血红素与蛋白质结合的过程在几乎所有生命形式中都很普遍,以控制许多重要的生物学特性,如O2结合,电子转移,气体传感或建立催化能力。在这些情况下,血红素通常与离散血红素结合袋中的蛋白质紧密结合(不可逆地),与一个或两个血红素配体提供的血红素铁最常见的His,Cys或Tyr残基。血红素结合也可以用作调节机制,例如在转录调节或离子通道控制中。当用作调节器时,血红素结合更弱,具有不同的血红素连接处,不需要离散的血红素口袋。这使得血红素调节蛋白的表征变得困难,并且需要新的方法来预测和理解血红素-蛋白质相互作用。我们应用ProFunc生物信息学工具的修改版本来识别来自蛋白质数据库(PDB)和AlphaFold模型的血红素依赖性调节蛋白测试集中的血红素结合位点。鉴定出的潜在血红素结合位点可以在PyMol和,如有必要,优化与RosettaDOCK。我们证明了该方法可用于鉴定蛋白质中的血红素结合位点,包括在没有晶体结构的情况下,但是当结构信息的质量较高时,该方法更准确。ProFunc工具,随着这项工作中使用的修改,可在https://www上公开获得。ebi.AC.uk/thornton-srv/databases/profunc,可以很容易地用于检查新的血红素结合目标。
The process of heme binding to a protein is prevalent in almost all forms of life to control many important biological properties, such as O2-binding, electron transfer, gas sensing or to build catalytic power. In these cases, heme typically binds tightly (irreversibly) to a protein in a discrete heme binding pocket, with one or two heme ligands provided most commonly to the heme iron by His, Cys or Tyr residues. Heme binding can also be used as a regulatory mechanism, for example in transcriptional regulation or ion channel control. When used as a regulator, heme binds more weakly, with different heme ligations and without the need for a discrete heme pocket. This makes the characterization of heme regulatory proteins difficult, and new approaches are needed to predict and understand the heme-protein interactions. We apply a modified version of the ProFunc bioinformatics tool to identify heme-binding sites in a test set of heme-dependent regulatory proteins taken from the Protein Data Bank and AlphaFold models. The potential heme binding sites identified can be easily visualized in PyMol and, if necessary, optimized with RosettaDOCK. We demonstrate that the methodology can be used to identify heme-binding sites in proteins, including in cases where there is no crystal structure available, but the methodology is more accurate when the quality of the structural information is high. The ProFunc tool, with the modification used in this work, is publicly available at https://www.ebi.ac.uk/thornton-srv/databases/profunc and can be readily adopted for the examination of new heme binding targets.