Acta Crystallographica Section D

Biological Crystallography

Volume 69, Part 6 (June 2013)

research papers

Acta Cryst. (2013). D69, 946-959    [ doi:10.1107/S0907444913003454 ]

Resolution of structural heterogeneity in dynamic crystallography

Z. Ren, P. W. Y. Chan, K. Moffat, E. F. Pai, W. E. Royer Jr, V. Srajer and X. Yang

Abstract: Dynamic behavior of proteins is critical to their function. X-­ray crystallography, a powerful yet mostly static technique, faces inherent challenges in acquiring dynamic information despite decades of effort. Dynamic `structural changes' are often indirectly inferred from `structural differences' by comparing related static structures. In contrast, the direct observation of dynamic structural changes requires the initiation of a biochemical reaction or process in a crystal. Both the direct and the indirect approaches share a common challenge in analysis: how to interpret the structural heterogeneity intrinsic to all dynamic processes. This paper presents a real-space approach to this challenge, in which a suite of analytical methods and tools to identify and refine the mixed structural species present in multiple crystallographic data sets have been developed. These methods have been applied to representative scenarios in dynamic crystallography, and reveal structural information that is otherwise difficult to interpret or inaccessible using conventional methods.

Keywords: dynamic crystallography; structural heterogeneity.

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Graphic Interchange Format (GIF) image (7265.5 kbytes)
[ doi:10.1107/S0907444913003454/lv5027sup1.gif ]
Simulation of structural heterogeneity in a crystal: simulation of the hypothetical reaction described in Fig. 1. The array of dots represent protein molecules in a crystal lattice. Their colors indicate the distinct structural states. Fractional concentrations of various states are displayed in the color bar. This simulation shows that molecules convert from one state to the next in a random thermodynamic fashion independently of one another, even when the reaction of each molecule is synchronously initiated (Moffat, 2001) at the same time point 0. The rates of the reaction steps govern when the concentration of each state will rise, peak and fall, and what concentration each state can reach. The reaction in one molecule is not tied to those in any other molecules by any force. Heterogeneity is intrinsic during any dynamic processes. This is true in both crystalline and solution states. A non-ideal experimental initiation of the reaction can only contribute further to heterogeneity.


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