Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555.
Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555
Proc Natl Acad Sci U S A. 2021 Jun 22;118(25). doi: 10.1073/pnas.2104020118.
Electrostatic potentials computed from three-dimensional structures of biomolecules by solving the Poisson-Boltzmann equation are widely used in molecular biophysics, structural biology, and medicinal chemistry. Despite the approximate nature of the Poisson-Boltzmann theory, validation of the computed electrostatic potentials around biological macromolecules is rare and methodologically limited. Here, we present a unique and powerful NMR method that allows for straightforward and extensive comparison with electrostatic models for biomolecules and their complexes. This method utilizes paramagnetic relaxation enhancement arising from analogous cationic and anionic cosolutes whose spatial distributions around biological macromolecules reflect electrostatic potentials. We demonstrate that this NMR method enables de novo determination of near-surface electrostatic potentials for individual protein residues without using any structural information. We applied the method to ubiquitin and the Antp homeodomain-DNA complex. The experimental data agreed well with predictions from the Poisson-Boltzmann theory. Thus, our experimental results clearly support the validity of the theory for these systems. However, our experimental study also illuminates certain weaknesses of the Poisson-Boltzmann theory. For example, we found that the theory predicts stronger dependence of near-surface electrostatic potentials on ionic strength than observed in the experiments. Our data also suggest that conformational flexibility or structural uncertainties may cause large errors in theoretical predictions of electrostatic potentials, particularly for highly charged systems. This NMR-based method permits extensive assessment of near-surface electrostatic potentials for various regions around biological macromolecules and thereby may facilitate improvement of the computational approaches for electrostatic potentials.
通过求解泊松-玻尔兹曼方程从生物分子的三维结构计算出的静电势在分子生物物理学、结构生物学和药物化学中得到了广泛应用。尽管泊松-玻尔兹曼理论具有近似性,但对生物大分子周围计算出的静电势进行验证的情况很少,而且方法上也受到限制。在这里,我们提出了一种独特而强大的 NMR 方法,可直接且广泛地与生物分子及其复合物的静电模型进行比较。该方法利用来自类似阳离子和阴离子共溶剂的顺磁弛豫增强,其在生物大分子周围的空间分布反映了静电势。我们证明,这种 NMR 方法无需使用任何结构信息即可从头确定单个蛋白质残基的近表面静电势。我们将该方法应用于泛素和 Antp 同源域-DNA 复合物。实验数据与泊松-玻尔兹曼理论的预测非常吻合。因此,我们的实验结果清楚地支持了这些系统的理论的有效性。然而,我们的实验研究也揭示了泊松-玻尔兹曼理论的某些弱点。例如,我们发现该理论预测近表面静电势对离子强度的依赖性比实验中观察到的要强。我们的数据还表明,构象灵活性或结构不确定性可能会导致理论预测静电势产生较大误差,尤其是对于高度带电的系统。这种基于 NMR 的方法允许对生物大分子周围的各种区域的近表面静电势进行广泛评估,从而可能有助于改进静电势的计算方法。