Binding of O2 and NO to heme in heme-nitric oxide/oxygen-binding (H-NOX) proteins. A theoretical study.
Binding of O2 and NO to heme in heme-nitric oxide/oxygen-binding (H-NOX) proteins. A theoretical study.
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DOI：
10.1021/jp403998u
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发表时间：
2013-09-05
期刊：
影响因子：
--
通讯作者：
Watts JD
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文献类型：
--
作者：
Liao MS;Huang MJ;Watts JD
血红素一氧化氮/氧结合 (H-NOX) 蛋白中 O2 和 NO 与血红素的结合已通过 DFT 以及色散校正 DFT 方法进行了研究。通过在研究系统中包括六个最近的周围残基来解释局部蛋白质环境。还关注了蛋白质环境（特别是远端 Tyr140）对近端铁组氨酸 (Fe-His) 结合的影响。测定铁卟啉 FeP(His)(AB)、肌红蛋白 Mb(AB)、H-NOX(AB) 和 Tyr140 → Phe 突变 H-NOX: Y140F(AB) 中的 Heme-AB (AB = O2, NO) 和 Fe-His 结合能进行比较。计算得出的 H-NOX 中结合 O2 的稳定性甚至比肌红蛋白 (Mb) 中的更高，这与 T. tengcongensis 的 H-NOX 结构域对其氧分子具有非常高的亲和力的观察结果一致。在 Tt H-NOX 蛋白的两种不同 X 射线晶体结构中，AB = O2 和 NO 的计算结果似乎支持 PDB 代码为 1XBN 的晶体结构，其中 Trp9 和 Asn74 残基不与 Tyr140 形成氢键网络。极性残基的氢键相互作用对 Fe-His 结合强度没有明显影响，但对 Ebind(Fe-His) 的色散贡献可能很重要，具体取决于所使用的晶体结构。我们推测，天然蛋白质脱氧形式的 Fe-His 结合强度可能是决定当 NO 与 Fe 结合时 His 与 Fe 的键是否断裂或维持的重要因素。
The binding of O2 and NO to heme in Heme-Nitric Oxide/OXygen-binding (H-NOX) proteins has been investigated with DFT as well as dispersion-corrected DFT methods. The local protein environment was accounted for by including the six nearest surrounding residues in the studied systems. Attention was also paid to the effects of the protein environment, particularly the distal Tyr140, on the proximal iron–histidine (Fe–His) binding. The Heme–AB (AB = O2, NO) and Fe–His binding energies in iron porphyrin FeP(His)(AB), myoglobin Mb(AB), H-NOX( AB), and Tyr140 → Phe mutated H-NOX: Y140F(AB) were determined for comparison. The calculated stabilization of bound O2 is even higher in H-NOX than in a myoglobin (Mb), consistent with the observation that the H-NOX domain of T. tengcongensis has a very high affinity for its oxygen molecule. Among the two different X-ray crystal structures for the Tt H-NOX protein, the calculated results for both AB = O2 and NO appear to support the crystal structure with the PDB code 1XBN, where the Trp9 and Asn74 residues do not form a hydrogen bonding network with Tyr140. A hydrogen bond interaction from the polar residue does not have obvious effects on the Fe–His binding strength, but a dispersion contribution to Ebind(Fe–His) may be significant, depending on the crystal structure used. We speculate that the Fe–His binding strength in the deoxy form of a native protein could be an important factor in determining whether the bond of His to Fe is broken or maintained upon binding of NO to Fe.
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