Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438 - Introductory Biochemistry - Spring 2013

Lecture Notes:

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Quaternary Protein Structure

Quaternary (4°) structures : Geometrically specific associations of protein subunits; the spatial arrangement of protein subunits. [Examples, Figure 4.26]: a = ₂{2 identical protomers with / barrel fold}; b = ₂{2 identical protomers, all fold}; c = ₄{4 identical protomers, all , three helices/subunit; 8 helix membrane spanning bundle}; d = ₃{3 identical protomers, sheets}; e = ₂₂; f = ₂.

Rationale for quaternary: There are a variety of advantages to large structures:

• Increasing the size of a protein allows better "fits" for catalysis and binding - many weak bonds are needed to maintain specific structures.
• Can bring sequential active sites of metabolic pathways into close proximity.
• However, large peptides have some problems:
  • The process of folding slows tremendously with increasing size, thus folding individual subunits, and assembling these subunits can greatly enhance folding efficiency.
  • Get about 1 error / 10³ aa residues due to the precision of the translation of messenger RNA to protein. Thus need to keep residue number down.
• Interacting subunits provide mechanisms for regulation.

Quaternary structures allows the assembly of large to extremely large structures. 

Note the occurance of oligomeric proteins of E. coli in the SWISSPROT database[Table 4.1]

Some of the large complexes are shown in Figure 4.27 for a bacterium with a very minimal genome (codes for only 689 proteins vs. about 5,000 for E. coli).

Note interactome diagram [Figure 4.30]—strengths of interactions are NOT indicated.

• IgG example domains, exons and evolution. [Figure 4.57] - Quaternary structure consisting of two heavy chains and two light chains ( or ₂₂), each heavy chain has four related domains (three constant and one variable domain) while each light chain consists of two related domains (one constant and one variable domain). All twelve domains have a "collapsed -barrel domain" or immunoglobin fold [Figure 4.58]. Note that the two heavy chains are identical to each other as are the two light chains.
  • The binding sites are composed of variable domains contributed by a heavy and light chain in each case - this enables a large number of different binding specificities (e.g. 100 H + 100 L gives 100x100 = 10,000 possibilities from 200 unique sequences).
  • Finally, note that the different variable domains are coded by different exons which can be shuffled during immunsystem cell development, serving as a model of evolutionary development - in each individual a unique population of cells in created which is then used as a pool for clonal development depending on the environment in response to antigen exposure.
• In a similar manner we see that many enzymes have active sites created between two domains, often one domain binds one substrate while the second binds a second substrate. Its as if these proteins were designed by taking "off-the-shelf" components, assembling them, and then over time (and generations) tuning the combination up.

Folding Hierarchy Overview

Let's look at how the various levels of structure go ingto making a typical multimeric protein:

FYI - Review/Enhancement: X-ray Diffraction determination of protein structure. Review x-ray diffraction learned in Chem 109 Note the each crystal point now becomes many points, each with its own "reflecting" plane. Rotation to determine relative locations in three space results in thousands of reflections Need to add heavy metals to act as "beacons" to locate positions in absolute space, and need to do a couple of times isomorphically (without altering the proteins structure - isomorphic replacements). Finally use Fourier transforms to convert angles and intensities of reflections to 3-D map of protein. Aside: The reality of X-ray diffraction structures. Trouble is that most of our detailed knowledge of protein 3-D structure is due to X-ray diffraction. Problem: Non-solution, look at very concentrated, crystal structures for proteins. Why do we think they represent reality? - Crystals very hydrated, in fact some enzymes maintain activities in crystal form! - Chemical exchange studies, such as deuterium exchange are consistent with residue exposure. - Chemical reactivity of residues are consistent with residue exposure. - Optical probes of overall shape (e.g. light and x-ray scattering) are consistent. - Hydrodynamic studies of size and shape (e.g. sedimentation, gel filtration) are consistent. - Optical probes of regularity/helicity (e.g. Circular dichroism and ORD) are consistent. - Probes of local environment (e.g. NMR, CD & ORD, Fluorescence, UV) are consistent. Note that any "non-rigid" region of the protein will not show up on X-ray diffraction image, or will be "fuzzy." Thus quite confident of structures.

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Last modified 13 February 2013