Intermolecular correlations are necessary to explain diffuse scattering from protein crystals.

Ariana Peck,Thomas J. Lane,Frédéric Poitevin

doi:10.1107/s2052252518001124

Ariana Peck, Thomas J. Lane + Show 1 more

Open Access

https://doi.org/10.1107/s2052252518001124

Copy DOI

Abstract

Conformational changes drive protein function, including catalysis, allostery and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to advance our understanding of biological dynamics. However, recent work has challenged this prevailing view, suggesting instead that diffuse scattering primarily originates from rigid-body motions and could therefore be applied to improve structure determination. To investigate the nature of the disorder giving rise to diffuse scattering, and thus the potential applications of this signal, a diverse repertoire of disorder models was assessed for its ability to reproduce the diffuse signal reconstructed from three protein crystals. This comparison revealed that multiple models of intramolecular conformational dynamics, including ensemble models inferred from the Bragg data, could not explain the signal. Models of rigid-body or short-range liquid-like motions, in which dynamics are confined to the biological unit, showed modest agreement with the diffuse maps, but were unable to reproduce experimental features indicative of long-range correlations. Extending a model of liquid-like motions to include disorder across neighboring proteins in the crystal significantly improved agreement with all three systems and highlighted the contribution of intermolecular correlations to the observed signal. These findings anticipate a need to account for intermolecular disorder in order to advance the interpretation of diffuse scattering to either extract biological motions or aid structural inference.

Highlights

X-ray diffraction images from macromolecular crystals frequently exhibit a diffuse background between and beneath the Bragg peaks (Wall, Adams et al, 2014; Welberry & Weber, 2016)
We found that multiple models of intramolecular conformational dynamics were unable to explain the observed diffuse scattering in all three systems
Our results call into question the practice of directly using a diffuse scattering map for either resolution extension or iterative phasing in cases that exhibit enhanced scattering at reciprocal-lattice positions, a feature observed in all three systems we studied and one that we have no physical or theoretical grounds to mask or model separately from the remainder of the diffuse signal

Summary

Introduction

X-ray diffraction images from macromolecular crystals frequently exhibit a diffuse background between and beneath the Bragg peaks (Wall, Adams et al, 2014; Welberry & Weber, 2016). In contrast to the Bragg reflections, which arise from coherent diffraction across the crystal, this diffuse signal results from disorder-induced incoherent diffraction. On the other hand, correlated disorder produces anisotropic diffuse scattering features whose spacing and intensity in reciprocal space are respectively determined by the length scale and amplitudes of the correlated atomic displacements involved (Benoit & Doucet, 1995). Diffuse scattering has routinely been cited as one such method that could provide unique insights into the collective motions responsible for biological functions

Methods

Results

Discussion

Conclusion