我们基于基于接触截止值的蛋白质残基富集的特异性来探测芳香族-蛋白质相互作用。因此,当残基与芳香族配体接触和不接触时,分析了155种蛋白质-NAD()/NADP()复合物在配体的芳香族基团的质心10埃内的富集。具体来说,氧化辅酶的中性腺嘌呤和阳离子烟酰胺基团引起了人们的兴趣,以了解电荷的对比度或共享的芳香性是否会在截止范围内的富集中表现出来。我们发现接触时,富集对烟酰胺和腺嘌呤-芳香结构具有高度特异性,因此基础可能很复杂,但是当不联系时,它们对于结构的收费和芳香性是通用的,因此,在基础上可能是具体的。接触残基的富集顺序是Tyr>Cys>Thr>His>Asn>Ser>Met>Ile>Phe针对烟酰胺-π()结构和Asp>Ile>Thr>His>Arg>Tyr>Gly>Val针对腺嘌呤-π结构,而非接触残基的顺序是Trp>Gly>His>Asn>Cys>Met>Tyr>Ser>Thr>Phe针对烟酰胺-π()结构和Asn>Thr>Ser>Gly>Cys>His>Val针对腺嘌呤-π结构。中立Trp,他的,Tyr,而Phe,但不是阳离子Arg,因此,是针对烟酰胺-π(+)结构特异性富集的非接触残基,而Asn,Gly,Thr,Ser,和Cys是通常针对烟酰胺-π(+)和腺嘌呤-π芳族结构富集的非接触残基。通过分析富集组的几何特异性,我们发现,针对烟酰胺阳离子的富集显示出预期的阳离子-π相互作用的特异性,针对烟酰胺-和腺嘌呤-芳香族基团的富集显示出预期的偶极-π相互作用的特异性。基于截止值的方法在探测所涉及的物理学中的蛋白质-配体相互作用方面被证明是有价值的。
We probed aromatic-protein interactions based on specificity of enrichment of protein residues across a contact-based cutoff. Thus, 155 protein-NAD(+)/
NADP(+) complexes were analyzed for enrichments within 10Å of centroids of aromatic groups of the ligand when the residues were contacted and not contacted with the aromatic ligand. Specifically, neutral-adenine and cationic-nicotinamide groups of the oxidized coenzymes evoked interest to know whether the contrast of charge or the shared aromaticity will manifest in the enrichments across the cutoff. We found that when in contact, the enrichments are highly specific for nicotinamide and adenine-aromatic structures, and thus possibly complex in the basis, but when not in contact, they are generic for charge and aromaticity of the structures, and thus possibly specific in the basis. The order of enrichments over the contacted residues is Tyr>Cys>Thr>His>Asn>Ser>Met>Ile>Phe against nicotinamide-π(+) structure and Asp>Ile>Thr>His>Arg>Tyr>Gly>Val against adenine-π structure, while the order over the non-contacted residues is Trp>Gly>His>Asn>Cys>Met>Tyr>Ser>Thr>Phe against nicotinamide-π(+) structure and Asn>Thr>Ser>Gly>Cys>His>Val against adenine-π structure. Neutral Trp, His, Tyr, and Phe, but not cationic Arg, are thus the non-contacted residues enriched specifically against nicotinamide-π(+) structure, while Asn, Gly, Thr, Ser, and Cys are the non-contacted residues enriched generically against both the nicotinamide-π(+) and adenine-π aromatic structures. By analyzing the enriched groups in their geometric specificities, we found that, the enrichments against nicotinamide cation manifest the specificity expected of cation-π interaction and against nicotinamide- and adenine-aromatic groups manifest the specificity expected of dipole-π interaction. The cutoff-based method is proven valuable in probing protein-ligand interactions in the physics involved.