Symmetry, Pseudo-symmetry and Evolution in Protein Structures

This poster was displayed at BioPhysChem 2011 at the University of Wollongong 3-6 December 2011. Reasoning from the effect of Natural Selection on symmetry, it shows examples of the arrangement of subunits in a complex and the alignment of "barrel" structures pointing towards the centre of the complex. Click on the title of this post or here to view the poster.

Effect of Crystallization on Protein Quaternary Structure

This talk was given at BioPhysChem2011 (3-6 December at the University of Wollongong) on 6 December 2011. It deals quantitatively with the expected changes to protein structure when the protein-in-water phase is changed to a water-in-protein phase during crystallization. For the first time there is a chemical explanation of why crystal structures differ from native structures as detailed throughout this blog. Click on the title of this post or here to view the slides, including animation.

Galactose oxidase now in the Gallery

The reassembled structure of galactose oxidase has been placed in the Gallery. My earlier work on this enzyme was posted, below, on September 30, 2007. I remarked then that the docking could be improved and I have done so in preparing the structure for the Gallery. The improved structure brings the copper centres of adjacent subunits closer together and the surrounding aromatic groups into closer contact. To achieve this I have accepted that the amino-acid chain 148-153 has been displaced by crystallization. This chain links the N-terminal auxilliary domain to the catalytic domain. It is quite likely that the N-terminal domain is also slightly out of place but it does not clash significantly with other subunits. The clash of 148-153 with the symmetry-related subunit can be seen in the reassembled structure but it is an artefact of crystallization.
Galactose oxidase shares many features with other proteins in the Gallery. Like hemocyanin it has pairs of copper-histidine centres but unlike hemocyanin, the partners in each pair are in different subunits. Like hemoglobin, the metal centres are electronically linked by an extended π-electron network. Like neuraminidases, the structural motif that focusses compressive force is a "propeller" of β-sheets. Also like some neuraminidases, galactose oxidase has auxilliary domains. These may have a role in interactions with the oligo- or poly-saccharides that are the natural substrates for both enzymes.
In coming days I will modify the preprint, linked through the 30 September 2007 post, to reflect the improved structure.

Hemocyanin structure

I was curious to see whether there were any obvious similarities in the subunit interactions of hemocyanin and hemoglobin. I downloaded 1NOL.pdb of Hazes et al. (1993). They reported it as a homohexamer and so I tried to dock the structure as a compact hexamer. In the crystal the hexamer has a large central cavity, which is unsatisfactory on physical grounds (see the first post of this Blog). Docking of a hexamer was unsatisfactory but a tetramer docked very well.
I have added the tetramer to the Gallery. The implication is that the tetramer has a physiological role.
Like hemoglobin, hemocyanin has an extensive aromatic network linked to the oxygen binding sites. Unlike hemoglobin the network does not appear to link oxygen binding sites on adjacent subunits. It is also unclear how the reported reverse Bohr effect could work.

Hemoglobin of the goose.

I have placed the R state and T state of hemoglobin from the Bar-Headed Goose, Anser indicus, in the Gallery. Inositol hexaphosphate is the polyanionic effector of avian hemoglobins and I have included a molecule of inositol hexaphosphate in the polyanion binding site of the T state. The positive charges of the polyanion binding site can be visualised by following the instructions in the Gallery. It can be seen that there are more positive charges than in human hemoglobin. The number of positive charges able to interact with the inositol hexaphosphate is more than appears at first sight, because allowance must be made for the flexibility of lysine side-chains. The larger number of positive charges accords with the fact that the avian effector has more negative charges than does diphosphoglycerate, the effector in human hemoglobin.

The Gallery can be accessed by clicking on the Title of this Post.

Quaternary Isomers of Hemoglobin

Perhaps a suitable term for the T state and R state conformations of hemoglobin would be "Quaternary Isomers". I have previously described them as interchangeable by subunit exchange. Subunit exchange is geometrically equivalent to concerted rotation of each subunit about its radial axis by 120º and perhaps this would be the preferred pathway of isomerisation in nature. For an α₂β₂ tetrahedron there are 3 different quaternary isomers. For vertebrate hemoglobins, a clockwise rotation of each subunit of the R state by 120º produces the T state with a polyanion binding site. An anticlockwise rotation of each R state subunit by 120º produces an alternate T state without an intact polyanion binding site. The alternate T state probably has a minor role physiologically. In the presence of the appropriate polyanion effector the isomerisation equilibrium would shift towards the main T state.
I have placed all 3 isomers in the Gallery.

Hemoglobin poster added to F1000 poster collection

The 2008 "Haemoglobin Revisited" poster presented at WATOC 08 has been accepted into the Faculty of 1000 Poster Collection and can be accessed by clicking on the heading of this post. It is slightly modified from the original by inclusion of the instructions for generating the structures and by crossing out the claim that the crystal structure cannot account for the inability to form crosslinks between the N-terminals of the beta chains. The crystal structure can account for this phenomenon if it is also assumed that the N-terminals are not very mobile. On the other hand, the native structure of the T-state proposed in the poster (click on the Gallery link) can account for the crosslinking properties only if the lysine side chains are considered mobile.
In summary, the crosslinking study cannot distinguish between these opposing views of protein structure.

Dihydrodipicolinate Synthase (DHDPS)

The structure of this enzyme from Bacillus anthracis is now available in the Gallery. It is the first alpha/beta barrel native quaternary structure to be reassembled. Using this structure as a template should help in the reassembly of other alpha/beta barrel structures. There is a ragged edge on the z-axis of this structure that corresponds to an area of inter-subunit contact in the crystal. Probably this is an example of damage to the tertiary structure caused by crystallization.

Dihydrofolate reductase Type 1 tetramer

In the course of discussions about Enzyme Function arising from the companion blog, I became aware that DHFR Type 1 is described as a monomer. It is divided into two sub-domains. As this is inconsistent with the physics of catalysis (see the first post of this blog), I explored possible dimeric and tetrameric complexes of this enzyme. The tetramer docks very well. The tetrameric structure is now included in the gallery. Click on the title of this post to study the 3D structure.
I checked the sources of reports that DHFR Type 1 is a monomer and found that the direct evidence came from experiments in the absence of cofactor. I am now planning to repeat the MW determination in the presence of cofactor.

Gallery of 3D Protein Structures

I have begun a gallery of 3D structures of the proteins mentioned on this blog. The structures are rendered by the powerful Jmol applet using the same graphic interface used by the Protein Data Bank. Jmol can display spacefill, backbone or cartoon representations. Jmol can calculate and display surfaces and cavities. It can rotate the structure in any way requested by the user and responds to scripts similar to those of RASMOL and other protein display programs. Click here to enter the gallery.