Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement

Argonaute (Ago) proteins and microRNAs (miRNAs) are central components in RNA interference, which is a key cellular mechanism for sequence-specific gene silencing. Despite intensive studies, molecular mechanisms of how Ago recognizes miRNA remain largely elusive. In this study, we propose a two-step mechanism for this molecular recognition: selective binding followed by structural re-arrangement. Our model is based on the results of a combination of Markov State Models (MSMs), large-scale protein-RNA docking, and molecular dynamics (MD) simulations. Using MSMs, we identify an open state of apo human Ago-2 in fast equilibrium with partially open and closed states. Conformations in this open state are distinguished by their largely exposed binding grooves that can geometrically accommodate miRNA as indicated in our protein-RNA docking studies. miRNA may then selectively bind to these open conformations. Upon the initial binding, the complex may perform further structural re-arrangement as shown in our MD simulations and eventually reach the stable binary complex structure. Our results provide novel insights in Ago-miRNA recognition mechanisms and our methodology holds great potential to be widely applied in the studies of other important molecular recognition systems.     

叶表面角质层在贝母属植物叶鉴定中的意义

叶表面角质层在贝母属植物叶鉴定中的意义李萍，濮祖茂，蒋鑫，刘惠娟，徐国钧（中国药科大学生药学教研室；分析中心电镜室南京２１０００９）ＴｈｅｄｉａｇｎｏｓｔｉｃｖａｌｕｅｏｆｔｈｅｃｕｔｉｃｌｅｉｎｔｈｅｌｅａｖｅｓｆｒｏｍｇｅｎｕｓＦｒｉｔｉｌｌａｒ...     

New calcium-sensitive ligand for nuclear magnetic resonance spectroscopy.

Fluorinated calcium-sensitive indicators such as 5,5'-difluoro-1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid (difluoro-BAPTA) will often be less sensitive under in vivo conditions than gyromagnetic ratio considerations alone would have predicted. This is due to the very broad line widths displayed by these molecules within the living cell. In order to provide a spectroscopic alternative to these molecules, we have synthesized 13C-enriched 1-(2-aminophenoxy)-2-(2-aminoethoxy)ethane-N,N,N',N'-tetraac etic acid or AATA. The rationale for the design of this molecule was the increased signal to noise ratio available by selective detection of 13C-attached protons in AATA using proton-observe carbon-edited spectroscopy or multiple-quantum coherence. AATA has the advantage of increased number of detectable nuclei and narrow line widths. As such, it should provide a 6-10-fold improvement in the signal to noise ratio over existing fluorinated indicators. As a hybrid between EGTA and BAPTA, AATA should display intermediate pKa's, exchange rates, and KD values. We have measured pKa values of 5.94 +/- 0.05 and 9.03 +/- 0.05 for AATA. KD values of 350 +/- 80 nM and 6.6 +/- 2.0 mM were obtained for the AATA-Ca2+ and AATA-Mg2+ interactions, respectively, at 37 degrees C in 0.1 M KCl. As such, this new ligand displays the expected selectivity for Ca2+ over Mg2+. This new approach to detection of intracellular probes with NMR can be readily extended to other probes for intracellular ions, pH, and membrane potential. In addition, the move toward carbon-selected proton spectroscopy should also permit more flexibility in synthetic approaches since the strong electronegativity of fluorine often hampers synthetic design.     

Preliminary studies of the complement fixation test to confirm the diagnosis of bovine ephemeral fever

A strain of bovine ephemeral fever (BEF) virus isolated in China in 1976 was adapted to growth in tissue cultures. A baby hamster kidney complement fixing (CF) antigen, stable at -20 degrees C for at least 120 days, was prepared from the BEF virus grown in tissue culture and used to test bovine sera for antibodies to that virus. CF antibodies were detected in all of 31 cattle after convalescence from experimental infection with BEF virus, in 208 (98%) of 213 cattle observed to have shown clinical ephemeral fever in an epidemic, in 96 cattle in these herds which did not show clinical signs of ephemeral fever and 16 cattle from herds in northern China outside the epidemic area. The CF antibodies to BEF virus were found to persist in 34 (89%) of 38 cattle which were bled 6 years after natural exposure to ephemeral fever. The CF antigen is economical to prepare and is suitable to differentiate ephemeral fever from other viral infections with which it could possibly be confused on clinical appearance.