Helical ensembles outperform ideal helices in molecular replacement.

Filomeno Sánchez Rodríguez,Owen R Davies,Daniel J Rigden,Adam J Simpkin,Ronan M Keegan

doi:10.1107/s205979832001133x

Filomeno Sánchez Rodríguez, Owen R Davies + Show 3 more

Open Access

https://doi.org/10.1107/s205979832001133x

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Abstract

The conventional approach in molecular replacement is the use of a related structure as a search model. However, this is not always possible as the availability of such structures can be scarce for poorly characterized families of proteins. In these cases, alternative approaches can be explored, such as the use of small ideal fragments that share high, albeit local, structural similarity with the unknown protein. Earlier versions of AMPLE enabled the trialling of a library of ideal helices, which worked well for largely helical proteins at suitable resolutions. Here, the performance of libraries of helical ensembles created by clustering helical segments is explored. The impacts of different B-factor treatments and different degrees of structural heterogeneity are explored. A 30% increase in the number of solutions obtained by AMPLE was observed when using this new set of ensembles compared with the performance with ideal helices. The boost in performance was notable across three different fold classes: transmembrane, globular and coiled-coil structures. Furthermore, the increased effectiveness of these ensembles was coupled to a reduction in the time required by AMPLE to reach a solution. AMPLE users can now take full advantage of this new library of search models by activating the `helical ensembles' mode.

Highlights

X-ray crystallography is the most prevalent technique for protein structure determination (Berman et al, 2002), but the phase problem remains one of its most challenging aspects
In order to form a set of structures that are representative of the different ranges of difficulty that it is possible to encounter while solving different Molecular replacement (MR) cases, the structures were organized into four bins according to their expected log-likelihood gain (eLLG) values obtained with a 40-residue polyalanine ideal helix as a search model and an expected r.m.s. value of 0.1
Using AMPLE’s ideal helix and helical ensemble modes, a solution was attempted for each of these structures using the original library of ideal helices and the members of the newly generated ensemble library as search models, respectively

Summary

Introduction

X-ray crystallography is the most prevalent technique for protein structure determination (Berman et al, 2002), but the phase problem remains one of its most challenging aspects. Molecular replacement (MR) is often the method of choice to obtain the missing phase information, primarily because of its speed and high potential for automation (Evans & McCoy, 2008) This approach relies on replacing the missing experimental phases of the unknown structure with the calculated phases of a similar solved structure (Rossmann, 1990) positioned appropriately in the unit cell. In nontrivial MR cases, the availability and detection of suitable search models can be a key limitation and alternative routes need to be explored. One such route is the use of small fragments such as -helices. Since most proteins contain -helices or -strands as secondarystructure elements, such standardized fragments are often a valid approximation to elements of the unknown structure

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