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地狱门血红蛋白 I(HGbI)的分子动力学研究:来自产甲烷嗜极生物的氧气迁移通过一个大腔。

Molecular dynamics study of hell's gate globin I (HGbI) from a methanotrophic extremophile: oxygen migration through a large cavity.

出版信息

J Mol Model. 2013 Jun;19(6):2265-71. doi: 10.1007/s00894-012-1739-y. Epub 2013 Feb 2.

Abstract

Hell's gate globin I (HGbI), a heme-containing protein from the extremophile Methylacidiphilum infernorum, has fast oxygen-binding/slow release characteristics due to its distal residues Gln and Tyr. The combination of Gln/Tyr distal iron coordination, adaptation to extreme environmental conditions, and lack of a D helix suggests that ligand migration in HGbI differs from other previously studied globins. Locally enhanced molecular dynamics trajectories of oxygen migration indicate a large internal cavity. This may increase the tendency of oxygen to exit from portals other than the most direct exit from the space near the heme. Oxygen may reside transiently in shallow surface depressions around the exits. Such surface trapping may enhance both oxygen uptake by increasing contact time between molecules, and decrease release by increasing the probability of oxygen reentry from the vicinity of the portal.

摘要

地狱门球蛋白 I(HGbI)是一种来自极端微生物嗜酸甲基球菌的含铁蛋白,由于其远端残基 Gln 和 Tyr,具有快速氧结合/缓慢释放的特性。Gln/Tyr 远端铁配位的结合、对极端环境条件的适应以及缺乏 D 螺旋表明,HGbI 中的配体迁移与其他先前研究过的球蛋白不同。局部增强的氧气迁移分子动力学轨迹表明存在一个大的内部空腔。这可能会增加氧气从除靠近血红素的空间的最直接出口以外的其他出口离开的趋势。氧气可能暂时存在于出口周围的浅层表面凹陷处。这种表面捕获可能会通过增加分子之间的接触时间来增加氧气的摄取,同时通过增加从门户附近重新进入氧气的概率来减少释放。

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