Kitova Elena N, Seo Mikyung, Roy Pierre-Nicholas, Klassen John S
Alberta Ingenuity Centre for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2.
J Am Chem Soc. 2008 Jan 30;130(4):1214-26. doi: 10.1021/ja075333b. Epub 2008 Jan 3.
The first detailed study of the intermolecular hydrogens bonds (H-bonds) within a desolvated, noncovalent protein-ligand complex is reported. Using both experimental and computational methods, the intermolecular H-bonds stabilizing protonated and deprotonated ions of a complex composed of a single chain fragment (scFv) of a monoclonal antibody and its native trisaccharide ligand, alphaGal[alphaAbe] alphaMan (1), are characterized. Using the blackbody infrared radiative dissociation-functional group replacement (BIRD/FGR) technique, three H-bond donor-acceptor pairs within the gaseous (scFv + 1)n+ ions are identified and quantified. Additional sites of interaction on the protein and ligand, for which the binding partner could not be elucidated, are also identified. Comparison of the gas-phase interaction maps with the crystal structure suggests that at least two of the specific H-bonds are conserved upon transfer of the complex from solution to the gas phase by electrospray ionization. However, new (nonspecific) interactions can also form in the gas phase. Notably, the nature and strength of the intermolecular interactions can vary significantly with charge state, and striking differences in the structures of the (scFv + 1)n+ and (scFv + 1)n- ions are evident. Intermolecular H-bonds are also identified from molecular dynamics (MD) simulations performed at the +8 and -8 charge states. Agreement is found for a majority of intermolecular interactions predicted for the (scFv + 1)8+ ion by the MD simulation and BIRD/FGR method; the agreement is less favorable in the case of the (scFv + 1)8- ion. However, both the computational and experimental results point to structural differences between the +8 and -8 ions. The computational results also provide insights into the structural changes that accompany the loss of interfacial waters from the complex.
报道了对去溶剂化的非共价蛋白质-配体复合物中分子间氢键（H键）的首次详细研究。使用实验和计算方法，对由单克隆抗体的单链片段（scFv）及其天然三糖配体αGal[αAbe]αMan（1）组成的复合物的质子化和去质子化离子的稳定分子间H键进行了表征。使用黑体红外辐射解离-官能团置换（BIRD/FGR）技术，确定并量化了气态（scFv + 1）n+离子中的三对H键供体-受体对。还确定了蛋白质和配体上无法阐明结合伙伴的其他相互作用位点。气相相互作用图谱与晶体结构的比较表明，通过电喷雾电离将复合物从溶液转移到气相时，至少有两个特定的H键得以保留。然而，新的（非特异性）相互作用也可以在气相中形成。值得注意的是，分子间相互作用的性质和强度会随电荷状态而显著变化，并且（scFv + 1）n+和（scFv + 1）n-离子的结构存在明显差异。还从在+8和-8电荷状态下进行的分子动力学（MD）模拟中识别出分子间H键。MD模拟和BIRD/FGR方法对（scFv + 1）8+离子预测的大多数分子间相互作用达成了一致；在（scFv + 1）8-离子的情况下，一致性较差。然而，计算和实验结果都表明+8和-8离子之间存在结构差异。计算结果还提供了对复合物中界面水损失伴随的结构变化的见解。
