1. Visualization of Biological Macromolecules Shuchismita Dutta, Ph.D.

2. Why Visualize? Julian Voss-Andreae www.hhmi.org/news/media/geis/geis.jpg Julian Voss-Andreae

3. Visualization Objectives Understand the structural data Visualize structural data (using software e.g. Chimera) – Atomic model (using coordinates from PDB) – Maps (computed using experimental data from PDB) Analyze protein/nucleic acid structures – Select and display specific atoms/groups of atoms and neighboring atoms/ligands – Draw hydrogen bonds – Measure distances/angles etc. Compare structures of related macromolecules Create figures of molecular structures that tell a story

4. Evolution of Visualization Jane Richardson Hand-drawn ribbon diagram of Triosephosphate isomerase http://en.wikipedia.org/wiki/Jane_S._Richardson http://www.wellcomecollection.org/full- image.aspx?page=1139&image=john-kendrew-and-maz-perutz John Kendrew and Max Perutz looking at the “forest of rods” model of myoglobin

5. Visit a Museum http://www.umass.edu/microbio/rasmol/history.htm

6. Visualize molecules on a computer 1. Coordinate file from PDB 2. Visualization software RasMol, Chimera, Swiss PDB Viewer etc. 3. Computer 4. Molecule image

7. What is in the PDB? Coordinate and experimental data files Details about sample preparation, data collection and structure solution Sequence(s) of polymers (proteins and nucleic acids) in the structure Information about ligands in the structure Links to various resources that describe the sequence, function and other properties of the molecule. Classification of structures by sequence, structure, function and other criteria Download/Use directly Link to/Find similar

8. A Tour of the RCSB PDB web-site Default View

9. Exploring a Specific Structure (PDB ID 4hhb)

10. Exploring 4hhb – contd.

11. Header

12. Composition of Structure Ligands Polymer sequence

13. Secondary Structure and Links

14. Origin and Coordinates

15. Visualization Metaphors/Conventions Spacefill WireframeRibbons What does a molecule look like? All atoms Backbone

16. What to Show and How Overlap of Gleevec & Sprycel bound to Abl kinase (PDB IDs 1iep, 2gqg) Gleevec bound to Abl Kinase PDB ID 1iep Sprycel bound to Abl Kinase PDB ID 2gqg Mira Patel Student 2008, 2009 Treating Chronic Myeloid Leukemia

17. Ligands Chemical Component Dictionary – access from RCSB PDB website OR – from http://ligand- expo.rcsb.org/ PNN: Penicillin G

18. Biological Assembly

19. Missing Pieces ATP Synthase: PDB entries 1c17, 1e79, 2a7u, 1l2p Illustrations from D. Goodsell

20. Split entries

21. NMR Ensemble Structures Sugarcane Defensin 5 protein, PDB ID 2ksk

22. Structure Comparison Sequence based Sequences with greater than 30% identity usually have similar structure Structure based Sequences with less than 30% similarity may also have similar structures Pairwise structure alignment: jFATCAT - flexible Pairwise sequence alignment: Smith-Waterman orange blue

23. Learning to Use Chimera Upload file and Save file/image/session Select chain/residue/atoms/neighbors/sequence Display, color atoms/ ribbons/ surface/ labels Structure analysis – H-bonds measure bond lengths Structure superposition Making a movie

24. Visualization Summary Understand the structural data Visualize (using software e.g. Chimera) – Atomic model (using coordinates from PDB) – Maps (computed using experimental data from PDB) Analyze protein/nucleic acid structures – Select and display specific atoms/groups of atoms – Identify neighboring atoms/ligands – Measure distances/angles etc. Compare structures of related macromolecules Create figures of molecular structures that tell a story

25. Telling a story with figures Selection – of atoms, residues, polymer chains Color – to denote identity, mark groups etc. Representation – suitable for main points being made Orientation – to clearly show the point being made Labels – to mark and explain Legened – to explain what is being shown

26. Tell a Story: How Hemoglobin Works Note the use of: Scroll Color Representation Orientation Labels

27. Structure of Kir2.2. (A) Stereoview of a ribbon representation of the Kir2.2 tetramer from the side with the extracellular solution above. Four subunits of the channel are uniquely colored. Approximate boundaries of the lipid bilayer are shown as gray bars. (B) A close-up view of the pore-region of a single subunit (in ribbon representation) with the turret, pore helix and selectivity filter labeled. Side chains of residues E139, R149 and a pair of disulfide-bonded cysteines (C123 and C155) are shown as sticks and colored according to atom type: carbon, yellow; nitrogen, blue; oxygen, red; and sulfur, green. Ionized hydrogen bonds are indicated by dashed black lines. The region flanked by the two disulfide-bonded cysteines is colored orange. (C) Electron density (blue wire mesh, 2Fo-Fc, calculated from 50 to 3.1Å using phases from the final model and contoured at 1.0 σ) is shown for the side chains of E139 and R149 [sticks, colored the same scheme as in (B)] forming a salt bridge. (D and E) K+ selectivity filter of the Kir2.2 channel (D) compared with that of the Kv1.2-Kv2.1 paddle chimera channel [(E), PDB ID 2R9R]. For clarity, only two of the four subunits [sticks, colored with the same scheme as in (B)] are shown. K+ (green spheres), water molecules (cyan spheres), and hydrogen bonds between R149 and E139 (Kir, dashed black lines), or between D379, M380 and waters (Kv, dashed black lines) are shown. Tao X, Avalos JL, Chen J, MacKinnon R., Science. 2009 Dec 18;326(5960):1668-74. Use of Selection, Color, Orientation, Labels and Legends