Structure and regulatory mechanism of human uncoupling protein 1

Abstract

Uncoupling protein 1 (UCP1) in the mitochondrial inner membrane is responsible for the thermogenic properties of brown adipose tissue. In response to cold exposure, UCP1 is activated by free fatty acids and catalyses proton leak, dissipating the proton motive force, which mitochondria use to drive ATP synthesis. Therefore, UCP1 uncouples the oxidation of nutrients from the phosphorylation of ADP, releasing heat instead of generating ATP. The thermogenic properties of UCP1 are regulated by cytosolic purine nucleotides, which inhibit proton conductance and therefore enable activation only in response to cold environments. This thesis aimed to determine the first high-resolution structure of UCP1 to address several unanswered questions about its overall structure and its nucleotide inhibition and activation mechanisms. Initially, attempts were made to grow three-dimensional crystals for X-ray crystallography, but later cryogenic electron microscopy (cryo-EM) and single particle analysis were used to determine the structure. Human UCP1 was purified from yeast mitochondria and modified with nanobody fiducials to develop a sample suitable for cryo-EM analysis. The resolved structure revealed that UCP1 has a similar fold to the mitochondrial ADP/ATP carrier in the cytoplasmic-open state, consisting of six transmembrane and three small matrix helices, and three bound cardiolipin molecules. The purine nucleotide binds in the central cavity, which is open to the intermembrane space, through ionic, polar and cation-π interactions with the positively charged central cavity. The structure clarifies the structural basis of the pH-dependency of nucleotide binding. The negatively charged phosphate groups of the nucleotide are positioned close to the negatively charged residues of the matrix gate, requiring proton-mediated bonds to prevent the electrostatic repulsion that occurs at higher pH levels. UCP1 has retained all of the key functional and structural features required for a mitochondrial carrier–like transport mechanism. Structural analyses show that inhibitor binding prevents the conformational changes that UCP1 might use to facilitate proton leak. Further analysis revealed that the nucleotide-binding specificity of UCP1 is not limited to purine nucleotides, but also includes pyrimidine nucleotides. Thus, all cytosolic nucleotides inhibit UCP1 proton conductance, regardless of the nucleobase, with only subtle differences in binding affinities.