Differential repair enzyme-substrate selection within dynamic DNA energy landscapes.

IF 7.2 2区 生物学 Q1 BIOPHYSICS
J Völker, K J Breslauer
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引用次数: 4

Abstract

We demonstrate that reshaping of the dynamic, bulged-loop energy landscape of DNA triplet repeat ensembles by the presence of an abasic site alters repair outcomes by the APE1 enzyme. This phenomenon depends on the structural context of the lesion, despite the abasic site always having the same neighbors in sequence space. We employ this lesion-induced redistribution of DNA states and a kinetic trap to monitor different occupancies of the DNA bulge loop states. We show how such dynamic redistribution and associated differential occupancies of DNA states impact APE1 repair outcomes and APE1 induced interconversions. We correlate the differential biophysical properties of the dynamic, DNA ensemble states, with their ability to be recognized and processed as substrates by the APE1 DNA repair enzyme. Enzymatic digestions and biophysical characterizations reveal that APE1 cuts a fraction (10-12%) of the dynamic, rollameric substrates within the initial kinetic distribution. APE1 interactions also 'induce' rollamer redistribution from a kinetically trapped distribution to an equilibrium distribution, the latter not containing viable APE1 substrates. We distinguish between kinetically controlled ensemble (re)distributions of potential DNA substrates, versus thermodynamically controlled ensemble (re)distribution; features of importance to DNA regulation. We conclude that APE1 activity catalyzes/induces ensembles that represent the thermodynamically optimal loop distribution, yet which also are nonviable substrate states for abasic site cleavage by APE1. We propose that by inducing substrate redistributions in a dynamic energy landscape, the enzyme actually reduces the available substrate competent species for it to process, reflective of a regulatory mechanism for enzymatic self-repression. If this is a general phenomenon, such a consequence would have a profound impact on slowing down and/or misdirecting DNA repair within dynamic energy landscapes, as exemplified here within triplet repeat domains. In short, APE1-instigated redistribution of potential substrates induces a preferred pathway to an equilibrium ensemble of enzymatically incompetent states.

动态DNA能量景观中的差异修复酶-底物选择。
我们证明,通过一个基本位点的存在,重塑DNA三联体重复序列的动态、膨出环能量景观会改变APE1酶的修复结果。这种现象取决于病变的结构背景,尽管基本位点在序列空间中总是具有相同的邻居。我们采用这种损伤诱导的DNA状态再分配和动力学陷阱来监测DNA凸起环状态的不同占用。我们展示了这种动态再分配和相关的DNA状态差异占用如何影响APE1修复结果和APE1诱导的相互转换。我们将动态DNA集合状态的不同生物物理特性与它们被APE1 DNA修复酶识别和加工为底物的能力联系起来。酶解和生物物理表征表明,在初始动力学分布中,APE1切割了一小部分(10-12%)的动态、滚动底物。APE1相互作用也“诱导”辊体从动力学捕获分布重新分布到平衡分布,后者不包含可行的APE1底物。我们区分了潜在DNA底物的动力学控制的系综(re)分布与热力学控制的系综(re)分布;对DNA调控很重要的特征。我们得出的结论是,APE1活性催化/诱导了代表热力学最佳环分布的综合体,但这也是APE1切割基本位点的不可活底物状态。我们提出,通过在动态能量环境中诱导底物重新分配,酶实际上减少了可供其加工的底物胜任物种,反映了酶自我抑制的调节机制。如果这是一种普遍现象,那么这种后果将对动态能量景观中减慢和/或误导DNA修复产生深远的影响,例如在三联体重复结构域中。简而言之,ape1诱导的潜在底物的重新分配诱导了一条通往酶无能状态平衡集合的首选途径。
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来源期刊
Quarterly Reviews of Biophysics
Quarterly Reviews of Biophysics 生物-生物物理
CiteScore
12.90
自引率
1.60%
发文量
16
期刊介绍: Quarterly Reviews of Biophysics covers the field of experimental and computational biophysics. Experimental biophysics span across different physics-based measurements such as optical microscopy, super-resolution imaging, electron microscopy, X-ray and neutron diffraction, spectroscopy, calorimetry, thermodynamics and their integrated uses. Computational biophysics includes theory, simulations, bioinformatics and system analysis. These biophysical methodologies are used to discover the structure, function and physiology of biological systems in varying complexities from cells, organelles, membranes, protein-nucleic acid complexes, molecular machines to molecules. The majority of reviews published are invited from authors who have made significant contributions to the field, who give critical, readable and sometimes controversial accounts of recent progress and problems in their specialty. The journal has long-standing, worldwide reputation, demonstrated by its high ranking in the ISI Science Citation Index, as a forum for general and specialized communication between biophysicists working in different areas. Thematic issues are occasionally published.
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