General Dynamics Information Technology, San Antonio, Texas 78234, USA.
J Phys Chem B. 2012 Sep 13;116(36):11032-40. doi: 10.1021/jp304310z. Epub 2012 Aug 29.
Understanding the conformational changes induced by small ligands noncovalently bound to proteins is a central problem in biophysics. We focus on the binding location of the water-soluble porphyrin, meso-tetrakis (p-sulfonatophenyl) porphyrin, to a globular protein, β-lactoglobulin, which has been observed to partially unfold when irradiated by laser light. Identifying the binding location is necessary to determine the mechanism of action as well as the atoms and residues involved in the photoinduced partial unfolding. Such atomic details are typically investigated by nuclear magnetic resonance or X-ray crystallography. However, for biomolecules in solution at the low concentrations (μM) required to deliver uniform laser irradiation, these traditional techniques do not currently provide sufficient information, and one must rely upon less direct spectroscopic methods. We describe a method that uses resonance Raman spectroscopy and density functional theory (DFT) to select the most likely binding configuration among a set of solutions yielded by computational docking algorithms. This methodology may be generalized to use with other ligand-protein complexes where the ligand structure is amenable to DFT simulations.
理解非共价结合小分子配体诱导的蛋白质构象变化是生物物理学的一个核心问题。我们关注的是水溶性卟啉，meso-四(对磺酸钠苯基)卟啉与球状蛋白质β-乳球蛋白的结合位置，当用激光照射时，β-乳球蛋白会部分展开。确定结合位置对于确定作用机制以及涉及光诱导部分展开的原子和残基是必要的。这些原子细节通常通过核磁共振或 X 射线晶体学来研究。然而，对于溶液中的生物分子，在为了实现均匀激光照射所需的低浓度（μM）下，这些传统技术目前无法提供足够的信息，因此必须依赖于不那么直接的光谱方法。我们描述了一种使用共振拉曼光谱和密度泛函理论（DFT）的方法，从计算对接算法生成的一组溶液中选择最可能的结合构型。这种方法可以推广到其他配体-蛋白质复合物中使用，只要配体结构适合 DFT 模拟即可。
