Literature DB >> 11854485

An NMR approach to structural proteomics.

Adelinda Yee1, Xiaoqing Chang, Antonio Pineda-Lucena, Bin Wu, Anthony Semesi, Brian Le, Theresa Ramelot, Gregory M Lee, Sudeepa Bhattacharyya, Pablo Gutierrez, Aleksej Denisov, Chang-Hun Lee, John R Cort, Guennadi Kozlov, Jack Liao, Grzegorz Finak, Limin Chen, David Wishart, Weontae Lee, Lawrence P McIntosh, Kalle Gehring, Michael A Kennedy, Aled M Edwards, Cheryl H Arrowsmith.   

Abstract

The influx of genomic sequence information has led to the concept of structural proteomics, the determination of protein structures on a genome-wide scale. Here we describe an approach to structural proteomics of small proteins using NMR spectroscopy. Over 500 small proteins from several organisms were cloned, expressed, purified, and evaluated by NMR. Although there was variability among proteomes, overall 20% of these proteins were found to be readily amenable to NMR structure determination. NMR sample preparation was centralized in one facility, and a distributive approach was used for NMR data collection and analysis. Twelve structures are reported here as part of this approach, which allowed us to infer putative functions for several conserved hypothetical proteins.

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Year:  2002        PMID: 11854485      PMCID: PMC122278          DOI: 10.1073/pnas.042684599

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  23 in total

1.  Assigning genomic sequences to CATH.

Authors:  F M Pearl; D Lee; J E Bray; I Sillitoe; A E Todd; A P Harrison; J M Thornton; C A Orengo
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

Review 2.  Automated protein modelling--the proteome in 3D.

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3.  Ansig for Windows: an interactive computer program for semiautomatic assignment of protein NMR spectra.

Authors:  M Helgstrand; P Kraulis; P Allard; T Härd
Journal:  J Biomol NMR       Date:  2000-12       Impact factor: 2.835

4.  Rapid determination of protein folds using residual dipolar couplings.

Authors:  C A Fowler; F Tian; H M Al-Hashimi; J H Prestegard
Journal:  J Mol Biol       Date:  2000-12-01       Impact factor: 5.469

5.  Structural proteomics of an archaeon.

Authors:  D Christendat; A Yee; A Dharamsi; Y Kluger; A Savchenko; J R Cort; V Booth; C D Mackereth; V Saridakis; I Ekiel; G Kozlov; K L Maxwell; N Wu; L P McIntosh; K Gehring; M A Kennedy; A R Davidson; E F Pai; M Gerstein; A M Edwards; C H Arrowsmith
Journal:  Nat Struct Biol       Date:  2000-10

6.  How representative are the known structures of the proteins in a complete genome? A comprehensive structural census.

Authors:  M Gerstein
Journal:  Fold Des       Date:  1998

7.  The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding.

Authors:  M Teplova; V Tereshko; R Sanishvili; A Joachimiak; T Bushueva; W F Anderson; M Egli
Journal:  Protein Sci       Date:  2000-12       Impact factor: 6.725

8.  A tracked approach for automated NMR assignments in proteins (TATAPRO).

Authors:  H S Atreya; S C Sahu; K V Chary; G Govil
Journal:  J Biomol NMR       Date:  2000-06       Impact factor: 2.835

9.  RFAC, a program for automated NMR R-factor estimation.

Authors:  W Gronwald; R Kirchhöfer; A Görler; W Kremer; B Ganslmeier; K P Neidig; H R Kalbitzer
Journal:  J Biomol NMR       Date:  2000-06       Impact factor: 2.835

10.  Three-dimensional structure of an evolutionarily conserved N-terminal domain of syntaxin 1A.

Authors:  I Fernandez; J Ubach; I Dulubova; X Zhang; T C Südhof; J Rizo
Journal:  Cell       Date:  1998-09-18       Impact factor: 41.582

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  75 in total

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Authors:  Bin Wu; Adelinda Yee; Antonio Pineda-Lucena; Anthony Semesi; Theresa A Ramelot; John R Cort; Jin-Won Jung; Aled Edwards; Weontae Lee; Michael Kennedy; Cheryl H Arrowsmith
Journal:  Protein Sci       Date:  2003-12       Impact factor: 6.725

2.  Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures.

Authors:  Alexander Stark; Robert B Russell
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

3.  Expression screening, protein purification and NMR analysis of human protein domains for structural genomics.

Authors:  G E Folkers; B N M van Buuren; R Kaptein
Journal:  J Struct Funct Genomics       Date:  2004

4.  The NMR solution structure of the 30S ribosomal protein S27e encoded in gene RS27_ARCFU of Archaeoglobus fulgidis reveals a novel protein fold.

Authors:  Catherine Herve du Penhoat; Hanudatta S Atreya; Yang Shen; Gaohua Liu; Thomas B Acton; Rong Xiao; Zhaohui Li; Diana Murray; Gaetano T Montelione; Thomas Szyperski
Journal:  Protein Sci       Date:  2004-05       Impact factor: 6.725

5.  Sonication of proteins causes formation of aggregates that resemble amyloid.

Authors:  Peter B Stathopulos; Guenter A Scholz; Young-Mi Hwang; Jessica A O Rumfeldt; James R Lepock; Elizabeth M Meiering
Journal:  Protein Sci       Date:  2004-09-30       Impact factor: 6.725

6.  Comparative analysis and "expression space" coverage of the production of prokaryotic membrane proteins for structural genomics.

Authors:  Sachin Surade; Markus Klein; Peggy C Stolt-Bergner; Cornelia Muenke; Ankita Roy; Hartmut Michel
Journal:  Protein Sci       Date:  2006-09       Impact factor: 6.725

7.  A novel member of the YchN-like fold: solution structure of the hypothetical protein Tm0979 from Thermotoga maritima.

Authors:  Joe A Gaspar; Chengsong Liu; Kenrick A Vassall; Gabriela Meglei; Ricardo Stephen; Peter B Stathopulos; Antonio Pineda-Lucena; Bin Wu; Adelinda Yee; Cheryl H Arrowsmith; Elizabeth M Meiering
Journal:  Protein Sci       Date:  2005-01       Impact factor: 6.725

8.  Interaction between the bacterial nucleoid associated proteins Hha and H-NS involves a conformational change of Hha.

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Journal:  Biochem J       Date:  2005-06-15       Impact factor: 3.857

9.  Structure and function of the Escherichia coli protein YmgB: a protein critical for biofilm formation and acid-resistance.

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Journal:  J Mol Biol       Date:  2007-08-02       Impact factor: 5.469

10.  Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm.

Authors:  John J Kuszewski; Robin Augustine Thottungal; G Marius Clore; Charles D Schwieters
Journal:  J Biomol NMR       Date:  2008-07-31       Impact factor: 2.835

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