Protein-chromophore interactions are a central component of a wide variety of critical biological processes, such as color vision and photosynthesis. To understand the fundamental elements that contribute to spectral tuning of a chromophore inside the protein cavity, we have redesigned human Cellular Retinol Binding Protein II (hCRBPII) to fully encapsulate all-trans-retinal and form a covalent bond as a protonated Schiff base. Using this system, the absorption maximum of the pigment was regulated from 425 nm to 644 nm using rational mutagenesis designed to alter the electrostatic environment within the binding pocket of the host protein. Employing only 9 point mutations, the hCRBPII mutants induce a systematic shift in the absorption profile of all trans-retinal of over 200 nm across the visible spectrum.

Background: 1,8-Cineole, a commercially important monoterpene, was identified as a fungal product. Results: The 1,8-cineole synthase was identified from a Hypoxylon fungal genome, and mutagenesis revealed a critical asparagine residue. Conclusion:The fungal 1,8-cineole synthase uses a mechanism similar to the plant version. Significance: This is the first identified fungal monoterpene synthase and may facilitate future terpene synthase identification and production.

Protein reengineering of cellular retinoic acid binding protein II (CRABPII) has yielded a genetically addressable system, capable of binding a profluorophoric chromophore that results in fluorescent protein/chromophore complexes. These complexes exhibit far-red emission, with high quantum efficiencies and brightness and also exhibit excellent pH stability spanning the range of 2–11. In the course of this study, it became evident that single mutations of L121E and R59W were most effective in improving the fluorescent characteristics of CRABPII mutants as well as the kinetics of complex formation. The readily crystallizable nature of these proteins was invaluable to provide clues for the observed spectroscopic behavior that results from single mutation of key residues.

Background: Fluoride is broadly toxic, and organisms use fluoride export (FEX) proteins to expel it. Results: FEX is a constitutively expressed fluoride channel, and mutations to the C-and N-terminal domains have asymmetric effects. Conclusion: Protection from fluoride is constantly needed, and a positive residue in the membrane is required. Significance: Understanding FEX furthers our knowledge of fluoride resistance mechanisms.

Reengineering of cellular retinoic acid binding protein II (CRABPII) to be capable of binding retinal as a protonated Schiff base is described. Through rational alterations of the binding pocket, electrostatic perturbations of the embedded retinylidene chromophore that favor delocalization of the iminium charge lead to exquisite control in the regulation of chromophoric absorption properties, spanning the visible spectrum (474–640 nm). The pKa of the retinylidene protonated Schiff base was modulated from 2.4 to 8.1, giving rise to a set of proteins of varying colors and pH sensitivities. These proteins were used to demonstrate a concentration-independent, ratiometric pH sensor.

The members of the rhodopsin family of proteins are involved in many essential light-dependent processes in biology. Specific photoisomerization of the protein-bound retinylidene PSB at a specified wavelength range of light is at the heart of all of these systems. Nonetheless, it has been difficult to reproduce in an engineered system. We have developed rhodopsin mimics, using intracellular lipid binding protein family members as scaffolds, to study fundamental aspects of protein/chromophore interactions. Herein we describe a system that specifically isomerizes the retinylidene protonated Schiff base both thermally and photochemically. This isomerization has been characterized at atomic resolution by quantitatively interconverting the isomers in the crystal both thermally and photochemically. This event is accompanied by a large pKa change of the imine similar to the pKa changes observed in bacteriorhodopsin and visual opsins during isomerization.

The fluoride export protein (FEX) in yeast and other fungi provides tolerance to fluoride (F-), an environmentally ubiquitous anion. FEX efficiently eliminates intracellular fluoride that otherwise would accumulate at toxic concentrations. The FEX homolog in bacteria, Fluc, is a ‘double-barreled’ channel formed by dimerization of two identical or similar subunits. FEX in yeast and other eukaryotes is a monomer resulting from covalent fusion of the two subunits. As a result, both potential fluoride pores are created from different parts of the same protein. Here we identify FEX proteins from two multicellular eukaryotes, a plant Arabidopsis thaliana and an animal Amphimedon queenslandica, by demonstrating significant fluoride tolerance when these proteins are heterologously expressed in the yeast Saccharomyces cerevisiae. Residues important for eukaryotic FEX function were determined by phylogenetic sequence alignment and functional analysis using a yeast growth assay. Key residues of the fluoride channel are conserved in only one of the two potential fluoride-transporting pores. FEX activity is abolished upon mutation of residues in this conserved pore, suggesting that only one of the pores is functional. The same topology is conserved for the newly identified FEX proteins from plant and animal. These data suggest that FEX family of fluoride channels in eukaryotes are ‘single-barreled’ transporters containing one functional pore and a second non-functional vestigial remnant of a homologous gene fusion event.

Shield and control: The application of a protein design strategy to interrogate the perception of color is described. Cellular retinoic acid binding protein II (see structure) was used first to show that complete encapsulation of the chromophore is critical to achieve an opsin shift comparable to the one observed for rod rhodopsin, and second to show that a rhodopsin protein mimic capable of binding a retinoid analogue responds to changes in electrostatic environments.