Consecutive non-natural PZ nucleobase pairs in DNA impact helical structure as seen in 50 μs molecular dynamics simulations

Little is known about the influence of multiple consecutive ‘non-standard’ (Z, 6-amino-5-nitro-2(1H)-pyridone, and P, 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one) nucleobase pairs on the structural parameters of duplex DNA. P:Z nucleobase pairs follow standard rules for Watson–Crick base pairing but have rearranged hydrogen bonding donor and acceptor groups. Using the X-ray crystal structure as a starting point, we have modeled the motions of a DNA duplex built from a self-complementary oligonucleotide (5΄-CTTATPPPZZZATAAG-3΄) in water over a period of 50 μs and calculated DNA local parameters, step parameters, helix parameters, and major/minor groove widths to examine how the presence of multiple, consecutive P:Z nucleobase pairs might impact helical structure. In these simulations, the PZ-containing DNA duplex exhibits a significantly wider major groove and greater average values of stagger, slide, rise, twist and h-rise than observed for a ‘control’ oligonucleotide in which P:Z nucleobase pairs are replaced by G:C. The molecular origins of these structural changes are likely associated with at least two differences between P:Z and G:C. First, the electrostatic properties of P:Z differ from G:C in terms of density distribution and dipole moment. Second, differences are seen in the base stacking of P:Z pairs in dinucleotide steps, arising from energetically favorable stacking of the nitro group in Z with π–electrons of the adjacent base

Facile C_sp²-C_sp² bond cleavage in oxalic acid-derived radicals

Oxalate decarboxylase (OxDC) catalyzes the Mn-dependent conversion of the oxalate monoanion into CO2 and formate. Many questions remain about the catalytic mechanism of OxDC although it has been proposed that the reaction proceeds via substrate-based radical intermediates. Using coupled cluster theory combined with implicit solvation models we have examined the effects of radical formation on the structure and reactivity of oxalic acid-derived radicals in aqueous solution. Our results show that the calculated solution-phase free-energy barrier for C–C bond cleavage to form CO2 is decreased from 34.2 kcal/mol for oxalic acid to only 9.3 kcal/mol and a maximum of 3.5 kcal/mol for the cationic and neutral oxalic acid-derived radicals, respectively. These studies also show that the C–C σ bonding orbital of the radical cation contains only a single electron, giving rise to an elongated C–C bond distance of 1.7 Å; a similar lengthening of the C–C bond is not observed for the neutral radical. This study provides new chemical insights into the structure and stability of plausible intermediates in the catalytic mechanism of OxDC, and suggests that removal of an electron to form a radical (with or without the concomitant loss of a proton) may be a general strategy for cleaving the unreactive C–C bonds between adjacent sp2-hybridized carbon atoms

Gas phase RDX decomposition pathways using coupled cluster theory

Electronic and free energy barriers for a series of gas-phase RDX decomposition mechanisms have been obtain using coupled cluster singles, doubles, and perturbative triples with complete basis set (CCSD(T)/CBS) electronic energies for MBPT(2)/cc-pVTZ structures. Importantly, we have located a well-defined transition state for NN homolysis, in the initial RDX decomposition step, thereby obtaining a true barrier for this reaction. These calculations support the view that HONO elimination is preferred at STP over other proposed mechanisms, including NN homolysis, “triple whammy” and NONO isomerization. Indeed, our calculated values of Arrhenius parameters are in agreement with experimental findings for gas phase RDX decomposition. We also investigate a number of new pathways leading to breakdown of the intermediate formed by the initial HONO elimination, and find that NN homolysis in this intermediate has an activation energy barrier comparable with that computed for HONO elimination

Monotherapy with boosted protease inhibitors as antiretroviral treatment simplification strategy in the clinical setting

