Intrinsic nucleic acid dynamics modulates HIV-1 nucleocapsid protein binding to its targets

HIV-1 nucleocapsid protein (NC) is involved in the rearrangement of nucleic acids occurring in key steps of reverse transcription. The protein, through its two zinc fingers, interacts preferentially with unpaired guanines in single-stranded sequences. In mini-cTAR stem-loop, which corresponds to the top half of the cDNA copy of the transactivation response element of the HIV-1 genome, NC was found to exhibit a clear preference for the TGG sequence at the bottom of mini-cTAR stem. To further understand how this site was selected among several potential binding sites containing unpaired guanines, we probed the intrinsic dynamics of mini-cTAR using (13)C relaxation measurements. Results of spin relaxation time measurements have been analyzed using the model-free formalism and completed by dispersion relaxation measurements. Our data indicate that the preferentially recognized guanine in the lower part of the stem is exempt of conformational exchange and highly mobile. In contrast, the unrecognized unpaired guanines of mini-cTAR are involved in conformational exchange, probably related to transient base-pairs. These findings support the notion that NC preferentially recognizes unpaired guanines exhibiting a high degree of mobility. The ability of NC to discriminate between close sequences through their dynamic properties contributes to understanding how NC recognizes specific sites within the HIV genome

PloS one

The HIV-1 nucleocapsid protein (NC) is a small basic protein containing two zinc fingers (ZF) separated by a short linker. It is involved in several steps of the replication cycle and acts as a nucleic acid chaperone protein in facilitating nucleic acid strand transfers occurring during reverse transcription. Recent analysis of three-dimensional structures of NC-nucleic acids complexes established a new property: the unpaired guanines targeted by NC are more often inserted in the C-terminal zinc finger (ZF2) than in the N-terminal zinc finger (ZF1). Although previous NMR dynamic studies were performed with NC, the dynamic behavior of the linker residues connecting the two ZF domains remains unclear. This prompted us to investigate the dynamic behavior of the linker residues. Here, we collected 15N NMR relaxation data and used for the first time data at several fields to probe the protein dynamics. The analysis at two fields allows us to detect a slow motion occurring between the two domains around a hinge located in the linker at the G35 position. However, the amplitude of motion appears limited in our conditions. In addition, we showed that the neighboring linker residues R29, A30, P31, R32, K33 displayed restricted motion and numerous contacts with residues of ZF1. Our results are fully consistent with a model in which the ZF1-linker contacts prevent the ZF1 domain to interact with unpaired guanines, whereas the ZF2 domain is more accessible and competent to interact with unpaired guanines. In contrast, ZF1 with its large hydrophobic plateau is able to destabilize the double-stranded regions adjacent to the guanines bound by ZF2. The linker residues and the internal dynamics of NC regulate therefore the different functions of the two zinc fingers that are required for an optimal chaperone activity

Unprocessed Viral DNA Could Be the Primary Target of the HIV-1 Integrase Inhibitor Raltegravir

Integration of HIV DNA into host chromosome requires a 3′-processing (3′-P) and a strand transfer (ST) reactions catalyzed by virus integrase (IN). Raltegravir (RAL), commonly used in AIDS therapy, belongs to the family of IN ST inhibitors (INSTIs) acting on IN-viral DNA complexes (intasomes). However, studies show that RAL fails to bind IN alone, but nothing has been reported on the behaviour of RAL toward free viral DNA. Here, we assessed whether free viral DNA could be a primary target for RAL, assuming that the DNA molecule is a receptor for a huge number of pharmacological agents. Optical spectroscopy, molecular dynamics and free energy calculations, showed that RAL is a tight binder of both processed and unprocessed LTR (long terminal repeat) ends. Complex formation involved mainly van der Waals forces and was enthalpy driven. Dissociation constants (Kds) revealed that RAL affinity for unbound LTRs was stronger than for bound LTRs. Moreover, Kd value for binding of RAL to LTRs and IC50 value (half concentration for inhibition) were in same range, suggesting that RAL binding to DNA and ST inhibition are correlated events. Accommodation of RAL into terminal base-pairs of unprocessed LTR is facilitated by an extensive end fraying that lowers the RAL binding energy barrier. The RAL binding entails a weak damping of fraying and correlatively of 3′-P inhibition. Noteworthy, present calculated RAL structures bound to free viral DNA resemble those found in RAL-intasome crystals, especially concerning the contacts between the fluorobenzyl group and the conserved 5′C4pA33′ step. We propose that RAL inhibits IN, in binding first unprocessed DNA. Similarly to anticancer drug poisons acting on topoisomerases, its interaction with DNA does not alter the cut, but blocks the subsequent joining reaction. We also speculate that INSTIs having viral DNA rather IN as main target could induce less resistance

The HIV-1 Integrase α4-Helix Involved in LTR-DNA Recognition Is also a Highly Antigenic Peptide Element

Monoclonal antibodies (MAbas) constitute remarkable tools to analyze the relationship between the structure and the function of a protein. By immunizing a mouse with a 29mer peptide (K159) formed by residues 147 to 175 of the HIV-1 integrase (IN), we obtained a monoclonal antibody (MAba4) recognizing an epitope lying in the N-terminal portion of K159 (residues 147–166 of IN). The boundaries of the epitope were determined in ELISA assays using peptide truncation and amino acid substitutions. The epitope in K159 or as a free peptide (pep-a4) was mostly a random coil in solution, while in the CCD (catalytic core domain) crystal, the homologous segment displayed an amphipathic helix structure (α4-helix) at the protein surface. Despite this conformational difference, a strong antigenic crossreactivity was observed between pep-a4 and the protein segment, as well as K156, a stabilized analogue of pep-a4 constrained into helix by seven helicogenic mutations, most of them involving hydrophobic residues. We concluded that the epitope is freely accessible to the antibody inside the protein and that its recognition by the antibody is not influenced by the conformation of its backbone and the chemistry of amino acids submitted to helicogenic mutations. In contrast, the AA →Glu mutations of the hydrophilic residues Gln148, Lys156 and Lys159, known for their interactions with LTRs (long terminal repeats) and inhibitors (

