Mottonen James M, Xu Minli, Jacobs Donald J, Livesay Dennis R
Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
Proteins. 2009 May 15;75(3):610-27. doi: 10.1002/prot.22273.
We compare various predicted mechanical and thermodynamic properties of nine oxidized thioredoxins (TRX) using a Distance Constraint Model (DCM). The DCM is based on a nonadditive free energy decomposition scheme, where entropic contributions are determined from rigidity and flexibility of structure based on distance constraints. We perform averages over an ensemble of constraint topologies to calculate several thermodynamic and mechanical response functions that together yield quantitative stability/flexibility relationships (QSFR). Applied to the TRX protein family, QSFR metrics display a rich variety of similarities and differences. In particular, backbone flexibility is well conserved across the family, whereas cooperativity correlation describing mechanical and thermodynamic couplings between the residue pairs exhibit distinctive features that readily standout. The diversity in predicted QSFR metrics that describe cooperativity correlation between pairs of residues is largely explained by a global flexibility order parameter describing the amount of intrinsic flexibility within the protein. A free energy landscape is calculated as a function of the flexibility order parameter, and key values are determined where the native-state, transition-state, and unfolded-state are located. Another key value identifies a mechanical transition where the global nature of the protein changes from flexible to rigid. The key values of the flexibility order parameter help characterize how mechanical and thermodynamic response is linked. Variation in QSFR metrics and key characteristics of global flexibility are related to the native state X-ray crystal structure primarily through the hydrogen bond network. Furthermore, comparison of three TRX redox pairs reveals differences in thermodynamic response (i.e., relative melting point) and mechanical properties (i.e., backbone flexibility and cooperativity correlation) that are consistent with experimental data on thermal stabilities and NMR dynamical profiles. The results taken together demonstrate that small-scale structural variations are amplified into discernible global differences by propagating mechanical couplings through the H-bond network.
我们使用距离约束模型（DCM）比较了九种氧化型硫氧还蛋白（TRX）的各种预测力学和热力学性质。DCM基于一种非加和自由能分解方案，其中熵贡献是根据基于距离约束的结构刚性和柔性来确定的。我们对约束拓扑结构的集合进行平均，以计算几个热力学和力学响应函数，这些函数共同产生定量稳定性/柔性关系（QSFR）。应用于TRX蛋白家族时，QSFR指标显示出丰富多样的异同。特别是，整个家族的主链柔性保存良好，而描述残基对之间力学和热力学耦合的协同相关性则表现出明显突出的独特特征。描述残基对之间协同相关性的预测QSFR指标的多样性在很大程度上由描述蛋白质内固有柔性程度的全局柔性序参量来解释。计算了作为柔性序参量函数的自由能景观，并确定了天然态、过渡态和未折叠态所在的关键值。另一个关键值确定了蛋白质全局性质从柔性转变为刚性的力学转变。柔性序参量的关键值有助于表征力学和热力学响应是如何联系的。QSFR指标的变化和全局柔性的关键特征主要通过氢键网络与天然态X射线晶体结构相关。此外，对三个TRX氧化还原对的比较揭示了热力学响应（即相对熔点）和力学性质（即主链柔性和协同相关性）的差异，这些差异与热稳定性和NMR动力学谱的实验数据一致。综合结果表明，小规模的结构变化通过氢键网络传播力学耦合而放大为可辨别的全局差异。
