Molecular dynamics study on the solvent dependent heme cooling following ligand photolysis in carbonmonoxy myoglobin.
Molecular dynamics study on the solvent dependent heme cooling following ligand photolysis in carbonmonoxy myoglobin.
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碳单氧肌红蛋白中配体光解后溶剂依赖性血红素冷却的分子动力学研究。
DOI：
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发表时间：
2007
影响因子：
3.3
通讯作者：
J. Straub
中科院分区：
文献类型：
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作者：
Yong Zhang;H. Fujisaki;J. Straub
用分子动力学模拟方法研究了肌红蛋白中血红素部分振动能弛豫的时间尺度和机理。研究了五种不同的溶剂模型，包括正常水、重水、正常甘油、氢化甘油和非极性溶剂，以及两种形式的血红素，一种是天然的，一种是缺少酸性侧链的。在天然肌红蛋白甘油溶液和天然肌红蛋白水溶液中观察到蛋白质结构的变化。在所研究的所有体系中，都观察到了配体光解后血红素过剩动能的单指数衰减。松弛速率取决于所使用的溶剂。然而，这种依赖关系不能用包括宏观热扩散在内的溶剂的整体输运性质来解释。血红素冷却的速度和机制取决于血红素和溶剂之间详细的微观相互作用。考虑了三种分子间的能量转移机制：(I)氢键介导的能量转移，(Ii)通过共振相互作用的直接振动-振动能量转移，(Iii)通过振动-平移或振动-旋转相互作用的能量转移，即热碰撞。在天然肌红蛋白水溶液和天然肌红蛋白甘油溶液中，血红素与溶剂分子之间的氢键相互作用和振动-振动相互作用主导着能量传递。对于修饰的肌红蛋白，与水溶液不同，在甘油溶液中振动-振动相互作用也是有效的。热碰撞形成了修饰肌红蛋白水溶液的主要能量传递途径，以及非极性环境中天然肌红蛋白和修饰肌红蛋白的能量传递途径。对于天然肌红蛋白在非极性溶剂溶液中，血红素异丙酸侧链和附近蛋白质残基之间的氢键是影响驰豫途径的关键相互作用，而改性的肌红蛋白非极性溶剂溶液中没有这种氢键。
The time scale and mechanism of vibrational energy relaxation of the heme moiety in myoglobin was studied using molecular dynamics simulation. Five different solvent models, including normal water, heavy water, normal glycerol, deuterated glycerol and a nonpolar solvent, and two forms of the heme, one native and one lacking acidic side chains, were studied. Structural alteration of the protein was observed in native myoglobin glycerol solution and native myoglobin water solution. The single-exponential decay of the excess kinetic energy of the heme following ligand photolysis was observed in all systems studied. The relaxation rate depends on the solvent used. However, this dependence cannot be explained using bulk transport properties of the solvent including macroscopic thermal diffusion. The rate and mechanism of heme cooling depends upon the detailed microscopic interaction between the heme and solvent. Three intermolecular energy transfer mechanisms were considered: (i) energy transfer mediated by hydrogen bonds, (ii) direct vibration-vibration energy transfer via resonant interaction, and (iii) energy transfer via vibration-translation or vibration-rotation interaction, or in other words, thermal collision. The hydrogen bond interaction and vibration-vibration interaction between the heme and solvent molecules dominates the energy transfer in native myoglobin aqueous solution and native myoglobin glycerol solutions. For modified myoglobin, the vibration-vibration interaction is also effective in glycerol solution, different from aqueous solution. Thermal collisions form the dominant energy transfer pathway for modified myoglobin in water solution, and for both native myoglobin and modified myoglobin in a nonpolar environment. For native myoglobin in a nonpolar solvent solution, hydrogen bonds between heme isopropionate side chains and nearby protein residues, absent in the modified myoglobin nonpolar solvent solution, are key interactions influencing the relaxation pathways.