Quaternary structure - Wikipedia, the free encyclopedia 2/1/09 9:42 PM

Quaternary structure
From Wikipedia, the free encyclopedia

In biochemistry, quaternary structure is the arrangement of multiple folded protein molecules in a multi-
subunit complex.

Contents
1 Description and examples
2 Nomenclature of quaternary structures
3 Determination of quaternary structure
3.1 Methods that measure mass of intact complex directly
3.2 Methods that measure the size of the intact complex directly
3.3 Methods that measure the size of the intact complex indirectly
4 Protein-protein interactions
5 Quaternary or Quartary?
6 See also
7 References
8 External links

Description and examples

Many proteins are actually assemblies of more than one polypeptide chain, which in the context of the larger
assemblage are known as protein subunits. In addition to the tertiary structure of the subunits, multiple-subunit
proteins possess a quaternary structure, which is the arrangement into which the subunits assemble.
Enzymes composed of subunits with diverse functions are sometimes called holoenzymes, in which some parts
may be known as regulatory subunits and the functional core is known as the catalytic subunit. Examples of
proteins with quaternary structure include hemoglobin, DNA polymerase, and ion channels. Other assemblies
referred to instead as multiprotein complexes also possess quaternary structure. Examples include nucleosomes
and microtubules. Changes in quaternary structure can occur through conformational changes within individual
subunits or through reorientation of the subunits relative to each other. It is through such changes, which
underlie cooperativity and allostery in "multimeric" enzymes, that many proteins undergo regulation and
perform their physiological function.

The above definition follows a classical approach to biochemistry, established at times when the distinction
between a protein and a functional, proteinaceous unit was difficult to elucidate. More recently, people refer to
protein-protein interaction when discussing quaternary structure of proteins and consider all assemblies of
proteins as protein complexes.

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Nomenclature of quaternary structures

The number of subunits in an oligomeric complex are described using names that end in -mer (Greek for "part,
subunit"). Formal Greco-Latinate names are generally used for the first ten types and can be used for up to
twenty subunits, whereas higher order complexes are usually described by the number of subunits, followed by
-meric.

1= monomer 7 = heptamer 13 = tridecamer 19 = nonadecamer

2= dimer 8 = octamer 14 = tetradecamer 20 = eicosamer
3= trimer 9 = nonamer 15 = pentadecamer* 21-mer
4= tetramer 10 = decamer 16 = hexadecamer 22-mer
5= pentamer 11 = undecamer 17 = heptadecamer* 23-mer*
6= hexamer 12 = dodecamer 18 = octadecamer etc.

*No known examples

Although complexes higher than octamers are rarely observed for most proteins, there are some important
exceptions. Viral capsids are often composed of multiples of 60 proteins. Several molecular machines are also
found in the cell, such as the proteasome (four heptameric rings = 28 subunits), the transcription complex and
the spliceosome. The ribosome is probably the largest molecular machine, and is composed of many RNA and
protein molecules.

In some cases, proteins form complexes that then assemble into even larger complexes. In such cases, one uses
the nomenclature, e.g., "dimer of dimers" or "trimer of dimers", to suggest that the complex might dissociate
into smaller sub-complexes before dissociating into monomers.

Determination of quaternary structure

Protein quaternary structure can be determined using a variety of experimental techniques that require a
sample of protein in a variety of experimental conditions. The experiments often provide an estimate of the
mass of the native protein and, together with knowledge of the masses and/or stoichiometry of the subunits,
allow the quaternary structure to be predicted with a given accuracy. It is not always possible to obtain a
precise determination of the subunit composition for a variety of reasons.

The number of subunits in a protein complex can often be determined by measuring the hydrodynamic
molecular volume or mass of the intact complex, which requires native solution conditions. For folded
proteins, the mass can be inferred from its volume using the partial specific volume of 0.73 ml/g. However,
volume measurements are less certain than mass measurements, since unfolded proteins appear to have a much
larger volume than folded proteins; additional experiments are required to determined whether a protein is
unfolded or has formed an oligomer.

