Beyond biochemistry : the mechanics of life.

Abstract

In the last half century, biologists have made great strides towards understanding the intricate structure of the cell and the relation between this structure and cellular function. Single-molecule techniques and advances in microscopy have also significantly changed the way in which biologists ask and answer questions. As biological measurements and techniques have become increasingly quantitative, they have allowed biologists to ask ever more quantitative questions: How do the molecular machines, which comprise the cell function microscopically? Can we understand the design principles that govern the structure and function of biological systems on a microscopic scale? One outcome of this new generation of quantitative biological questions is the need to greet quantitative experiments with models at a higher level of abstraction than the traditional cartoons of molecular biology. In this thesis, I present two such quantitative models. In the first half of this thesis, I present a physical model for mechanotransduction. Mechanosensitive channels are the central agents employed by cells to transduce mechanical stimuli. Our senses of hearing and touch are both examples of this functional motif. The Mechanosensitive Channel of Large conductance (MscL) is arguably the simplest and best studied mechanosensitive channel. I present analytic estimates for the forces and free energy generated by bilayer deformation which reveal a compelling and intuitive model for the function of the MscL channel, analogous to the nucleation of a second phase. The competition between hydrophobic mismatch of the protein with the surrounding membrane and tension results in a surprisingly rich story which can provide both a quantitative comparison to measurements of the opening tension for MscL when reconstituted in bilayers of different thickness and qualitative insights into the function of the MscL channel and other transmembrane proteins. In the second half of this thesis, I examine models for the mechanics of DNA. DNA bending, on length scales shorter than a persistence length, plays a central role in the translation of genetic information from DNA to cellular function. Quantitative experimental studies of these biological systems have led to a renewed interest in the short-contour-length polymer statistics relevant for describing the conformational free energy of DNA bending induced by protein-DNA complexes. The recent DNA cyclization studies of Cloutier and Widom have questioned the applicability of the canonical semiflexible polymer theory, the wormlike chain model, to DNA bending on biological length scales. We describe a new class of polymer models that can resolve the proposed discrepancy between short and long-contour-length bending. These models explain the spectacular success of the wormlike chain model in describing many traditional DNA mechanics experiments, as well as its failure to describe the short-contour-length mechanics of DNA. In particular, I present two toy models for DNA bending which capture the short-contour-length behavior observed by Cloutier and Widom. These toy models make quantitative predictions for chain statistics of DNA, observable in DNA mechanics experiments and of central importance to the qualitative description of cellular function, from chromosomal DNA packaging to transcription and gene regulation to viral packaging.