論文紹介：Investigating the relationship between ATP synthase and the TCA cycle by crosslinking mass spectrometry
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July 21, 26
スライド概要
ATP合成酵素とTCA回路の相互作用（近接性）をプロテオミクス、具体的にはXL-MSとBN-PAGEによって測定した論文です。
ミトコンドリアの酸化的リン酸化において、ATP合成酵素はTCA回路と高い近接性を持っており、Lrpprcマウスを用いた実験でミトコンドリアの機能不全によってその相互作用はより強くなることがわかりました。
ATP合成酵素がOXPHOSシステムとTCA回路を繋ぐ役割を持つことや、ミトコンドリアの欠損によってATPの分解抑制機構が変化することが示唆されました。
重要な結果に絞って抽出してまとめました。
I am Shunichi, a second-year master's student at the Graduate School of Pharmaceutical Sciences, Kyoto University. I belong to a laboratory specializing in proteomics, where I conduct applied research in machine learning. My work particularly focuses on generative models such as mixture distribution models, and I am especially interested in language models for proteins and chemical compounds.
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E-JOURNAL Investigating the relationship between ATP synthase and the TCA cycle by crosslinking mass spectrometry KEY POINTS Visualized ATP synthase – TCA cycle enzyme physical links ATP synthase structural changes under mtDNA stress condition Inhibitor (ATIF1) reaction to mitochondria dysfunction WT vs Lrpprc-KO mitochondria ATP control Pérez Pañeda, Misic, Kadavá, Larsson & Heck Nature Communications Published 23 June 2026
BACKGROUND Does ATP synthase in OXPHOS system interact with TCA? Mitochondria — essential organelles with functions in energy conversion, metabolism, and signaling The oxidative phosphorylation (OXPHOS) system make most cellular ATP. OXPHOS system electrons: I, II → III → IV → V ATP synthase (Complex V) mitochondrial Intermembrane space I II III known link (only known bridge) IV F0 TCA cycle ? this study F1 head ADP + Pi → ATP
APPROACH Two structural read-outs: proximity and complex assembly 1 In-situ XL-MS 2 Complexome profiling primary method added in revision to validate XL-MS high MW intact complex DSSO protein protein –NH₂ –NH₂ (Lys / N-term) low MW fragmented / free proteins native BN-PAGE DSSO bonds nearby –NH₂ groups (Lys/N-term) Native gel sorts INTACT complexes → in-situ physical proximity . → each protein's assembly state . digest → MS identifies each linked pair 24 slices → LC-MS/MS MODEL heart Lrpprc knockout mice — impaired mtDNA translation lowers OXPHOS & ATP synthase → mitochondrial dysfunction
RESULT · WILD-TYPE HEART The F₁ head of ATP synthase contacts TCA enzymes ↻ Reanalysis ATP synthase - TCA-cycle links were found most — far more than Complex II Driven by the F₁ α/β subunits (ATPA, ATPB) Conserved in bovine & human mitochondria Fig. 1A — reanalysis of published WT mouse-heart XL-MS
RESULT · LRPPRC KNOCKOUT ATP synthase destabilizes in Lrpprc KO mouse — the detached F₁ head binds TCA enzymes Complexome profiling a detached F₁ head accumulated dimers / oligomers were lost BN-PAGE F₁ (ATPA) co-migrates with the TCA enzyme MDHM KEY CONTROL F₁ and TCA-enzyme abundances are unchanged (bottom-up + Western) — the extra crosslinks reflect proximity, not expression.
REGULATION · TAKE-HOME ATIF1 clamps the detached F₁ head — an energy-preserving switch WHAT WE MEASURED PREDICTED MECHANISM XL-MS · ATIF1 interlinks 6 → 136 ATIF1–ATP synthase interlinks (WT → KO) BN-PAGE + LC-MS/MS · complexome predicts Take-home Active ATIF1 (dimer) binds the detached F₁ head and blocks reverse ATP hydrolysis — an energy-preserving state.