Mining Patterns in Mobile Network Logs

Alarm logs are a valuable source of information and play a crucial role in network management. Network devices such as backbone routers or 3G/4G base stations generate verbose and detailed logs that network managers process to detect problems and identify their root causes. Manual analysis of such logs is extremely time-consuming because of the extensive amount of data. Therefore, finding suitable automatic methods to process logs is an important problem in the network analysis area.In this paper, we target the automatic extraction of situations, i.e., sequences of events occurring close in time and space which identify common and recurring patterns. We adopt an unsupervised machine learning approach to automatically mine logs and provide information and correlations in network failures. We face a real use case processing more than 2 million alarms generated by 2 months of TIM Network Operations Center in Northern Italy. Most of the features are categorical and call for specific methodologies to process them. We choose rule mining of frequent items. We focus on event logs and apply rule mining methods to extract temporal-spatial correlations and co-occurrences, i.e., situations. To ease the analyst work, we highlight the most important rules and offer visualization techniques in both spatial and temporal dimensions. Results have been verified to be helpful to recognize common situations and identify possible future anomalies

Nickelation of PCP- and POCOP-Type Pincer Ligands: Kinetics and Mechanism

This report describes the results of a combined experimental and computational investigation on the kinetics and mechanism of the C–H metalation step involved in the formation of PCP- and POCOP-type complexes of nickel. The kinetics of the C–H nickelation reaction was probed through competition studies involving two ligands reacting with a substoicheometric quantity of {(<i>i-</i>PrCN)­NiBr₂}_<i>n</i>. These experiments have confirmed that metalation is more facile for aromatic ligands 1,3-(<i>i</i>-Pr₂PE)₂C₆H₄ vs their aliphatic counterparts 1,3-(<i>i</i>-Pr₂PECH₂)₂CH₂ (sp² C–H > sp³ C–H; E = O, CH₂), ligands bearing phosphine moieties vs those with phosphinite moieties (PCP > POCOP), ligands bearing P substituents <i>i</i>-Pr₂P vs <i>t</i>-Bu₂P and Ph₂P, and POC_sp²OP ligands 1,3-(<i>i</i>-Pr₂PO)₂C₆R_<i>n</i>H_4–<i>n</i> bearing electron-donating vs electron-withdrawing substituents (<i>p</i>-OMe ≈ <i>m</i>-OMe > <i>p</i>-Me > <i>m</i>-CO₂Me > <i>p</i>-CO₂Me > <i>m,m</i>-Cl₂). Among the latter, there is a 6-fold difference in C–H metalation rate between ligands bearing <i>p</i>-OMe and <i>p</i>-COOMe, whereas the most readily metalating ligand, 1,3-(<i>i</i>-Pr₂PCH₂)₂C₆H₄, is metalated ca. 270 times more readily relative to the least reactive ligand, 1,3-(<i>i</i>-Pr₂POCH₂)₂CH₂. Density functional calculations indicate that PCP- or POCOP-type pincer ligands react with NiBr₂ to generate nonmetalated intermediates that form the corresponding pincer complexes via a two-step mechanism involving an ionic dissociation of the bromide to give a tight ion pair intermediate, followed by bromide-assisted deprotonation of the C–H bond. The type of structure adopted by the nonmetalated intermediates (mono- or dinuclear; tetrahedral, cis or trans square planar) and the energy barriers for the metalation transition states depend on the steric properties of the PR₂ moiety. The presence of a base that can neutralize the HBr generated in the metalation step is crucial for rendering the metalation process exergonic. One rationale for the more facile metalation of PCP ligands in comparison to their POCOP counterparts is the greater donor character of phosphine moieties, which allows a more effective stabilization of the coordination and metalation transition states wherein the strongly donor halide ligand is displaced by a much weaker C–H bond donor. The aromatic ligands metalate more readily than their aliphatic analogues for multiple reasons, including the higher ground state energy of the nonmetalated intermediates formed with aromatic ligands, the stronger C_sp²–Ni bond formed via metalation, and the more stabilized anionic charge on the C atom being metalated

Nanotechnology-assisted RNA delivery. From nucleic acid therapeutics to COVIDvaccines

In recent years, the main quest of science has been the pioneering of the groundbreaking biomedical strategies needed for achieving a personalized medicine. Ribonucleic acids (RNAs) are outstanding bioactive macromolecules identified as pivotal actors in regulating a wide range of biochemical pathways. The ability to intimately control the cell fate and tissue activities makes RNA-based drugs the most fascinating family of bioactive agents. However, achieving a widespread application of RNA therapeutics in humans is still a challenging feat, due to both the instability of naked RNA and the presence of biological barriers aimed at hindering the entrance of RNA into cells. Recently, material scientists’ enormous efforts have led to the development of various classes of nanostructured carriers customized to overcome these limitations. This work systematically reviews the current advances in developing the next generation of drugs based on nanotechnology-assisted RNA delivery. The features of the most used RNA molecules are presented, together with the development strategies and properties of nanostructured vehicles. Also provided is an in-depth overview of various therapeutic applications of the presented systems, including coronavirus disease vaccines and the newest trends in the field. Lastly, emerging challenges and future perspectives for nanotechnology-mediated RNA therapies are discussed