To automate or not to automate: this is the question

Abstract

New protocols and instrumentation significantly boost the outcome of structural biology, which has resulted in significant growth in the number of deposited Protein Data Bank structures. However, even an enormous increase of the productivity of a single step of the structure determination process may not significantly shorten the time between clone and deposition or publication. For example, in a medium size laboratory equipped with the LabDB and HKL-3000 systems, we show that automation of some (and integration of all) steps of the X-ray structure determination pathway is critical for laboratory productivity. Moreover, we show that the lag period after which the impact of a technology change is observed is longer than expected.

Structural and Immunologic Characterization of Ara h 1, a Major Peanut Allergen

“…Tracking and analysis of the crystallization experiments were performed with Xtaldb (28,29). Despite testing ϳ1500 conditions, no crystals of natural Ara h 1 were obtained.…”

Molecular Determinants for Antibody Binding on Group 1 House Dust Mite Allergens

“…Design of Site-directed Mutagenesis-Four amino acids of the mAb 4C1 epitope were selected for site-directed mutagenesis and expression as single mutants of pro-rDer p 1 (Arg 17 Table S2). Arg 17 also participated in a cation-interaction with Tyr 102 from the heavy chain (3.3 Å).…”

“…The protein solution was mixed with the well solution in a 1:1 ratio. Tracking and analysis of the crystallization experiments were performed with the XTALDB crystallization system (16,17). Crystallization and cryocooling conditions are summarized in supplemental Table S1.…”

The Protein Maker: an automated system for high-throughput parallel purification

“…Although suitable for a research environment (Walls et al, 2011), most standard instrumentation does not allow parallel purification or testing to investigate a large number of purification conditions simultaneously. To address this critical need on a structural genomics scale, much research and development has gone into the creation of pipelines designed to deliver the necessary high-quality materials at a rapid pace (Kim et al, 2008;Cymborowski et al, 2010;Stols et al, 2002;Dieckman et al, 2002;Steen et al, 2006). To facilitate rapid purification of proteins for structural genomics, we have developed the Protein Maker, a high-throughput parallel liquid-chromatography system that is capable of purifying up to 24 protein targets in a single unattended run (Fig.…”