Euplotes nobilii and Euplotes raikovi are phylogenetically closely allied species of marine ciliates, living in polar and temperate waters, respectively. Their evolutional relation and the sharply ...different temperatures of their natural environments make them ideal organisms to investigate thermal-adaptation. We perform a comparative study of the thermal unfolding of disulfide-rich protein pheromones produced by these ciliates. Recent circular dichroism (CD) measurements have shown that the two psychrophilic (E. nobilii) and mesophilic (E. raikovi) protein families are characterized by very different melting temperatures, despite their close structural homology. The enhanced thermal stability of the E. raikovi pheromones is realized notwithstanding the fact that these proteins form, as a rule, a smaller number of disulfide bonds. We perform Monte Carlo (MC) simulations in a structure-based coarse-grained (CG) model to show that the higher stability of the E. raikovi pheromones is due to the lower locality of the disulfide bonds, which yields a lower entropy increase in the unfolding process. Our study suggests that the higher stability of the mesophilic E. raikovi phermones is not mainly due to the presence of a strongly hydrophobic core, as it was proposed in the literature. In addition, we argue that the molecular adaptation of these ciliates may have occurred from cold to warm, and not from warm to cold. To provide a testable prediction, we identify a point-mutation of an E. nobilii pheromone that should lead to an unfolding temperature typical of that of E. raikovi pheromones.
Circular dichroism (CD) is known to be an excellent tool for the determination of protein secondary structure due to fingerprint signatures of α and β domains. However, CD spectra are also sensitive ...to the 3D arrangement of the chain as a result of the excitonic nature of additional signals due to the aromatic residues. This double sensitivity, when extended to time-resolved experiments, should allow protein folding to be monitored with high spatial resolution. To date, the exploitation of this very appealing idea has been limited, due to the difficulty in relating the observed spectral evolution to specific configurations of the chain. Here, we demonstrate that the combination of atomistic molecular dynamics simulations of the folding pathways with a quantum chemical evaluation of the excitonic spectra provides the missing key. This is exemplified for the folding of canine milk lysozyme protein.
The internal dynamics ol strongly interacting systems and that ol bio-polymers such as proteins display several important analogies, despite the huge difference in their characteristic energy and ...length scales. For example, in all such systems, collective excitations, cooperative transitions and phase transitions emerge as the result of the interplay of strong correlations with quantum or thermal fluctuations. In view of such an observation, some theoretical methods initially developed in the context of theoretical nuclear physics have been adapted to investigate the dynamics of biomolecules. In this talk, we review some of our recent studies performed along this direction. In particular, we discuss how the path integral formulation of the molecular dynamics allows to overcome some of the long-standing problems and limitations which emerge when simulating the protein folding dynamics at the atomistic level of detail.
A global analysis of ATLAS and CMS measurements reveals that, at mid-rapidity, the directly-produced
χ
c
1
,
χ
c
2
and J/
ψ
mesons have differential cross sections of seemingly identical shapes, when ...presented as a function of the mass-rescaled transverse momentum,
p
T
/
M
. This identity of kinematic behaviours among S- and P-wave quarkonia is certainly not a natural expectation of non-relativistic QCD (NRQCD), where each quarkonium state is supposed to reflect a specific family of elementary production processes, of significantly different
p
T
-differential cross sections. Remarkably, accurate kinematic cancellations among the various NRQCD terms (colour singlets and octets) of its factorization expansion can lead to a surprisingly good description of the data. This peculiar tuning of the NRQCD mixtures leads to a clear prediction regarding the
χ
c
1
and
χ
c
2
polarizations, the only observables not yet measured: they should be almost maximally different from one another, and from the J/
ψ
polarization, a striking exception in the global panorama of quarkonium production. Measurements of the difference between the
χ
c
1
,
χ
c
2
and J/
ψ
polarizations, complementing the observed identity of momentum dependences, represent a decisive probe of NRQCD.
The process q q A= ? Z Z ? 4 l , dominant background for new physics signals in the four-lepton channel, is characterized by a fully transverse polarization of the two Z bosons with respect to the q ...and q A= directions. We show that the Z decay angular distributions can be described by a simple, analytical function of the event kinematics, not depending on parton distributions. Using the search for a heavy Higgs boson as an example, we show that the angular discrimination improves the sensitivity to rare signals and is especially beneficial when the background contribution is large.
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