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Acta Cryst. (2014). A70, C347
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Molecular Replacement (MR) is an increasingly popular route to protein structure solution. AMPLE[1] is a software pipeline that uses either cheaply obtained ab inito protein models, or NMR structures to extend the scope of MR, allowing it to solve entirely novel protein structures in a completely automated pipeline on a standard desktop computer. AMPLE employs a cluster-and-truncate approach, combined with multiple modes of side chain treatment, to analyse the candidate models and extract the consensual features most likely to solve the structure. The search models generated in this way are screened by MrBump using Phaser and Molrep and correct solutions are detected using main chain tracing and phase modification with Shelxe. AMPLE proved capable of processing rapidly obtained ab initio structure predictions into successful search models and more recently proved effective in assembling NMR structures for MR[2]. Coiled-coil proteins are a distinct class of protein fold whose structure solution by MR is not typically straightforward. We show here that AMPLE can quickly and routinely solve most coiled-coil structures using ab initio predictions from Rosetta. The predictions are generally not globally accurate, but by encompassing different degrees of truncation of clustered models, AMPLE succeeds by sampling across a range of search models. These sometimes succeed through capturing locally well-modelled conformations, but often simply contain small helical units. Remarkably, the latter regularly succeed despite out-of-register placement and poor MR statistics. We demonstrate that single structures derived from successful ensembles perform less well, and comparable ideal helices solve few targets. Thus, both modelling of distortions from ideal helical geometry and the ensemble nature of the search models contribute to success. AMPLE is a framework applicable to any set of input structures in which variability is correlated with inaccuracy. We also present preliminary data demonstrating structure solution of transmembrane helical structures using Rosetta modelling. We finally consider future sources of starting models which offer the hope that MR with AMPLE, in the absence of close homology between a known structure and the target, may soon be possible with larger proteins.

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Acta Cryst. (2014). A70, C734
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The use of intermetallic compounds in catalysis is a promising means of achieving well-defined catalytic active sites with high selectivity. Simultaneously, it is desirable to nanostructure the catalyst to maximize activity. However in nanoparticulate form, structures and properties quite distinct from bulk systems may arise. Thorough characterization of the nano-sized catalyst is therefore required, for which the high-resolution analysis provided by transmission electron microscopy (TEM) can be invaluable. The directly interpretable imaging provided by aberration-corrected annular dark-field scanning TEM especially, can reveal atomic-scale intricacies and intrapopulation heterogeneities with clarity. Recently, a promising new class of selective hydrogenation catalyst has emerged based on intermetallic Ga-Pd compounds [1]. In foundational studies, use of bulk or powdered model systems led to insights into the relationship between structural and electronic properties and catalytic performance. Aiming for industrial applicability, attention is now being given to high-performance nanoparticulate Ga-Pd catalysts. Through high-resolution imaging, spectroscopic and 3D tomographic TEM studies, significant insight into the crystallographic status of unsupported Ga-Pd nanocatalysts, GaPd2 in particular, has been possible [2,3]. Further to direct verification of the distinctive intermetallic structure in nano-sized particles, catalytically significant and crystallographically intriguing deviations compared to the 'ideal' bulk crystal are revealed. These include strong surface segregation, lattice relaxation and particularly interesting morphologies of the small (<10 nm) particles that comprise both nanocrystalline 'fcc-like' and 'non-crystallographic' five-fold twinned structures. The extent to which the intermetallic structure may be maintained in nanoscale morphologies and the nature of the resultant catalytically active sites are important aspects to be addressed.
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