Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs

Guanine-adenine (GA) base pairs play important roles in determining the structure, dynamics, and stability of RNA. In RNA internal loops, GA base pairs often occur in tandem arrangements and their structure is context and sequence dependent. Calculations reported here test the thermodynamic integration (TI) approach with the amber99 force field by comparing computational predictions of free energy differences with the free energy differences expected on the basis of NMR determined structures of the RNA motifs (5′-GCGGACGC-3′)2, (5′-GCiGGAiCGC-3′)2, (5′-GGCGAGCC-3′)2, and (5′-GGiCGAiGCC-3′)2. Here, iG and iC denote isoguanosine and isocytidine, which have amino and carbonyl groups transposed relative to guanosine and cytidine. The NMR structures show that the GA base pairs adopt either imino (cis Watson−Crick/Watson−Crick A-G) or sheared (trans Hoogsteen/Sugar edge A-G) conformations depending on the identity and orientation of the adjacent base pair. A new mixing function for the TI method is developed that allows alchemical transitions in which atoms can disappear in both the initial and final states. Unrestrained calculations gave ΔG° values 2−4 kcal/mol different from expectations based on NMR data. Restraining the structures with hydrogen bond restraints did not improve the predictions. Agreement with NMR data was improved by 0.7 to 1.5 kcal/mol, however, when structures were restrained with weak positional restraints to sample around the experimentally determined NMR structures. The amber99 force field was modified to partially include pyramidalization effects of the unpaired amino group of guanosine in imino GA base pairs. This provided little or no improvement in comparisons with experiment. The marginal improvement is observed when the structure has potential cross-strand out-of-plane hydrogen bonding with the G amino group. The calculations using positional restraints and a nonplanar amino group reproduce the signs of ΔG° from the experimental results and are, thus, capable of providing useful qualitative insights complementing the NMR experiments. Decomposition of the terms in the calculations reveals that the dominant terms are from electrostatic and interstrand interactions other than hydrogen bonds in the base pairs. The results suggest that a better description of the backbone is key to reproducing the experimental free energy results with computational free energy predictions

Acetylcholinesterase enzyme activity in carp brain and muscle after acute exposure to diafuran Atividade da enzima acetilcolinesterase em cérebro e músculo de carpas após exposição aguda ao diafuran

Sublethal adverse effects may result from exposure of aquatic organisms to insecticides at environmentally relevant concentrations. Fingerlings of the common carp (Cyprinus carpio, Linnaeus, 1758), grass carp (Ctenopharyngodon idella, Valenciennes, 1844), and bighead carp (Aristichthys nobilis, Richardson, 1845) were exposed to diafuran, an insecticide widely used during rice cultivation in Southern Brazil. The aim of this study was to verify the relationship between the lethal concentration (LC50) of diafuran and the acetylcholinesterase (AChE) activity in brain and muscle tissues of these species as a possible early biomarker of exposure to this insecticide. LC50 was determined for fish exposed to diafuran concentrations during 96 h (short term): common carp: control, 0.5, 1.0, 1.5, 2.0, 2.5 and 3.0 mg L-1; grass carp: control, 1.0, 2.0, 3.0 and 3.5 mg L-1 and, bighead carp: control, 0.5, 1.0, 1.5, 2.0, 3.0 and 4.0 mg L-1, as well as the determination of AChE at concentrations near LC50 for these species. LC50 values (nominal concentrations) were 1.81 mg L-1 for the common carp, 2.71 mg L-1 for the grass carp and, 2.37 mg L-1 for the bighead carp. All carps exposed to diafuran were lethargic (lower concentrations) or immobile. Diafuran inhibited the acetylcholinesterase activity in brain (~38%) and muscle (~50%) of all species. Muscle of bighead carp under control treatment showed higher specific AChE activity than brain (14.44 against 5.94 µmol min-1 g protein-1, respectively). Concentrations of diafuran used for rice cropping may affect Cyprinus carpio, Ctenopharyngodon idella and Aristichthys nobilis behaviors and the AChE activities in brain and muscle of these species may be an early biomarker of toxicity of this insecticide.<br>Exposição a inseticidas em concentrações elevadas no ambiente podem ocasionar efeitos adversos subletais em organismos aquáticos. Alevinos de carpa húngara (Cyprinus carpio, Linnaeus, 1758), carpa capim (Ctenopharyngodon idella, Valenciennes, 1844) e carpa cabeça grande (Aristichthys nobilis, Richardson, 1845) foram expostos ao diafuran, um inseticida utilizado na cultura do arroz no sul do Brasil. O objetivo deste estudo foi verificar a relação entre concentração letal mediana (CL50) do diafuran e a atividade da enzima acetilcolinesterase (AChE) em cérebro e músculo dessas espécies, como um possível biomarcador inicial da exposição a este inseticida. A CL50 foi determinada com peixes expostos a concentrações de diafuran em 96 h: carpa húngara: controle; 0,5; 1,0; 1,5; 2,0; 2,5 e 3,0 mg L-1; carpa capim: controle; 1,0; 2,0; 3,0 e 3,5 mg L-1 e carpa cabeça grande: controle; 0,5; 1,0; 1,5; 2,0; 3,0 e 4,0 mg L-1, bem como a determinação da AChE em concentrações próximas da CL50 para essas espécies. Valores de CL50 (concentrações nominais) foram de 1,81 mg L-1 para carpa húngara, 2,71 mg L-1 para carpa capim e 2,37 mg L-1 para carpa cabeça grande. Todas as carpas expostas ao diafuran estavam letárgicas (menores concentrações) ou imóveis. Diafuran inibiu significativamente a atividade da AChE em cérebro (~38 %) e músculo (~50 %) de todas as espécies estudadas. Atividade da AChE em músculo para carpa cabeça grande foi mais alta que cérebro (14,44 contra 5,94 µmol min-1 g proteína-1, respectivamente). Este estudo demonstrou que concentrações de diafuran utilizadas na cultura do arroz podem afetar o comportamento de Cyprinus carpio, Ctenopharyngodon idella e Aristichthys nobilis, e a atividade da acetilcolinesterase cerebral e muscular pode ser um biomarcador inicial de toxicidade deste inseticida