# Interactions of Arachidonic Acid with AAC1 and UCP1

## TL;DR

This study explores how arachidonic acid interacts with two mitochondrial proteins, AAC1 and UCP1, using molecular dynamics simulations to understand their roles in proton transport and potential drug targets.

## Contribution

The paper provides new insights into the binding and transport mechanisms of arachidonic acid in AAC1 and UCP1 through extensive molecular dynamics simulations.

## Key findings

- Arachidonic acid binds to specific regions of AAC1 and UCP1, primarily from the intermembrane space-facing leaflet.
- Water wires connecting the intermembrane space and matrix were identified in both proteins, with distinct electrostatic barriers observed.
- Molecular dynamics simulations revealed detailed interactions and structural insights not previously observed in experimental structures.

## Abstract

The inner mitochondrial membrane proteins ATP/ADP carrier protein 1 (AAC1) and Uncoupling protein 1 (UCP1) belong to the SLC25 mitochondrial carrier family. AAC1 is responsible for ATP/ADP exchange, while UCP1-dependent proton transport, which also requires small molecules known as activators, is the basis of brown fat thermogenesis. Arachidonic acid (AA) is an endogenous activator capable of inducing proton transport in both proteins. As such, both AAC1- and UCP1-dependent proton transport are potential targets of weight loss drugs. While AAC1 structures have long been available, only recently have structures of UCP1 been determined. Unfortunately, no AA-bound structure of either protein is available. To explore their interactions with AA, we performed molecular dynamics (MD) simulations of both proteins. Six parallel simulations of each protein were run with an average length of just over 6 μs, for a total of 75 μs of aggregate simulation across both proteins. AA bound deeply between transmembrane helix (TM) helices or in the central cavity of AAC1 in 14 events and between TM helices of UCP1 in 6 events. All AA involved in these deep binding events came from the intermembrane space-facing (C) leaflet. In AAC1, AA most often bound between TM1/TM2 and TM5/TM6. In four cases the fatty acid bound at the bottom of the central cavity rather than in an interhelical groove. In UCP1, all but one deeply bound AA sat between TM5 and TM6. No AA fully entered the cavity as observed in AAC1. In addition to entering the proteins, AAs were enriched around them in the surrounding membrane adjacent to the TM helices. While both protein structures exhibit hydrophobic stretches separating the intermembrane space (IMS) from the matrix, water wires formed through both AAC1 and UCP1, connecting the bulk water in both regions. Grotthuss shuttling along water wires has been proposed as a possible mechanism of AAC1/UCP1-dependent proton transport, but water wires are not present in experimental structures and have not previously been reported in MD simulations. Calculations of electric potentials along these water wires find a large 0.75–1 V electrostatic barrier along water wires through AAC1 and a substantially smaller such barrier of ~0.5 V through UCP1.