It had been observed that in some DNA-binding proteins, hydrophobic amino acid side-chains intercalate between two base pairs of the DNA, often leading to curvature or kink. Some of these proteins pre-dominantly interact through the minor groove and are often described as not having strong sequence preference. In contrast, lac-repressor binds to DNA with strong sequence specificity, also interacts with the minor groove of its operator by partially intercalating two Leucine side-chains between two CG base pairs, in addition to its interaction with the major groove base atoms. The role of this interaction in the operator recognition has not been fully elucidated. We have done extensive quantum chemical calculations, from molecular dynamics derived snapshots, using dispersion-corrected density functional theory to show that this unstacking is energetically slightly unfavorable. However, among all the base-amino acid pairs studied, the CG/CG-Leucine pair, the natural sequence, is among the most stable ones. The bending of the DNA resulting from this intercalation is important for aligning the major dimeric protein and the DNA interfaces. Thus, the sacrifice of modest binding energy enhances the sequence-specificity. Given many prokaryotic repressors belong to the lac repressor family, this could be a general mechanism for augmenting sequence specificity.

已经观察到，在一些DNA结合蛋白中，疏水性氨基酸侧链插在DNA的两个碱基对之间，通常导致弯曲或扭结。这些蛋白质中的一些主要通过小沟相互作用，通常被描述为不具有较强的序列偏好性。相反，lac-阻遏物以很强的序列特异性与DNA结合，除了其与主要沟碱基原子的相互作用外，还通过部分插入两个CG碱基对之间的两条亮氨酸侧链与其操纵子的次要沟相互作用。这种交互作用在操作员识别中的作用尚未完全阐明。我们已经从分子动力学得出的快照中进行了广泛的量子化学计算，使用色散校正的密度泛函理论来证明这种分解在能量上稍微不利。但是，在所有研究的碱基氨基酸对中，天然序列CG / CG-亮氨酸对是最稳定的。由这种插入引起的DNA弯曲对于对准主要的二聚体蛋白质和DNA界面很重要。因此，牺牲适度的结合能增强了序列特异性。鉴于许多原核生物阻遏物都属于lac阻遏物家族，这可能是增强序列特异性的一般机制。由这种插入引起的DNA弯曲对于对准主要的二聚体蛋白质和DNA界面很重要。因此，牺牲适度的结合能增强了序列特异性。鉴于许多原核生物阻遏物都属于lac阻遏物家族，这可能是增强序列特异性的一般机制。由这种插入引起的DNA弯曲对于比对主要的二聚体蛋白质和DNA界面是重要的。因此，牺牲适度的结合能增强了序列特异性。鉴于许多原核生物阻遏物都属于lac阻遏物家族，这可能是增强序列特异性的一般机制。