PMC:1867812 / 44723-46474 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1867812","sourcedb":"PMC","sourceid":"1867812","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1867812","text":"4.1 Detecting and Ordering Folding Events\nWe summarize both folding trajectories of BBA5 into a sequence of SOAPs as illustrated in Figure 9. Coincidently, both summarized trajectories consist of 64 conformations.\nBased on these summarized trajectories, we can quickly identify all the conformations where the first α-helix-like or β-turn-like local motifs were formed. For trajectory T23, the first α-helix-like motif was identified in frame 26, and the first β-turn-like local motif was formed in frame 63. For the other trajectory T24, the frames were 29 and 38. This is in accordance with experimental results that α-helices generally fold more rapidly than β-turns. However, since we only consider frequent SOAPs, it is very possible that we might miss the actual first formation of such local motifs. To address this issue, we might need to consider rarely occurring SOAPs. We plan to investigate this in the future. For the two events related to β-turn formation, formation of two extended strands and formation of the turn, we found that for both trajectories, the formation of extended strands preceded the formation of the turn.\nAlso, we identify two conformations in each trajectory that show native-like structure. We do this by locating the conformations associated with the generalized SOAP (β.1 α.2). Figure 10 presents the 3D structure of these native-like conformations along with the native conformation of BBA5. One can see that our SOAP-based comparison does well in identifying similar 3D conformations.\nFigure 10 The native-like conformations identified in the two BBA5 trajectories. According to the SOAP-based summarization of the two BBA5 folding trajectories, two native-like conformations are identified in each trajectory.","divisions":[{"label":"title","span":{"begin":0,"end":41}},{"label":"p","span":{"begin":42,"end":213}},{"label":"p","span":{"begin":214,"end":1138}},{"label":"p","span":{"begin":1139,"end":1524}},{"label":"label","span":{"begin":1525,"end":1534}}],"tracks":[]}