A large-scale, high-efficiency and low-cost platform for structural genomics studies

Su, Xiao Dong; Liang, Yu-He; Li, Lanfen; Nan, Jie; Bröstromer, Erik; Liu, Peng; Dong, Yuhui; Xian, Dingchang

doi:10.1107/s0907444906024395

Cited by 16 publications

(16 citation statements)

References 23 publications

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“…At Paul Scherrer Institute, we have adopted the second approach. In accordance with smaller SG initiatives [14], we find that it is more cost effective to buy one large liquid handling robot equipped with hardware to run a variety of diverse HTP protocols rather than several smaller robots handling one or two dedicated protocols like in larger SG consortia.…”

Section: Robotics: From Minimum To Integrated Workflowsupporting

confidence: 62%

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Pipelines, Robots, Crystals and Biology: What Use High Throughput Solving Structures of Challenging Targets?

Kambach

2007

CPPS

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With recent advances in the technology and software underlying crystallographic structure solution, demands on both output and functional significance of X-ray structures are soaring. To achieve the required speed and quality also with ever larger and more difficult targets, combining HTP screening methods (robotics based or not) adopted from structural genomics initiatives with thorough expertise and dedicated characterization effort for each individual target is almost a must. I present concepts, practical considerations, and experiences on implementing an HTP technology platform for structural and functional studies on complexes, membrane proteins and other challenging targets. Emphasis lies on the environment of small academic groups engaged exclusively in hypothesis driven projects focused on specific biological systems. Suitability of given HTP protocols for particular target classes, benchmarking and quality control for procedures, and project management issues at the interface between extensive, broad parameter screening and intensive individual target work required by non-SG amenable targets are discussed.

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Section: Robotics: From Minimum To Integrated Workflowsupporting

confidence: 62%

“…Hence, the vast majority of larger SG initiatives rely on recombination based cloning systems, and in general only cost considerations can prompt a group to use classical, restriction/ligation based schemes [14] (but see [26], JCSG). A recent overview of available cloning schemes is given in [27].…”

Section: Cloning Systems For Single Cistron and Coexpressionmentioning

confidence: 99%

Pipelines, Robots, Crystals and Biology: What Use High Throughput Solving Structures of Challenging Targets?

Kambach

2007

CPPS

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“…Our structural study of YcbY-related proteins began with orthologs from S. mutans (44). The two S. mutans proteins Smu472 and Smu776 are about 400 amino acids in length and each possesses one distinctive methyltransferase domain plus auxiliary domains.…”

Section: Resultsmentioning

confidence: 99%

Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m 7 G2069 and m 2 G2445 modifications in Escherichia coli 23S rRNA

Wang

Desmolaize

Nan

et al. 2012

Nucleic Acids Research

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The 23S rRNA nucleotide m2G2445 is highly conserved in bacteria, and in Escherichia coli this modification is added by the enzyme YcbY. With lengths of around 700 amino acids, YcbY orthologs are the largest rRNA methyltransferases identified in Gram-negative bacteria, and they appear to be fusions from two separate proteins found in Gram-positives. The crystal structures described here show that both the N- and C-terminal halves of E. coli YcbY have a methyltransferase active site and their folding patterns respectively resemble the Streptococcus mutans proteins Smu472 and Smu776. Mass spectrometric analyses of 23S rRNAs showed that the N-terminal region of YcbY and Smu472 are functionally equivalent and add the m2G2445 modification, while the C-terminal region of YcbY is responsible for the m7G2069 methylation on the opposite side of the same helix (H74). Smu776 does not target G2069, and this nucleotide remains unmodified in Gram-positive rRNAs. The E.coli YcbY enzyme is the first example of a methyltransferase catalyzing two mechanistically different types of RNA modification, and has been renamed as the Ribosomal large subunit methyltransferase, RlmKL. Our structural and functional data provide insights into how this bifunctional enzyme evolved.

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“…The Su lab has started to establish an SG platform several years ago at the level of a university laboratory [201, 202], adopting automation and HTP techniques from other SG centers, and further developing crystallization tools and imaging equipment etc. methods.…”

Section: Recent and Future Perspectives: Structural Genomics And X-ramentioning

confidence: 99%

Protein crystallography from the perspective of technology developments

Terwilliger

Liljas

et al. 2014

Crystallography Reviews

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Early on, crystallography was a domain of mineralogy and mathematics and dealt mostly with symmetry properties and imaginary crystal lattices. This changed when Wilhelm Conrad Röntgen discovered X-rays in 1895, and in 1912 Max von Laue and his associates discovered X-ray irradiated salt crystals would produce diffraction patterns that could reveal the internal atomic periodicity of the crystals. In the same year the father-and-son team, Henry and Lawrence Bragg successfully solved the first crystal structure of sodium chloride and the era of modern crystallography began. Protein crystallography (PX) started some 20 years later with the pioneering work of British crystallographers. In the past 50-60 years, the achievements of modern crystallography and particularly those in protein crystallography have been due to breakthroughs in theoretical and technical advancements such as phasing and direct methods; to more powerful X-ray sources such as synchrotron radiation (SR); to more sensitive and efficient X-ray detectors; to ever faster computers and to improvements in software. The exponential development of protein crystallography has been accelerated by the invention and applications of recombinant DNA technology that can yield nearly any protein of interest in large amounts and with relative ease. Novel methods, informatics platforms, and technologies for automation and high-throughput have allowed the development of large-scale, high efficiency macromolecular crystallography efforts in the field of structural genomics (SG). Very recently, the X-ray free-electron laser (XFEL) sources and its applications in protein crystallography have shown great potential for revolutionizing the whole field again in the near future.

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A large-scale, high-efficiency and low-cost platform for structural genomics studies

Cited by 16 publications

References 23 publications

Pipelines, Robots, Crystals and Biology: What Use High Throughput Solving Structures of Challenging Targets?

Pipelines, Robots, Crystals and Biology: What Use High Throughput Solving Structures of Challenging Targets?

Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m 7 G2069 and m 2 G2445 modifications in Escherichia coli 23S rRNA

Protein crystallography from the perspective of technology developments

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