Structure of the HIV-1 Full-Length Capsid Protein in a Conformationally Trapped Unassembled State Induced by Small-Molecule Binding

The capsid protein (CA) plays crucial roles in HIV-infection and replication, essential to viral maturation. The absence of high-resolution structural data on unassembled CA hinders the development of antivirals effective in inhibiting assembly. Unlike enzymes that have targetable functional substrate binding sites, the CA does not have a known site that affects catalytic or other innate activity, which can be more readily targeted in drug development efforts. We report the crystal structure of the HIV-1 CA, revealing the domain organization in context of the wild-type full-length (FL) unassembled CA. The FL CA adopts an antiparallel dimer (APD) configuration, exhibiting a domain organization sterically incompatible with capsid assembly. A small compound, generated in-situ during crystallization, is bound tightly at a hinge-site (“H-site”), indicating that binding at this interdomain region stabilizes the ADP conformation. Electron microscopy studies on nascent crystals reveal both dimeric and hexameric lattices coexisting within a single condition, in agreement with the interconvertibility of oligomeric forms and supporting the feasibility of promoting assembly-incompetent dimeric states. Solution characterization in the presence of the H-site ligand shows predominantly unassembled dimeric CA, even under conditions that promote assembly. Our structure elucidation of the HIV-1 FL CA and characterization of a potential allosteric binding site provides 3D views of an assembly-defective conformation, a state targeted in and, thus, directly relevant to, inhibitor development. Based on our findings, we propose an unprecedented means of preventing CA assembly, by ‘conformationally-trapping’ CA in assembly-incompetent conformational states, induced by H-site binding

Formation Mechanism of Char and Coke in Biomass Catalytic Pyrolysis

Thermochemical conversion of biomass via pyrolysis can play an important role in renewable fuel production. Introduction of catalyst in biomass pyrolysis is an effective way to upgrade the quality of bio-oil via de-oxygenation reactions. However, in catalytic pyrolysis, char and coke are formed via primary decomposition of biomass and secondary catalytic reactions of pyrolysis intermediates, respectively. The formation of coke and char is the main reaction competing with the production of favorable aromatic compounds and can significantly deteriorate catalyst activity. Control of coke and char formation during pyrolysis could be possible through innovative catalyst and process designs, in which fundamental understanding of the formation mechanisms of char and coke should be viewed as a prerequisite. This study utilizes various experimental and modeling techniques in order to measure and interpret the physicochemical characteristics of char and coke and gain mechanistic insights of their origins during biomass catalytic pyrolysis. This study includes design and testing of a conical spouted bed reactor for in-situ biomass catalytic pyrolysis, investigation of the effect of key operating parameters on pyrolysis product distribution, characterization of char and coke structures and a structured model compound exploration of coke formation mechanisms. It is shown that char and coke have different origins. They cannot be lumped as one, since they occupy different locations on the catalyst surface and, thus, contribute differently to catalyst deactivation. Char, a product from thermal reactions, forms as an external layer on the catalyst surface and in its macropores, whereas coke, a catalytic product, forms inside the zeolite micropores. By studying the coke formation using biomass model compounds, it is concluded that the chemical structure of coke depends on its chemical precursors. The formation of coke from olefins, aromatic hydrocarbons and aromatic oxygenates are all directly related to the so-called “hydrocarbon pool” mechanism, following mainly hydrogen transfer and cyclization reactions

Synthesis and Evaluation of LaBaCo_2−<i>x</i>Mo<i>_x</i>O_5+<i>δ</i> Cathode for Intermediate-Temperature Solid Oxide Fuel Cells

