Gupta Pooja, Chakroborty Sristi, Rathod Arun K, Kumar K Ranjith, Bhat Shreya, Ghosh Suparna, Rao T Pallavi, Yele Kameshwari, Bakthisaran Raman, Nagaraj R, Manna Moutusi, Raychaudhuri Swasti
CSIR- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad - 500007, India.
Academy of Scientific and Innovative Research (AcSIR), Ghaziabad - 201002, India.
Nat Commun. 2025 Feb 27;16(1):2044. doi: 10.1038/s41467-025-57295-7.
Sequence evolution of protein complexes (PCs) is constrained by protein-protein interactions (PPIs). PPI-interfaces are predominantly conserved and hotspots for disease-related mutations. How do lipid-protein interactions (LPIs) constrain sequence evolution of membrane-PCs? We explore Respiratory Complexes (RCs) as a case study as these allow to compare sequence evolution in subunits exposed to both lipids in inner-mitochondrial membrane (IMM) and lipid-free aqueous matrix. We find that lipid-exposed surfaces of the IMM-subunits but not of the matrix subunits are populated with non-PPI disease-causing mutations signifying LPIs in stabilizing RCs. Further, IMM-subunits including their exposed surfaces show high intra-kingdom sequence conservation but remarkably diverge beyond. Molecular Dynamics simulation suggests contrasting LPIs of structurally superimposable but sequence-wise diverged IMM-exposed helices of Complex I (CI) subunit Ndufa1 from human and Arabidopsis depending on kingdom-specific unsaturation of cardiolipin fatty acyl chains. in cellulo assays consolidate inter-kingdom incompatibility of Ndufa1-helices due to the lipid-exposed amino acids. Plant-specific unsaturated fatty acids in human cells also trigger CI-instability. Taken together, we posit that altered LPIs calibrate sequence evolution at the IMM-arms of eukaryotic RCs.
蛋白质复合物（PCs）的序列进化受到蛋白质-蛋白质相互作用（PPIs）的限制。PPI界面主要是保守的，并且是疾病相关突变的热点。脂质-蛋白质相互作用（LPIs）如何限制膜PCs的序列进化？我们以呼吸复合物（RCs）为例进行研究，因为这有助于比较线粒体内膜（IMM）中暴露于脂质的亚基和无脂质的水相基质中亚基的序列进化。我们发现，IMM亚基的脂质暴露表面而非基质亚基的表面存在非PPI致病突变，这表明LPIs在稳定RCs中发挥作用。此外，包括其暴露表面在内的IMM亚基在同一界内显示出高度的序列保守性，但在界外则明显不同。分子动力学模拟表明，人类和拟南芥中复合物I（CI）亚基Ndufa1的结构可叠加但序列不同的IMM暴露螺旋的LPIs存在差异，这取决于心磷脂脂肪酰链的界特异性不饱和度。细胞内实验证实了由于脂质暴露的氨基酸导致Ndufa1螺旋在界间的不兼容性。人类细胞中的植物特异性不饱和脂肪酸也会引发CI不稳定。综上所述，我们认为改变的LPIs校准了真核生物RCs的IMM臂上的序列进化。
