Literature DB >> 21360289

PSI:Biology-materials repository: a biologist's resource for protein expression plasmids.

Catherine Y Cormier1, Jin G Park, Michael Fiacco, Jason Steel, Preston Hunter, Jason Kramer, Rajeev Singla, Joshua LaBaer.   

Abstract

The Protein Structure Initiative:Biology-Materials Repository (PSI:Biology-MR; MR; http://psimr.asu.edu ) sequence-verifies, annotates, stores, and distributes the protein expression plasmids and vectors created by the Protein Structure Initiative (PSI). The MR has developed an informatics and sample processing pipeline that manages this process for thousands of samples per month from nearly a dozen PSI centers. DNASU ( http://dnasu.asu.edu ), a freely searchable database, stores the plasmid annotations, which include the full-length sequence, vector information, and associated publications for over 130,000 plasmids created by our laboratory, by the PSI and other consortia, and by individual laboratories for distribution to researchers worldwide. Each plasmid links to external resources, including the PSI Structural Biology Knowledgebase ( http://sbkb.org ), which facilitates cross-referencing of a particular plasmid to additional protein annotations and experimental data. To expedite and simplify plasmid requests, the MR uses an expedited material transfer agreement (EP-MTA) network, where researchers from network institutions can order and receive PSI plasmids without institutional delays. As of March 2011, over 39,000 protein expression plasmids and 78 empty vectors from the PSI are available upon request from DNASU. Overall, the MR's repository of expression-ready plasmids, its automated pipeline, and the rapid process for receiving and distributing these plasmids more effectively allows the research community to dissect the biological function of proteins whose structures have been studied by the PSI.

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Year:  2011        PMID: 21360289      PMCID: PMC3184641          DOI: 10.1007/s10969-011-9100-8

Source DB:  PubMed          Journal:  J Struct Funct Genomics        ISSN: 1345-711X


  42 in total

1.  A new vector for high-throughput, ligation-independent cloning encoding a tobacco etch virus protease cleavage site.

Authors:  Lucy Stols; Minyi Gu; Lynda Dieckman; Rosemarie Raffen; Frank R Collart; Mark I Donnelly
Journal:  Protein Expr Purif       Date:  2002-06       Impact factor: 1.650

2.  The Protein Data Bank and structural genomics.

Authors:  John Westbrook; Zukang Feng; Li Chen; Huanwang Yang; Helen M Berman
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

Review 3.  Target selection and determination of function in structural genomics.

Authors:  James D Watson; Annabel E Todd; James Bray; Roman A Laskowski; Aled Edwards; Andrzej Joachimiak; Christine A Orengo; Janet M Thornton
Journal:  IUBMB Life       Date:  2003 Apr-May       Impact factor: 3.885

4.  The protein target list of the Northeast Structural Genomics Consortium.

Authors:  Zeba Wunderlich; Thomas B Acton; Jinfeng Liu; Gregory Kornhaber; John Everett; Phil Carter; Ning Lan; Nathaniel Echols; Mark Gerstein; Burkhard Rost; Gaetano T Montelione
Journal:  Proteins       Date:  2004-08-01

5.  The state of the Protein Structure Initiative.

Authors:  Eaton Lattman
Journal:  Proteins       Date:  2004-03-01

6.  Structural genomics projects in Japan.

Authors:  S Yokoyama; H Hirota; T Kigawa; T Yabuki; M Shirouzu; T Terada; Y Ito; Y Matsuo; Y Kuroda; Y Nishimura; Y Kyogoku; K Miki; R Masui; S Kuramitsu
Journal:  Nat Struct Biol       Date:  2000-11

7.  Expression of a highly toxic protein, Bax, in Escherichia coli by attachment of a leader peptide derived from the GroES cochaperone.

Authors:  M I Donnelly; P W Stevens; L Stols; S X Su; S Tollaksen; C Giometti; A Joachimiak
Journal:  Protein Expr Purif       Date:  2001-08       Impact factor: 1.650

Review 8.  The Seattle Structural Genomics Center for Infectious Disease (SSGCID).

Authors:  P J Myler; R Stacy; L Stewart; B L Staker; W C Van Voorhis; G Varani; G W Buchko
Journal:  Infect Disord Drug Targets       Date:  2009-11

9.  Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms.

Authors:  Karen R Christie; Shuai Weng; Rama Balakrishnan; Maria C Costanzo; Kara Dolinski; Selina S Dwight; Stacia R Engel; Becket Feierbach; Dianna G Fisk; Jodi E Hirschman; Eurie L Hong; Laurie Issel-Tarver; Robert Nash; Anand Sethuraman; Barry Starr; Chandra L Theesfeld; Rey Andrada; Gail Binkley; Qing Dong; Christopher Lane; Mark Schroeder; David Botstein; J Michael Cherry
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

10.  Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline.

