Lujun Luo, Tarikul I Milon, Elijah K Tandoh, Walter J Galdamez, Andrei Y Chistoserdov, Jianping Yu, Jan Kern, Yingchun Wang, Wu Xu
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(ii) There are two electron transfer chains (A and B branches) in PS I. Are the cofactors on both branches structurally different? (iii) Are the amino acids in cofactor binding sites structurally different from those not in cofactor binding sites?</p><p><strong>Results: </strong>The key contributions and important findings include: (i) a novel TSR-based method for representing 3D structures of pigments as well as for quantifying pigment structures was developed; (ii) the results revealed that the redox cofactor, P700, are structurally conserved and different from other redox factors. Similar situations were also observed for both A<sub>-1</sub> and A<sub>0</sub>; (iii) the results demonstrated structural differences between A and B branches for the redox cofactors P700, A<sub>-1</sub>, A<sub>0</sub> and A<sub>1</sub> as well as their cofactor binding sites; (iv) the tryptophan residues close to A<sub>0</sub> and A<sub>1</sub> are structurally conserved; (v) The TSR-based method outperforms the Root Mean Square Deviation (RMSD) and the Ultrafast Shape Recognition (USR) methods.</p><p><strong>Conclusions: </strong>The structural analyses of redox cofactors and their binding sites provide a foundation for understanding the unique chemical and physical properties of each redox cofactor in PS I, which are essential for modulating the rate and direction of energy and electron transfers.</p>","PeriodicalId":8958,"journal":{"name":"BMC Bioinformatics","volume":"26 1","pages":"15"},"PeriodicalIF":2.9000,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11731568/pdf/","citationCount":"0","resultStr":"{\"title\":\"Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I.\",\"authors\":\"Lujun Luo, Tarikul I Milon, Elijah K Tandoh, Walter J Galdamez, Andrei Y Chistoserdov, Jianping Yu, Jan Kern, Yingchun Wang, Wu Xu\",\"doi\":\"10.1186/s12859-025-06038-y\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>All chemical forms of energy and oxygen on Earth are generated via photosynthesis where light energy is converted into redox energy by two photosystems (PS I and PS II). 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引用次数: 0
摘要
背景：地球上所有化学形式的能量和氧气都是通过光合作用产生的，其中光能通过两个光系统（PS I和PS II）转化为氧化还原能。蛋白质数据库（PDB）中储存的PS I 3D结构越来越多。基于三角空间关系（TSR）的算法将三维结构转换为整数（TSR键）。利用PS I的三维结构和基于tsr的算法进行了全面的研究，回答了三个问题：(I)电子辅助因子包括P700， A-1和A0，它们是化学上相同的叶绿素，在结构上是否不同？（ii） PS i中有两个电子传递链（A支和B支），两个支上的辅因子在结构上是否不同？（iii）辅因子结合位点上的氨基酸与非辅因子结合位点上的氨基酸在结构上是否不同？结果：主要贡献和重要发现包括：(i)开发了一种新的基于tsr的颜料三维结构表征方法和定量颜料结构的方法；（ii）结果显示，氧化还原辅因子P700在结构上是保守的，与其他氧化还原因子不同。A-1和A0也观察到类似的情况；（iii）结果表明，氧化还原辅助因子P700、A-1、A0和A1及其辅助因子结合位点在A和B分支之间存在结构差异；（iv）靠近A0和A1的色氨酸残基在结构上是保守的；(v)基于tsr的方法优于均方根偏差（RMSD）和超快速形状识别（USR）方法。结论：氧化还原辅助因子及其结合位点的结构分析为了解PS I中每个氧化还原辅助因子独特的化学和物理性质提供了基础，这些性质对调节能量和电子转移的速率和方向至关重要。
Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I.
Background: All chemical forms of energy and oxygen on Earth are generated via photosynthesis where light energy is converted into redox energy by two photosystems (PS I and PS II). There is an increasing number of PS I 3D structures deposited in the Protein Data Bank (PDB). The Triangular Spatial Relationship (TSR)-based algorithm converts 3D structures into integers (TSR keys). A comprehensive study was conducted, by taking advantage of the PS I 3D structures and the TSR-based algorithm, to answer three questions: (i) Are electron cofactors including P700, A-1 and A0, which are chemically identical chlorophylls, structurally different? (ii) There are two electron transfer chains (A and B branches) in PS I. Are the cofactors on both branches structurally different? (iii) Are the amino acids in cofactor binding sites structurally different from those not in cofactor binding sites?
Results: The key contributions and important findings include: (i) a novel TSR-based method for representing 3D structures of pigments as well as for quantifying pigment structures was developed; (ii) the results revealed that the redox cofactor, P700, are structurally conserved and different from other redox factors. Similar situations were also observed for both A-1 and A0; (iii) the results demonstrated structural differences between A and B branches for the redox cofactors P700, A-1, A0 and A1 as well as their cofactor binding sites; (iv) the tryptophan residues close to A0 and A1 are structurally conserved; (v) The TSR-based method outperforms the Root Mean Square Deviation (RMSD) and the Ultrafast Shape Recognition (USR) methods.
Conclusions: The structural analyses of redox cofactors and their binding sites provide a foundation for understanding the unique chemical and physical properties of each redox cofactor in PS I, which are essential for modulating the rate and direction of energy and electron transfers.
期刊介绍：
BMC Bioinformatics is an open access, peer-reviewed journal that considers articles on all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology.
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