Insights into the mobility of methyl-bearing side chains in proteins from 3JCC and 3JCN couplings
Insights into the mobility of methyl-bearing side chains in proteins from 3JCC and 3JCN couplings
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DOI：
10.1021/ja029972s
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发表时间：
2003-07-23
影响因子：
15
通讯作者：
Bax, A
中科院分区：
文献类型：
--
作者：
Chou, JJ;Case, DA;Bax, A
蛋白质中的侧链动力学可以通过C-13和2 h弛豫速率的NMR测量来表征。对相应光谱密度的评估限制了可以定量研究的最慢的运动，以达到总体分子滚动的时间尺度。可以从（3）j（c'-cgamma）和（3）J（n- cgamma）耦合。这些耦合可以高精度测量，尤其是对于THR，LLE和VAL残基。结合蛋白质G的泛素和第三个IgG结合结构的已知主链结构，以及在定向培养基中使用的广泛的C-13-H-1侧链偶尔偶联测量值，使用这些（3）J耦合参数化（3）j（c'-cgamma）和（3）j（n-cgamma）的经验karplus关系。这些karplus曲线与DFT计算的结果非常吻合，包括异常的相移，导致最大值（3）J（CC）和（3）J（CN）耦合发生在二面角略小于180的二面角，尤其是在残留物。新的karplus曲线允许确定X，扭转角的旋转体种群。类似的旋转体种群可以从侧链偶极耦合中得出。这些旋转群体将这些旋转群体转换为广义有序参数，S-J（2）和S-D（2），提供了侧链动力学的视图，这些动力学与从C-13和H-2弛豫获得的互补。平均而言，结果与泛素和艾滋病毒蛋白酶中H-2 - - 释放衍生的S-REL（2）值的文献值非常吻合，但也确定了S-J，D（2）<s-Rel的一部分残基（ 2）。这表明某些Rotameric平均发生在时间尺度上发生得太慢，无法在传统的放松测量中观察到。
Side-chain dynamics in proteins can be characterized by the NMR measurement of C-13 and 2 H relaxation rates. Evaluation of the corresponding spectral densities limits the slowest motions that can be studied quantitatively to the time scale on which the overall molecular tumbling takes place. A different measure for the degree of side-chain order about the C-alpha-C-beta bond (chi(1) angle) can be derived from (3)J(C'-Cgamma) and (3)J(N-Cgamma) couplings. These couplings can be measured at high accuracy, in particular for Thr, lle, and Val residues. In conjunction with the known backbone structures of ubiquitin and the third IgG-binding domain of protein G, and an extensive set of C-13-H-1 side-chain dipolar coupling measurements in oriented media, these (3)J couplings were used to parametrize empirical Karplus relationships for (3)J(C'-Cgamma) and (3)J(N-Cgamma). These Karplus curves agree well with results from DFT calculations, including an unusual phase shift, which causes the maximum (3)J(CC) and (3)J(CN) couplings to occur for dihedral angles slightly smaller than 180, particularly noticeable in Thr residues. The new Karplus curves permit determination of rotamer populations for the X, torsion angles. Similar rotamer populations can be derived from side-chain dipolar couplings. Conversion of these rotamer populations into generalized order parameters, S-J(2) and S-D(2), provides a view of side-chain dynamics that is complementary to that obtained from C-13 and H-2 relaxation. On average, results agree well with literature values for H-2-relaxation-derived S-rel(2) values in ubiquitin and HIV protease, but also identify a fraction of residues for which S-J,D(2) < S-rel(2). This indicates that some of the rotameric averaging occurs on a time scale too slow to be observable in traditional relaxation measurements.