Mechanical Biochemistry of Proteins One Molecule at a Time

Mariano Carrión-Vázquez,Andres F. Oberhauser

doi:10.1074/jbc.r700050200

Abstract

The activity of proteins and their complexes often involves the conversion of chemical energy (stored or supplied) into mechanical work through conformational changes. Mechanical forces are also crucial for the regulation of the structure and function of cells and tissues. Thus, the shape of eukaryotic cells (and by extension, that of the multicellular organisms they form) is the result of cycles of mechanosensing, mechanotransduction, and mechanoresponse. Recently developed single-molecule atomic force microscopy techniques can be used to manipulate single molecules, both in real time and under physiological conditions, and are ideally suited to directly quantify the forces involved in both intra- and intermolecular protein interactions. In combination with molecular biology and computer simulations, these techniques have been applied to characterize the unfolding and refolding reactions in a variety of proteins. Single-molecule mechanical techniques are providing fundamental information on the structure and function of proteins and are becoming an indispensable tool to understand how these molecules fold and work.

Highlights

The activity of proteins and their complexes often involves the conversion of chemical energy into mechanical work through conformational changes
Modern biochemistry tends to regard the cell as a factory crowded with specialized molecular “nanomachines,” mainly proteins acting as single polypeptides or complexes [1]
With the recent advent of single-molecule manipulation techniques such as AFM,3 we can investigate these new biochemical pathways by directly probing bond dynamics in real time and under physiological conditions. These new techniques allow the use of mechanical force as an additional parameter in a biochemical reaction (Fig. 1), which can dramatically affect its rates in both directions

Summary

Mechanical Force as a New Biochemical Parameter

Modern biochemistry tends to regard the cell as a factory crowded with specialized molecular “nanomachines,” mainly proteins acting as single polypeptides or complexes [1]. With the recent advent of single-molecule manipulation techniques such as AFM, we can investigate these new biochemical pathways by directly probing bond dynamics in real time and under physiological conditions These new techniques allow the use of mechanical force as an additional parameter in a biochemical reaction (Fig. 1), which can dramatically affect its rates in both directions. Using an analytical solution of this type, it is possible to calculate the kinetic parameters for the process: ku0 (spontaneous rate of unfolding) and ⌬xu (width of the activation energy barrier: distance on the reaction coordinate over which the force must be applied to reach the transition state). In addition to single polypeptides, a few protein complexes have been studied (27, 40 – 42)

Molecular Determinants of Mechanical Stability in Proteins

How Well Do SMFS Experiments Mimic in Vivo Protein Mechanics?

Concluding Remarks and Perspectives