Hildebrand Nils, Michaelis Monika, Wurzler Nina, Li Zhuo, Hirst Jonathan D, Micsonai András, Kardos József, Gil-Ley Alejandro, Bussi Giovanni, Köppen Susan, Delle Piane Massimo, Ciacchi Lucio Colombi
Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen, Am Fallturm 1, Bremen 28359, Germany.
School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom.
ACS Biomater Sci Eng. 2018 Dec 10;4(12):4036-4050. doi: 10.1021/acsbiomaterials.8b00819. Epub 2018 Nov 15.
Adsorption of enzymes on solid surfaces may lead to conformational changes that reduce their catalytic conversion activity and are thus detrimental to the efficiency of biotechnology or biosensing applications. This work is a joint theoretical and experimental endeavor in which we identify and quantify the conformational changes that chymotrypsin undergoes when in contact with the surface of amorphous silica nanoparticles. For this purpose, we use circular dichroism spectroscopy, standard molecular dynamics, and advanced-sampling methods. Only the combination of these techniques allowed us to pinpoint a destabilization effect of silica on specific structural motifs of chymotrypsin. They are linked by the possibility of theoretically predicting CD spectra, allowing us to elucidate the source of the experimentally observed spectral changes. We find that chymotrypsin loses part of its helical content upon adsorption, with minor perturbation of its overall tertiary structure, associated with changes in the aromatic interactions. We demonstrate that the C-terminal helical fragment is unfolded as an isolated oligopeptide in pure water, folded as an α-helix as terminus of chymotrypsin in solution, and again partly disordered when the protein is adsorbed on silica. We believe that the joint methodology introduced in this manuscript has a direct general applicability to investigate any biomolecule-inorganic surface system. Methods to theoretically predict circular dichroism spectra from atomistic simulations were compared and improved. The drawbacks of the approaches are discussed; in particular, the limited capability of advanced-sampling MD schemes to explore the conformational phase space of large proteins and the dependency of the predicted ellipticity bands on the choice of calculation parameters.
酶在固体表面的吸附可能导致构象变化，从而降低其催化转化活性，进而对生物技术或生物传感应用的效率产生不利影响。这项工作是一项理论与实验相结合的研究，我们识别并量化了胰凝乳蛋白酶与无定形二氧化硅纳米颗粒表面接触时所经历的构象变化。为此，我们使用了圆二色光谱、标准分子动力学和高级采样方法。只有这些技术的结合才能让我们确定二氧化硅对胰凝乳蛋白酶特定结构基序的去稳定化作用。它们通过理论预测圆二色光谱的可能性联系在一起，使我们能够阐明实验观察到的光谱变化的来源。我们发现，胰凝乳蛋白酶在吸附后失去了部分螺旋结构，其整体三级结构受到轻微扰动，这与芳香族相互作用的变化有关。我们证明，C端螺旋片段在纯水中作为孤立的寡肽展开，在溶液中作为胰凝乳蛋白酶的末端折叠成α螺旋，而当蛋白质吸附在二氧化硅上时又部分无序。我们相信，本文中介绍的联合方法对于研究任何生物分子 - 无机表面系统具有直接的普遍适用性。我们比较并改进了从原子模拟理论预测圆二色光谱的方法。讨论了这些方法的缺点；特别是，高级采样分子动力学方案探索大蛋白质构象相空间的能力有限，以及预测的椭圆率带对计算参数选择的依赖性。
