Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
J Phys Chem B. 2010 Jun 3;114(21):7359-70. doi: 10.1021/jp906421v.
Mature antibodies (Abs) that are exquisitely specific for virtually any foreign molecule may be produced by affinity maturation of naïve (or germline) Abs. However, the finite number of germline Abs available suggests that, in contrast to mature Abs, germline Abs must be broadly polyspecific so that they are able to recognize a wide range of ligands. Thus, affinity maturation must play a role in mediating Ab specificity. One biophysical property that distinguishes polyspecificity from specificity is protein flexibility; a flexible combining site is able to adopt different conformations that recognize different foreign molecules (or antigens), while a rigid combining site is locked into a conformation that is specific for a given antigen. Recent studies (Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 8821-8826) have examined, at the atomic level, the structural properties that mediate changes in flexibility at four stages of affinity maturation in the 4-4-20 Ab. These studies employed molecular dynamics simulations to reveal a network of residue interactions that mediate the flexibility changes accompanying maturation. The flexibility of the Ab combining sites in these molecular systems was originally measured using three-pulse photon echo spectroscopy (3PEPS). The present investigation extends this work by providing a concrete link between structural properties of the Ab molecules and features of the spectroscopic measurements used to characterize their flexibility. Results obtained from the simulations are in good qualitative agreement with the experimental measurements and indicate that the spectroscopic signal is sensitive to protein dynamics distributed throughout the entire combining site. Thus, the simulations provide a molecular-level interpretation of the changes induced by affinity maturation of the Ab. The results suggest that 3PEPS spectroscopy in combination with molecular dynamics simulations can provide a detailed description of protein dynamics and, in this case, how it is evolved for biological function.
成熟的抗体 (Abs) 对几乎任何外来分子都具有高度特异性，可以通过幼稚 (或种系) Abs 的亲和力成熟来产生。然而，可用的种系 Abs 的数量有限，这表明与成熟的 Abs 相比，种系 Abs 必须具有广泛的多特异性，以便能够识别广泛的配体。因此，亲和力成熟必须在介导 Ab 特异性方面发挥作用。区分多特异性和特异性的一个生物物理特性是蛋白质的灵活性；一个灵活的结合位点能够采用不同的构象来识别不同的外来分子 (或抗原)，而一个刚性的结合位点则被锁定在一种特定的抗原构象中。最近的研究（Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 8821-8826）在原子水平上研究了 4-4-20 Ab 亲和力成熟的四个阶段中，介导灵活性变化的结构特性。这些研究采用分子动力学模拟揭示了介导成熟伴随的灵活性变化的残基相互作用网络。这些分子系统中的 Ab 结合位点的灵活性最初使用三脉冲光声光谱法 (3PEPS) 进行测量。本研究通过提供 Ab 分子结构特性与用于表征其灵活性的光谱测量特征之间的具体联系，扩展了这项工作。模拟结果与实验测量结果具有良好的定性一致性，并表明光谱信号对整个结合位点分布的蛋白质动力学敏感。因此，模拟为 Ab 的亲和力成熟所诱导的变化提供了分子水平的解释。结果表明，3PEPS 光谱学与分子动力学模拟相结合可以提供蛋白质动力学的详细描述，并且在这种情况下，可以描述它如何适应生物功能而进化。
