4 research outputs found
Structural attributes of nucleotide sequences in promoter regions of supercoiling-sensitive genes: how to relate microarray expression data with genomic sequences
The level of supercoiling in the chromosome can affect gene expression. To
clarify the basis of supercoiling sensitivity, we analyzed the structural
features of nucleotide sequences in the vicinity of promoters for the genes
with expression enhanced and decreased in response to loss of chromosomal
supercoiling in E. coli. Fourier analysis of promoter sequences for
supercoiling-sensitive genes reveals the tendency in selection of sequences
with helical periodicities close to 10 nt for relaxation-induced genes and to
11 nt for relaxation-repressed genes. The helical periodicities in the subsets
of promoters recognized by RNA polymerase with different sigma factors were
also studied. A special procedure was developed for study of correlations
between the intensities of periodicities in promoter sequences and the
expression levels of corresponding genes. Significant correlations of
expression with the AT content and with AT periodicities about 10, 11, and 50
nt indicate their role in regulation of supercoiling-sensitive genes.Comment: 38 pages, 12 figure
Structural coordinates: A novel approach to predict protein backbone conformation
Motivation Local protein structure is usually described via classifying each peptide to a unique class from a set of pre-defined structures. These classifications may differ in the number of structural classes, the length of peptides, or class attribution criteria. Most methods that predict the local structure of a protein from its sequence first rely on some classification and only then proceed to the 3D conformation assessment. However, most classification methods rely on homologous proteins' existence, unavoidably lose information by attributing a peptide to a single class or suffer from a suboptimal choice of the representative classes. Results To alleviate the above challenges, we propose a method that constructs a peptide's structural representation from the sequence, reflecting its similarity to several basic representative structures. For 5-mer peptides and 16 representative structures, we achieved the Q16 classification accuracy of 67.9%, which is higher than what is currently reported in the literature. Our prediction method does not utilize information about protein homologues but relies only on the amino acids' physicochemical properties and the resolved structures' statistics. We also show that the 3D coordinates of a peptide can be uniquely recovered from its structural coordinates, and show the required conditions under various geometric constraints