Conformational variability of matrix metalloproteinases: Beyond a single 3D structure
Conformational variability of matrix metalloproteinases: Beyond a single 3D structure
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DOI：
10.1073/pnas.0407106102
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发表时间：
2005-04-12
影响因子：
11.1
通讯作者：
Turano, P
中科院分区：
文献类型：
--
作者：
Bertini, I;Calderone, V;Turano, P
基质金属蛋白酶12的催化结构域中的乙酰异羟肟酸和N-异丁基-N-[4-甲氧基苯磺酰基]甘氨酰异羟肟酸的存在下，已解决了由X-射线衍射在结晶状态下在1.0和1.3埃分辨率，分别，并与先前公布的X-射线结构在1.2埃分辨率的加合物与巴马司他。N-异丁基-N-[4-甲氧基苯磺酰基]甘氨酰异羟肟酸加合物的结构已通过溶液中的NMR解析。三种X射线结构和溶液结构相似但不完全相同，环中的差异明显更高。我们建议，许多循环显示在各种时间尺度上的动态行为的解决方案。在不同的晶体环境中，可以观察到蛋白质的一些柔性区域的不同构象被“冻结”。通过NMR研究的溶液中的迁移率揭示了在可接近的时间尺度内的构象平衡，即，从10（-5）秒到更多。一些剩余偶极耦合的平均值与进一步运动一致，下降到10（-9）s。最后，在100 K的结晶状态下，每个冻结构象的局部热运动与皮秒时间尺度上的局部运动相关。灵活性/构象异质性的催化结构域的关键部分是一个规则，而不是一个例外，在基质金属蛋白酶，其程度可能被低估的一个X射线结构的检查。骨架的灵活性可能发挥作用，在选择性抑制剂的设计中遇到的困难，而它可能是一个必要的底物结合和广泛的底物特异性。
The structures of the catalytic domain of matrix metalloproteinase 12 in the presence of acetohydroxamic acid and N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid have been solved by x-ray diffraction in the crystalline state at 1.0 and 1.3-angstrom resolution, respectively, and compared with the previously published x-ray structure at 1.2-angstrom resolution of the adduct with batimastat. The structure of the N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid adduct has been solved by NMR in solution. The three x-ray structures and the solution structure are similar but not identical to one another, the differences being sizably higher in the loops. We propose that many of the loops show a dynamical behavior in solution on a variety of time scales. Different conformations of some flexible regions of the protein can be observed as "frozen" in different crystalline environments. The mobility in solution studied by NMR reveals conformational equilibria in accessible time scales, i.e., from 10(-5) s toms and more. Averaging of some residual dipolar couplings is consistent with further motions down to 10(-9) s. Finally, local thermal motions of each frozen conformation in the crystalline state at 100 K correlate well with local motions on the picosecond time scale. Flexibility/conformational heterogeneity in crucial parts of the catalytic domain is a rule rather than an exception in matrix metalloproteinases, and its extent may be underestimated by inspection of one x-ray structure. Backbone flexibility may play a role in the difficulties encountered in the design of selective inhibitors, whereas it may be a requisite for substrate binding and broad substrate specificity.