LaBaCo2−xMoxO5+δ (LBCMx, x = 0–0.08) cathodes synthesized by a sol-gel method were evaluated for intermediate-temperature solid oxide fuel cells. The limit of the solid solubility of Mo in LBCMx was lower than 0.08. As the content of Mo increased gradually from 0 to 0.06, the thermal expansion coefficient decreased from 20.87 × 10−6 K−1 to 18.47 × 10−6 K−1. The introduction of Mo could increase the conductivity of LBCMx, which varied from 464 S cm−1 to 621 S cm−1 at 800 °C. The polarization resistance of the optimal cathode LBCM0.04 in air at 800 °C was 0.036 Ω cm2, reduced by a factor of 1.67 when compared with the undoped Mo cathode. The corresponding maximum power density of a single cell based on a YSZ electrolyte improved from 165 mW cm−2 to 248 mW cm−2 at 800 °C

The Crystal Structure of Non‐Modified and Bipyridine‐Modified PNA Duplexes

Peptide nucleic acid (PNA) is a synthetic analogue of DNA that commonly has an N-aminoethlyl-glycine backbone. The crystal structure of two PNA duplexes, one containing eight standard nucleobase pairs (GGCATCGG)(2) (pdb: 3MBS), and the other containing the same nucleobase pairs and a central pair of bipyridine ligands (pdb: 3MBU), has been solved with a resolution of 1.2 Å and 1.05 Å, respectively. The non-modified PNA duplex adopts a P-type helical structure s i m i l a r t o that of previously characterized PNAs. The atomic-level resolution of the structures allowed us to observe for the first time specific modes of interaction between the terminal lysines of the PNA and the backbone and nucleobases situated in the vicinity of the lysines, which are considered an important factor in the induction of a preferred handedness in PNA duplexes. These results support the notion that while PNA typically adopts a P-type helical structure, its flexibility is relatively high. For example, the base pair rise in the bipyridine-containing PNA is the largest measured to date in a PNA homoduplex. The two bipyridines are bulged out of the duplex and are aligned parallel to the minor groove of the PNA. In the case of the bipyridine-containing PNA, two bipyridines from adjacent PNA duplexes form a π-stacked pair that relates the duplexes within the crystal. The bulging out of the bipyridines causes bending of the PNA duplex, which is in contrast to the structure previously reported for biphenyl-modified DNA duplexes in solution, where the biphenyls are π-stacking with adjacent nucleobase pairs and adopt an intrahelical geometry [Johar et al., Chem. Eur. J., 2008, 14, 2080]. This difference shows that relatively small perturbations can significantly impact the relative position of nucleobase analogues in nucleic acid duplexes

The Crystal Structure of Non-Modified and Bipyridine-Modified PNA Duplexes

Peptide nucleic acid (PNA) is a synthetic analogue of DNA that commonly has an N-aminoethlyl-glycine backbone. The crystal structure of two PNA duplexes, one containing eight standard nucleobase pairs (GGCATCGG)(2) (pdb: 3MBS), and the other containing the same nucleobase pairs and a central pair of bipyridine ligands (pdb: 3MBU), has been solved with a resolution of 1.2 Å and 1.05 Å, respectively. The non-modified PNA duplex adopts a P-type helical structure s i m i l a r t o that of previously characterized PNAs. The atomic-level resolution of the structures allowed us to observe for the first time specific modes of interaction between the terminal lysines of the PNA and the backbone and nucleobases situated in the vicinity of the lysines, which are considered an important factor in the induction of a preferred handedness in PNA duplexes. These results support the notion that while PNA typically adopts a P-type helical structure, its flexibility is relatively high. For example, the base pair rise in the bipyridine-containing PNA is the largest measured to date in a PNA homoduplex. The two bipyridines are bulged out of the duplex and are aligned parallel to the minor groove of the PNA. In the case of the bipyridine-containing PNA, two bipyridines from adjacent PNA duplexes form a π-stacked pair that relates the duplexes within the crystal. The bulging out of the bipyridines causes bending of the PNA duplex, which is in contrast to the structure previously reported for biphenyl-modified DNA duplexes in solution, where the biphenyls are π-stacking with adjacent nucleobase pairs and adopt an intrahelical geometry [Johar et al., Chem. Eur. J., 2008, 14, 2080]. This difference shows that relatively small perturbations can significantly impact the relative position of nucleobase analogues in nucleic acid duplexes

