Massimo Sammito

Exploiting tertiary structure through local folds for crystallographic phasing.

We describe an algorithm for phasing protein crystal X-ray diffraction data that identifies, retrieves, refines and exploits general tertiary structural information from small fragments available in the Protein Data Bank. The algorithm successfully phased, through unspecific molecular replacement combined with density modification, all-helical, mixed alpha-beta, and all-beta protein structures. The method is available as a software implementation: Borges.

Practical structure solution with ARCIMBOLDO

ARCIMBOLDO combines the location of small fragments with Phaser and density modification with SHELXE of all possible Phaser solutions. Its uses are explained and illustrated through practical test cases.

Macromolecular ab initio phasing enforcing secondary and tertiary structure

ARCIMBOLDO replaces the atomicity constraints required for ab initio phasing by enforcement of model stereochemistry. Small model fragments and local folds are exploited at resolutions up to 2 Å in different contexts, from supercomputers to the standalone ARCIMBOLDO_LITE, which solves straightforward cases on a single multicore machine.

Structure solution with ARCIMBOLDO using fragments derived from distant homology models

Molecular replacement, one of the general methods used to solve the crystallographic phase problem, relies on the availability of suitable models for placement in the unit cell of the unknown structure in order to provide initial phases. ARCIMBOLDO, originally conceived for ab initio phasing, operates at the limit of this approach, using small, very accurate fragments such as polyalanine α‐helices. A distant homolog may contain accurate building blocks, but it may not be evident which sub‐structure is the most suitable purely from the degree of conservation. Trying out all alternative possibilities in a systematic way is computationally expensive, even if effective. In the present study, the solution of the previously unknown structure of MltE, an outer membrane‐anchored endolytic peptidoglycan lytic transglycosylase from Escherichia coli, is described. The asymmetric unit contains a dimer of this 194 amino acid protein. The closest available homolog was the catalytic domain of Slt70 (PDB code 1QTE). Originally, this template was used omitting contiguous spans of aminoacids and setting as many ARCIMBOLDO runs as models, each aiming to locate two copies sequentially with PHASER. Fragment trimming against the correlation coefficient prior to expansion through density modification and autotracing in SHELXE was essential. Analysis of the figures of merit led to the strategy to optimize the search model against the experimental data now implemented within ARCIMBOLDO‐SHREDDER (http://chango.ibmb.csic.es/SHREDDER). In this strategy, the initial template is systematically shredded, and fragments are scored against each unique solution of the rotation function. Results are combined into a score per residue and the template is trimmed accordingly.

Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries

The structure solution of DNA-binding protein structures and complexes based on the combination of location of DNA-binding protein motif fragments with density modification in a multi-solution frame is described.

Combining phase information in reciprocal space for molecular replacement with partial models

ARCIMBOLDO allows ab initio phasing of macromolecular structures below atomic resolution by exploiting the location of small model fragments combined with density modification in a multisolution frame. The model fragments can be either secondary-structure elements predicted from the sequence or tertiary-structure fragments. The latter can be derived from libraries of typical local folds or from related structures, such as a low-homology model that is unsuccessful in molecular replacement. In all ARCIMBOLDO applications, fragments are searched for sequentially. Correct partial solutions obtained after each fragment-search stage but lacking the necessary phasing power can, if combined, succeed. Here, an analysis is presented of the clustering of partial solutions in reciprocal space and of its application to a set of different cases. In practice, the task of combining model fragments from an ARCIMBOLDO run requires their referral to a common origin and is complicated by the presence of correct and incorrect solutions as well as by their not being independent. The F-weighted mean phase difference has been used as a figure of merit. Clustering perfect, non-overlapping fragments dismembered from test structures in polar and nonpolar space groups shows that density modification before determining the relative origin shift enhances its discrimination. In the case of nonpolar space groups, clustering of ARCIMBOLDO solutions from secondary-structure models is feasible. The use of partially overlapping search fragments provides a more favourable circumstance and was assessed on a test case. Applying the devised strategy, a previously unknown structure was solved from clustered correct partial solutions.

Structure of a 13-fold superhelix (almost) determined from first principles

A peptide fortuitously crystallized to form a motif exhibiting 13-fold non-crystallographic symmetry as judged by self-rotation function analysis. Molecular-replacement phasing used a small α-helix as the search model and was only successful with the recently deployed ARCIMBOLDO_LITE.

Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement

Maximum-likelihood rigid-body refinement can be carried out to improve oriented models before the translation-function step of molecular replacement.

New in the ARCIMBOLDO toolbox for phasing with small fragments

ARCIMBOLDO (1) combines the search of small and accurate fragments with PHASER (2), with their expansion to a full structure solution through density modification and autotracing with SHELXE (3). Fragments can be as small and general as a single ideal polyalanine helix, libraries of tertiary structure local folds such as beta sheets, or even fragments extracted from a distant homolog. These three approaches are accessible through our programs ARCIMBOLDO_LITE, ARCIMBOLDO_BORGES, and ARCIMBOLDO_SHREDDER. Our recent implementations include strategies tailored to deal with challenging cases, tackling lower resolution, larger size, data pathologies or the ambiguity in the crystal contents. This communication will focus on the latest developments in our group, illustrated through examples of their application to previously unknown structures. Coiled coil structures required to develop new features in order to tackle their inherent phasing difficulties. PHASER’s new packing constraints can now be used at the translation search, and automatic handling of the anisotropy and translational non crystallographic symmetry corrections have been included. Both helix directions are tested for all fragments in partial solutions to increase the search base at low resolution. Moreover, we now make use of a different autotracing algorithm from the SHELXE beta version. ARCIMBOLDO_SHREDDER derives and improves model fragments starting from a distant homolog template, and implements new approaches to refine them in order to reduce the deviations within an overall correct fold. Finally, we also have the possibility of using phase combination of partial solutions in order to increase their information content of the starting map to be expanded into a full solution. [1] Millan, C., Sammito, M. & Uson, I. (2015). IUCrJ 2, 95-105. [2] McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. & Read, R. J. (2007). J Appl Crystallogr 40, 658-674. [3] Sheldrick, G. M. (2010). Acta Cryst. D66, 479-485.

Phasing Through Location of Small Fragments and Density Modification with ARCIMBOLDO

The International School of Crystallography held a course at the Ettore Majorana Centre in Erice in 1997 on “Direct methods for solving macromolecular structures”. In those days, Dual Space recycling methods, introduced by Hauptman and Weeks had allowed the breakthrough of extending atomic resolution phasing to macromolecules. The largest previously unknown macromolecule to have been phased by such methods was hirustasin at 1.2 A resolution, with 400 independent atoms. At the time of the meeting, triclinic lysozyme at 1.0 A, with 1,001 equal atoms was solved with SHELXD. Fifteen years later, ab Initio phasing has pushed the size and resolution limits of the problems it can tackle. Macromolecules with several thousands of atoms in the asymmetric unit can be solved from medium resolution data. One of the successful approaches is the combination of fragment location with the program PHASER and density modification with the program SHELXE in a supercomputing frame. The method is implemented in the program ARCIMBOLDO, described in this chapter.