Overview
This lecture introduces tools and concepts for visualizing and understanding 3D protein structures, culminating in a slide-based report project on a chosen enzyme.
Getting Started with the Software
- Use Firefox, Chrome, Safari, or Edge for visualization; avoid Internet Explorer.
- Visit Atlas.MolviZ.Org, choose a "STRAIGHTFORWARD" protein, and open it in FirstGlance for practice.
- The practice enzyme is just for software familiarization, not for the final project.
Project Goals
- Review protein 3D structure principles.
- Select an experimentally-determined protein model for your Enzyme Paper Project.
- Learn to use FirstGlance in Jmol for analyzing structure-function relationships.
- Prepare a PowerPoint report with protein snapshots answering specific questions.
Protein Structure & Structural Bioinformatics
- Protein function is determined by its amino acid sequence and 3D conformation.
- Proteins can have stable folds or intrinsically unstructured regions; both may exist in one molecule.
- 3D structures are mostly determined experimentally by X-ray crystallography, NMR, and cryo-EM.
- All experimentally-derived structures are stored with unique PDB codes in the Protein Data Bank.
- The asymmetric unit may differ from the biological unit; biological unit represents the functional molecule.
Choosing an Enzyme
- Use RCSB Protein Data Bank, Atlas.MolviZ.Org, or Proteopedia to find PDB codes.
- Select a unique, experimentally-determined enzyme that catalyzes a reaction and has a cofactor.
- Ensure the structure is resolved to 3Å or better, and note its 4-character PDB code.
- Post your chosen enzyme and PDB code to Canvas, ensuring no duplicates.
Exploring Your Enzyme in FirstGlance
- Enter your enzyme’s PDB code into FirstGlance and explore various views.
- Hydrophobic/polar view distinguishes surface features, indicating solubility or membrane association.
- Charge view reveals surface charge patterns important in molecular interactions.
Report Slides: Required Sections
- Section 1: Identity — Provide your name, enzyme name, PDB code, function, experimental method, resolution, and a snapshot.
- Section 2: Composition — List numbers of protein, DNA, RNA chains, and all ligands/cofactors with their abbreviations and names.
- Section 3: Evolutionary Conservation — Show snapshots of conserved and variable regions; discuss their function.
- Section 4: Hydrophobic/Polar — Determine solubility and support with a relevant snapshot.
- Section 5: Hydrophobic Core — Identify hydrophobic cores in domains; support with "slab" view snapshot.
- Section 6: Charge — Identify and illustrate areas with uniform surface charge.
- Section 7: Cation-Pi Interactions — Provide a snapshot and CaPTURE report of a significant cation-pi interaction.
- Section 8: Biological Unit — Show side-by-side snapshots of the asymmetric and biological units; indicate chain counts.
- Section 9: Animation from Polyview-3D — Create and insert an animated GIF of your enzyme structure.
- Section 10: Contacts/Non-covalent Bonds — Show a snapshot of a hydrogen bond between specified residues or ligands.
- Section 11: Structure-Function Relationship — Write ≥75 words on how structure supports enzyme function, citing credible sources.
Key Terms & Definitions
- PDB code — Unique 4-character identifier for a protein structure in the Protein Data Bank.
- Asymmetric unit — Smallest part of a crystal structure used to generate the full lattice.
- Biological unit — Functional form of a protein complex as it exists in nature.
- Hydrophobic core — Interior region of a protein composed mainly of hydrophobic amino acids.
- Cation-pi interaction — Non-covalent interaction between a cation and the face of an aromatic ring.
Action Items / Next Steps
- Explore a sample protein in FirstGlance for practice.
- Select and register your unique enzyme and PDB code on Canvas.
- Create a PowerPoint report following all section guidelines and include all required snapshots.
- Submit your completed report by the syllabus due date.