Mechanism for APOBEC3G catalytic exclusion of RNA and non-substrate DNA

The potent antiretroviral protein APOBEC3G (A3G) specifically targets and deaminates deoxycytidine nucleotides, generating deoxyuridine, in single stranded DNA (ssDNA) intermediates produced during HIV replication. A non-catalytic domain in A3G binds strongly to RNA, an interaction crucial for recruitment of A3G to the virion; yet, A3G displays no deamination activity for cytidines in viral RNA. Here, we report NMR and molecular dynamics (MD) simulation analysis for interactions between A3Gctd and multiple substrate or non-substrate DNA and RNA, in combination with deamination assays. NMR ssDNA-binding experiments revealed that the interaction with residues in helix1 and loop1 (T201-L220) distinguishes the binding mode of substrate ssDNA from non-substrate. Using 2\u27-deoxy-2\u27-fluorine substituted cytidines, we show that a 2\u27-endo sugar conformation of the target deoxycytidine is favored for substrate binding and deamination. Trajectories of the MD simulation indicate that a ribose 2\u27-hydroxyl group destabilizes the pi-pi stacking of the target cytosine and H257, resulting in dislocation of the target cytosine base from the catalytic position. Interestingly, APOBEC3A, which can deaminate ribocytidines, retains the ribocytidine in the catalytic position throughout the MD simulation. Our results indicate that A3Gctd catalytic selectivity against RNA is dictated by both the sugar conformation and 2\u27-hydroxyl group

Crystal structure of the catalytic domain of HIV-1 restriction factor APOBEC3G in complex with ssDNA

The human APOBEC3G protein is a cytidine deaminase that generates cytidine to deoxy-uridine mutations in single-stranded DNA (ssDNA), and capable of restricting replication of HIV-1 by generating mutations in viral genome. The mechanism by which APOBEC3G specifically deaminates 5\u27-CC motifs has remained elusive since structural studies have been hampered due to apparently weak ssDNA binding of the catalytic domain of APOBEC3G. We overcame the problem by generating a highly active variant with higher ssDNA affinity. Here, we present the crystal structure of this variant complexed with a ssDNA substrate at 1.86 A resolution. This structure reveals atomic-level interactions by which APOBEC3G recognizes a functionally-relevant 5\u27-TCCCA sequence. This complex also reveals a key role of W211 in substrate recognition, implicating a similar recognition in activation-induced cytidine deaminase (AID) with a conserved tryptophan

Antimicrobial Prophylaxis in Lower Uterine Segment Caesarean Section: A Prospective Observational Data-based Study

Introduction: Any major surgery like lower uterine Caesarean Section (CS) can be hazardous due to postoperative nosocomial infection. Pregnant mothers are at greater risk during such surgical intervention as compared to vaginal delivery. Prophylactic antibiotic administration is a standard practice across the globe to prevent such anticipated postoperative infection. Aim: To evaluate the prophylactic antimicrobial use with regards to the choice of antimicrobials, dose, route, timing and duration, any possible Adverse Drug Reaction (ADR) as well as to assess the frequency of the postoperative morbidity due to infection (if any). Materials and Methods: A prospective observational data-based study was conducted in the Department of Pharmacology in collaboration with Department of Obstetrics and Gynaecology, Burdwan Medical College and Hospital, Burdwan, West Bengal, India, from February 2016 to October 2017. Study was conducted on 1944 pregnant women of reproductive age group planned or scheduled for elective/emergency lower segment CS, but otherwise healthy and received prophylactic antimicrobials for the surgery. They were prospectively observed regarding the treatment they received with focus on antimicrobial agents from the period of antimicrobial prophylaxis during their stay at hospital to till their discharge. Demographic data, vital signs, indication of CS, postoperative infections and ADR if any were recorded in predesigned proforma. The study population was divided into two groups: group A included 995 mothers, who received ceftriaxone sodium (1 g intravenously) and metronidazole (15 mg/kg) infusion and group B included 949 mothers, who received ampicillin (2 g intravenously), metronidazole (15 mg/kg) infusion and injection gentamycin (5 mg/kg) for 0.5 hour before initiation of CS. The data were statistically analysed by standard statistical software Microsoft Excel 2010 and Statistical Package for the Social Sciences (SPSS) sotware version 27.0 (SPSS Inc., Chicago, IL, USA) expressed as mean and standard deviation and percentage. Independent t- test and Chi-square test were used for analysis. Results: The mean age of group A was 22.36±3.07 years and group B was 22.76±2.47 years. Endomyometritis was documented in 4 (0.4%) from group A and 2 (0.21%) from the group B. Wound infection was present in 3 (0.3%) for group A and five (0.5%) for the group B. Infection related complications like chest infection seen in 7 (0.7%) for group A and in 3 (0.31%) for group B and urinary tract infection was noticed in 6 (0.6%) for group A and 5 (0.52%) for group B. Any incidence of maternal mortality was not evident among the two study groups and statistically insignificant ADR like vomiting and maculopapular rash (p-value=0.324) was observed in both the study groups with the use of above-mentioned antimicrobial therapy. Conclusion: Prophylactic use of ceftriaxone plus metronidazole and combination of triple antimicrobial therapy of ampicillin, metronidazole, and gentamycin therapy at the usual standard dose were commonly used antimicrobials at the present set up and they are safe and equally effective in decreasing considerably the incidence of post caesarean maternal infection thereby reducing their morbidity and mortality

