Senior Author

The ways in which proteins and RNAs fold and unfold, and the shapes they form, fascinate molecular biologists. Imaging techniques such as X-ray crystallography have provided snapshots of the molecules in their stable forms. And optical tweezers allow researchers to stretch out the folded molecules and watch them refold. But measuring the free-energy differences between folded and unfolded states using optical tweezers has proved problematic, as much of the energy measured dissipates as heat rather than as work done by the refolding molecule. Theoretical physicists have derived general fluctuation theorems that can be used to obtain the free-energy values for refolding. On page 231, Carlos Bustamante and his team provide an experimental verification for these predictions, and then use them to obtain RNA folding free energies. Nature caught up with Bustamante, the senior author on the paper, to find out more.

Why is it so hard to get at these molecules' folding free energy?

The molecules are very complex, and there is a catch 22. If you try to measure the energies accurately, it would take far too long. Alternatively, you can pull the molecules quickly, but then you lose the information about refolding energies.

How did you overcome this obstacle?

We tested the Crooks fluctuation theorem and then used it to extract the folding free energy of a molecule that dissipated a lot of energy as it refolded. The theorem passed the test with flying colours and we got the molecule's folding energy.

How many stretches did you have to do?

A few hundred pulls sufficed.

How broadly applicable is your technique?

It should be valid for most biological molecules.

What are the other authors up to now?

The first author, Delphine Collins, is at Merck, where she is working on nanobiotechnology projects. The work she did here at Berkeley was very interdisciplinary, so it served her well. The second author, Felix Ritort, is a professor at the University of Barcelona. I feel both happy and guilty that I converted a theoretician into an experimentalist. And Ignacio Tinoco, my colleague in the chemistry department, and I continue to work on the thermodynamics of small systems and single molecules.

You did 35 drafts before submitting this paper. Why so many?

I'm a little bit of an obsessive when it comes to wording. This is an abstract, somewhat difficult, subject and the challenge is to write something clear for the reader.