Recognizing protein–protein interfaces with empirical potentials and reduced amino acid alphabets-0

<p><b>Copyright information:</b></p><p>Taken from "Recognizing protein–protein interfaces with empirical potentials and reduced amino acid alphabets"</p><p>http://www.biomedcentral.com/1471-2105/8/270</p><p>BMC Bioinformatics 2007;8():270-270.</p><p>Published online 27 Jul 2007</p><p>PMCID:PMC2034607.</p><p></p>imized, 20-class energy matrix (left). The Pearson Correlation coefficent of each cluster is given for the lefthand tree

Recognizing protein–protein interfaces with empirical potentials and reduced amino acid alphabets-2

<p><b>Copyright information:</b></p><p>Taken from "Recognizing protein–protein interfaces with empirical potentials and reduced amino acid alphabets"</p><p>http://www.biomedcentral.com/1471-2105/8/270</p><p>BMC Bioinformatics 2007;8():270-270.</p><p>Published online 27 Jul 2007</p><p>PMCID:PMC2034607.</p><p></p>imized, 20-class energy matrix (left). The Pearson Correlation coefficent of each cluster is given for the lefthand tree

Recognizing protein–protein interfaces with empirical potentials and reduced amino acid alphabets-3

<p><b>Copyright information:</b></p><p>Taken from "Recognizing protein–protein interfaces with empirical potentials and reduced amino acid alphabets"</p><p>http://www.biomedcentral.com/1471-2105/8/270</p><p>BMC Bioinformatics 2007;8():270-270.</p><p>Published online 27 Jul 2007</p><p>PMCID:PMC2034607.</p><p></p>tein length (number of amino acids). The corresponding energy functions are those derived for fold recognition, using the Monomeric Optimization Set. The mean number of decoys is shown vs. protein length (grey bars; righthand graduations)

Recognizing protein–protein interfaces with empirical potentials and reduced amino acid alphabets-1

<p><b>Copyright information:</b></p><p>Taken from "Recognizing protein–protein interfaces with empirical potentials and reduced amino acid alphabets"</p><p>http://www.biomedcentral.com/1471-2105/8/270</p><p>BMC Bioinformatics 2007;8():270-270.</p><p>Published online 27 Jul 2007</p><p>PMCID:PMC2034607.</p><p></p>tein length (number of amino acids). The corresponding energy functions are those derived for fold recognition, using the Monomeric Optimization Set. The mean number of decoys is shown vs. protein length (grey bars; righthand graduations)

Global Analysis of CPEBs Reveals Sequential and Non-Redundant Functions in Mitotic Cell Cycle

<div><p>CPEB (Cytoplasmic Polyadenylation Element Binding) proteins are a family of four RNA-binding proteins that regulate the translation of maternal mRNAs controlling meiotic cell cycle progression. But CPEBs are not limited to the transcriptionally silent germline; they are also expressed, in various combinations, in somatic cells, yet their role in regulation of mitosis-related gene expression is largely unknown. Deregulation of CPEB1 and CPEB4 have been linked to tumor development. However, a systematic analysis addressing their requirements for the temporal regulation of mitotic gene expression has yet to be performed. This study addresses the requirements of each of the four CPEBs for mitotic phase transitions, with a particular focus on cytoplasmic polyadenylation and translational regulation. We demonstrate that CPEB3 is the only member dispensable for mitotic cell division, whereas the other three members, CPEB1, 2, and 4, are essential to successful mitotic cell division. Thus, CPEB1 is required for prophase entry, CPEB2 for metaphase and CPEB4 for cytokinesis. These three CPEBs have sequential non-redundant functions that promote the phase-specific polyadenylation and translational activation of CPE-regulated transcripts in the mitotic cell cycle.</p></div

CPEB1 is required for prophase entry; CPEB2 for metaphase-to-anaphase transition and CPEB4 for cytokinesis.

<p>(A) HEK-293 cells stably expressing an IPTG-inducible system for each CPEB knock-down were induced or not with IPTG. Two days after induction, cells were transfected with a plasmid encoding fluorescent histon H2B. After one additional day cells were recorded by live imaging experiments. Images were acquired every 10 minutes and analyzed for mitotic progression. Representative images are shown for individual cells in interphase or during specific phases of mitosis that are readily identified by chromosome condensation state and organisation. (B) Mitotic-stage analysis of 50 cells from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138794#pone.0138794.s002" target="_blank">S1</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138794#pone.0138794.s006" target="_blank">S5</a> Videos as in Fig 2A. On Y axis, each lane represents one cell. On X axis, time is represented as minutes. Colors represent the indicated mitotic phases. Mitotic entry was determined by analyzing the first signs of DNA condensation cross-reinforced with cell-rounding. Mitotic exit was scored based on chromosome segregation at anaphase and DNA decondensation. Sh, short-hairpin; CTRL, control.</p

CPEB1, CPEB2 and CPEB4 are required for cell cycle progression.

<p>(A) HEK-293 cells stably expressing an IPTG-inducible system for CPEB1,2 and 4 knock-down were induced or not with IPTG. Two days after induction cells were synchronized through double thymidine blockade (DTB). Samples were harvested at the indicated time points and protein lysates were analyzed on SDS–PAGE followed by immunoblotting for the indicated proteins. α-tubulin was used as a loading control. (B) HEK-293 cells stably expressing an IPTG-inducible system for each CPEB knock-down were induced or not with IPTG. Three days after induction, cells were marked with EdU for two hours and then released. Samples were harvested at the indicated time points, stained for DNA content with PI and analyzed by FACS. Mean EdU⁺ cell-population: 23100 for control, 10800 for CPEB1-KD cells, 16400 for CPEB2-KD cells, 20900 for CPEB3-KD cells, 18900 for CPEB4-KD cells). Sh, short-hairpin; CTRL, control; IPTG, Isopropyl β-D-1-thiogalactopyranoside; DTB, double-thymidine block; Edu, 5-ethynyl-2'-deoxyuridine; PI, propidium iodide; ES, early S-phase; MS, middle S-phase; LS, late S-phase; FACS, fluorescence-activated cell sorter.</p

CPEB1, CPEB2 and CPEB4 are required for proper GFP translation at G2 and M phases.

<p>(A) HEK-293 cells stably expressing an IPTG-inducible system for each CPEB knock-down and carrying a GFP-3'UTR +/-CPE together with a RFP-3'UTR were induced or not with IPTG. Two days after induction, cells were recorded by live imaging experiments and analyzed for GFP expression (see Fig I in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138794#pone.0138794.s001" target="_blank">S1 File</a>, for RFP expression). Representative images from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138794#pone.0138794.s007" target="_blank">S6</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138794#pone.0138794.s012" target="_blank">S11</a> Videos are shown. (B) HEK-293 cells stably expressing an IPTG-inducible system for each CPEB knock-down and cells carrying a GFP-3'UTR with mutated CPE (CPE-) were induced or not with IPTG. Two days after induction cells were synchronized by double thymidine blockade (DTB). Samples were collected at the indicated phases of the cell cycle and GFP expression was measured by FACS. Results are shown as the mean value from six experiments, error bars indicate s.d; au, arbitrary units; Sh, short-hairpin; CTRL, control.</p