Computational tools and approaches for aquaporin (AQP) research

Aquaporins (AQPs), a water transporter protein present in almost all living organisms, is also known to transport many other small solutes like H 2 O 2 , urea, CO 2 , boron, and silicon. Very high numbers of AQPs are found in plants compared with animals, which are further diversified into five primary subfamilies. Each of the plant AQP subfamilies has unique features like localization to specific cellular compartments, a wide range of solutes they transport, and expression regulation in particular tissues. Detailed knowledge about molecular aspects like protein structure, solute transport dynamics, protein interactions, gene expression, localization, and molecular evolution is required for better understanding of the AQP transport system. This chapter highlights current understanding and knowledge gaps in AQP biology more particularly related to its molecular structure. Distribution of AQPs, genome-wide characterization, and functional predictions performed in numerous plant species has been addressed. A catalog of various techniques, bioinformatics tools and approaches to study AQPs was provided. Progress achieved in prediction of AQP tertiary structures using both electron and X-ray crystallography techniques and subsequent utilization of the information for functional annotation has been described in detail. The chapter provides a state-of-the-art account of numerous computational tools and techniques useful to understand the AQP transport system.