Investigation on migration process of oxygen and carbon monoxide in human hemoglobin

doi:10.11949/0438-1157.20190862

Abstract

Abstract:

To reveal the relationship between CO and O₂ competitive binding to the heme site of human hemoglobin (HbA) and its relationship with HbA structural transition, we used all-atom molecular dynamics simulations (MD) combined with Markov state models (MSMs) to study the migration of O₂ and CO molecules from the aqueous solution into the heme site of α and β chains of HbA. Molecular dynamics simulations revealed the steady binding sites and instantaneous binding sites to O₂ and CO of α and β chains of HbA, migration pathways and structural changes of HbA. It is shown that all discrete Xe binding sites and O₂ migration pathways observed in experiments can be reproduced by molecular dynamics simulations. Molecular dynamics simulations revealed structural changes in the homeostatic binding sites and transient binding sites, migration channels, and alpha chains of O₂ and CO binding αand β chains. Above results demonstrate the importance of instantaneous migration pathways formed due to the flexibility of HbA for gas migration. In addition, MSMs and transition path theory(TPT) were used to investigate the conformational transitions among different microstates in α chain, which provides the mechanism between gases migration behavior and HbA conformational transitions.

Key words: human hemoglobin, heme, oxygen, carbon monoxide, molecular simulation, Markov state models, gas migration

摘要：

为了揭示CO和O₂竞争性结合人血红蛋白血红素位点的机制及其与人血红蛋白结构转换之间的关系，本文采用全原子分子动力学模拟（MD）结合马尔科夫状态模型（MSMs）研究氧气（O₂）和一氧化碳（CO）分子从水溶液迁移进入人血红蛋白四聚体α链和β链的全过程。分子动力学模拟揭示了O₂和CO结合α链和β链的稳态结合位点和瞬态结合位点、迁移通道以及α链的结构变化。结果显示，分子模拟不仅仅能够再现全部实验中所观察到的离散Xe结合位点和分子扩散通道，而且揭示了实验中无法观测的瞬态结合位点和多重气体迁移途径。上述结果表明人血红蛋白因其结构柔性所形成的瞬态通道对于气体分子迁移过程的重要性。除此之外，利用MSM和过渡路径理论（TPT）构建了人血红蛋白α链结构变化与气体分子迁移之间的关系，阐释了血红蛋白中影响气体迁移的关键结构及其微观机制。

关键词: 人血红蛋白, 血红素, 氧气, 一氧化碳, 分子模拟, 马尔科夫状态模型, 气体迁移

CLC Number:

TQ 028.8

Xue PENG, Chenlin LU, Diannan LU. Investigation on migration process of oxygen and carbon monoxide in human hemoglobin[J]. CIESC Journal, 2020, 71(2): 724-735.

彭雪, 芦琛璘, 卢滇楠. 氧气和一氧化碳在人血红蛋白迁移过程研究[J]. 化工学报, 2020, 71(2): 724-735.

Figures/Tables 12

Fig.1 O2 binding sites and 6 major migration pathways in α chain of human hemoglobin(blue ball: O2 sites; line with arrow: migration trajectories of O2; cyan belt: backbone of α chain of human hemoglobin; brown stick: heme; Xe1—Xe6: Xe binding sites determined by experiments; DP: distal path site determined by experiemnts; Ph1— Ph5: instant cavities; MbXe1 — MbXe4: Xe binding sites of myoglobin determined by experiments)

Fig.4 CO binding sites and 6 major migration pathways in β chain of human hemoglobin(red ball: CO sites; line with arrow: migration trajectories of CO; pink belt: backbone of β chain of human hemoglobin; brown stick: heme; Xe1—Xe6: Xe binding sites determined by experiments; DP: distal path site determined by experiemnts; Ph1—Ph3: instant cavities; MbXe1—MbXe4: Xe binding sites of myoglobin determined by experiments)

