Visualization of Biological Macromolecules

Shuchismita Dutta, Ph.D.

Why Visualize?

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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

Evolution of Visualization

Jane Richardson

Hand-drawn ribbon diagram of Triosephosphate isomerasehttp://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

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Visualize molecules on a computer1. Coordinate file from PDB

2. Visualization softwareRasMol, Chimera, Swiss PDB Viewer etc.

3. Computer4. Molecule image

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

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A Tour of the RCSB PDB web-siteDefault View

Exploring a Specific Structure (PDB ID 4hhb)

Exploring 4hhb – contd.

Header

Composition of Structure

Ligands

Polymer sequence

Secondary Structure and Links

Origin and Coordinates

Visualization Metaphors/Conventions

Spacefill

Wireframe Ribbons

What does a molecule look like?

All atoms Backbone

What to Show and How

Overlap of Gleevec &Sprycel bound to Abl kinase (PDB IDs 1iep, 2gqg)

Gleevec bound to Abl KinasePDB ID 1iep

Sprycel bound to Abl Kinase

PDB ID 2gqg

Mira PatelStudent 2008, 2009

Treating Chronic Myeloid Leukemia

Ligands

• Chemical Component Dictionary– access from RCSB

PDB websiteOR– from http://ligand-

expo.rcsb.org/

PNN: Penicillin G

Biological Assembly

Missing Pieces

ATP Synthase:PDB entries1c17, 1e79,2a7u, 1l2p

Illustrations from D. Goodsell

Split entries

NMR Ensemble Structures

Sugarcane Defensin 5 protein, PDB ID 2ksk

Structure ComparisonSequence 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

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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

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

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

Tell a Story: How Hemoglobin Works

Note the use of:• Scroll• Color• Representation• Orientation• Labels

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