RbGd{sub 2}Br{sub 7}:Ce scintillators for gamma ray and thermal neutron detection

In this paper, we report on gamma ray and thermal neutron detection with RbGd2Br7:Ce scintillators. RbGd2Br7:Ce (RGB) is a new scintillator material, which shows high light output (56,000 photons/MeV) and has a fast principal decay constant (45 ns) when doped with 10% Ce. These properties make RGB an attractive scintillator for g-ray detection. Also, due to the presence of Gd as a constituent, RGB has a high cross section for thermal neutron absorption and can achieve close to 100% stopping efficiency with 0.5 mm thick RGB crystals. Crystals of RGB with three different Ce concentrations (0.1, 5, and 10%) have been grown and their basic scintillation properties such as light output, decay time, and emission spectrum have been measured. In addition, high efficiency thermal neutron detection has been confirmed in our studies

Crystal Structure of a Soluble APOBEC3G Variant Suggests ssDNA to Bind in a Channel that Extends between the Two Domains

APOBEC3G (A3G) is a single-stranded DNA (ssDNA) cytosine deaminase that can restrict HIV-1 infection by mutating the viral genome. A3G consists of a non-catalytic N-terminal domain (NTD) and a catalytic C-terminal domain (CTD) connected by a short linker. While the CTD catalyzes cytosine deamination, the NTD is believed to provide additional affinity for ssDNA. Structures of both A3G domains have been solved individually; however, a full-length A3G structure has been challenging. Recently, crystal structures of full-length rhesus macaque A3G variants were solved which suggested dimerization mechanisms and RNA binding surfaces, whereas the dimerization appeared to compromise catalytic activity. We determined the crystal structure of a soluble variant of human A3G (sA3G) at 2.5 A and from these data generated a model structure of wild-type A3G. This model demonstrated that the NTD was rotated 90 degrees relative to the CTD along the major axis of the molecule, an orientation that forms a positively charged channel connected to the CTD catalytic site, consisting of NTD loop-1 and CTD loop-3. Structure-based mutations, in vitro deamination and DNA binding assays, and HIV-1 restriction assays identify R24, located in the NTD loop-1, as essential to a critical interaction with ssDNA. Furthermore, sA3G was shown to bind a deoxy-cytidine dinucleotide near the catalytic Zn(2+), yet not in the catalytic position, where the interactions between deoxy-cytidines and CTD loop-1 and loop-7 residues were different from those formed with substrate. These new interactions suggest a mechanism explaining why A3G exhibits a 3\u27 to 5\u27 directional preference in processive deamination

Nanoscale Characterization of Interaction of APOBEC3G with RNA

The human cytidine deaminase APOBEC3G (A3G) is a potent inhibitor of the HIV-1 virus in the absence of viral infectivity factor (Vif). The molecular mechanism of A3G antiviral activity is primarily attributed to deamination of single-stranded DNA (ssDNA); however, the nondeamination mechanism also contributes to HIV-1 restriction. The interaction of A3G with ssDNA and RNA is required for its antiviral activity. Here we used atomic force microscopy to directly visualize A3G–RNA and A3G–ssDNA complexes and compare them to each other. Our results showed that A3G in A3G–RNA complexes exists primarily in monomeric–dimeric states, similar to its stoichiometry in complexes with ssDNA. New A3G–RNA complexes in which A3G binds to two RNA molecules were identified. These data suggest the existence of two separate RNA binding sites on A3G. Such complexes were not observed with ssDNA substrates. Time-lapse high-speed atomic force microscopy was applied to characterize the dynamics of the complexes. The data revealed that the two RNA binding sites have different affinities for A3G. On the basis of the obtained results, a model for the interaction of A3G with RNA is proposed

Correction: A narrow amide I vibrational band observed by sum frequency generation spectroscopy reveals highly ordered structures of a biofilm protein at the air/water interface

Correction for 'A narrow amide I vibrational band observed by sum frequency generation spectroscopy reveals highly ordered structures of a biofilm protein at the air/water interface' by Zhuguang Wang et al., Chem. Commun., 2016, 52, 2956-2959

A narrow amide I vibrational band observed by sum frequency generation spectroscopy reveals highly ordered structures of a biofilm protein at the air/water interface

We characterized BslA, a bacterial biofilm protein, at the air/water interface using vibrational sum frequency generation spectroscopy and observed one of the sharpest amide I band ever reported. Combining methods of surface pressure measurements, thin film X-ray reflectivity, and atomic force microscopy, we showed extremely ordered BslA at the interface