Graduate Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.
Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, USA.
Protein Sci. 2022 Aug;31(8):e4373. doi: 10.1002/pro.4373.
Numerous studies have investigated the differences and similarities between protein structures determined by solution NMR spectroscopy and those determined by X-ray crystallography. A fundamental question is whether any observed differences are due to differing methodologies or to differences in the behavior of proteins in solution versus in the crystalline state. Here, we compare the properties of the hydrophobic cores of high-resolution protein crystal structures and those in NMR structures, determined using increasing numbers and types of restraints. Prior studies have reported that many NMR structures have denser cores compared with those of high-resolution X-ray crystal structures. Our current work investigates this result in more detail and finds that these NMR structures tend to violate basic features of protein stereochemistry, such as small non-bonded atomic overlaps and few Ramachandran and sidechain dihedral angle outliers. We find that NMR structures solved with more restraints, and which do not significantly violate stereochemistry, have hydrophobic cores that have a similar size and packing fraction as their counterparts determined by X-ray crystallography at high resolution. These results lead us to conclude that, at least regarding the core packing properties, high-quality structures determined by NMR and X-ray crystallography are the same, and the differences reported earlier are most likely a consequence of methodology, rather than fundamental differences between the protein in the two different environments.
许多研究都调查了通过溶液 NMR 光谱学和 X 射线晶体学确定的蛋白质结构之间的差异和相似之处。一个基本问题是，观察到的差异是由于不同的方法学还是由于蛋白质在溶液中和结晶状态下的行为差异所致。在这里，我们比较了高分辨率蛋白质晶体结构和 NMR 结构中疏水区核心的性质，这些结构是使用越来越多的约束类型和数量确定的。先前的研究报告称，与高分辨率 X 射线晶体结构相比，许多 NMR 结构的核心密度更高。我们当前的工作更详细地研究了这一结果，发现这些 NMR 结构往往违反了蛋白质立体化学的基本特征，例如小的非键原子重叠和很少的 Ramachandran 和侧链二面角异常值。我们发现，使用更多约束条件解决且不显著违反立体化学的 NMR 结构，其疏水区核心的大小和堆积分数与通过高分辨率 X 射线晶体学确定的对应物相似。这些结果使我们得出结论，至少就核心堆积特性而言，通过 NMR 和 X 射线晶体学确定的高质量结构是相同的，而早期报道的差异很可能是方法学的结果，而不是蛋白质在两种不同环境中的基本差异。
