Evolutionary Covariance Combined with Molecular Dynamics Predicts a Framework for Allostery in the MutS DNA Mismatch Repair Protein

Mismatch
repair (MMR) is an essential, evolutionarily conserved
pathway that maintains genome stability by correcting base-pairing
errors in DNA. Here we examine the sequence and structure of MutS
MMR protein to decipher the amino acid framework underlying its two
key activitiesrecognizing mismatches in DNA and using ATP
to initiate repair. Statistical coupling analysis (SCA) identified
a network (sector) of coevolved amino acids in the MutS protein family.
The potential functional significance of this SCA sector was assessed
by performing molecular dynamics (MD) simulations for alanine mutants
of the top 5% of 160 residues in the distribution, and control nonsector
residues. The effects on three independent metrics were monitored:
(i) MutS domain conformational dynamics, (ii) hydrogen bonding between
MutS and DNA/ATP, and (iii) relative ATP binding free energy. Each
measure revealed that sector residues contribute more substantively
to MutS structure–function than nonsector residues. Notably,
sector mutations disrupted MutS contacts with DNA and/or ATP from
a distance via contiguous pathways and correlated motions, supporting
the idea that SCA can identify amino acid networks underlying allosteric
communication. The combined SCA/MD approach yielded novel, experimentally
testable hypotheses for unknown roles of many residues distributed
across MutS, including some implicated in Lynch cancer syndrome.

错配修复（Mismatch Repair，MMR）是一类进化保守的核心通路，可通过校正DNA中的碱基配对错误维持基因组稳定性。本研究针对MutS错配修复蛋白的序列与结构展开分析，解析其两项核心活性背后的氨基酸架构：识别DNA错配与利用ATP启动修复。研究人员通过统计耦合分析（Statistical Coupling Analysis，SCA），在MutS蛋白家族中鉴定出一个共进化氨基酸网络（sector）。为评估该SCA区段的潜在功能意义，我们对分布排名前5%的160个残基构建丙氨酸突变体，并以非区段残基作为对照，开展分子动力学（Molecular Dynamics，MD）模拟。我们监测了三项独立指标的变化：(i) MutS结构域的构象动力学；(ii) MutS与DNA/ATP之间的氢键相互作用；(iii) ATP结合相对自由能。所有指标均显示，区段残基对MutS的结构-功能贡献显著高于非区段残基。值得注意的是，区段突变可通过连续通路与协同运动，从远端破坏MutS与DNA和/或ATP的相互作用，这一结果支持了“SCA可鉴定介导变构通讯的氨基酸网络”这一观点。本研究结合SCA与MD的研究策略，为分布于MutS蛋白各处的众多残基的未知功能提供了全新的、可通过实验验证的假说，其中部分残基与林奇癌症综合征（Lynch Cancer Syndrome）相关。