Authors:  Scott A Lesley; Peter Kuhn; Adam Godzik; Ashley M Deacon; Irimpan Mathews; Andreas Kreusch; Glen Spraggon; Heath E Klock; Daniel McMullan; Tanya Shin; Juli Vincent; Alyssa Robb; Linda S Brinen; Mitchell D Miller; Timothy M McPhillips; Mark A Miller; Daniel Scheibe; Jaume M Canaves; Chittibabu Guda; Lukasz Jaroszewski; Thomas L Selby; Marc-Andre Elsliger; John Wooley; Susan S Taylor; Keith O Hodgson; Ian A Wilson; Peter G Schultz; Raymond C Stevens
Journal:  Proc Natl Acad Sci U S A       Date:  2002-08-22       Impact factor: 11.205

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  31 in total

1.  The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource.

Authors:  Lida K Gifford; Lester G Carter; Margaret J Gabanyi; Helen M Berman; Paul D Adams
Journal:  J Struct Funct Genomics       Date:  2012-04-06

2.  Target selection for structural genomics based on combining fold recognition and crystallisation prediction methods: application to the human proteome.

Authors:  James E Bray
Journal:  J Struct Funct Genomics       Date:  2012-02-22

3.  Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of human dihydrouridine synthase.

Authors:  Sam Griffiths; Robert T Byrne; Alfred A Antson; Fiona Whelan
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2012-02-22

4.  Binding of Substrates to the Central Pore of the Vps4 ATPase Is Autoinhibited by the Microtubule Interacting and Trafficking (MIT) Domain and Activated by MIT Interacting Motifs (MIMs).

Authors:  Han Han; Nicole Monroe; Jörg Votteler; Binita Shakya; Wesley I Sundquist; Christopher P Hill
Journal:  J Biol Chem       Date:  2015-04-01       Impact factor: 5.157

5.  Structure and function of a novel LD-carboxypeptidase a involved in peptidoglycan recycling.

Authors:  Debanu Das; Mireille Hervé; Marc-André Elsliger; Rameshwar U Kadam; Joanna C Grant; Hsiu-Ju Chiu; Mark W Knuth; Heath E Klock; Mitchell D Miller; Adam Godzik; Scott A Lesley; Ashley M Deacon; Dominique Mengin-Lecreulx; Ian A Wilson
Journal:  J Bacteriol       Date:  2013-10-11       Impact factor: 3.490

6.  Distinct Fcγ receptors mediate the effect of serum amyloid p on neutrophil adhesion and fibrocyte differentiation.

Authors:  Nehemiah Cox; Darrell Pilling; Richard H Gomer
Journal:  J Immunol       Date:  2014-07-14       Impact factor: 5.422

Review 7.  High-throughput protein purification and quality assessment for crystallization.

Authors:  Youngchang Kim; Gyorgy Babnigg; Robert Jedrzejczak; William H Eschenfeldt; Hui Li; Natalia Maltseva; Catherine Hatzos-Skintges; Minyi Gu; Magdalena Makowska-Grzyska; Ruiying Wu; Hao An; Gekleng Chhor; Andrzej Joachimiak
Journal:  Methods       Date:  2011-08-31       Impact factor: 3.608

8.  Annotation of proteins of unknown function: initial enzyme results.

Authors:  Talia McKay; Kaitlin Hart; Alison Horn; Haeja Kessler; Greg Dodge; Keti Bardhi; Kostandina Bardhi; Jeffrey L Mills; Herbert J Bernstein; Paul A Craig
Journal:  J Struct Funct Genomics       Date:  2015-01-29

9.  Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative.

Authors:  Kamil Khafizov; Carlos Madrid-Aliste; Steven C Almo; Andras Fiser
Journal:  Proc Natl Acad Sci U S A       Date:  2014-02-24       Impact factor: 11.205

10.  Antiviral antibody profiling by high-density protein arrays.

Authors:  Xiaofang Bian; Peter Wiktor; Peter Kahn; Al Brunner; Amritpal Khela; Kailash Karthikeyan; Kristi Barker; Xiaobo Yu; Mitch Magee; Clive H Wasserfall; David Gibson; Madeleine E Rooney; Ji Qiu; Joshua LaBaer
Journal:  Proteomics       Date:  2015-05-15       Impact factor: 3.984

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