Treffer: 10-11 bp periodicities in complete genomes reflect protein structure and DNA folding

Title:
10-11 bp periodicities in complete genomes reflect protein structure and DNA folding
Authors:
HERZEL, H, WEISS, O, TRIFONOV, E. N
Source:
Selection of papers presented at the German Conference on Bioinformatics (GCB'98, Cologne, Germany, October 1998Bioinformatics (Oxford. Print). 15(3):187-193
Publisher Information:
Oxford: Oxford University Press, 1999.
Publication Year:
1999
Physical Description:
print, 36 ref
Original Material:
INIST-CNRS
Subject Terms:
Bioinformatics, Bioinformatique, Sciences biologiques et medicales, Biological and medical sciences, Sciences biologiques fondamentales et appliquees. Psychologie, Fundamental and applied biological sciences. Psychology, Generalites, General aspects, Mathématiques biologiques. Statistiques. Modèles. Métrologie. Informatique en biologie (généralités), Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects), Traitement informatique, Computerized processing, Tratamiento informático, Archaeobacteria, Bactérie, Bacteria, DNA, Oligodésoxyribonucléotide, Oligodeoxyribonucleotide, Oligodesoxirribonucleótido, Protéine, Protein, Proteína, Périodicité, Periodicity, Periodicidad, Relation structure propriété, Property structure relationship, Relación estructura propiedad, Repliement, Refolding, Repliegue, Structure superhélice, Superhelical structure, Estructura superhelicoidal, Structure tertiaire, Tertiary structure, Estructura terciaria, Séquence répétée, Repeated sequence, Secuencia repetida
Document Type:
Konferenz Conference Paper
File Description:
text
Language:
English
Author Affiliations:
Institute for Theoretical Biology, Humboldt University Invalidenstr. 43, 10115 Berlin, Germany
Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
ISSN:
1367-4803
Access URL:
http://pascal-francis.inist.fr/vibad/index.php?action=search&terms=1832270
Rights:
Copyright 1999 INIST-CNRS
CC BY 4.0
Sauf mention contraire ci-dessus, le contenu de cette notice bibliographique peut être utilisé dans le cadre d’une licence CC BY 4.0 Inist-CNRS / Unless otherwise stated above, the content of this bibliographic record may be used under a CC BY 4.0 licence by Inist-CNRS / A menos que se haya señalado antes, el contenido de este registro bibliográfico puede ser utilizado al amparo de una licencia CC BY 4.0 Inist-CNRS
Notes:
Biological sciences. Generalities. Modelling. Methods

Generalities in biological sciences
Accession Number:
edscal.1832270
Database:
PASCAL Archive

Weitere Informationen

Motivation: Completely sequenced genomes allow for detection and analysis of the relatively weak periodicities of 10-11 basepairs (bp). Two sources contribute to such signals: correlations in the corresponding protein sequences due to the amphipatic character of α-helices and the folding ofDNA (nucleosomal patterns, DNA supercoiling). Since the topological state of genomic DNA is of importance for its replication, recombination and transcription, there is an immediate interest to obtain information about the supercoiled state from sequence periodicities. Results: We show that correlations within proteins affect mainly the oscillations at distances below 35 bp. The long-ranging correlations up to 100 bp reflect primarily DNA folding. For the yeast genome these oscillations are consistent in detail with the chromatin structure. For eubacteria and archaea the periods deviate significantly from the 10.55 bp value for free DNA. These deviations suggest that while a period of 11 bp in bacteria reflects negative supercoiling, the significantly different period of thermophilic archaea close to 10 bp corresponds to positive supercoiling of thermophilic archaeal genomes. Availability: Protein sets and Cprograms for the calculation of correlation functions are available on request from the authors (see http://itb.biologie. hu-berlin.de).