Changes in Active Site Hydrogen Bonding upon Formation of the Electronically Excited State of Photoactive Yellow Protein

Abstract

Light plays three main roles in biology. First, light from the sun provides the main source of energy driving the biosphere through chlorophyll-based electron transfer in photosynthetic reaction centers and retinal-based proton pumping in rhodopsins [1]. Second, light is a source of information about the environment for many organisms using photosensory proteins, including animals, plants, fungi and bacteria [2,3]. Third, light can cause damage to biological systems. Light from the near-UV region can damage DNA [4], and excess visible light can damage the photosynthetic machinery in photoinhibition [5]. Thus, light is of great importance for a wide range of biological processes.Proteins that perform photosynthesis or light sensing consist of an apoprotein and a bound chromophore. Only a small number of chromophores account for most known processes in photobiology: chlorophyll and linear tetrapyrroles, caretoids and retinal, flavins and p-coumaric acid [2]. In many cases the chromophore has strong and functionally important interactions with the protein binding pocket, particularly charge-charge interactions and hydrogen bonding interactions. While many different proteins interact with light in a wide range of organisms, almost all of these systems are based on key types of photochemical processes, including electron transfer, C¼C double bond isomerization and the formation of chemical bonds [2,6]. These photochemical events often trigger a cascade of thermal reactions in the protein that extends to the millisecond and minute range, and that result in a biologically relevant output. If the cascade of thermal reactions results in the re-formation of the initial state, the process is referred to as a photocycle. It is the initial ultrafast