Combined Approaches to Study Virus Structures

Abstract

A virus particle must work as a safe box for protecting its genome, but at the same time it has to undergo dramatic conformational changes in order to preserve itself by propagating in a cell infection. Thus, viruses are miniaturized wonders whose structural complexity requires them to be investigated by a combination of different techniques that can tackle both static and dynamic processes. In this chapter we will illustrate how major structural techniques such as X-ray crystallography and electron microscopy have been and can be combined with other techniques to determine the structure of complex viruses. The power of these hybrid method approaches are revealed through the various examples provided.

From lows to highs: using low-resolution models to phase X-ray data

“…EM, SAXS and X-ray crystallography provide structural information at different but overlapping resolution ranges (Johnson, 2008;Steven & Baumeister, 2008;Badia-Martinez et al, 2013;Fig. 2).…”

“…Since molecular replacement works by the cross-correlation of Patterson vectors, either three-dimensional atomic models or electron-density maps can be given as search models. Thus, any structural information obtained by SAXS, EM, X-ray crystallography and NMR can, in theory, be used (for more discussion on how a one-dimensional tool such as SAXS can lead to three-dimensional results, see Svergun & Koch, 2002;Badia-Martinez et al, 2013). Undeniably, the original successes in virus phasing using unrelated virus structures boosted confidence in phasing high-resolution X-ray data from low-resolution models.…”

“…Recently, EM and X-ray crystallography have taken the leading role in the development of hybrid methods (Chiu & Smith, 1994;Rossmann, 2000;Gilbert et al, 2003;Rossmann et al, 2005;Johnson, 2008;Steven & Baumeister, 2008), although useful techniques now also include nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS). Together, these methods are helping to realise a vision of the cellular landscape spanning a continuum in the å ngströ m to nanometre resolution range (Badia-Martinez et al, 2013).…”