ABSTRACT
This chapter explores how nanoscale machines and engines work. In biology, molecular machines perform energy conversion, signal transduction, regulation, transcription, ion pumping, molecular transport, and more. A molecular machine can be as simple as a single protein or nucleic acid molecule. The chapter also explores the principles of biomolecular machines using binding polynomials. It discusses oxygen binding to globin proteins, probably the best understood process of coupled binding and cooperativity in biology. The chapter considers a single type of ligand: one oxygen molecule binds, changing hemoglobin's affinity to bind another oxygen. Carbon monoxide can also bind to hemoglobin, displacing oxygen, leading to toxicity and asphyxiation. Coupled binding is the basis for signaling, transduction, inhibition, activation, and regulation in biology. Biological function depends on biochemical and genetic circuits. The principles of operation derive from coupled and cooperative binding and conformational changes of ligands with the biomolecules.
