Spial: analysis of subtype-specific features in multiple sequence alignments of proteins

Motivation: Spial (Specificity in alignments) is a tool for the comparative analysis of two alignments of evolutionarily related sequences that differ in their function, such as two receptor subtypes. It highlights functionally important residues that are either specific to one of the two alignments or conserved across both alignments. It permits visualization of this information in three complementary ways: by colour-coding alignment positions, by sequence logos and optionally by colour-coding the residues of a protein structure provided by the user. This can aid in the detection of residues that are involved in the subtype-specific interaction with a ligand, other proteins or nucleic acids. Spial may also be used to detect residues that may be post-translationally modified in one of the two sets of sequences

The hadron-quark phase transition in dense matter and neutron stars

We study the hadron-quark phase transition in the interior of neutron stars (NS's). We calculate the equation of state (EOS) of hadronic matter using the Brueckner-Bethe-Goldstone formalism with realistic two-body and three-body forces, as well as a relativistic mean field model. For quark matter we employ the MIT bag model constraining the bag constant by using the indications coming from the recent experimental results obtained at the CERN SPS on the formation of a quark-gluon plasma. We find necessary to introduce a density dependent bag parameter, and the corresponding consistent thermodynamical formalism. We calculate the structure of NS interiors with the EOS comprising both phases, and we find that the NS maximum masses fall in a relatively narrow interval, $1.4 M_\odot \leq M_{\rm max} \leq 1.7 M_\odot$. The precise value of the maximum mass turns out to be only weakly correlated with the value of the energy density at the assumed transition point in nearly symmetric nuclear matter.Comment: 25 pages, Revtex4, 16 figures included as postscrip

Modeling the strangeness content of hadronic matter

The strangeness content of hadronic matter is studied in a string-flip model that reproduces various aspects of the QCD-inspired phenomenology, such as quark clustering at low density and color deconfinement at high density, while avoiding long range van der Waals forces. Hadronic matter is modeled in terms of its quark constituents by taking into account its internal flavor (u,d,s) and color (red, blue, green) degrees of freedom. Variational Monte-Carlo simulations in three spatial dimensions are performed for the ground-state energy of the system. The onset of the transition to strange matter is found to be influenced by weak, yet not negligible, clustering correlations. The phase diagram of the system displays an interesting structure containing both continuous and discontinuous phase transitions. Strange matter is found to be absolutely stable in the model.Comment: 14 pages, 1 table, 8 eps figures, revtex. Submitted to Phys. Rev. C, Presented at INPC2001 Berkeley, Ca. july 29-Aug

Hybrid stars with the color dielectric and the MIT bag models

We study the hadron-quark phase transition in the interior of neutron stars (NS). For the hadronic sector, we use a microscopic equation of state (EOS) involving nucleons and hyperons derived within the Brueckner-Bethe-Goldstone many-body theory, with realistic two-body and three-body forces. For the description of quark matter, we employ both the MIT bag model with a density dependent bag constant, and the color dielectric model. We calculate the structure of NS interiors with the EOS comprising both phases, and we find that the NS maximum masses are never larger than 1.7 solar masses, no matter the model chosen for describing the pure quark phase.Comment: 11 pages, 5 figures, submitted to Phys. Rev.

Insights into congenital stationary night blindness based on the structure of G90D rhodopsin

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102109/1/embr201344.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/102109/2/embr201344.reviewer_comments.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/102109/3/embr201344-sup-0001.pd

