Structural Basis of the Association of HIV-1 Matrix Protein with DNA

HIV-1 matrix (MA) is a multifunctional protein that is synthesized as a polyprotein that is cleaved by protease during viral maturation. MA contains a cluster of basic residues whose role is controversial. Proposed functions include membrane anchoring, facilitating viral assembly, and directing nuclear import of the viral DNA. Since MA has been reported to be a component of the preintegration complex (PIC), we have used NMR to probe its interaction with other PIC components. We show that MA interacts with DNA and this is likely sufficient to account for its association with the PIC

Electronic and Structural Properties of a 4d-Perovskite: Cubic Phase of SrZrO3_3

First-principles density functional calculations are performed within the local density approximation to study the electronic properties of SrZrO$_3$, an insulating 4d-perovskite, in its high-temperature cubic phase, above 1400 K, as well as the generic 3d-perovskite SrTiO$_3$, which is also a d^0-insulator and cubic above 105 K, for comparison reasons. The energy bands, density of states and charge density distributions are obtained and a detailed comparison between their band structures is presented. The results are discussed also in terms of the existing data in the literature for both oxides.Comment: 5 pages, 2 figure

Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy

Many biomolecular interactions proceed via a short-lived encounter state, consisting of multiple, lowly-populated species invisible to most experimental techniques. Recent development of paramagnetic relaxation enhancement (PRE) nuclear magnetic resonance (NMR) spectroscopy has allowed to directly visualize such transient intermediates in a number of protein-protein and protein-DNA complexes. Here we present an analysis of the recently published PRE NMR data for a protein complex of yeast cytochrome c (Cc) and cytochrome c peroxidase (CcP). First, we describe a simple, general method to map out the spatial and temporal distributions of binding geometries constituting the Cc-CcP encounter state. We show that the spatiotemporal mapping provides a reliable estimate of the experimental coverage and, at higher coverage levels, allows to delineate the conformational space sampled by the minor species. To further refine the encounter state, we performed PRE-based ensemble simulations. The generated solutions reproduce well the experimental data and lie within the allowed regions of the encounter maps, confirming the validity of the mapping approach. The refined encounter ensembles are distributed predominantly in a region encompassing the dominant form of the complex, providing experimental proof for the results of classical theoretical simulations

Jahn-Teller effects and surface interactions in multiply-charged fullerene anions and the effect on scanning tunneling microscopy images

We investigate the combined effects of Jahn-Teller (JT) coupling and interactions with a surface substrate on fullerene anions C$_{60}^{2-}$ to C$_{60}^{4-}$. JT coupling alone causes the C$_{60}$ ions to instantaneously distort from the icosahedral symmetry of the neutral molecule to a lower symmetry, with the molecule moving dynamically between a set of equivalent distortions. When adsorbed on a surface, the number of equivalent minimum-energy distortions is reduced. The implications of this on observed scanning tunneling microscopy (STM) images will be discussed, and comparisons made with existing experimental data. We show that a consistent interpretation of the images from all of the charge states of C$_{60}$ can only be obtained using a JT model in which the symmetry is further reduced by surface interactions. The comparison with experimental data also allows us to determine relationships between the quadratic Jahn-Teller coupling and surface interaction parameters

Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target-methylated DNA sequence

The epigenetic code of DNA methylation is interpreted chiefly by methyl cytosine binding domain (MBD) proteins which in turn recruit multiprotein co-repressor complexes. We previously isolated one such complex, MBD2-NuRD, from primary erythroid cells and have shown it contributes to embryonic/fetal β-type globin gene silencing during development. This complex has been implicated in silencing tumor suppressor genes in a variety of human tumor cell types. Here we present structural details of chicken MBD2 bound to a methylated DNA sequence from the ρ-globin promoter to which it binds in vivo and mediates developmental transcriptional silencing in normal erythroid cells. While previous studies have failed to show sequence specificity for MBD2 outside of the symmetric mCpG, we find that this domain binds in a single orientation on the ρ-globin target DNA sequence. Further, we show that the orientation and affinity depends on guanine immediately following the mCpG dinucleotide. Dynamic analyses show that DNA binding stabilizes the central β-sheet, while the N- and C-terminal regions of the protein maintain mobility. Taken together, these data lead to a model in which DNA binding stabilizes the MBD2 structure and that binding orientation and affinity is influenced by the DNA sequence surrounding the central mCpG

