Genomics Project (genomics + project)

Distribution by Scientific Domains

Kinds of Genomics Project

  • structural genomics project

  • Selected Abstracts

    Amino acid profiling in plant cell cultures: An inter-laboratory comparison of CE-MS and GC-MS

    ELECTROPHORESIS, Issue 9 2007
    Brad J. Williams
    Abstract A CE-MS method for metabolic profiling of amino acids was developed and used in an integrated functional genomics project to study the response of Medicago truncatula liquid suspension cell cultures to stress. This project required the analysis of more than 500 root cell culture extracts. The CE-MS method profiled 20 biologically important amino acids. The CE-MS method required no sample derivatization prior to injection and used minimal sample preparation. The method is described in terms of CE and MS operational parameters, reproducibility of migration times and response ratios, sample preparation, sample throughput, and reliability. This method was then compared with a previously published report that used GC-MS metabolic profiling for the same tissues. The data reveal a high level of similarity between the CE-MS and GC-MS amino acid profiling methods, thus supporting these as complementary technologies for metabolomics. We conclude that CE-MS is a valid alternative to GC-MS for targeted profiling of metabolites, such as amino acids, and possesses some significant advantages over GC-MS. [source]

    The hypothetical protein Atu4866 from Agrobacterium tumefaciens adopts a streptavidin-like fold

    PROTEIN SCIENCE, Issue 1 2008
    Xuanjun Ai
    Abstract Atu4866 is a 79-residue conserved hypothetical protein of unknown function from Agrobacterium tumefaciens. Protein sequence alignments show that it shares ,60% sequence identity with 20 other hypothetical proteins of bacterial origin. However, the structures and functions of these proteins remain unknown so far. To gain insight into the function of this family of proteins, we have determined the structure of Atu4866 as a target of a structural genomics project using solution NMR spectroscopy. Our results reveal that Atu4866 adopts a streptavidin-like fold featuring a ,-barrel/sandwich formed by eight antiparallel ,-strands. Further structural analysis identified a continuous patch of conserved residues on the surface of Atu4866 that may constitute a potential ligand-binding site. [source]

    On the use of DXMS to produce more crystallizable proteins: Structures of the T. maritima proteins TM0160 and TM1171

    PROTEIN SCIENCE, Issue 12 2004
    Glen Spraggon
    DXMS, deuterium exchange mass spectroscopy Abstract The structure of two Thermotoga maritima proteins, a conserved hypothetical protein (TM0160) and a transcriptional regulator (TM1171), have now been determined at 1.9 and 2.3 resolution, respectively, as part of a large-scale structural genomics project. Our first efforts to crystallize full-length versions of these targets were unsuccessful. However, analysis of the recombinant purified proteins using the technique of enhanced amide hydrogen/deuterium exchange mass spectroscopy (DXMS) revealed substantial regions of rapid amide deuterium hydrogen exchange, consistent with flexible regions of the structures. Based on these exchange data, truncations were designed to selectively remove the disordered C-terminal regions, and the resulting daughter proteins showed greatly enhanced crystallizability. Comparative DXMS analysis of full-length protein versus truncated forms demonstrated complete and exact preservation of the exchange rate profiles in the retained sequence, indicative of conservation of the native folded structure. This study presents the first structures produced with the aid of the DXMS method for salvaging intractable crystallization targets. The structure of TM0160 represents a new fold and highlights the use of this approach where any prior structural knowledge is absent. The structure of TM1171 represents an example where the lack of a substrate/cofactor may impair crystallization. The details of both structures are presented and discussed. [source]

    On increasing protein-crystallization throughput for X-ray diffraction studies

    Ashit K. Shah
    Two recent developments, a novel screening/optimization strategy that considerably reduces the number of trials required to produce diffraction-size crystals and a simple modification that doubles the screening capacity of the Douglas Instruments ORYX 1-6 protein-crystallization robot, have been implemented into a structural genomics project. The new two-step screening/optimization strategy yields diffraction-quality crystals directly from the screening process, reducing the need for further optimization. The ORYX modification involves the addition of extensions to the sample- and oil-delivery arms and software modifications that allow two plates to be set up simultaneously. [source]

    Structure of a conserved hypothetical protein, TTHA0849 from Thermus thermophilus HB8, at 2.4, resolution: a putative member of the StAR-related lipid-transfer (START) domain superfamily

    Makoto Nakabayashi
    The crystal structure of a conserved hypothetical protein, TTHA0849 from Thermus thermophilus HB8, has been determined at 2.4, resolution as a part of a structural and functional genomics project on T. thermophilus HB8. The main-chain folding shows a compact ,+, motif, forming a hydrophobic cavity in the molecule. A structural similarity search reveals that it resembles those steroidogenic acute regulatory proteins that contain the lipid-transfer (START) domain, even though TTHA0849 shows comparatively weak sequence identity to polyketide cyclases. However, the size of the ligand-binding cavity is distinctly smaller than other START domain-containing proteins, suggesting that it catalyses the transfer of smaller ligand molecules. [source]

    Computer-aided NMR assay for detecting natively folded structural domains,

    PROTEIN SCIENCE, Issue 4 2006
    Takayuki Hondoh
    Abstract Structural genomics projects require strategies for rapidly recognizing protein sequences appropriate for routine structure determination. For large proteins, this strategy includes the dissection of proteins into structural domains that form stable native structures. However, protein dissection essentially remains an empirical and often a tedious process. Here, we describe a simple strategy for rapidly identifying structural domains and assessing their structures. This approach combines the computational prediction of sequence regions corresponding to putative domains with an experimental assessment of their structures and stabilities by NMR and biochemical methods. We tested this approach with nine putative domains predicted from a set of 108 Thermus thermophilus HB8 sequences using PASS, a domain prediction program we previously reported. To facilitate the experimental assessment of the domain structures, we developed a generic 6-hour His-tag-based purification protocol, which enables the sample quality evaluation of a putative structural domain in a single day. As a result, we observed that half of the predicted structural domains were indeed natively folded, as judged by their HSQC spectra. Furthermore, two of the natively folded domains were novel, without related sequences classified in the Pfam and SMART databases, which is a significant result with regard to the ability of structural genomics projects to uniformly cover the protein fold space. [source]

    An improved protocol for rapid freezing of protein samples for long-term storage

    Rapid freezing of protein samples
    Freezing of purified protein drops directly in liquid nitrogen is a convenient technique for the long-term storage of protein samples. Although this enhances reproducibility in follow-up crystallization experiments, some protein samples are not amenable to this technique. It has been discovered that plunging PCR tubes containing protein samples into liquid nitrogen results in more rapid freezing of the samples and can safely preserve some proteins that are damaged by drop-freezing. The PCR-tube method can also be adapted to a PCR-plate freezing method with applications for high-throughput and structural genomics projects. [source]