Integrated Analysis of Molecular Assemblies using Chimera
A Demonstration with Alpha Crystallin

NCRR Site Visit
November 17, 2011

Purpose of this Demonstration

Software for Analysis of Large Molecular Assemblies

Example System: Alpha Crystallin

Modeling Alpha Crystallin

Demo Outline

24 copies of alpha crystallin form oligomer
seen by electron microscopy (20 Angstrom resolution).
Human alpha crystallin is 2 beta sheets.

How Alpha Crystallin Binds to Itself: Evidence from X-ray, NMR, SAXS

Various crystal structures show several biological dimerization modes. C-terminal tail binds to edge of beta-sheet. Binds in 180 degree flipped orientation too. Binding sequence is palindrome. Side-by-side beta sheet dimer.

Beta-sheet dimer observed with 3 different registrations in crystals and NMR. Some literature suggests all are present allowing different oligomers to form.

Small-angle x-ray scattering in solution shows only one registration is present at physiological conditions (NMR registration). Shifted human dimer with C-terminal tails for building 24-mer.

Building the Model: Fitting and Optimization

Deduce map symmetry. Fit dimer in EM map. Movie. Symmetry copies of fit dimer.
Hexamer with 6 C-terminal tails. Moved C-terminal tails to bind hexamer. Made C-terminal tails connect 4 hexamers. Movie. Fit of 24-mer model to map.

Mechanism of Chaperone Activity: A Hypothesis

Molecular surface with orange hydrophobic regions. C-terminal strands cover hydrophobic grooves. Literature says binding unfolded proteins requires oligomer to disassemble.

Comparison to an Archaeal Chaperone

M jannaschii octahedral small heat shock protein 24-mer (1shs), 20% sequence identity to human alpha-crystallin. Same C-terminal tail binding pattern as our alpha-crystallin model. Alpha-crystallin is larger. Two inequivalent of 3-fold axes in alpha-crystallin are equivalent in M jannaschii sHSP.
Aligned alpha-crystallin (red) and sHSP (blue) monomers. Aligned alpha-crystallin dimer (red), sHSP dimer (blue). Movie. All 12 alpha-crystallin structures show edge-to-edge dimers. None show sHSP type strand swapping. Comparison of alpha-crystallin EM map and simulated map from sHSP crystal structure. Movie.

Chimera Capabilities used for this Example Analysis

We used 16 Chimera capabilities in this example, only about 1/5 of the available Chimera molecular assembly modeling tools.

Main message of the demonstration