FPbase is an open-source, community-editable online database dedicated to fluorescent proteins (FPs) and their properties. It serves as a centralized and comprehensive resource for researchers and developers working with these biological tools. The platform collects and organizes structured, searchable data about FPs.
Understanding Fluorescent Proteins
Fluorescent proteins are naturally occurring proteins that can absorb light at one wavelength and then emit it at a longer wavelength, resulting in a visible glow. The most well-known example is Green Fluorescent Protein (GFP), initially discovered in the jellyfish Aequorea victoria in the early 1960s. Since this initial discovery, scientists have identified and engineered many other fluorescent proteins from diverse marine organisms, expanding the available color palette from blue to red and beyond.
Scientists use fluorescent proteins in biological research because they can be genetically fused to other molecules without disrupting function. This allows researchers to “tag” specific cells, proteins, or cellular processes, making them visible under a microscope. For example, GFP can be used to track gene expression or visualize cancer metastasis in living organisms. These genetically encoded markers provide a non-invasive way to observe dynamic biological events in real-time.
The wide array of available FPs, each with unique spectral properties, brightness, and stability, highlights the need for a structured database. Researchers often require specific FP characteristics for their experiments, such as a particular emission color for multicolor imaging or a highly stable protein for long-term tracking. A comprehensive database helps navigate this diversity, ensuring scientists can select the most appropriate FP for their specific research questions.
Key Features of Fpbase
FPbase offers various functionalities and data types for exploring and comparing FPs. Each protein within the database has a dedicated page providing detailed information. This includes the full amino acid sequence, along with relevant accession IDs from public databases like GenBank and UniProt.
Users can view the evolutionary lineage and specific mutations that distinguish FP variants. The database also catalogs fluorescence attributes, such as excitation and emission spectra, presented as interactive curves. Measurements of brightness, photostability (how resistant the protein is to fading), and oligomerization state (whether the protein exists as a single unit or forms complexes) are also available.
FPbase integrates tools for comparing spectra with common filters and light sources, helping researchers assess FP performance with their microscopy setup. The platform also provides structural data and references to primary literature that introduced or characterized each protein. Users can perform advanced searches based on over 20 characteristics, filter proteins by oligomerization or switching type, and explore relationships between various FP properties using interactive charts.
Real-World Applications
Researchers use FPbase to streamline experimental design and improve outcomes in various biological disciplines. A primary application involves selecting the optimal FP for specific experiments, such as advanced microscopy or flow cytometry. By comparing spectral properties, brightness, and photostability on FPbase, scientists can choose an FP that matches their microscope’s filters and light sources, maximizing signal and minimizing background noise.
The database also assists in troubleshooting experimental issues related to FP performance. If an FP is not performing as expected, researchers can consult FPbase to review its known properties, such as sensitivity to pH or temperature, which might explain unexpected results. This helps in identifying potential causes for low fluorescence or rapid photobleaching, leading to adjustments in experimental conditions or the selection of a more robust FP.
FPbase aids in designing new genetic constructs by providing access to protein sequences and information on how mutations affect FP characteristics. This allows scientists to engineer novel FP fusions or modify existing ones for improved performance or specific applications. The platform’s interactive tools, such as the spectra viewer and FRET calculator, further enable researchers to predict how different FPs will interact in complex labeling schemes, saving time and resources.