107 research outputs found
Number of natively unfolded proteins scales with genome size
Natively unfolded proteins exist as an ensemble of flexible conformations
lacking a well defined tertiary structure along a large portion of their
polypeptide chain. Despite the absence of a stable configuration, they are
involved in important cellular processes. In this work we used from three
indicators of folding status, derived from the analysis of mean packing and
mean contact energy of a protein sequence as well as from VSL2, a disorder
predictor, and we combined them into a consensus score to identify natively
unfolded proteins in several genomes from Archaea, Bacteria and Eukarya. We
found a high correlation among the number of predicted natively unfolded
proteins and the number of proteins in the genomes. More specifically, the
number of natively unfolded proteins scaled with the number of proteins in the
genomes, with exponent 1.81 +- 0.10. This scaling law may be important to
understand the relation between the number of natively unfolded proteins and
their roles in cellular processes.Comment: Submitted to Biophysics and Bioengineering Letters
http://padis2.uniroma1.it:81/ojs/index.php/CISB-BB
Causal influence in linear response models
The intuition of causation is so fundamental that almost every research study
in life sciences refers to this concept. However a widely accepted formal
definition of causal influence between observables is still missing. In the
framework of linear Langevin networks without feedbacks (linear response
models) we developed a measure of causal influence based on a decomposition of
information flows over time. We discuss its main properties and compare it with
other information measures like the Transfer Entropy. Finally we outline some
difficulties of the extension to a general definition of causal influence for
complex systems.Comment: 9 pages, 9 figure
Bacterial protein interaction networks: connectivity is ruled by gene conservation, essentiality and function
Protein-protein interaction (PPI) networks are the backbone of all processes
in living cells. In this work we relate conservation, essentiality and
functional repertoire of a gene to the connectivity of the corresponding
protein in the PPI networks. Focusing on a set of 42 bacterial species with
reasonably separated evolutionary trajectories, we investigate three issues: i)
whether the distribution of connectivity values changes between PPI subnetworks
of essential and nonessential genes; ii) how gene conservation, measured both
by the evolutionary retention index (ERI) and by evolutionary pressures
(evaluated through the ratio and ENC plots) is related to the the
connectivity of the corresponding protein; iii) how PPI connectivities are
modulated by evolutionary and functional relationships, as represented by the
Clusters of Orthologous Proteins (COGs). We show that conservation,
essentiality and functional specialization of genes control in a quite
universal way the topology of the emerging bacterial PPI networks. Noteworthy,
a structural transition in the network is observed such that, for
connectivities , bacterial PPI networks are mostly populated by genes
that are conserved, essential and which, in most cases, belong to the COG
cluster J, related to ribosomal functions and to the processing of genetic
information
Codon Bias Patterns of 's Interacting Proteins
Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino
acid, are used differently across the variety of living organisms. The
biological meaning of this phenomenon, known as codon usage bias, is still
controversial. In order to shed light on this point, we propose a new codon
bias index, , that is based on the competition between cognate and
near-cognate tRNAs during translation, without being tuned to the usage bias of
highly expressed genes. We perform a genome-wide evaluation of codon bias for
, comparing with other widely used indices: , , and
. We show that and capture similar information by being
positively correlated with gene conservation, measured by ERI, and
essentiality, whereas, and appear to be less sensitive to
evolutionary-functional parameters. Notably, the rate of variation of and
with ERI allows to obtain sets of genes that consistently belong to
specific clusters of orthologous genes (COGs). We also investigate the
correlation of codon bias at the genomic level with the network features of
protein-protein interactions in . We find that the most densely
connected communities of the network share a similar level of codon bias (as
measured by and ). Conversely, a small difference in codon bias
between two genes is, statistically, a prerequisite for the corresponding
proteins to interact. Importantly, among all codon bias indices, turns
out to have the most coherent distribution over the communities of the
interactome, pointing to the significance of competition among cognate and
near-cognate tRNAs for explaining codon usage adaptation
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