Zocchi Laboratory for Molecular Biophysics

The main research topic in our group is the study of conformational changes of biological macromolecules (proteins, DNA). The goal is to understand the physical principles underlying the internal organization of these molecules and their mutual interactions, which translate into their function. This also leads to designing our own artificial nanomachines.

We use nanomechanical and optical techniques to study conformational changes of single bio-molecules. Single molecule experiments are advantageous for exploring the dynamics.

Through ensemble experiments we study equilibrium properties and engineer new devices at the nm scale. For example, one mechanical component which, unlike nuts and bolts, can be shrunk to the nanoscale is the spring. By inserting a “molecular spring” on a protein we can control the protein’s conformation, and thus its function. We create artificial molecular devices based on allosteric control.

DNA is the molecule which encodes the masterplan for the cell. Decoding this information, i.e. the process of expressing and controlling genes, involves a variety of conformational changes of DNA caused by protein - DNA interactions.

Proteins are the molecular machines which perform the tasks in the living cell. This includes catalysis, molecular recognition, and mechanical motion. Virtually all these tasks involve a change of conformation of the protein. Allosteric control, whereby a chemical signal modifies a protein’s conformation, is the molecular basis of life.

Research in the Zocchi Lab is supported / has been supported by:
The National Science Foundation / DMR ; the US-Israel Binational Science Foundation ; the US Department of Defense / DMEA

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Proteins are soft – can undergo large reversible deformations. Mechanical forces naturally couple to such conformational changes. With the molecular springs, we have introduced an ensemble method to exert localized mechanical forces on proteins. Technically, this allows for high-throughput experiments and for the construction of devices. Conceptually, we have learned how to establish a field – the force field – which naturally couples to the relevant degrees of freedom of the protein. Usually this leads eventually to the discovery of new effects and a better understanding of the physics of the system

Physics in Molecular Biology