The effect of compressive strain on the Raman modes of the dry and hydrated BaCe0.8Y0.2O3 proton conductor

The BaCe0.8Y0.2O3-{\delta} proton conductor under hydration and under compressive strain has been analyzed with high pressure Raman spectroscopy and high pressure x-ray diffraction. The pressure dependent variation of the Ag and B2g bending modes from the O-Ce-O unit is suppressed when the proton conductor is hydrated, affecting directly the proton transfer by locally changing the electron density of the oxygen ions. Compressive strain causes a hardening of the Ce-O stretching bond. The activation barrier for proton conductivity is raised, in line with recent findings using high pressure and high temperature impedance spectroscopy. The increasing Raman frequency of the B1g and B3g modes thus implies that the phonons become hardened and increase the vibration energy in the a-c crystal plane upon compressive strain, whereas phonons are relaxed in the b-axis, and thus reveal softening of the Ag and B2g modes. Lattice toughening in the a-c crystal plane raises therefore a higher activation barrier for proton transfer and thus anisotropic conductivity. The experimental findings of the interaction of protons with the ceramic host lattice under external strain may provide a general guideline for yet to develop epitaxial strained proton conducting thin film systems with high proton mobility and low activation energy

High-resolution structure determination of the CylR2 homodimer using paramagnetic relaxation enhancement and structure-based prediction of molecular alignment

Structure determination of homooligomeric proteins by NMR spectroscopy is difficult due to the lack of chemical shift perturbation data, which is very effective in restricting the binding interface in heterooligomeric systems, and the difficulty of obtaining a sufficient number of intermonomer distance restraints. Here we solved the high-resolution solution structure of the 15.4 kDa homodimer CylR2, the regulator of cytolysin production from Enterococcus faecalis, which deviates by 1.1 Å from the previously determined X-ray structure. We studied the influence of different experimental information such as long-range distances derived from paramagnetic relaxation enhancement, residual dipolar couplings, symmetry restraints and intermonomer Nuclear Overhauser Effect restraints on the accuracy of the derived structure. In addition, we show that it is useful to combine experimental information with methods of ab initio docking when the available experimental data are not sufficient to obtain convergence to the correct homodimeric structure. In particular, intermonomer distances may not be required when residual dipolar couplings are compared to values predicted on the basis of the charge distribution and the shape of ab initio docking solutions

Modular protein-RNA interactions regulating mRNA metabolism: a role for NMR

Here we review the role played by transient interactions between multi-functional proteins and their RNA targets in the regulation of mRNA metabolism, and we describe the important function of NMR spectroscopy in the study of these systems. We place emphasis on a general approach for the study of different features of modular multi-domain recognition that uses well-established NMR techniques and that has provided important advances in the general understanding of post-transcriptional regulation

Cooling quasiparticles in A(3)C(60) fullerides by excitonic mid-infrared absorption

Long after its discovery, superconductivity in alkali fullerides A(3)C(60) still challenges conventional wisdom. The freshest inroad in such ever-surprising physics is the behaviour under intense infrared excitation. Signatures attributable to a transient superconducting state extending up to temperatures ten times higher than the equilibrium T-c similar to 20 K have been discovered in K3C60 after ultra-short pulsed infrared irradiation-an effect which still appears as remarkable as mysterious. Motivated by the observation that the phenomenon is observed in a broad pumping frequency range that coincides with the mid-infrared electronic absorption peak still of unclear origin, rather than to transverse optical phonons as has been proposed, we advance here a radically new mechanism. First, we argue that this broad absorption peak represents a 'super-exciton' involving the promotion of one electron from the t(1u) half-filled state to a higher-energy empty t(1g) state, dramatically lowered in energy by the large dipole-dipole interaction acting in conjunction with the Jahn-Teller effect within the enormously degenerate manifold of (t(1u))(2)(t(1g))(1) states. Both long-lived and entropy-rich because they are triplets, the infrared-induced excitons act as a sort of cooling mechanism that permits transient superconductive signals to persist up to much higher temperatures