Methods that measure mass of intact complex directly

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sedimentation-equilibrium analytical ultracentrifugation

electrospray mass spectrometry

Methods that measure the size of the intact complex directly

static light scattering

size exclusion chromatography (requires calibration)

Methods that measure the size of the intact complex indirectly

sedimentation-velocity analytical ultracentrifugation (measures the translational diffusion constant)

dynamic light scattering (measures the translational diffusion constant)
pulsed-gradient protein nuclear magnetic resonance (measures the translational diffusion constant)
fluorescence polarization (measures the rotational diffusion constant)
dielectric relaxation (measures the rotational diffusion constant)

Methods that measure the mass or volume under unfolding conditions (such as MALDI-TOF mass
spectrometry and SDS-PAGE) are generally not useful, since non-native conditions usually cause the complex
to dissociate into monomers. However, these may sometimes be applicable; for example, the experimenter
may apply SDS-PAGE after first treating the intact complex with chemical cross-linking reagents.

Protein-protein interactions
Proteins are capable of forming very tight complexes. For example, ribonuclease inhibitor binds to
ribonuclease A with a roughly 20 fM dissociation constant. Other proteins have evolved to bind specifically to
unusual moieties on another protein, e.g., biotin groups (avidin), phosphorylated tyrosines (SH2 domains) or
proline-rich segments (SH3 domains).

Quaternary or Quartary?
In biology, the non-standard usage "Quaternary structure" is so firmly entrenched that to refer to "Quartary
structure" would be incorrect. The correct term should really be "Quartary":

Quartary (from Latin: quartarius) is the fourth member of an ordinal number word series beginning
with (primary, secondary, tertiary) and continuing with (quintary, sextary, ...). [1]
Quaternary (from Latin: quaternarius) is the fourth member of a distributive number word series
beginning with (singular, binary, ternary) and continuing with (quinary, senary, septenary, octonary ...
centenary).[2][3]

See also
primary structure
secondary structure
tertiary structure

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structural biology

References
1. ^ quartarius (http://www.perseus.tufts.edu/cgi-bin/ptext?
doc=Perseus%3Atext%3A1999.04.0059%3Aentry%3D%2340027)
2. ^ quaternarius – Charlton T. Lewis, Charles Short, A Latin Dictionary (http://www.perseus.tufts.edu/cgi-bin/ptext?
doc=Perseus%3Atext%3A1999.04.0059%3Aentry%3D%2340050) .
3. ^ E. T. Bell, Representations of Integers in Certain Binary, Ternary, Quaternary and Quinary Quadratic Forms and
Allied Class Number Relations (http://links.jstor.org/sici?sici=0003-
486X(192409%2F12)2%3A26%3A1%2F2%3C155%3AROIICB%3E2.0.CO%3B2-B) , 1924

External links
The Macromolecular Structure Database (http://www.ebi.ac.uk/msd/) (MSD) at the European
Bioinformatics Institute (EBI) serves a list of the Probabable Quaternary Structure (PQS) for every
protein in the Protein Data Bank (PDB).
PQS server (http://pqs.ebi.ac.uk/)
The Protein Interfaces, Surfaces and Assemblies (Pisa) server (http://www.ebi.ac.uk/msd-
srv/prot_int/pistart.html) at the MSD.
3D complex (http://www.mrc-lmb.cam.ac.uk/genomes/elevy/3dcomplex/Home.cgi) Structural
classification of protein complexes
Proteopedia — Proteopedia Home Page (http://www.proteopedia.org) The collaborative, 3D
encyclopedia of proteins and other molecules.
PDBWiki — PDBWiki Home Page (http://PDBWiki.Org) - a website for community annotation of PDB
structures.

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Categories: Protein structure | Stereochemistry

This page was last modified on 19 January 2009, at 19:54.

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