591 research outputs found
Parallel computing and molecular dynamics of biological membranes
In this talk I discuss the general question of the portability of Molecular
Dynamics codes for diffusive systems on parallel computers of the APE family.
The intrinsic single precision arithmetics of the today available APE platforms
does not seem to affect the numerical accuracy of the simulations, while the
absence of integer addressing from CPU to individual nodes puts strong
constraints on the possible programming strategies. Liquids can be very
satisfactorily simulated using the "systolic" method. For more complex systems,
like the biological ones at which we are ultimately interested in, the "domain
decomposition" approach is best suited to beat the quadratic growth of the
inter-molecular computational time with the number of elementary components of
the system. The promising perspectives of using this strategy for extensive
simulations of lipid bilayers are briefly reviewed.Comment: 4 pages LaTeX, 2 figures included, espcrc2.sty require
Ab initio simulations of Cu binding sites in the N-terminal region of PrP
The prion protein (PrP) binds Cu2+ ions in the octarepeat domain of the
N-terminal tail up to full occupancy at pH=7.4. Recent experiments show that
the HGGG octarepeat subdomain is responsible for holding the metal bound in a
square planar coordination. By using first principle ab initio molecular
dynamics simulations of the Car-Parrinello type, the Cu coordination mode to
the binding sites of the PrP octarepeat region is investigated. Simulations are
carried out for a number of structured binding sites. Results for the complexes
Cu(HGGGW)+(wat), Cu(HGGG) and the 2[Cu(HGGG)] dimer are presented. While the
presence of a Trp residue and a H2O molecule does not seem to affect the nature
of the Cu coordination, high stability of the bond between Cu and the amide
Nitrogens of deprotonated Gly's is confirmed in the case of the Cu(HGGG)
system. For the more interesting 2[Cu(HGGG)] dimer a dynamically entangled
arrangement of the two monomers, with intertwined N-Cu bonds, emerges. This
observation is consistent with the highly packed structure seen in experiments
at full Cu occupancy.Comment: 4 pages, conference proceedin
A simple atomistic model for the simulation of the gel phase of lipid bilayers
In this paper we present the results of a large-scale numerical investigation
of structural properties of a model of cell membrane, simulated as a bilayer of
flexible molecules in vacuum. The study was performed by carrying out extensive
Molecular Dynamics simulations, in the (NVE) micro-canonical ensemble, of two
systems of different sizes (2x32 and 2x256 molecules), over a fairly large set
of temperatures and densities, using parallel platforms and more standard
serial computers. Depending on the dimension of the system, the dynamics was
followed for physical times that go from few hundred of picoseconds for the
largest system to 5--10 nanoseconds for the smallest one. We find that the
bilayer remains stable even in the absence of water and neglecting Coulomb
interactions in the whole range of temperatures and densities we have
investigated. The extension of the region of physical parameters that we have
explored has allowed us to study significant points in the phase diagram of the
bilayer and to expose marked structural changes as density and temperature are
varied, which are interpreted as the system passing from a crystal to a gel
phase.Comment: 41 pages, 13 figure
Measuring shared electrons in extended molecular systems: Covalent bonds from plane-wave representation of wave function
In the study of materials and macromolecules by first-principle methods, the bond order is a useful tool to represent molecules, bulk materials and interfaces in terms of simple chemical concepts. Despite the availability of several methods to compute the bond order, most applications have been limited to small systems because a high spatial resolution of the wave function and an all-electron representation of the electron density are typically required. Both limitations are critical for large-scale atomistic calculations, even within approximate density-functional theory (DFT) approaches. In this work, we describe our methodology to quickly compute delocalization indices for all atomic pairs, while keeping the same representation of the wave function used in most compute-intensive DFT calculations on high-performance computing equipment. We describe our implementation into a post-processing tool, designed to work with Quantum ESPRESSO, a popular open-source DFT package. In this way, we recover a description in terms of covalent bonds from a representation of wave function containing no explicit information about atomic types and positions
Zn-induced interactions between SARS-CoV-2 orf7a and BST2/Tetherin
