Bridging Conformational Dynamics and Function Using Single-Molecule Spectroscopy
In a typical structure-function relation study, the primary structure of proteins or nucleic acids is changed by mutagenesis and its functional effect is measured via biochemical means. Single-molecule spectroscopy has begun to give a whole new meaning to the "structure-function relation" by measuring the real-time conformational changes of individual biological macromolecules while they are functioning. This review discusses a few recent examples: untangling internal chemistry and conformational dynamics of a ribozyme, branch migration landscape of a Holliday junction at a single-step resolution, tRNA selection and dynamics in a ribosome, repetitive shuttling and snapback of a helicase, and discrete rotation of an ATP synthase.
Abstract The coordinate conditions usually used to describe the open string and its boundary conditions are intrinsically singular at the boundary. As a result, the boundary conditions are difficult to understand or interpret geometrically. The physical requirement that the variation of the string at the boundary yield a vanishing contribution to the variation of the action may be accomplished by the requirement that the induced metric, in non-singular coordinates, have signature (0, — 1) at the boundary and that the metric be C 1 on the boundary. These geometrically simple by analytically somewhat complicated requirements are equivalent to the usual boundary conditions. Lastly it is shown that the open string is, in a strict sense, a special case of the closed string. Some of the peculiar behavior of characteristic curves on the open string becomes clear in this context.