PMC:2728246 / 45088-49568 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/2728246","sourcedb":"PMC","sourceid":"2728246","source_url":"https://www.ncbi.nlm.nih.gov/pmc/2728246","text":"Correlation between (CC) and (NH)\nExtending the investigation of side chains dynamics to the supra-τc time windows reveals substantial additional mobility slower than τc, which is likely to be composed of rotameric jumps around torsion angles and of small-scale rapid fluctuations around equilibrium positions. Whereas the mechanism underlying these motions is too complex to decipher with the approach used in this study, it would be intriguing to study whether these substantial movements might have an effect on the motions at the level of the backbone, especially considering that the important rearrangements associated with rotameric jumps may require local structural accommodations even from the backbone. Mechanisms of such transfer of motion have already been suggested and applied to improve side chain conformational variability models (Davis et al. 2006; Friedland et al. 2008).\nRecently, a tendency was observed that residues with solvent exposed side chains appear more mobile in protein backbone. A transfer of motion from the side chains to the protein backbone had already been hypothesized (Lakomek et al. 2005). Due to the lack of dynamic information for the side chains, conclusions were based on the assumption that solvent-exposed side chains were more mobile than those in the core of the protein. Now that direct experimental information about side chain dynamics in a time window from pico- to milliseconds becomes available, it is of interest to investigate whether there is a direct correlation between the order parameters of the methyl groups and those of the backbone amides to which they are directly bonded.\nIn Figure 5a and b, the order parameters of methyl groups are plotted against the order parameters of the same (i) and of the following (i + 1) NH group over different time scales and the linear correlation coefficients are summarized in Table 2. For pairs of values where the correlation is deemed “significant” based on p-values smaller than 0.1 (probability that this correlation would occur by chance, in brackets), a few observation can be made. On all time scales, S2(CCi) show better correlation with S2(NHi) than with S2(NHi+1). This is the case for fs-ms dynamics with Pearson coefficients of ri = 0.49 and ri+1 = 0.34, as well as for fs-ns dynamics  = 0.60 and  = 0.41. These numbers show that a possible mechanism of transfer of motion from the side chain to the backbone is more prevalent from the side chain to the amide group of the same residue than to the next one as has been postulated earlier (Lakomek et al. 2005).\nFig. 5 Correlation of RDC-based order parameters from side chains at residue position i from methyl Cγ (full circles) and Cδ (open circles) with RDC-based backbone NH order parameters at the corresponding i and i + 1 positions taken from (Lakomek et al. 2008a). Short and long dashed lines correspond to the linear function fitting for Cγ and Cδ order parameters\nTable 2 Pearson correlation coefficient of side chain and backbone order parameters over various time scales\nTime scale Order parameters S2(NHi)a,b No. of data S2(NHi+1)a,b No. of data\nfs–ms (CCi) 0.49 (0.006) 30 0.34 (0.07) 29\n(CCγi) 0.50 (0.06) 15 0.19 (0.52) 13\n(CCδi) 0.46 (0.11) 13 0.26 (0.37) 14\nfs–ns (CCi) 0.60 (0.003) 23 0.41 (0.06) 22\n(CCγi) −0.17 (0.58) 13 0.36 (0.33) 9\n(CCδi) 0.76 (0.02) 9 0.48 (0.10) 13\naNumber in brackets is the null-hypothesis p-value\nbOnly correlations in bold are considered significant. All the others (in italic) are not significant\nWhen classifying the data according to the distance of the methyl group to the backbone, it seems that the order parameters at the Cγ methyl show practically the same correlations to the amide motion on the same residue as the Cδ methyl groups (e.g., ri(γ) = 0.50 vs. ri(δ) = 0.46). The slope of the linear correlation is, however, roughly twice for Cδ compared to Cγ, indicating that the methyl group motion transfer are significantly dampened through the degrees of freedom of the linear side chain.