Table 1 Frequency and probability of O2 migration pathways in α chain

路径	次数	概率/%
1: 水溶液→Xe6→Ph3→Xe5→DP	49	49.0
2: 水溶液→Ph2→Xe1→Xe5→DP	18	18.0
3: 水溶液→Ph3→Xe1→Xe5→DP	3	3.0
4: 水溶液→Ph5→Xe5→Xe4→DP	12	12.0
5: 水溶液→DP	6	6.0
6: 水溶液→Ph1→Xe3→DP	10	10.0
其他	2	2.0

Fig.2 CO binding sites and 6 major migration pathways in α chain of human hemoglobin(red ball: CO sites; line with arrow: migration trajectories of CO; cyan belt: backbone of α chain of human hemoglobin; brown stick: heme; Xe1—Xe6: Xe binding sites determined by experiments; DP: distal path site determined by experiemnts; Ph1—Ph6: instant cavities; MbXe1—MbXe4: Xe binding sites of myoglobin determined by experiment)

Table 2 Frequency and probability of CO migration pathways in α chain

路径	次数	概率/%
1: 水溶液→Xe6→Ph3→Xe4→DP	21	17.9
2: 水溶液→Xe6→Ph2→Xe5→DP	5	4.3
3: 水溶液→Ph5→Ph6→DP	5	4.3
4: 水溶液→DP	34	29.0
5: 水溶液→Ph1→Xe3→DP	37	31.6
6: 水溶液→Ph4→Xe2→Xe4→DP	12	10.3
其他	3	2.6

Fig.3 O2 binding sites and 6 major migration pathways in β chain of human hemoglobin(blue ball: O2 sites; line with arrow: migration trajectories of O2; pink belt: backbone of β chain of human hemoglobin; brown stick: heme; Xe1—Xe6: Xe binding sites determined by experiments; DP: distal path site determined by experiemnts; Ph1: instant cavities; MbXe1 — MbXe4: Xe binding sites of myoglobin determined by experiments)

Table 3 Frequency and probability of O2 migration pathways in β chain

路径	次数	概率/%
1: 水溶液→Xe6→Xe1→Xe5→DP	25	25.0
2: 水溶液→Xe5→DP	11	11.0
3: 水溶液→Xe1→Xe5→DP	36	36.0
4: 水溶液→Ph1→Xe5→→DP	5	5.0
5: 水溶液→DP	4	4.0
6: 水溶液→Xe2→Xe4→DP	16	16.0
其他	3	3.0

Table 4 Frequency and probability of CO migration pathways in β chain

路径	次数	概率/%
1: 水溶液→Xe6→Xe1→Xe5→DP	14	13.0
2: 水溶液→Xe1→Xe2→Xe4→DP	18	16.7
3: 水溶液→Xe1→Xe5→DP	7	6.5
4: 水溶液→Ph1→Xe5→DP	18	16.7
5: 水溶液→Ph2→Ph3→DP	7	6.4
6: 水溶液→DP	40	37.0
其他	4	3.7

Fig.5 Gyration and RMSD/RMSF in four protein models

Fig.6 Protein secondary structure changes

Fig.7 Tructural transition pathways of α chain of human hemoglobin during O2 migration processes(gray ribbon model: crystal structure of α chain of human hemoglobin; O2_MS1 in red: initial structure, i.e., O2 unbinding state; O2_MS2 in yellow and O2_MS3 in pink: middle states, i.e., key structures during O2 migration; O2_MS4 in orange: final O2 binding state; lines with arrow: transition pathways among different states, their thickness reflects transition probability; circles with different color: different states, their sizes reflect appearance probability; ribbon model with different color: corresponding structures of α chain of human hemoglobin; green ball model: heme molecule)

Fig.8 Structural transition pathways of α chain of human hemoglobin during CO migration processes(gray ribbon model: crystal structure of α chain of human hemoglobin; CO _MS1 in red: initial structure, i.e., CO unbinding state; CO _MS2 in yellow and CO _MS3 in pink: middle states, i.e., key structures during CO migration; CO _MS0 in purple: independent state, i.e., a structure not in transition network; CO _MS4 in orange: final CO binding state; lines with arrow: transition pathways among different states, their thickness reflects transition probability; circles with different color: different states, their sizes reflect appearance probability; ribbon model with different color: corresponding structures of α chain of human hemoglobin; green ball model: heme molecule)

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