BioDolphin As a Comprehensive Database of Lipid-protein Binding Interactions

Overview

Journal Commun Chem

Publisher Springer Nature

Specialty Chemistry

Date 2024 Dec 5

PMID 39633021

Authors

Li-Yen Yang

Kaike Ping

Yunan Luo

Andrew C McShan

Affiliations

Soon will be listed here.

Abstract

Lipid-protein interactions are crucial for virtually all biological processes in living cells. However, existing structural databases focusing on these interactions are limited to integral membrane proteins. A systematic understanding of diverse lipid-protein interactions also encompassing lipid-anchored, peripheral membrane and soluble lipid binding proteins remains to be elucidated. To address this gap and facilitate the research of universal lipid-protein assemblies, we developed BioDolphin - a curated database with over 127,000 lipid-protein interactions. BioDolphin provides comprehensive annotations, including protein functions, protein families, lipid classifications, lipid-protein binding affinities, membrane association type, and atomic structures. Accessible via a publicly available web server ( www.biodolphin.chemistry.gatech.edu ), users can efficiently search for lipid-protein interactions using a wide range of options and download datasets of interest. Additionally, BioDolphin features interactive 3D visualization of each lipid-protein complex, facilitating the exploration of structure-function relationships. BioDolphin also includes detailed information on atomic-level intermolecular interactions between lipids and proteins that enable large scale analysis of both paired complexes and larger assemblies. As an open-source resource, BioDolphin enables global analysis of lipid-protein interactions and supports data-driven approaches for developing predictive machine learning algorithms for lipid-protein binding affinity and structures.

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