Basics of Protein structure in bioinformatics
- 1. Protein Structures XBT707 BIOINFORMATICS Asma Shajahan (121011101438) Priyadharahini (121011101440) IV year Department of Biotechnology Submitted To P. Mala Department of Biotechnology
- 2. What Are Proteins? • - Essential biomolecules in all living organisms • - Perform functions like catalysis, structural support, and signaling • - Composed of amino acid chains
- 3. Levels of Protein Structure • - Primary: Sequence of amino acids • - Secondary: Alpha helices and beta sheets • - Tertiary: 3D folding of a single polypeptide • - Quaternary: Assembly of multiple polypeptides
- 4. Importance of Protein Structure • - Structure determines function • - Misfolding can lead to diseases (e.g., Alzheimer's, Parkinson's) • - Key for drug design and biotechnology
- 5. Protein Structure Prediction • - Predicting 3D structure from amino acid sequence • - Key methods: • 1. Homology modeling • 2. Ab initio prediction • 3. Threading
- 6. Tools for Protein Structure Analysis • - Popular tools: • - PyMOL: Visualization • - AlphaFold: Prediction • - SWISS-MODEL: Homology modeling • - Chimera: Molecular graphics
- 7. Databases in Bioinformatics • - Protein Data Bank (PDB): Repository of 3D structures • - UniProt: Comprehensive protein sequence database • - Pfam: Protein families and domains
- 8. Protein Folding • - Process by which a protein assumes its functional 3D shape • - Driven by interactions like hydrogen bonds, hydrophobic effects • - Folding pathways are crucial for correct function
- 9. Protein Misfolding • - Misfolded proteins can form aggregates • - Linked to diseases such as: • - Alzheimer's • - Parkinson's • - Cystic fibrosis
- 10. Experimental Methods for Structure Determination • - X-ray Crystallography: High-resolution 3D structures • - NMR Spectroscopy: Structures in solution • - Cryo-Electron Microscopy: Large complexes
- 11. Homology Modeling • - Predicts protein structure based on similar known structures • - Steps: • 1. Template selection • 2. Sequence alignment • 3. Model building and refinement
- 12. Role of AlphaFold in Bioinformatics • - Revolutionized structure prediction • - Uses AI to predict accurate 3D structures • - Accessible and widely used in research
- 13. Challenges in Protein Structure Prediction • - Handling large, flexible proteins • - Accurately modeling protein-ligand interactions • - Predicting membrane protein structures
- 14. Conclusion • - Protein structure is vital to understanding biological function • - Bioinformatics tools and databases enhance prediction and analysis • - Advancements like AlphaFold are transforming the field