Phase Combination and its Application to the Solution of Macromolecular Structures: Developing ALIXE and SHREDDER

Abstract

Phasing X-ray data within the frame of the ARCIMBOLDO programs requires very accurate models and a sophisticated evaluation of the possible hypotheses. ARCIMBOLDO uses small fragments, that are placed with the maximum likelihood molecular replacement program Phaser, and are subject to density modification and autotracing with the program SHELXE. The software receives its name from the Italian painter Giuseppe Arcimboldo, who used to compose portraits out of common objects such as vegetables or flowers. Out of most possible arrangements of such objects, only a still-life will result, and just a few ones will truly produce a portrait. In a similar way, from all possible placements with small protein fragments, only a few will be correct and will allow to get the full “protein’s portrait”.

The work presented in this thesis has explored new ways to exploit partial information and increase the signal in the process of phasing with fragments. This has been achieved through two main pieces of software, ALIXE and SHREDDER. With the spherical mode in ARCIMBOLDO_SHREDDER, the aim is to derive compact fragments starting from a distant homolog to our unknown protein of interest. Then, locations for these fragments are searched with Phaser. These include strategies for refining the fragments against the experimental data and giving them more degrees of freedom. With ALIXE, the aim is to combine information in reciprocal space from partial solutions, such as the ones produced by SHREDDER, and use the coherence between them to guide their merging and to increase the information content, so that the step of density modification and autotracing starts from a more complete solution. Even if partial solutions contain both correct and incorrect information, the combination of solutions that share some similarity will allow to get a better approximation to the correct structure.

Both ARCIMBOLDO_SHREDDER and ALIXE have been used on test data for development and optimisation but also on datasets from previously unknown structures, which have been solved thanks to these programs. These programs are distributed through the website of the group but also through software suites of general use in the crystallographic community such as CCP4 and SBGrid.