A computational study of water and CO migration sites and channels inside myoglobin.
A computational study of water and CO migration sites and channels inside myoglobin.
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DOI：
10.1021/ct300862j
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发表时间：
2013-02-12
影响因子：
5.5
通讯作者：
Abrams, Cameron F.
中科院分区：
文献类型：
--
作者：
Lapelosa, Mauro;Abrams, Cameron F.
在一个完全原子化、显式求解的模型系统中，使用单扫描法和零温弦方法计算了H2O和CO在肌红蛋白(Mb)中的传输路径。我们对CO运输途径中的位置和障碍的预测与以前的研究一致。对于H2O，我们预测在远端口袋(Dp)有一个结合位点，这与结晶学观察一致，另一个靠近Leu29的结合位点解释了该残基在控制口袋的疏水性方面的重要性，以及在主要无极氙腔中的无序极小。特别是，H2O可以占据XE4、XE2和XE3的氙腔并在其间过渡。我们的结果支持这样的假设，即热力学上对H2O最有利的进出入口是所谓的组氨酸门(HG)，与CO一样。这一结果，以及对DP和非极性Xe空腔水分占用的观察，表明水和CO等气体小分子竞争进入蛋白质内部，因此蛋白质内气体分子运输的模型也应该明确考虑水运输。
Pathways are computed for transport of H2O and CO in myoglobin (Mb), using the single sweep and zero-temperature string methods in a fully atomistic, explicitly solvated model system. Our predictions of sites and barriers in the pathways for CO transport agree with previous studies. For H2O, we predict a binding site in the distal pocket (DP), in agreement with crystallographic observations, and another one close to Leu 29 which explains the importance of this residue in controlling the pocket’s hydrophobicity, as well as disordered minima in the largely apolar xenon cavities. In particular, H2O can occupy and transition among the xenon cavities, Xe4, Xe2, and Xe3. Our results support the hypothesis that the thermodynamically most favorable entry/exit portal for H2O is the so-called histidine gate (HG), the same as for CO. This result, along with the observation of water occupation of both DP and apolar Xe cavities, suggest that water and small gas molecules like CO compete for access to the protein interior, and therefore models of gas molecule transport within proteins should also explicitly consider water transport.
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DOI：
10.1073/pnas.0914540107
发表时间：
2010-03-16
影响因子：
11.1
作者：
Abrams, Cameron F.;Vanden-Eijnden, Eric
通讯作者：
Vanden-Eijnden, Eric
影响因子：
3.4
作者：
Anselmi, Massimiliano;Di Nola, Alfredo;Amadei, Andrea
通讯作者：
Amadei, Andrea
影响因子：
3.4
作者：
Bossa, C;Anselmi, M;Di Nola, A
通讯作者：
Di Nola, A
影响因子：
13.8
作者：
Brunori, M
通讯作者：
Brunori, M
影响因子：
15
作者：
Goldbeck, Robert A.;Pillsbury, Marlisa L.;Jensen, Russell A.;Mendoza, Juan L.;Nguyen, Rosa L.;Olson, John S.;Soman, Jayashree;Kliger, David S.;Esquerra, Raymond M.
通讯作者：
Esquerra, Raymond M.