Antiretroviral treatment simplification with darunavir/ritonavir or lopinavir/ritonavir monotherapy maintains sustained HIV viremia suppression in clinical trials. However, data about the efficacy of this strategy in routine clinical practice is still limited, and no direct comparison between darunavir/ritonavir and lopinavir/ritonavir has been performed to date. We retrospectively studied all HIV-1-infected subjects who initiated monotherapy with darunavir/ritonavir or lopinavir/ritonavir while having plasma VL<50 c/mL, and had at least 1 subsequent follow-up visit in our clinic. When two consecutive PI-monotherapy regimens were used, each regimen was considered separately. The primary endpoint was the percentage of patients who maintained virological suppression (HIV-1 VL <50 c/mL) through follow-up. Virological failure was defined as at least two consecutive HIV-1 VL >50 c/mL. We also evaluated other reasons for treatment discontinuation. Analyses were performed considering all regimens (full dataset analysis) either as “on treatment” or as “treatment switch equals failure”. Five hundred and seventy-three PI-monotherapy regimens corresponding to 520 subjects were included, 262 with darunavir/ritonavir and 311 with lopinavir/ritonavir. Medians (IQR) follow-up were 50 (26.3–107.6) and 85.6 (36.9–179.1) weeks for subjects on darunavir/ritonavir and lopinavir/ritonavir, respectively (p<0.001). Overall, 67 (11.7%) subjects experienced virological failure, 23 (8.7%) were on darunavir/ritonavir and 42 (13.5%) were on lopinavir/ritonavir (p=0.796). Two hundred and three (77.5%) patients on darunavir/ritonavir and 154 (49.5%) on lopinavir/ritonavir maintained virological suppression in the “treatment switch equals failure” (p=0.002). Other reasons for treatment discontinuation were gastrointestinal toxicity and dyslipidemia in 7.2% and 5.9% of cases, respectively. Gastrointestinal toxicities and dyslipidemia leading to treatment discontinuation were more frequent in patients on lopinavir/ritonavir (10.6% and 10.3%, respectively) than in patients on darunavir/ritonavir (3.1% and 0.8%, respectively). Monotherapy with darunavir/ritonavir or lopinavir/ritonavir as simplification strategy appears to be effective and safe in subjects with virological suppression in clinical practice. Virological efficacy seems to be similar between regimens. However, rates of discontinuation due to toxicities were higher in subjects on lopinavir/ritonavir than darunavir/ritonavir

Deciphering the Potential Coding of Human Cytomegalovirus: New Predicted Transmembrane Proteome

CMV is a major cause of morbidity and mortality in immunocompromised individuals that will benefit from the availability of a vaccine. Despite the efforts made during the last decade, no CMV vaccine is available. An ideal CMV vaccine should elicit a broad immune response against multiple viral antigens including proteins involved in virus-cell interaction and entry. However, the therapeutic use of neutralizing antibodies targeting glycoproteins involved in viral entry achieved only partial protection against infection. In this scenario, a better understanding of the CMV prote-ome potentially involved in viral entry may provide novel candidates to include in new potential vaccine design. In this study, we aimed to explore the CMV genome to identify proteins with puta-tive transmembrane domains to identify new potential viral envelope proteins. We have performed in silico analysis using the genome sequences of nine different CMV strains to predict the trans-membrane domains of the encoded proteins. We have identified 77 proteins with transmembrane domains, 39 of which were present in all the strains and were highly conserved. Among the core proteins, 17 of them such as UL10, UL139 or US33A have no ascribed function and may be good candidates for further mechanistic studies

Cluster scaling relations from cosmological hydrodynamic simulations in dark energy dominated universe

Clusters are potentially powerful tools for cosmology provided their observed properties such as the Sunyaev-Zel'dovich (SZ) or X-ray signals can be translated into physical quantities like mass and temperature. Scaling relations are the appropriate mean to perform this translation. It is therefore, important to understand their evolution and their modifications with respect to the physics and to the underlying cosmology. In this spirit, we investigate the effect of dark energy on the X-ray and SZ scaling relations. The study is based on the first hydro-simulations of cluster formation for diferent models of dark energy. We present results for four dark energy models which differ from each other by their equations of state parameter, $w$. Namely, we use a cosmological constant model $w=-1$ (as a reference), a perfect fluid with constant equation of state parameter $w=-0.8$ and one with $w = -1.2$ and a scalar field model (or quintessence) with varying $w$. We generate N-body/hydrodynamic simulations that include radiative cooling with the public version of the Hydra code, modified to consider an arbitrary dark energy component. We produce cluster catalogues for the four models and derive the associated X-ray and SZ scaling relations. We find that dark energy has little effect on scaling laws making it safe to use the $\Lambda$CDM scalings for conversion of observed quantities into temperature and masses.Comment: 9 pages, 7 figures, submitted to A&

Association of the Chromosome Replication Initiator DnaA with the Escherichia coli Inner Membrane In Vivo: Quantity and Mode of Binding

DnaA initiates chromosome replication in most known bacteria and its activity is controlled so that this event occurs only once every cell division cycle. ATP in the active ATP-DnaA is hydrolyzed after initiation and the resulting ADP is replaced with ATP on the verge of the next initiation. Two putative recycling mechanisms depend on the binding of DnaA either to the membrane or to specific chromosomal sites, promoting nucleotide dissociation. While there is no doubt that DnaA interacts with artificial membranes in vitro, it is still controversial as to whether it binds the cytoplasmic membrane in vivo. In this work we looked for DnaA-membrane interaction in E. coli cells by employing cell fractionation with both native and fluorescent DnaA hybrids. We show that about 10% of cellular DnaA is reproducibly membrane-associated. This small fraction might be physiologically significant and represent the free DnaA available for initiation, rather than the vast majority bound to the datA reservoir. Using the combination of mCherry with a variety of DnaA fragments, we demonstrate that the membrane binding function is delocalized on the surface of the protein’s domain III, rather than confined to a particular sequence. We propose a new binding-bending mechanism to explain the membrane-induced nucleotide release from DnaA. This mechanism would be fundamental to the initiation of replication