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Random Walks and the Structure of Macromolecules

We have already belabored the idea that the study of structure is often a prerequisite to being able to tackle the more interesting question of the functional dynamics of a particular macromolecule or macromolecular assembly. Indeed, this notion of the relation between structure and function has been elevated to the status of the true central dogma of molecular biology, namely, “sequence determines structure determines function” (Petsko and Ringe, 2004), wherein our mission is to uncover the relation between sequence and consequence. We have also already noted that the idea of structure is hierarchical and subtle, with the relevant detail that is needed to uncover function often living at totally disparate spatial scales. For example, in thinking about phosphorylation-induced conformational changes, an atom-by-atom description is required, whereas in thinking about cell division, a much coarser description of DNA is likely more useful. The key message of the present chapter is that there is much to be gained in some circumstances by abandoning the deterministic, pdb mentality described in earlier chapters for a statistical description in which we attempt only to characterize certain average properties of the structure. Indeed, we will argue that this type of thinking permits immediate and potent contact with a range of experiments. To elaborate, we continue with an aside on the concept of structure itself with the aim of probing the subtlety that attends this idea. The use of the word