81,763 research outputs found
Loop-closure principles in protein folding
Simple theoretical concepts and models have been helpful to understand the
folding rates and routes of single-domain proteins. As reviewed in this
article, a physical principle that appears to underly these models is loop
closure.Comment: 27 pages, 5 figures; to appear in Archives of Biochemistry and
Biophysic
Single DNA conformations and biological function
From a nanoscience perspective, cellular processes and their reduced in vitro
imitations provide extraordinary examples for highly robust few or single
molecule reaction pathways. A prime example are biochemical reactions involving
DNA molecules, and the coupling of these reactions to the physical
conformations of DNA. In this review, we summarise recent results on the
following phenomena: We investigate the biophysical properties of DNA-looping
and the equilibrium configurations of DNA-knots, whose relevance to biological
processes are increasingly appreciated. We discuss how random DNA-looping may
be related to the efficiency of the target search process of proteins for their
specific binding site on the DNA molecule. And we dwell on the spontaneous
formation of intermittent DNA nanobubbles and their importance for biological
processes, such as transcription initiation. The physical properties of DNA may
indeed turn out to be particularly suitable for the use of DNA in nanosensing
applications.Comment: 53 pages, 45 figures. Slightly revised version of a review article,
that is going to appear in the J. Comput. Theoret. Nanoscience; some typos
correcte
Modeling Structure and Resilience of the Dark Network
While the statistical and resilience properties of the Internet are no more
changing significantly across time, the Darknet, a network devoted to keep
anonymous its traffic, still experiences rapid changes to improve the security
of its users. Here, we study the structure of the Darknet and we find that its
topology is rather peculiar, being characterized by non-homogenous distribution
of connections -- typical of scale-free networks --, very short path lengths
and high clustering -- typical of small-world networks -- and lack of a core of
highly connected nodes.
We propose a model to reproduce such features, demonstrating that the
mechanisms used to improve cyber-security are responsible for the observed
topology. Unexpectedly, we reveal that its peculiar structure makes the Darknet
much more resilient than the Internet -- used as a benchmark for comparison at
a descriptive level -- to random failures, targeted attacks and cascade
failures, as a result of adaptive changes in response to the attempts of
dismantling the network across time.Comment: 8 pages, 5 figure
Recommended from our members
The Rabl configuration limits topological entanglement of chromosomes in budding yeast.
The three dimensional organization of genomes remains mostly unknown due to their high degree of condensation. Biophysical studies predict that condensation promotes the topological entanglement of chromatin fibers and the inhibition of function. How organisms balance between functionally active genomes and a high degree of condensation remains to be determined. Here we hypothesize that the Rabl configuration, characterized by the attachment of centromeres and telomeres to the nuclear envelope, helps to reduce the topological entanglement of chromosomes. To test this hypothesis we developed a novel method to quantify chromosome entanglement complexity in 3D reconstructions obtained from Chromosome Conformation Capture (CCC) data. Applying this method to published data of the yeast genome, we show that computational models implementing the attachment of telomeres or centromeres alone are not sufficient to obtain the reduced entanglement complexity observed in 3D reconstructions. It is only when the centromeres and telomeres are attached to the nuclear envelope (i.e. the Rabl configuration) that the complexity of entanglement of the genome is comparable to that of the 3D reconstructions. We therefore suggest that the Rabl configuration is an essential player in the simplification of the entanglement of chromatin fibers
Testing simplified protein models of the hPin1 WW domain
The WW domain of the human Pin1 protein for its simple topology and the large
amount of experimental data is an ideal candidate to assess theoretical
approaches to protein folding. The purpose of the present work is to compare
the reliability of the chemically-based Sorenson/Head-Gordon (SHG) model and a
standard native centric model in reproducing through molecular dynamics
simulations some of the well known features of the folding transition of this
small domain. Our results show that the G\={o} model correctly reproduces the
cooperative, two-state, folding mechanism of the WW-domain, while the SHG model
predicts a transition occurring in two stages: a collapse followed by a
structural rearrangement. The lack of a cooperative folding in the SHG
simulations appears to be related to the non-funnel shape of the energy
landscape featuring a partitioning of the native valley in sub-basins
corresponding to different chain chiralities. However the SHG approach remains
more reliable in estimating the -values with respect to G\={o}-like
description. This may suggest that the WW-domain folding process is stirred by
energetic and topological factors as well, and it highlights the better
suitability of chemically-based models in simulating mutations.Comment: RevTex4: 12 pages and 13 eps-figure file
- …