Tubulin Database Application Design
From the perspective of the tubulin research community, here are the key elements your database application should incorporate:
Structural Classifications
- Isotype tracking: Alpha/beta/gamma tubulin variants with their distinct structural features
- PTM mapping: Comprehensive post-translational modification sites (acetylation, tyrosination, polyglutamylation, etc.)
- Conformational states: Straight vs. curved, GTP vs. GDP-bound states
- Lattice arrangements: A vs. B lattice, protofilament number variations (13 vs. non-13)
- Interface classifications: Lateral and longitudinal contact regions
- Seam structures: Variations in microtubule seam architecture
Biologically Relevant Operations
- PTM pattern search: Query by specific modification patterns
- Structural alignment tools: Compare conformational changes between states
- Pharmacological binding site analysis: Drug interaction surfaces
- MAP binding region identification: Sites for motor proteins and other MAPs
- Evolutionary conservation mapping: Highlight conserved regions across species
- Disease-associated mutation correlation: Link mutations to structural changes
Critical Loci
- Nucleotide binding pockets: GTP/GDP binding sites
- Taxane-binding site: And other drug-binding domains
- E-site/M-site: Exchangeable vs. non-exchangeable nucleotide sites
- C-terminal tails: Highly variable regions subject to most PTMs
- Inter-dimer interfaces: Critical for polymerization dynamics
- Loop regions: T5, H1-S2, M, etc. that change conformation during dynamics
Additional Functionalities
- Dynamics prediction: Tools to correlate structure with dynamic behavior
- Resolution-based filtering: Quality assessment of structural data
- Experimental method classification: Cryo-EM vs. X-ray crystallography sources
- Taxonomic organization: Species-specific tubulin structures
- Integrated visualization: Direct linking to molecular viewers with highlighting options
Would you like me to expand on any particular aspect of this database design?