...
  • 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>Biochemistry >Computational study of the binding affinity and selectivity of the bacterial ammonium transporter AmtB
【24h】

Computational study of the binding affinity and selectivity of the bacterial ammonium transporter AmtB

机译：细菌铵转运蛋白AmtB的结合亲和力和选择性的计算研究

获取原文
获取原文并翻译 | 示例
           
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

We report results from microscopic molecular dynamics and free energy perturbation simulations of substrate binding and selectivity for the Escherichia coli high-affinity ammonium transporter AmtB. The simulation system consists of the protein embedded in a model membrane/water surrounding. The calculated absolute binding free energies for the external NH4+ ions are between -5.8 and -7.3 kcal/mol and are in close agreement with experimental data. The apparent pK(a) of the bound NH4+ increases by more than 4 units, indicating a preference for binding ammonium ion and not neutral ammonia. The external binding site is also selective for NH4+ toward monovalent metal cations by 2.4-4.4 kcal/mol. The externally bound NH4+ shows strong electrostatic interactions with the proximal buried Asp160, stabilized in the anionic form, whereas the interactions with the aromatic rings of Phe107 and Trp148, lining the binding cavity, are less pronounced. Simulated mutation of the highly conserved Asp160 to Asn reduces the pK(a) of the bound ammonium ion by similar to 7 units and causes loss of its binding. The calculations further predict that the substrate affinity of E. coli AmtB depends on the ionization state of external histidines. The computed free energies of hypothetical intermediate states related to transfer of NH3, NH4+, or H2O from the external binding site to the first position inside the internal channel pore favor permeation of the neutral species through the channel interior. However, the predicted change in the apparent pK(a) of NH4+ upon translocation from the external site, Am1, to the first internal site, Am2, indicates that ammonium ion becomes deprotonated only when it enters the channel interior.
机译：我们报告的结果从微观分子动力学和基质结合和选择性的大肠杆菌高亲和力铵转运蛋白AmtB选择性的自由能摄动模拟。该模拟系统由嵌入模型膜/水周围环境中的蛋白质组成。外部NH4 +离子的绝对结合自由能的计算值介于-5.8和-7.3 kcal / mol之间，与实验数据非常吻合。结合的NH4 +的表观pK（a）增加了4个以上的单位，表明偏好结合铵离子而不是中性氨。外部结合位点对NH 4+对单价金属阳离子的选择性也为2.4-4.4 kcal / mol。外部结合的NH4 +与稳定的阴离子形式的近端埋入式Asp160表现出强烈的静电相互作用，而与结合腔内衬的Phe107和Trp148芳香环的相互作用则不太明显。高度保守的Asp160突变为Asn的模拟突变将结合的铵离子的pK（a）降低了约7个单位，并导致其结合丧失。该计算进一步预测大肠杆菌AmtB的底物亲和力取决于外部组氨酸的电离状态。与NH 3，NH 4+或H 2 O从外部结合位点转移到内部通道孔内第一位置有关的假设中间态的计算自由能有利于中性物质通过通道内部的渗透。但是，从外部位点Am1转移到第一个内部位点Am2时，NH4 +的表观pK（a）的预测变化表明，铵离子只有在进入通道内部时才会去质子化。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号