A journey into the enigmatic mitochondrion

Our researchers take a deep dive into Polytomella mitochondria to study the structure of ATP synthase in its native environment

You have heard about mitochondria as the powerhouses of the cell, but have you ever wondered how they generate power? The enigmatic molecular machine known as ATP synthase works as a proton-driven turbine as it produces adenosine triphosphate (ATP), the universal energy currency of living organisms. Scientists at the Max Planck Institute of Biophysics have resolved the structure of the dynamic ATP synthase in its native membrane environment, setting new standards for structural biology inside cells.
 

Text: Pamela Ornelas

The process of generating energy through respiration is known as oxidative phosphorylation, and in eukaryotes, it takes place in mitochondria. In the respiratory chain, protons pass from the matrix into the intermembrane space through a series of molecular machines in the inner mitochondrial membrane. The resulting electrochemical potential drives protons back into the matrix through the ATP synthase. As the protons flow, this molecular generator makes ATP from adenosine diphosphate (ADP) and phosphate.

ATP synthase in its native environment

The Department of Structural Biology at the Max Planck Institute of Biophysics, led by Werner Kühlbrandt, has a long-standing relationship with ATP synthase. After publishing multiple structures of ATP synthases obtained by single-particle electron cryo-microscopy, the team has now taken their analysis to the next level. Postdoc and first author of the article published in Science, Lea Dietrich, used cryo-tomography to image ATP synthase in flash-frozen cells of Polytomella sp.

In their publication, the authors describe how extremely thin slivers, called lamellae, of the cells are milled down to a thickness of 60 to 200 nm, as required for high-resolution electron tomography. In this way, they collected spatial images of the complex environment inside the cell. Inside mitochondria, they identified crowded rows of ATP synthase dimers, shaping the cristae of the inner mitochondrial membrane. The resulting 3D volumes provide a mesmerisingly detailed view of this textbook organelle.

The structure of ATP synthase dimer is stabilized by a symmetrical stalk, resolved in this study to an unusually high resolution for tomography. Each copy of the stalk holds a catalytic head facing the matrix, and a rotating ring embedded in the membrane. It is worth noting that the authors were able to identify different catalytically relevant states of the rotating subunits in native operating conditions for the first time.

Protein assemblies in their context

The study of protein assemblies without isolation or manipulation opens a new window for therapeutic applications. Furthermore, understanding the structure and function of ATP synthase within its native context brings us one step closer to unlocking the mysteries of life. Through their work, the authors prove the power of cryo-tomography, not only in resolving protein structures at high resolution, but also in capturing their essential dynamics.