64,313 research outputs found
Heteropolymers in a Solvent at an Interface
Exact bounds are obtained for the quenched free energy of a polymer with
random hydrophobicities in the presence of an interface separating a polar from
a non polar solvent. The polymer may be ideal or have steric self-interactions.
The bounds allow to prove that a ``neutral'' random polymer is localized near
the interface at any temperature, whereas a ``non-neutral'' chain is shown to
undergo a delocalization transition at a finite temperature. These results are
valid for a quite general a priori probability distribution for both
independent and correlated hydrophobic charges. As a particular case we
consider random AB-copolymers and confirm recent numerical studies.Comment: 4 pages, no figure
Melting behavior and different bound states in three-stranded DNA models
Thermal denaturation of DNA is often studied with coarse-grained models in
which native sequential base pairing is mimicked by the existence of attractive
interactions only between monomers at the same position along strands (Poland
and Scheraga models). Within this framework, the existence of a three strand
DNA bound state in conditions where a duplex DNA would be in the denaturated
state was recently predicted from a study of three directed polymer models on
simplified hierarchical lattices () and in dimensions. Such
phenomenon which is similar to the Efimov effect in nuclear physics was named
Efimov-DNA. In this paper we study the melting of the three-stranded DNA on a
Sierpinski gasket of dimensions by assigning extra weight factors to fork
openings and closings, to induce a two-strand DNA melting. In such a context we
can find again the existence of the Efimov-DNA-like state but quite
surprisingly we discover also the presence of a different phase, to be called a
mixed state, where the strands are pair-wise bound but without three chain
contacts. Whereas the Efimov DNA turns out to be a crossover near melting, the
mixed phase is a thermodynamic phase.Comment: corrected file uploade
From A. rhizogenes RolD to Plant P5CS: Exploiting Proline to Control Plant Development
The capability of the soil bacterium Agrobacterium rhizogenes to reprogram plant development and induce adventitious hairy roots relies on the expression of a few root-inducing genes (rol A, B, C and D), which can be transferred from large virulence plasmids into the genome of susceptible plant cells. Contrary to rolA, B and C, which are present in all the virulent strains of A. rhizogenes and control hairy root formation by affecting auxin and cytokinin signalling, rolD appeared non-essential and not associated with plant hormones. Its role remained elusive until it was discovered that it codes for a proline synthesis enzyme. The finding that, in addition to its role in protein synthesis and stress adaptation, proline is also involved in hairy roots induction, disclosed a novel role for this amino acid in plant development. Indeed, from this initial finding, proline was shown to be critically involved in a number of developmental processes, such as floral transition, embryo development, pollen fertility and root elongation. In this review, we present a historical survey on the rol genes focusing on the role of rolD and proline in plant development
Geometrical model for the native-state folds of proteins
We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci.
USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which
incorporates, in an approximate manner, several key features such as the
inherent anisotropy of a chain molecule, the geometrical and energetic
constraints placed by the hydrogen bonds and sterics, and the role played by
hydrophobicity. Within this framework, marginally compact conformations
resembling the native state folds of proteins emerge as broad competing minima
in the free energy landscape even for a homopolymer. Here we show how the
introduction of sequence heterogeneity using a simple scheme of just two types
of amino acids, hydrophobic (H) and polar (P), and sequence design allows a
selected putative native fold to become the free energy minimum at low
temperature. The folding transition exhibits thermodynamic cooperativity, if
one neglects the degeneracy between two different low energy conformations
sharing the same fold topology.Comment: 12 pages, 3 figure
Invariant mass distribution of jet pairs produced in association with a W boson at CDF
We present a study of the invariant mass spectra of jets produced in association with a W boson decaying into a lepton and a neutrino. Events of this signature are critical to studies of vector boson pair production, top-quark physics,
Higgs boson physics, and searches for beyond the standard model particles. We present a search for high-mass resonances decaying into jets, and find no significant excess above the standard model background prediction
Protein sequence and structure: Is one more fundamental than the other?
We argue that protein native state structures reside in a novel "phase" of
matter which confers on proteins their many amazing characteristics. This phase
arises from the common features of all globular proteins and is characterized
by a sequence-independent free energy landscape with relatively few low energy
minima with funnel-like character. The choice of a sequence that fits well into
one of these predetermined structures facilitates rapid and cooperative
folding. Our model calculations show that this novel phase facilitates the
formation of an efficient route for sequence design starting from random
peptides.Comment: 7 pages, 4 figures, to appear in J. Stat. Phy
Fibril elongation mechanisms of HET-s prion-forming domain: Topological evidence for growth polarity
The prion-forming C-terminal domain of the fungal prion HET-s forms
infectious amyloid fibrils at physiological pH. The conformational switch from
the non-prion soluble form to the prion fibrillar form is believed to have a
functional role, since HET-s in its prion form participates in a recognition
process of different fungal strains. Based on the knowledge of the
high-resolution structure of HET-s(218-289) (the prion forming-domain) in its
fibrillar form, we here present a numerical simulation of the fibril growth
process which emphasizes the role of the topological properties of the
fibrillar structure. An accurate thermodynamic analysis of the way an
intervening HET-s chain is recruited to the tip of the growing fibril suggests
that elongation proceeds through a dock and lock mechanism. First, the chain
docks onto the fibril by forming the longest -strands. Then, the
re-arrangement in the fibrillar form of all the rest of molecule takes place.
Interestingly, we predict also that one side of the HET-s fibril is more
suitable for substaining its growth with respect to the other. The resulting
strong polarity of fibril growth is a consequence of the complex topology of
HET-s fibrillar structure, since the central loop of the intervening chain
plays a crucially different role in favouring or not the attachment of the
C-terminus tail to the fibril, depending on the growth side.Comment: 16 pages, 10 figure
Continuum model for polymers with finite thickness
We consider the continuum limit of a recently-introduced model for
discretized thick polymers, or tubes. We address both analytically and
numerically how the polymer thickness influences the decay of tangent-tangent
correlations and find how the persistence length scales with the thickness and
the torsional rigidity of the tube centerline. At variance with the worm-like
chain model, the phase diagram that we obtain for a continuous tube is richer;
in particular, for a given polymer thickness there exists a threshold value for
the centerline torsional rigidity separating a simple exponential decay of the
tangent-tangent correlation from an oscillatory one.Comment: 8 pages, 4 figures. Accepted for publication in J. Phys.
Proline affects the size of the root meristematic zone in Arabidopsis
We reported previously that root elongation in Arabidopsis is promoted by exogenous proline, raising the possibility that this amino acid may modulate root growth. To evaluate this hypothesis we used a combination of genetic, pharmacological and molecular analyses, and showed that proline specifically affects root growth by modulating the size of the root meristem. The effects of proline on meristem size are parallel to, and independent from, hormonal pathways, and do not involve the expression of genes controlling cell differentiation at the transition zone. On the contrary, proline appears to control cell division in early stages of postembryonic root development, as shown by the expression of the G2/M-specific CYCLINB1;1 (CYCB1;1) gene. The overall data suggest that proline can modulate the size of root meristematic zone in Arabidopsis likely controlling cell division and, in turn, the ratio between cell division and cell differentiation
- …