This award by the Biomaterials program in the Division of Materials Research to University of California Los Angeles is to build a fundamental understanding of the mechanochemistry of proteins and to calibrate the forces produced by DNA oligomers. The biological cell is a miniature chemical factory operated by molecular daemons called enzymes. Each daemon may speed up a specific chemical reaction enormously. The objective of this project is to learn how to control the daemons mechanically, ultimately achieving mechanical control of chemical reactions. Specifically, the project will use a ?molecular spring? to stress the enzyme, and measure the effect on the chemical reaction controlled by that enzyme. This study brings mechanical tools such as springs and levers to bear at the molecular scale, opening a new nanotechnology direction. Scientifically, it will build up our knowledge of the mechano-chemistry of enzymes. Several graduate students and one postdoctoral fellow will be trained in the experimental and theoretical methods of this emerging field, which cuts across disciplines from physics to chemistry to molecular biology and thus offers optimal opportunities to broaden the scientific outlook of young researchers. This research also provides a splendid opportunity to educate the public in these exciting developments in modern science, through public lectures, interactions with LA area teachers (through the facilities of California NanoSystem Institute), and web-based dissemination of important results.

Enzymes as biological catalysts, couple mechanical motion and forces to chemical reactions through conformational transitions. Moving beyond structural descriptions, the objective of this project is to build a dynamic understanding of these complex structures, in terms of the elastic energies and forces which couple to the chemistry. Through a unique method which uses DNA as "molecular springs" attached to the enzyme, the investigators will apply controlled mechanical stresses to several proteins and measure the effect on the different steps which determine the reaction rate. Parallel experiments will answer the longstanding question of what is the elastic energy of sharply bent configurations of DNA, in other words, will calibrate the DNA springs. The knowledge will be applied to the parametrization of nonlinear models of DNA mechanics. This research explores fundamental physics at the boundary of chemistry and mechanics. It provides the vehicle for training graduate students and postdoctoral fellows in paradigm-changing biological physics research, both experimental and theoretical.

Project Report

With this project we created new supra-molecular constructions where a DNA "molecular spring" coupled to an enzyme exerts a mechanical stress on the enzyme (see figure). We developed a unique set of experiments where a non-destructive mechanical stress is applied to the enzyme and the effect on the chemical reaction cycle is monitored. Enzymes are the catalysts which perform all molecular tasks in the chemical factory which is the living cell. This project demonstrated experimentally that enzymes are continuously deformable molecules, in the very general sense of showing that enzymatic catalysis can be artificially controlled (turned on and off) by mechanical stress. This new paradigm in mechano–chemistry should be seen as a nanotechnology enabled generalization of the induced fit mechanism discovered by Koshland fifty years ago. The most important outcome of this project is therefore conceptual: the realization that enzymes – the molecules we are made of – are continuously deformable. Derived from this concept is the paradigm of mechanical control of chemical reactions, also established by this study, which is now open to thousands of chemical reactions. Practical applications may follow through advances in composite materials science and nanotechnology. Another part of this study concentrated on the mechanics of the DNA spring. We solved the long standing problem of the nonlinear bending elasticity of the DNA double helix. To this end we developed a method for the direct measurements of the elastic energy of a 10 nm long DNA molecule constrained into a highly bent conformation. The result has simplicity and beauty: for DNA bending, there is a softening transition characterized by a critical internal torque τc = 30 pN×nm at which the DNA molecule develops a kink. The beauty is that, this nonlinearity in the mechanics of a 10 nm size molecule is mathematically analogous to the buckling instability of macroscopic rods, first understood by Euler in the 18th century. In conclusion, the outcome of this project is a fundamental insight into enzyme mechanics.

National Science Foundation (NSF)
Division of Materials Research (DMR)
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Joseph A. Akkara
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University of California Los Angeles
Los Angeles
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