Shining a light on relationships between chlorophyll structures and optical properties

Protein studies have come a long way in the last few decades. Crystallographic data has revealed the detailed structural picture of thousands of proteins, while spectroscopic analysis has led to a better understanding of their optical properties. But relating these advances remains challenging, and photosynthesis research hinges on a clear idea of how energy moves through large protein complexes.

To facilitate this understanding, Ahad et al. developed PigmentHunter, an analysis tool designed to automate the process of calculating optical and electronic properties of chlorophyll proteins from their crystal structure. This makes a complicated process accessible to many researchers.

“Only a handful of research groups have the computational resources and specialized expertise to make realistic estimates of how to connect chlorophyll protein structure and spectroscopy,” said author Mike Reppert. “The goal with PigmentHunter is to democratize that process.”

With PigmentHunter, any researcher can upload a protein crystal structure, run molecular dynamics simulations, and use the resulting data to identify optical properties such as absorption and fluorescence. The software also allows for batch analysis of many structures and for determining the effects of point mutations on resulting pigments.

The authors hope PigmentHunter not only serves as a useful tool for studying existing proteins, but also as a way to build new proteins with desired properties.

“Some groups are starting to design new chlorophyll proteins to build synthetic light-harvesting complexes,” said Reppert. “At some level, they are still in the dark because they do not know what the optical properties will be. We want to predict what will happen when changing a structure or making a new structure.”

Source: “PigmentHunter: A point-and-click application for chlorophyll-protein simulations,” by Safa Ahad, Chientzu Lin, and Mike Reppert, Journal of Chemical Physics (2024). The article can be accessed at https://doi.org/10.1063/5.0198443 .