PMID: 11933060Apr 5, 2002Paper

Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds

Proteins
Hedi HegyiMark Gerstein

Abstract

We conducted a structural genomics analysis of the folds and structural superfamilies in the first 20 completely sequenced genomes by focusing on the patterns of fold usage and trying to identify structural characteristics of typical and atypical folds. We assigned folds to sequences using PSI-blast, run with a systematic protocol to reduce the amount of computational overhead. On average, folds could be assigned to about a fourth of the ORFs in the genomes and about a fifth of the amino acids in the proteomes. More than 80% of all the folds in the SCOP structural classification were identified in one of the 20 organisms, with worm and E. coli having the largest number of distinct folds. Folds are particularly effective at comprehensively measuring levels of gene duplication, because they group together even very remote homologues. Using folds, we find the average level of duplication varies depending on the complexity of the organism, ranging from 2.4 in M. genitalium to 32 for the worm, values significantly higher than those observed based purely on sequence similarity. We rank the common folds in the 20 organisms, finding that the top three are the P-loop NTP hydrolase, the ferrodoxin fold, and the TIM-barrel, and discuss in...Continue Reading

References

Nov 1, 1990·Journal of Molecular Evolution·R F DoolittleM R Alberro
Apr 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·W R Pearson, D J Lipman
Jul 28, 1995·Science·R D FleischmannJ M Merrick
Oct 20, 1995·Science·C M FraserJ C Venter
Dec 15, 1994·Nature·C A OrengoJ M Thornton
Apr 26, 1996·Journal of Molecular Biology·G MerJ F Lefèvre
Jan 1, 1996·Methods in Enzymology·W R Pearson
Jan 1, 1996·Methods in Enzymology·J C Wootton, S Federhen
Oct 25, 1996·Science·A GoffeauS G Oliver
Nov 15, 1996·Nucleic Acids Research·R HimmelreichR Herrmann
Dec 10, 1996·Proceedings of the National Academy of Sciences of the United States of America·T L Blundell, N Srinivasan
Apr 15, 1997·Proceedings of the National Academy of Sciences of the United States of America·H LiC L Lawson
Aug 1, 1997·Nature Structural Biology·D Frishman, H W Mewes
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Sep 5, 1997·Science·F R BlattnerY Shao
Aug 15, 1997·Structure·C A OrengoJ M Thornton
Oct 29, 1997·Proceedings of the National Academy of Sciences of the United States of America·D Fischer, D Eisenberg
Feb 21, 1998·Nucleic Acids Research·L Holm, C Sander
Mar 26, 1998·Journal of Molecular Biology·W R Pearson
Jul 17, 1998·Journal of Molecular Biology·M HuynenP Bork
Jul 29, 1998·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Y KawarabayasiH Kikuchi
Oct 17, 1998·Microbial & Comparative Genomics·I DubchakS H Kim
Nov 13, 1998·Proceedings of the National Academy of Sciences of the United States of America·R Sánchez, A Sali

❮ Previous
Next ❯

Citations

Apr 21, 2004·Journal of Molecular Biology·Juan A G RaneaChristine A Orengo
Jun 27, 2002·Journal of Molecular Biology·Paul M Harrison, Mark Gerstein
Jan 28, 2003·Current Opinion in Chemical Biology·Vivek AnantharamanEugene V Koonin
Jul 4, 2008·Journal of Biomolecular Structure & Dynamics·Zakharia M Frenkel
Nov 8, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Zakharia M Frenkel, Edward N Trifonov
Jul 4, 2003·Genome Research·Gustavo Caetano-Anollés, Derek Caetano-Anollés
Apr 6, 2004·BMC Bioinformatics·Artem Cherkasov, Steven J M Jones
May 9, 2006·PLoS Computational Biology·Philip Wong, Dmitrij Frishman
May 6, 2004·Proceedings of the National Academy of Sciences of the United States of America·Yang Zhang, Jeffrey Skolnick
Sep 28, 2006·Proceedings of the National Academy of Sciences of the United States of America·Einat SprinzakHanah Margalit
Jul 17, 2008·Comparative and Functional Genomics·Michal Linial
Feb 10, 2007·Expert Review of Proteomics·Jimmy Lin, Jiang Qian
Dec 2, 2014·Structure·Hong Li
Jul 8, 2005·Proteins·Sanne Abeln, Charlotte M Deane
Nov 2, 2007·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Julia Hartling, Junhyong Kim
Oct 17, 2008·Proteomics·Hema Prasad NarraHoward Ochman
Feb 1, 2005·Trends in Genetics : TIG·Juan A G RaneaChristine A Orengo
Nov 25, 2004·Journal of Molecular Biology·Philipp PagelDmitrij Frishman
Jun 21, 2005·Current Opinion in Structural Biology·Russell F Doolittle
Apr 28, 2005·Journal of Molecular Biology·Annabel E ToddChristine A Orengo
Apr 21, 2018·Proteins·Anni Kauko, Kirsi Lehto
May 11, 2005·Journal of Molecular Evolution·Gustavo Caetano-Anollés, Derek Caetano-Anollés
Dec 20, 2019·PloS One·Rafael Hernandez-GuerreroErnesto Pérez-Rueda

❮ Previous
Next ❯

Related Concepts

Related Feeds

Archaeogenetics

Recent advances in genomic sequencing has led to the discovery of new strains of Archaea and shed light on their evolutionary history. Discover the latest research on Archaeogenetics here.