---
title: 論文紹介：Investigating the relationship between ATP synthase and the TCA cycle by crosslinking mass spectrometry
tags:  #proteomics #xl-ms #interactome  
author: [Shunichi Ito](https://docswell.com/user/shunichi1100921)
site: [Docswell](https://www.docswell.com/)
thumbnail: https://bcdn.docswell.com/page/VJPKRR6NE8.jpg?width=480
description: 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。
published: July 21, 26
canonical: https://docswell.com/s/shunichi1100921/53J9PP-paper-xlms
---
# Page. 1

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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


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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


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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


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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


# Page. 5

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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.


# Page. 6

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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.