New paradigm for macromolecular crystallography experiments at SSRL: automated crystal screening and remote data collection

Soltis, S. Michael; Cohen, Aina E.; Deacon, Ashley M.; Eriksson, Thomas; González, Ana; McPhillips, S.E.; Chui, H.; Dunten, Pete; Hollenbeck, Michael; Mathews, I.I.; Miller, Mitchell D.; Moorhead, Penjit; Phizackerley, R. P.; Smith, Clyde A.; Song, Jianguo; Bedem, H. van dem; Ellis, P.J.; Kühn, Peter; McPhillips, Timothy M.; Sauter, Nicholas K.; Sharp, Kenneth G.; Tsyba, Irina; Wolf, Guenter

doi:10.1107/s0907444908030564

Cited by 119 publications

(89 citation statements)

References 29 publications

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“…KSI X-Ray Crystallography. Single-crystal diffraction data were collected at the Stanford Synchrotron Radiation Lightsource Beamline BL9-1 using a wavelength of 0.98 Å (42). The reflections were indexed and integrated and with the programs XDS (43); the intensities were scaled, merged, and converted Table S3.…”

Section: Experimental Methodsmentioning

confidence: 99%

Use of anion–aromatic interactions to position the general base in the ketosteroid isomerase active site

Schwans¹,

Sunden²,

Lassila³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Although the cation-pi pair, formed between a side chain or substrate cation and the negative electrostatic potential of a pi system on the face of an aromatic ring, has been widely discussed and has been shown to be important in protein structure and protein-ligand interactions, there has been little discussion of the potential structural and functional importance in proteins of the related anion-aromatic pair (i.e., interaction of a negatively charged group with the positive electrostatic potential on the ring edge of an aromatic group). We posited, based on prior structural information, that anion-aromatic interactions between the anionic Asp general base and Phe54 and Phe116 might be used instead of a hydrogen-bond network to position the general base in the active site of ketosteroid isomerase from Comamonas testosteroni as there are no neighboring hydrogenbonding groups. We have tested the role of the Phe residues using site-directed mutagenesis, double-mutant cycles, and high-resolution X-ray crystallography. These results indicate a catalytic role of these Phe residues. Extensive analysis of the Protein Data Bank provides strong support for a catalytic role of these and other Phe residues in providing anion-aromatic interactions that position anionic general bases within enzyme active sites. Our results further reveal a potential selective advantage of Phe in certain situations, relative to more traditional hydrogen-bonding groups, because it can simultaneously aid in the binding of hydrophobic substrates and positioning of a neighboring general base.enzyme catalysis | general-base catalysis | noncovalent interactions E nzymes use the same functional groups to achieve "chemical catalysis" as small-molecule catalysts, and yet enzymes attain much greater rate enhancements. A distinguishing feature of enzymes is that their reactions occur in highly specialized active sites that use noncovalent interactions to precisely position enzymatic functional groups relative to substrates and relative to other active-site features. Understanding how these groups are positioned within enzyme active sites is key for understanding the differences between enzymes and small-molecule catalysts.It is generally recognized that hydrophobic interactions can help bind and position substrates in enzyme active sites (1, 2). Beyond hydrophobic interactions, much attention has focused on the importance of hydrogen bonds in precisely positioning active-site groups directly involved in the chemical reaction (e.g., the catalytic triad in serine proteases), and the importance of hydrogen-bonding groups is supported by mutagenesis in many cases (e.g., refs. 1 and 3-5).In addition to hydrogen bonds, the cation-pi pair, formed between a side-chain or substrate cation and the negative electrostatic potential associated with the face of a pi system, has been widely discussed in hundreds of literature reports and has been shown to be important in both protein structure and proteinligand interactions (e.g., refs. 6 and 7). There has been much ...

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Section: Experimental Methodsmentioning

confidence: 99%

Use of anion–aromatic interactions to position the general base in the ketosteroid isomerase active site

Schwans¹,

Sunden²,

Lassila³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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“…The combination of highly intense focused X-ray beams, automatic sample changers, automated beam delivery, online data analysis and fast readout detectors at synchrotron macromolecular crystallography (MX) beamlines now allows for the collection of hundreds of datasets during each assigned experimental session (Arzt et al, 2005;Beteva et al, 2006;Bourenkov & Popov, 2010;Bowler et al, 2010;Cherezov et al, 2009;Cipriani et al, 2006;de Sanctis et al, 2012;Flot et al, 2010;Gabadinho et al, 2010;Incardona et al, 2009;Jacquamet et al, 2009;Leslie et al, 2002;McCarthy et al, 2009;McPhillips et al, 2002;Nurizzo et al, 2006;Soltis et al, 2008). In many cases, complete diffraction datasets can be collected in under one minute (Hü lsen et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF

et al. 2013

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The development of automated high-intensity macromolecular crystallography (MX) beamlines at synchrotron facilities has resulted in a remarkable increase in sample throughput. Developments in X-ray detector technology now mean that complete X-ray diffraction datasets can be collected in less than one minute. Such high-speed collection, and the volumes of data that it produces, often make it difficult for even the most experienced users to cope with the deluge. However, the careful reduction of data during experimental sessions is often necessary for the success of a particular project or as an aid in decision making for subsequent experiments. Automated data reduction pipelines provide a fast and reliable alternative to user-initiated processing at the beamline. In order to provide such a pipeline for the MX user community of the European Synchrotron Radiation Facility (ESRF), a system for the rapid automatic processing of MX diffraction data from single and multiple positions on a single or multiple crystals has been developed. Standard integration and data analysis programs have been incorporated into the ESRF data collection, storage and computing environment, with the final results stored and displayed in an intuitive manner in the ISPyB (information system for protein crystallography beamlines) database, from which they are also available for download. In some cases, experimental phase information can be automatically determined from the processed data. Here, the system is described in detail.

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“…Remote users, who ship their samples to a facility for data collection, also require more robust data management and movement infrastructure. Advances in the technology and automation at these shared facilities are producing higher data rates, with an anticipated need to process terabytes per day in the near future (Soltis et al, 2008). These challenges are similar to those faced by genomics research or high-energy physics: centralized data collection at a shared facility by a large group of users with independent affiliations and collaborations.…”

Section: Introductionmentioning

confidence: 96%

Adapting federated cyberinfrastructure for shared data collection facilities in structural biology

Stokes-Rees

Levesque

Murphy

et al. 2012

J Synchrotron Radiat

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Early stage experimental data in structural biology is generally unmaintained and inaccessible to the public. It is increasingly believed that this data, which forms the basis for each macromolecular structure discovered by this field, must be archived and, in due course, published. Furthermore, the widespread use of shared scientific facilities such as synchrotron beamlines complicates the issue of data storage, access and movement, as does the increase of remote users. This work describes a prototype system that adapts existing federated cyberinfrastructure technology and techniques to significantly improve the operational environment for users and administrators of synchrotron data collection facilities used in structural biology. This is achieved through software from the Virtual Data Toolkit and Globus, bringing together federated users and facilities from the Stanford Synchrotron Radiation Lightsource, the Advanced Photon Source, the Open Science Grid, the SBGrid Consortium and Harvard Medical School. The performance and experience with the prototype provide a model for data management at shared scientific facilities.

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New paradigm for macromolecular crystallography experiments at SSRL: automated crystal screening and remote data collection

Cited by 119 publications

References 29 publications

Use of anion–aromatic interactions to position the general base in the ketosteroid isomerase active site

Use of anion–aromatic interactions to position the general base in the ketosteroid isomerase active site

Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF

Adapting federated cyberinfrastructure for shared data collection facilities in structural biology

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