GeNMR (GEnerate NMR structures) is a web server for rapidly generating accurate 3D protein structures using sequence data, NOE-based distance restraints and/or NMR chemical shifts as input. GeNMR accepts distance restraints in XPLOR or CYANA format as well as chemical shift files in either SHIFTY or BMRB formats. The web server produces an ensemble of PDB coordinates for the protein within 15–25 min, depending on model complexity and completeness of experimental restraints. GeNMR uses a pipeline of several pre-existing programs and servers to calculate the actual protein structure. In particular, GeNMR combines genetic algorithms for structure optimization along with homology modeling, chemical shift threading, torsion angle and distance predictions from chemical shifts/NOEs as well as ROSETTA-based structure generation and simulated annealing with XPLOR-NIH to generate and/or refine protein coordinates. GeNMR greatly simplifies the task of protein structure determination as users do not have to install or become familiar with complex stand-alone programs or obscure format conversion utilities. Tests conducted on a sample of 90 proteins from the BioMagResBank indicate that GeNMR produces high-quality models for all protein queries, regardless of the type of NMR input data. GeNMR was developed to facilitate rapid, user-friendly structure determination of protein structures via NMR spectroscopy. GeNMR is accessible at http://www.genmr.ca.
Oestrogen receptor (ER) is a ligand-activated transcription factor which plays an important role in many physiological processes. The aim of this study was to explore the difference between agonist and antagonist recognition mode. Molecular dynamics simulation of ER/diethylstilbestrol and ER/4-hydroxytamoxifen complexes was carried out. Our research results indicate that Glu353 participates in both agonist and antagonist recognition; His524 is the key residue in agonist recognition; Met343, Leu346, Thr347 and Asp351 are the key residues in the antagonist recognition.
Apoptosis-inducing factor (AIF) is a caspase-independent death effector. Normally residing in the mitochondrial intermembrane space, AIF is released and translocated to the nucleus in response to proapoptotic stimuli. Nuclear AIF binds to DNA and induces chromatin condensation and DNA fragmentation, characteristics of apoptosis. Until now, it remained to be clarified how the mitochondrial-nuclear translocation of AIF is regulated. Here we report that steroid receptor coactivator-interacting protein (SIP) interacts directly with AIF in mitochondria and specifically inhibits caspase-independent and AIF-dependent apoptosis. Challenging cells with apoptotic stimuli leads to rapid degradation of SIP, and subsequently AIF is liberated from mitochondria and translocated to the nucleus to induce apoptosis. Together, our data demonstrate that SIP is a novel regulator in caspase-independent and AIF-mediated apoptosis.
Oncolytic viruses are promising treatments for many kinds of solid tumors. In this study, we constructed a novel oncolytic herpes simplex virus type 2: oHSV2. We investigated the cytopathic effects of oHSV2 in vitro and tested its antitumor efficacy in a 4T1 breast cancer model. We compared its effect on the cell cycle and its immunologic impact with the traditional chemotherapeutic agent doxorubicin. In vitro data showed that oHSV2 infected most of the human and murine tumor cell lines and was highly oncolytic. oHSV2 infected and killed 4T1 tumor cells independent of their cell cycle phase, whereas doxorubicin mainly blocked cells that were in S and G2/M phase. In vivo study showed that both oHSV2 and doxorubicin had an antitumor effect, though the former was less toxic. oHSV2 treatment alone not only slowed down the growth of tumors without causing weight loss but also induced an elevation of NK cells and mild decrease of Tregs in spleen. In addition, combination therapy of doxorubicin followed by oHSV2 increased survival with weight loss than oHSV2 alone. The data showed that the oncolytic activity of oHSV2 was similar to oHSV1 in cell lines examined and in vivo. Therefore, we concluded that our virus is a safe and effective therapeutic agent for 4T1 breast cancer and that the sequential use of doxorubicin followed by oHSV2 could improve antitumor activity without enhancing doxorubicin's toxicity.
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