Muroni Alessia, Erba Fulvio, Domenichelli Leonardo, Di Paola Luisa, Sinibaldi Federica, Mei Giampiero, Di Venere Almerinda, Minicozzi Velia
Department of Physics, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133, Rome, Italy.
Section of Roma Tor Vergata, INFN, Via Della Ricerca Scientifica 1, 00133, Rome, Italy.
Eur Biophys J. 2025 Jul 25. doi: 10.1007/s00249-025-01783-7.
Cytochrome C is a key protein involved in electron transport within the mitochondrial respiratory chain and in apoptosis mechanisms. In this work, we provide a detailed theoretical analysis of the binding mechanism between cytochrome-C and a cardiolipin-containing membrane. Molecular dynamics simulations, along with protein contact network and fractal dimension analyses were employed to investigate the structural changes in cytochrome-C during the binding process. Our results suggest that cytochrome-C follows a two-step binding mechanism, starting with a rapid initial interaction, followed by slower conformational rearrangements. We identified two different cytochrome-C conformations at the membrane: a compact, native-like structure and an extended form. The latter, stabilized by Lys72, exhibits a higher binding affinity (≈ 2 kcal/mol) compared to the former. Protein extension also correlates with increased protein-membrane contact and altered heme ring orientation, suggesting that the partial unfolding of cytochrome-C could be crucial for its peroxidase activity and its role in apoptosis. These findings enhance the understanding of the cytochrome-C's membrane interactions and its diverse functions.
细胞色素C是一种关键蛋白质，参与线粒体呼吸链中的电子传递以及细胞凋亡机制。在这项工作中，我们对细胞色素C与含心磷脂膜之间的结合机制进行了详细的理论分析。采用分子动力学模拟以及蛋白质接触网络和分形维数分析来研究细胞色素C在结合过程中的结构变化。我们的结果表明，细胞色素C遵循两步结合机制，首先是快速的初始相互作用，随后是较慢的构象重排。我们在膜上鉴定出两种不同的细胞色素C构象：一种紧凑的、类似天然的结构和一种伸展形式。后者由赖氨酸72稳定，与前者相比表现出更高的结合亲和力（约2千卡/摩尔）。蛋白质伸展还与蛋白质-膜接触增加和血红素环取向改变相关，这表明细胞色素C的部分展开可能对其过氧化物酶活性及其在细胞凋亡中的作用至关重要。这些发现增进了对细胞色素C膜相互作用及其多种功能的理解。