Conversion of Polyethylene Terephthalate Based Waste Carpet to Benzene-Rich Oils through Thermal, Catalytic, and Catalytic Steam Pyrolysis

Management of carpet wastes has become a substantial environmental issue in the United States. Specifically, reutilization of polyethylene terephthalate (PET) from waste carpet is increasingly problematic because of the steadily growing market share of PET-based carpets and the very low value of their wastes. In this work, we investigate pyrolysis as an option for repurposing PET carpet wastes. In particular, slow and fast, thermal and catalytic pyrolyses, with and without the co-feeding of steam, are investigated in terms of their selectivity to monoaromatic products. It is seen that higher temperatures increase the conversion of PET to aromatic hydrocarbons. Pyrolysis at slow heating rates is very selective to benzene production. Thermal pyrolysis of waste carpet produces significant amounts of benzoic acid and acetylbenzoic acid as liquid products, whereas catalytic pyrolysis enhances the decarboxylation of these acids, producing aromatic hydrocarbons. ZSM-5 and CaO are effective catalysts for enhancing deoxygenation reactions during catalytic pyrolysis of waste carpet but with significantly different selectivities. Catalytic steam pyrolysis is seen to accomplish the highest selectivity to benzene among all the pyrolysis options studied, due to the enhancement of hydrolysis reactions. The essentially pure benzene organic liquid product from steam pyrolysis of carpet-originated PET presents a unique opportunity for the reutilization of this unsustainable waste

Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair

UV light-induced photoproducts are recognized and removed by the nucleotide-excision repair (NER) pathway. In humans, the UV-damaged DNA-binding protein (UV-DDB) is part of a ubiquitin E3 ligase complex (DDB1-CUL4ADDB2) that initiates NER by recognizing damaged chromatin with concomitant ubiquitination of core histones at the lesion. We report the X-ray crystal structure of the human UV-DDB in a complex with damaged DNA and show that the N-terminal domain of DDB2 makes critical contacts with two molecules of DNA, driving N-terminal-domain folding and promoting UV-DDB dimerization. The functional significance of the dimeric UV-DDB [(DDB1-DDB2)2], in a complex with damaged DNA, is validated by electron microscopy, atomic force microscopy, solution biophysical, and functional analyses. We propose that the binding of UV-damaged DNA results in conformational changes in the N-terminal domain of DDB2, inducing helical folding in the context of the bound DNA and inducing dimerization as a function of nucleotide binding. The temporal and spatial interplay between domain ordering and dimerization provides an elegant molecular rationale for the unprecedented binding affinities and selectivities exhibited by UV-DDB for UV-damaged DNA. Modeling the DDB1-CUL4ADDB2 complex according to the dimeric UV-DDB-AP24 architecture results in a mechanistically consistent alignment of the E3 ligase bound to a nucleosome harboring damaged DNA. Our findings provide unique structural and conformational insights into the molecular architecture of the DDB1-CUL4ADDB2 E3 ligase, with significant implications for the regulation and overall organization of the proteins responsible for initiation of NER in the context of chromatin and for the consequent maintenance of genomic integrity

Antiretroviral Drug Discovery Targeting the HIV-1 Nef Virulence Factor

While antiretroviral drugs have transformed the lives of HIV-infected individuals, chronic treatment is required to prevent rebound from viral reservoir cells. People living with HIV also are at higher risk for cardiovascular and neurocognitive complications, as well as cancer. Finding a cure for HIV-1 infection is therefore an essential goal of current AIDS research. This review is focused on the discovery of pharmacological inhibitors of the HIV-1 Nef accessory protein. Nef is well known to enhance HIV-1 infectivity and replication, and to promote immune escape of HIV-infected cells by preventing cell surface MHC-I display of HIV-1 antigens. Recent progress shows that Nef inhibitors not only suppress HIV-1 replication, but also restore sufficient MHC-I to the surface of infected cells to trigger a cytotoxic T lymphocyte response. Combining Nef inhibitors with latency reversal agents and therapeutic vaccines may provide a path to clearance of viral reservoirs