Refined solution structure of the 82-kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints
Refined solution structure of the 82-kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints
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DOI：
10.1007/s10858-007-9211-5
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发表时间：
2008-02-01
影响因子：
2.7
通讯作者：
Bax, Ad
中科院分区：
文献类型：
--
作者：
Grishaev, Alexander;Tugarinov, Vitali;Bax, Ad
通过NMR确定大蛋白质的精确三维结构仍然具有挑战性，这是由于经常先决条件全氘化导致的实验限制密度的损失。解决方案小角度散射，携带远程平移信息，提供了一个机会，以提高结构的准确性，衍生模型结合使用时，与全球定向NMR的限制，如残留偶极耦合（RDC）和残留化学位移各向异性（RCSA）。我们已经量化了使用该策略可以获得的82 kDa酶苹果酸合酶G（MSG），目前最大的单链蛋白质溶液NMR解决的准确性的改善。对NMR和散射数据的联合细化导致结构准确度的提高，如通过衍生模型和高分辨率X射线结构（PDB代码1D 8 C）之间的骨架rmsd从近似4.5埃降低到近似3.3埃所证明的。这种改进主要是由于中等角度的散射数据，它编码的整体分子形状，而不是最低角度的数据，主要确定回转半径和最大颗粒尺寸。由内部密度波动主导的较高角度数据的影响虽然有益，但也被发现相对较小。我们的研究结果表明，联合NMR/SAXS细化可以显着提高溶液结构测定的准确性，并将特别适合于有限的NMR限制，如大蛋白质，寡核苷酸，或其复合物的系统的研究。
Determination of the accurate three-dimensional structure of large proteins by NMR remains challenging due to a loss in the density of experimental restraints resulting from the often prerequisite perdeuteration. Solution small-angle scattering, which carries long-range translational information, presents an opportunity to enhance the structural accuracy of derived models when used in combination with global orientational NMR restraints such as residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs). We have quantified the improvements in accuracy that can be obtained using this strategy for the 82 kDa enzyme Malate Synthase G (MSG), currently the largest single chain protein solved by solution NMR. Joint refinement against NMR and scattering data leads to an improvement in structural accuracy as evidenced by a decrease from similar to 4.5 to similar to 3.3 angstrom of the backbone rmsd between the derived model and the high-resolution X-ray structure, PDB code 1D8C. This improvement results primarily from medium-angle scattering data, which encode the overall molecular shape, rather than the lowest angle data that principally determine the radius of gyration and the maximum particle dimension. The effect of the higher angle data, which are dominated by internal density fluctuations, while beneficial, is also found to be relatively small. Our results demonstrate that joint NMR/SAXS refinement can yield significantly improved accuracy in solution structure determination and will be especially well suited for the study of systems with limited NMR restraints such as large proteins, oligonucleotides, or their complexes.