Light 1-+ exotics: molecular resonances

Highlights in the search for nonconventional (non qqbar) meson states are the pi_1(1400) and pi_1(1600) exotic candidates. Should they exist, mounting theoretical arguments suggest that they are tetraquark molecular resonances excitable by meson rescattering. We report a new tetraquark calculation within a model field theory approximation to Quantum Chromodynamics in the Coulomb gauge supporting this conjecture. We also strengthen this claim by consistently contrasting results with exotic state predictions for hybrid (q qbar g) mesons within the same theoretical framework. Our findings confirm that molecular-like configurations involving two color singlets (a resonance, not a bound state) are clearly favored over hybrid or color-exotic tetraquark meson (q qbar q qbar atoms) formation. Finally, to assist needed further experimental searches we document a useful off-plane correlator for establishing the structure of these exotic systems along with similar, but anticipated much narrower, states that should exist in the charmonium and bottomonium spectra.Comment: 12 pages, 8 figure

Meson and tetra-quark mixing

The mixing between q-qbar meson and qqbar-qqbar tetra-quark states is examined within an effective QCD Coulomb gauge Hamiltonian model. Mixing matrix elements of the Hamiltonian are computed and then diagonalized yielding an improved prediction for the low-lying J^{PC} = 0^{+/- +}, 1^{--} isoscalar spectra. Mixing effects were found significant for the scalar hadrons but not for the 1^{--} states, which is consistent with the ideal mixing of vector mesons. A perturbative assessment of the exact QCD kernel is also reported.Comment: 7 pages, 6 figure

ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones

The versatile functions of the heat shock protein 70 (Hsp70) family of molecular chaperones rely on allosteric interactions between their nucleotide-binding and substrate-binding domains, NBD and SBD. Understanding the mechanism of interdomain allostery is essential to rational design of Hsp70 modulators. Yet, despite significant progress in recent years, how the two Hsp70 domains regulate each other's activity remains elusive. Covariance data from experiments and computations emerged in recent years as valuable sources of information towards gaining insights into the molecular events that mediate allostery. In the present study, conservation and covariance properties derived from both sequence and structural dynamics data are integrated with results from Perturbation Response Scanning and in vivo functional assays, so as to establish the dynamical basis of interdomain signal transduction in Hsp70s. Our study highlights the critical roles of SBD residues D481 and T417 in mediating the coupled motions of the two domains, as well as that of G506 in enabling the movements of the α-helical lid with respect to the β-sandwich. It also draws attention to the distinctive role of the NBD subdomains: Subdomain IA acts as a key mediator of signal transduction between the ATP- and substrate-binding sites, this function being achieved by a cascade of interactions predominantly involving conserved residues such as V139, D148, R167 and K155. Subdomain IIA, on the other hand, is distinguished by strong coevolutionary signals (with the SBD) exhibited by a series of residues (D211, E217, L219, T383) implicated in DnaJ recognition. The occurrence of coevolving residues at the DnaJ recognition region parallels the behavior recently observed at the nucleotide-exchange-factor recognition region of subdomain IIB. These findings suggest that Hsp70 tends to adapt to co-chaperone recognition and activity via coevolving residues, whereas interdomain allostery, critical to chaperoning, is robustly enabled by conserved interactions. © 2014 General et al

Structure and dynamics of Penetratin’s association and translocation to a lipid bilayer

Penetratin belongs to the important class of small and positively charged peptides, capable of entering cells. The determination of the optimal peptidic structure for translocation is challenging; results obtained so far are varied and dependent on several factors. In this work, we review the dynamics of association of Penetratin with a modeled dioleoyl-phosphatidylcholine (DOPC) lipid membrane using molecular dynamics simulations with last generation force fields. Penetratin’s structural preferences are determined using a Markov state model. It is observed that the peptide retains a helical form in the membrane associated state, just as in water, with the exception of both termini which lose helicity, facilitating the interaction of terminal residues with the phosphate groups on the membrane’s outer layer. The optimal orientation for insertion is found to be with the peptide’s axis forming a small angle with the interface, and with R1 stretching toward the bilayer. The interaction between arginine side-chains and phosphate groups is found to be greater than the corresponding to lysine, mainly due to a higher number of hydrogen bonds between them. The free energy profile of translocation is qualitatively studied using Umbrella Sampling. It is found that there are different paths of penetration, that greatly differ in size of free energy barrier. The lowest path is compatible with residues R10 to K13 leading the way through the membrane and pulling the rest of the peptide. When the other side is reached, the C-terminus overtakes those residues, and finally breaks out of the membrane. The peptide’s secondary structure during this traversal suffers some changes with respect to the association structure but, overall, conserves its helicity, with both termini in a more disordered state

QCD Coulomb Gauge Approach to Exotic Hadrons

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