Phase transitions of hadronic to quark matter at finite T and \mu_B

The phase transition of hadronic to quark matter and the boundaries of the mixed hadron-quark coexistence phase are studied within the two Equation of State (EoS) model. The relativistic effective mean field approach with constant and density dependent meson-nucleon couplings is used to describe hadronic matter, and the MIT Bag model is adopted to describe quark matter. The boundaries of the mixed phase for different Bag constants are obtained solving the Gibbs equations. We notice that the dependence on the Bag parameter of the critical temperatures (at zero chemical potential) can be well reproduced by a fermion ultrarelativistic quark gas model, without contribution from the hadron part. At variance the critical chemical potentials (at zero temperature) are very sensitive to the EoS of the hadron sector. Hence the study of the hadronic EoS is much more relevant for the determination of the transition to the quark-gluon-plasma at finite baryon density and low-T. Moreover in the low temperature and finite chemical potential region no solutions of the Gibbs conditions are existing for small Bag constant values, B < (135 MeV)^4. Isospin effects in asymmetric matter appear relevant in the high chemical potential regions at lower temperatures, of interest for the inner core properties of neutron stars and for heavy ion collisions at intermediate energies.Comment: 24 pages and 16 figures (revtex4

The importance of the mixed phase in hybrid stars built with the Nambu-Jona-Lasinio model

We investigate the structure of hybrid stars based on two different constructions: one is based on the Gibbs condition for phase coexistence and considers the existence of a mixed phase (MP), and the other is based on the Maxwell construction and no mixed phase is obtained. The hadron phase is described by the non-linear Walecka model (NLW) and the quark phase by the Nambu-Jona-Lasinio model (NJL). We conclude that the masses and radii obtained are model dependent but not significantly different for both constructions.Comment: 8 pages, 7 figures, 3 table

Crystal structure of rhodopsin in complex with a mini-G_o sheds light on the principles of G protein selectivity

Selective coupling of G protein (heterotrimeric guanine nucleotide–binding protein)–coupled receptors (GPCRs) to specific Gα-protein subtypes is critical to transform extracellular signals, carried by natural ligands and clinical drugs, into cellular responses. At the center of this transduction event lies the formation of a signaling complex between the receptor and G protein. We report the crystal structure of light-sensitive GPCR rhodopsin bound to an engineered mini-Go protein. The conformation of the receptor is identical to all previous structures of active rhodopsin, including the complex with arrestin. Thus, rhodopsin seems to adopt predominantly one thermodynamically stable active conformation, effectively acting like a “structural switch,” allowing for maximum efficiency in the visual system. Furthermore, our analysis of the well-defined GPCR–G protein interface suggests that the precise position of the carboxyl-terminal “hook-like” element of the G protein (its four last residues) relative to the TM7/helix 8 (H8) joint of the receptor is a significant determinant in selective G protein activation

Are strange stars distinguishable from neutron stars by their cooling behaviour?

The general statement that strange stars cool more rapidly than neutron stars is investigated in greater detail. It is found that the direct Urca process could be forbidden not only in neutron stars but also in strange stars. If so, strange stars would be slowly cooling and their surface temperatures would be more or less indistinguishable from those of slowly cooling neutron stars. The case of enhanced cooling is reinvestigated as well. It is found that strange stars cool significantly more rapidly than neutron stars within the first $\sim 30$ years after birth. This feature could become particularly interesting if continued observation of SN 1987A would reveal the temperature of the possibly existing pulsar at its centre.Comment: 10 pages, 3 ps-figures, to appear in the proceedings of the International Symposium on ''Strangeness in Quark Matter 1997``, April 14--18, Thera (Santorini), Hella

Strange quark stars within the Nambu-Jona-Lasinio model

We investigate the properties of charge-neutral $\beta$-equilibrium cold quark matter within the Nambu-Jona-Lasinio model. The calculations are carried out for different ratios of coupling constants characterizing the vector and scalar 4-fermion interaction, $\xi\equiv G_V/G_S$. It is shown that for $\xi < 0.4$ matter is self-bound and for $\xi < 0.65$ it has a first order phase transition of the liquid-gas type. The Gibbs conditions in the mixed phase are applied for the case of two chemical potentials associated with the baryon number and electric charge. The characteristics of the quark stars are calculated for $\xi = 0, 0.5$ and 1. It is found that the phase transition leads to a strong density variation at the surface of these stars. For $\xi = 1$ the properties of quark stars show behaviors typical for neutron stars. At \xi\goo 0.4 the stars near to the maximum mass have a large admixture of strange quarks in their interiors.Comment: 22 pages, 8 ps-figures, Submitted to PR