Balamurugan Kanagasabai, Pisabarro M Teresa
Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg 47-51, 01307 Dresden, Germany.
ACS Omega. 2021 Sep 23;6(39):25350-25360. doi: 10.1021/acsomega.1c03264. eCollection 2021 Oct 5.
In this work, anion-π interactions between sulfate groups (SO ) and protein aromatic amino acids (AAs) (histidine protonated (HisP), histidine neutral (HisN), tyrosine (Tyr), tryptophan (Trp), and phenylalanine (Phe)) in an aqueous environment have been analyzed using quantum chemical (QC) calculations and molecular dynamics (MD) simulations. Sulfates can occur naturally in solution and can be contained in biomolecules playing relevant roles in their biological function. In particular, the presence of sulfate groups in glycosaminoglycans such as heparin and heparan sulfate has been shown to be relevant for protein and cellular communication and, consequently, for tissue regeneration. Therefore, anion-π interactions between sulfate groups and aromatic residues represent a relevant aspect to investigate. QC results show that such an anion-π mode of interaction between SO and aromatic AAs is only possible in the presence of water molecules, in the absence of any other cooperative non-covalent interactions. Protonated histidine stands out in terms of its enhancement in the magnitude of interaction strength on solvation. Other AAs such as non-protonated histidine, tyrosine, and phenylalanine can stabilize anion-π interactions on solvation, albeit with weak interaction energy. Tryptophan does not exhibit any anion-π mode of interaction with SO . The order of magnitude of the interaction of aromatic AAs with SO on microsolvation is HisP > HisN > Tyr > Trp > Phe. Atoms in molecules (AIM) analysis illustrates the significance of water molecules in stabilizing the divalent SO anion over the π surface of the aromatic AAs. MD simulation analysis shows that the order of magnitude of the interaction of SO with aromatic AAs in macroscopic solvation is HisP > HisN, Tyr, Trp > Phe, which is very much in line with the QC results. Spatial distribution function analysis illustrates that protonated histidine alone is capable of establishing the anion-π interaction with SO in the solution phase. This study sheds light on the understanding of anion-π interactions between SO and aromatic AAs such as His and Tyr observed in protein crystal structures and the significance of water molecules in stabilizing such interactions, which is not feasible otherwise.
在本研究中,利用量子化学(QC)计算和分子动力学(MD)模拟,分析了水环境中硫酸根离子(SO₄²⁻)与蛋白质芳香族氨基酸(AAs)(质子化组氨酸(HisP)、中性组氨酸(HisN)、酪氨酸(Tyr)、色氨酸(Trp)和苯丙氨酸(Phe))之间的阴离子 - π相互作用。硫酸根可自然存在于溶液中,并且可包含在对其生物学功能起相关作用的生物分子中。特别地,已证明诸如肝素和硫酸乙酰肝素等糖胺聚糖中硫酸根的存在与蛋白质和细胞通讯相关,因此与组织再生相关。因此,硫酸根与芳香族残基之间的阴离子 - π相互作用是一个值得研究的相关方面。量子化学计算结果表明,在不存在任何其他协同非共价相互作用的情况下,只有在水分子存在时,SO₄²⁻与芳香族氨基酸之间才可能存在这种阴离子 - π相互作用模式。质子化组氨酸在溶剂化时相互作用强度的增强方面表现突出。其他氨基酸,如非质子化组氨酸、酪氨酸和苯丙氨酸,虽然相互作用能较弱,但在溶剂化时可稳定阴离子 - π相互作用。色氨酸与SO₄²⁻不表现出任何阴离子 - π相互作用模式。芳香族氨基酸与SO₄²⁻在微溶剂化时相互作用的量级顺序为HisP>HisN>Tyr>Trp>Phe。分子中的原子(AIM)分析说明了水分子在稳定芳香族氨基酸π表面上的二价SO₄²⁻阴离子方面所起的重要作用。分子动力学模拟分析表明,在宏观溶剂化中,SO₄²⁻与芳香族氨基酸相互作用的量级顺序为HisP>HisN、Tyr、Trp>Phe,这与量子化学计算结果非常一致。空间分布函数分析表明,仅质子化组氨酸就能在溶液相中与SO₄²⁻建立阴离子 - π相互作用。这项研究有助于理解在蛋白质晶体结构中观察到的SO₄²⁻与His和Tyr等芳香族氨基酸之间的阴离子 - π相互作用,以及水分子在稳定这种相互作用中的重要性,否则这是不可行的。