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人8-氧代鸟嘌呤-DNA糖基化酶(hOgg1)可能的单功能活性的ONIOM和分子动力学研究

An ONIOM and MD Investigation of Possible Monofunctional Activity of Human 8-Oxoguanine-DNA Glycosylase (hOgg1).

作者信息

Kellie Jennifer L, Wilson Katie A, Wetmore Stacey D

机构信息

Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada, T1K 3M4.

出版信息

J Phys Chem B. 2015 Jun 25;119(25):8013-23. doi: 10.1021/acs.jpcb.5b04051. Epub 2015 Jun 9.

Abstract

Since the formation of 8-oxoguanine (OG) is one of the most common DNA-damaging events, cells have evolved efficient repair processes to avoid the mutagenic effects associated with this lesion, including base excision repair (BER) initiated by hOgg1. In the present work, three distinct mechanisms for deglycosylation catalyzed by hOgg1 that represent monofunctional activity were characterized using a combination of molecular dynamics (MD) simulations on the full DNA-enzyme complex and ONIOM calculations on a truncated DNA-protein model. The initial lysine activation step common to all pathways involves proton transfer from (cationic) K249 to (anionic) C253 and subsequent active-site rearrangement to align key amino acids and/or water for the next reaction step. In the first mechanism, K249 initiates deglycosylation as the nucleophile and the resulting DNA-protein cross-link is hydrolyzed to generate an abasic site. In the remaining two mechanisms, an active-site water molecule is the nucleophile, which is activated by either K249 or D268. These latter mechanisms are supported by MD simulations that reveal an abundance of water in the active site that could function as the nucleophile. Our ONIOM model suggests that the most likely mechanism involves water nucleophile activation by K249, which allows the active-site aspartate (D268) to electrostatically stabilize the charge buildup on the sugar residue throughout the entire reaction pathway. This newly conjectured mechanism is consistent with the proposed activity of other monofunctional glycosylases. In addition to providing the first atomic level evidence for a monofunctional hOgg1 catalytic pathway, the mechanistic details revealed in the present work can be used to direct future large-scale reaction modeling on the entire DNA-protein complex, which can be coupled with experimental kinetic data to afford a reliable comparison of the potential mono- and bifunctional activity of this crucial enzyme.

摘要

由于8-氧代鸟嘌呤(OG)的形成是最常见的DNA损伤事件之一,细胞已经进化出高效的修复过程,以避免与该损伤相关的诱变效应,包括由hOgg1启动的碱基切除修复(BER)。在本研究中,结合对完整DNA-酶复合物的分子动力学(MD)模拟和对截短的DNA-蛋白质模型的ONIOM计算,表征了hOgg1催化的去糖基化的三种不同机制,这些机制代表单功能活性。所有途径共有的初始赖氨酸活化步骤涉及质子从(阳离子)K249转移到(阴离子)C253,随后活性位点重排,以使关键氨基酸和/或水对齐,以便进行下一步反应。在第一种机制中,K249作为亲核试剂启动去糖基化,并且由此产生的DNA-蛋白质交联被水解以产生无碱基位点。在其余两种机制中,活性位点水分子是亲核试剂,其被K249或D268激活。MD模拟支持了后一种机制,该模拟揭示了活性位点中大量的水可以作为亲核试剂起作用。我们的ONIOM模型表明,最可能的机制涉及K249对水亲核试剂的激活,这使得活性位点天冬氨酸(D268)在整个反应途径中静电稳定糖残基上的电荷积累。这种新推测的机制与其他单功能糖基化酶的假定活性一致。除了为单功能hOgg1催化途径提供第一个原子水平的证据外,本研究中揭示的机制细节可用于指导未来对整个DNA-蛋白质复合物的大规模反应建模,这可以与实验动力学数据相结合,以可靠地比较这种关键酶的潜在单功能和双功能活性。

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