reconstructing three-dimensional shape envelopes from time-resolved small-angle X-ray scattering data

“…Data from techniques such as electron microscopy, which produces images but not scattering curves, are also hard to compare. Finally, there have been recent efforts to combine low-resolution data, atomic resolution data and computer modeling to maximize the information gained from each technique (Grossmann, 2007;Suhre et al, 2006). Timeresolved reconstructions used in conjunction with these techniques will provide deeper insight into the changes that take place in a molecule.…”

“…In addition, these ab initio algorithms allow users to propose molecular shapes without relying on previous knowledge. These reconstruction programs have produced shape envelopes for many proteins (Svergun & Koch, 2002;Grossmann, 2007) and nucleic acids (Nö llmann et al, 2004;Funari et al, 2000), enabling straightforward comparison between SAXS measurements and structural models.…”

Synchrotron radiation studies of non-crystalline systems

“…79 X-ray solution scattering results can also usefully be combined with those of sedimentation and viscometry 80 as shown for the human pyruvate dehydrogenase complex 81 or for PEGylated antibody fragments. 82 SAXS results have been reviewed by various authors during the past two years [83][84][85][86] and descriptions of the most popular data analysis and modelling software are also available. 87 In the simplest applications the contribution of SAXS to structural studies lies in the verification of the similarity between the models and those obtained by crystallography, [88][89][90][91][92][93][94] nuclear magnetic resonance (NMR), as in the case of the Josephin domain of ataxin-3, 95 or homology modelling, as for the natural killer inhibitory receptor Irp60.…”

Multiscale simulation of surfactant–aquaporin complex formation and water permeability

“…Because membrane proteins and surfactant molecules have distinctly different electron densities, their complex formation makes the analysis of SANS or SAXS data extremely difficult. 11 Recently, Berthaud et al reported that, at adequate conditions, n-dodecyl-b-D-maltopyranoside molecules and aquaporins form an elliptical, toroid-shaped corona in an aqueous solution. The shape of the protein-surfactant complex was deduced from complementary results from size exclusion chromatography, SAXS, refractometry experiments and coarsegrained modelling.…”