We present in this work a first X-ray Absorption Spectroscopy study of the interactions of Zn with human BST2/tetherin and SARS-CoV-2 orf7a proteins as well as with some of their complexes. The analysis of the XANES region of the measured spectra shows that Zn binds to BST2, as well as to orf7a, thus resulting in the formation of BST2-orf7a complexes. This structural information confirms the the conjecture, recently put forward by some of the present Authors, according to which the accessory orf7a (and possibly also orf8) viral protein are capable of interfering with the BST2 antiviral activity. Our explanation for this behavior is that, when BST2 gets in contact with Zn bound to the orf7a Cys(15) ligand, it has the ability of displacing the metal owing to the creation of a new disulfide bridge across the two proteins. The formation of this BST2-orf7a complex destabilizes BST2 dimerization, thus impairing the antiviral activity of the latter
The role of Zn ions in the interaction between SARS-CoV-2 orf7a protein and BST2/tetherin
In this paper, we provide evidence that Zn2+ ions play a role in the SARS-CoV-2 virus strategy to escape the immune response mediated by the BST2-tetherin host protein. This conclusion is based on sequence analysis and molecular dynamics simulations as well as X-ray absorption experiments [1]
The role of Zn ions in the interaction between SARS-CoV-2 orf7a protein and BST2/tetherin
In this paper, we provide evidence that Zn2+ ions play a role in the SARS-CoV-2 virus strategy to escape the immune response mediated by the BST2-tetherin host protein. This conclusion is based on sequence analysis and molecular dynamics simulations as well as X-ray absorption experiments
Metal ion binding in wild-type and mutated frataxin: a stability study
This work studies the stability of wild-type frataxin and some of its variants found in cancer tissues upon Co2+ binding. Although the physiologically involved metal ion in the frataxin enzymatic activity is Fe2+, as it is customarily done, Co2+ is most often used in experiments because Fe2+ is extremely unstable owing to the fast oxidation reaction Fe2+ → Fe3+. Protein stability is monitored following the conformational changes induced by Co2+ binding as measured by circular dichroism, fluorescence spectroscopy, and melting temperature measurements. The stability ranking among the wild-type frataxin and its variants obtained in this way is confirmed by a detailed comparative analysis of the XAS spectra of the metal-protein complex at the Co K-edge. In particular, a fit to the EXAFS region of the spectrum allows positively identifying the frataxin acidic ridge as the most likely location of the metal-binding sites. Furthermore, we can explain the surprising feature emerging from a detailed analysis of the XANES region of the spectrum, showing that the longer 81-210 frataxin fragment has a smaller propensity for Co2+ binding than the shorter 90-210 one. This fact is explained by the peculiar role of the N-terminal disordered tail in modulating the protein ability to interact with the metal
Optical response of a misaligned and suspended Fabry-Perot cavity
The response to a probe laser beam of a suspended, misaligned and detuned
optical cavity is examined. A five degree of freedom model of the fluctuations
of the longitudinal and transverse mirror coordinates is presented. Classical
and quantum mechanical effects of radiation pressure are studied with the help
of the optical stiffness coefficients and the signals provided by an FM
sideband technique and a quadrant detector, for generic values of the product
of the fluctuation frequency times the cavity round trip. A
simplified version is presented for the case of small misalignments. Mechanical
stability, mirror position entanglement and ponderomotive squeezing are
accommodated in this model. Numerical plots refer to cavities under test at the
so-called Pisa LF facility.Comment: 14 pages (4 figures) submitted to Phys. Rev.
Displacement power spectrum measurement of a macroscopic optomechanical system at thermal equilibrium
The mirror relative motion of a suspended Fabry-Perot cavity is studied in
the frequency range 3-10 Hz. The experimental measurements presented in this
paper, have been performed at the Low Frequency Facility, a high finesse
optical cavity 1 cm long suspended to a mechanical seismic isolation system
identical to that one used in the VIRGO experiment. The measured relative
displacement power spectrum is compatible with a system at thermal equilibrium
within its environmental. In the frequency region above 3 Hz, where seismic
noise contamination is negligible, the measurement distribution is stationary
and Gaussian, as expected for a system at thermal equilibrium. Through a simple
mechanical model it is shown that: applying the fluctuation dissipation theorem
the measured power spectrum is reproduced below 90 Hz and noise induced by
external sources are below the measurement.Comment: 11 pages, 9 figures, 2 tables, to be submitte
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