PMC:2724026 / 18161-19874 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/2724026","sourcedb":"PMC","sourceid":"2724026","source_url":"https://www.ncbi.nlm.nih.gov/pmc/2724026","text":"The transition state for folding in human FADD DD\nIn the TS of the human FADD DD, all three cores are partially structured. Helices H3 and H6, which are peripheral to the structure, are essentially detached from the protein. H3 is the only element of secondary structure that is completely unstructured, and H6 is only pinned to H5 via a helix-turn-helix interaction mediated through V173. In contrast, all four central elements of structure are already associated in the TS: three helices (H1, H2 and H5) contribute to central core packing, with the fourth helix (H4) pinned into the core at one end. However, H2 and H4 clearly interact with each other via residues that are packed in the B2 core. Thus, in the TS, helices H1, H2, H4 and H5 are apparently aligned in two parallel pairs (H1/H5 and H2/H4) and the pairs are packed against each other through interactions between H2 and the H1/H5 pair. Long-range packing interactions (H1 – H5, H2 – H4 and H2 – H1/H5) have a predominant role in the formation of structure in the central four-helix bundle, and in B2. Only in the formation of the B1 core do short-range side-chain interactions appear to be significant (in the formation of the helix 5-turn-helix 6 motif).\nAnalysis of the secondary structure propensity of FADD DD (as determined using the program AGADIR31) suggests that the level of overall helical propensity is very low; only two regions of the protein, the N-terminal region of H4 and the C-terminal region of H6, show any significant helical propensity (\u003e 10%). Interestingly, neither of these regions is involved in forming the central topology-defining core, although the N-terminal region of H4 appears to be important in the folding of B2.","divisions":[{"label":"title","span":{"begin":0,"end":49}},{"label":"p","span":{"begin":50,"end":1220}}],"tracks":[{"project":"2_test","denotations":[{"id":"19362094-9095674-62520524","span":{"begin":1318,"end":1320},"obj":"9095674"}],"attributes":[{"subj":"19362094-9095674-62520524","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93d6ec","default":true}]}]}}