\nWhen comparing the correlation of motion between side chains and backbone for the fast (ps to ns) to the full (ps to ms) time window detected by RDCs a better correlation from faster motions is obtained. This suggests that the major contribution of this transfer already occurs at time-scales faster than the correlation time (τc). These findings encourage further investigations of a possible transfer mechanism of motion from the side chains to the protein backbone.","divisions":[{"label":"title","span":{"begin":0,"end":33}},{"label":"p","span":{"begin":34,"end":891}},{"label":"p","span":{"begin":892,"end":1640}},{"label":"p","span":{"begin":1641,"end":3509}},{"label":"figure","span":{"begin":2576,"end":2938}},{"label":"label","span":{"begin":2576,"end":2582}},{"label":"caption","span":{"begin":2583,"end":2938}},{"label":"p","span":{"begin":2583,"end":2938}},{"label":"table-wrap","span":{"begin":2939,"end":3509}},{"label":"label","span":{"begin":2939,"end":2946}},{"label":"caption","span":{"begin":2947,"end":3047}},{"label":"p","span":{"begin":2947,"end":3047}},{"label":"table","span":{"begin":3048,"end":3356}},{"label":"tr","span":{"begin":3048,"end":3123}},{"label":"th","span":{"begin":3048,"end":3058}},{"label":"th","span":{"begin":3059,"end":3075}},{"label":"th","span":{"begin":3076,"end":3086}},{"label":"th","span":{"begin":3087,"end":3098}},{"label":"th","span":{"begin":3099,"end":3111}},{"label":"th","span":{"begin":3112,"end":3123}},{"label":"tr","span":{"begin":3124,"end":3166}},{"label":"td","span":{"begin":3124,"end":3129}},{"label":"td","span":{"begin":3130,"end":3135}},{"label":"td","span":{"begin":3136,"end":3148}},{"label":"td","span":{"begin":3149,"end":3151}},{"label":"td","span":{"begin":3152,"end":3163}},{"label":"td","span":{"begin":3164,"end":3166}},{"label":"tr","span":{"begin":3167,"end":3203}},{"label":"td","span":{"begin":3167,"end":3173}},{"label":"td","span":{"begin":3174,"end":3185}},{"label":"td","span":{"begin":3186,"end":3188}},{"label":"td","span":{"begin":3189,"end":3200}},{"label":"td","span":{"begin":3201,"end":3203}},{"label":"tr","span":{"begin":3204,"end":3240}},{"label":"td","span":{"begin":3204,"end":3210}},{"label":"td","span":{"begin":3211,"end":3222}},{"label":"td","span":{"begin":3223,"end":3225}},{"label":"td","span":{"begin":3226,"end":3237}},{"label":"td","span":{"begin":3238,"end":3240}},{"label":"tr","span":{"begin":3241,"end":3283}},{"label":"td","span":{"begin":3241,"end":3246}},{"label":"td","span":{"begin":3247,"end":3252}},{"label":"td","span":{"begin":3253,"end":3265}},{"label":"td","span":{"begin":3266,"end":3268}},{"label":"td","span":{"begin":3269,"end":3280}},{"label":"td","span":{"begin":3281,"end":3283}},{"label":"tr","span":{"begin":3284,"end":3320}},{"label":"td","span":{"begin":3284,"end":3290}},{"label":"td","span":{"begin":3291,"end":3303}},{"label":"td","span":{"begin":3304,"end":3306}},{"label":"td","span":{"begin":3307,"end":3318}},{"label":"td","span":{"begin":3319,"end":3320}},{"label":"tr","span":{"begin":3321,"end":3356}},{"label":"td","span":{"begin":3321,"end":3327}},{"label":"td","span":{"begin":3328,"end":3339}},{"label":"td","span":{"begin":3340,"end":3341}},{"label":"td","span":{"begin":3342,"end":3353}},{"label":"td","span":{"begin":3354,"end":3356}},{"label":"table-wrap-foot","span":{"begin":3357,"end":3509}},{"label":"p","span":{"begin":3357,"end":3407}},{"label":"p","span":{"begin":3408,"end":3509}},{"label":"p","span":{"begin":3510,"end":4011}}],"tracks":[{"project":"2_test","denotations":[{"id":"19652920-16472746-56190991","span":{"begin":862,"end":866},"obj":"16472746"},{"id":"19652920-18547586-56190992","span":{"begin":885,"end":889},"obj":"18547586"},{"id":"19652920-16276548-56190993","span":{"begin":1125,"end":1129},"obj":"16276548"},{"id":"19652920-16276548-56190994","span":{"begin":2569,"end":2573},"obj":"16276548"}],"attributes":[{"subj":"19652920-16472746-56190991","pred":"source","obj":"2_test"},{"subj":"19652920-18547586-56190992","pred":"source","obj":"2_test"},{"subj":"19652920-16276548-56190993","pred":"source","obj":"2_test"},{"subj":"19652920-16276548-56190994","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93caec","default":true}]}]}}