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Information about Quaternary Structure

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

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.

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.

  • 13 = tridecamer
  • 14 = tetradecamer
  • 15 = pentadecamer*
  • 16 = hexadecamer
  • 17 = heptadecamer*
  • 18 = octadecamer
  • 19 = nonadecamer
  • 20 = eicosamer
  • 21-mer
  • 22-mer
  • 23-mer*
  • 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

Methods that measure the size of the intact complex directly

Methods that measure the size of the intact complex indirectly

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).

See also

External links

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Protein quaternary structure
GeneralGlobular protein
DimersLeucine zipper
TrimersCollagen
TetramersHemoglobin
HexamersDnaB helicase
OctamersNucleosome
FibrilsActin
ComplexesPreinitiation complex
MachinesProteasome
VirusCapsid
PrecipitatesSalting out
MethodsUltracentrifugation
Biochemistry is the study of the chemical processes in living organisms.[1] The word "biochemistry" comes from the Greek word βιοχημεία biochēmeia, which means "the chemistry of life.
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Protein folding is the physical process by which a polypeptide folds into its characteristic three-dimensional structure.[1] Each protein begins as a polypeptide, translated from a sequence of mRNA as a linear chain of amino acids.
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Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues.
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Peptides (from the Greek πεπτίδια, "small digestibles") are short polymers formed from the linking, in a defined order, of α-amino acids.
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In structural biology, a protein subunit or subunit protein is a single protein molecule that assembles (or "coassembles") with other protein molecules to form a multimeric or oligomeric protein.
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In biochemistry and chemistry, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.[1]

Relationship to primary sequence


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Enzymes are proteins that catalyze (i.e. accelerate) chemical reactions.[1] In enzymatic reactions, the molecules at the beginning of the process are called substrates, and the enzyme converts them into different molecules, the products.
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Hemoglobin, also spelled haemoglobin and abbreviated Hb, is the iron-containing oxygen-transport metalloprotein in the red blood cells of the blood in vertebrates and other animals.
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Pol I: implicated in DNA repair; has both 5'->3'(Nick translation) and 3'->5' (Proofreading) exonuclease activity.
  • Pol II: involved in replication of damaged DNA; has both 5'->3'chain extension ability and 3'->5' exonuclease activity.
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    • Ion channels are pore-forming proteins that help to establish and control the small voltage gradient across the plasma membrane of all living cells (see cell potential) by allowing the flow of ions down their electrochemical gradient.
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    Nucleosomes are the fundamental repeating subunits of all eukaryotic chromatin (except when packaged in sperm). They package DNA into chromosomes inside the cell nucleus and control gene expression.
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    Microtubules are one of the components of the cytoskeleton. They have diameter of ~ 24 nm and length varying from several micrometers to possibly millimeters in axons of nerve cells.
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    Conformation generally means structural arrangement.

    In science, it may refer to:
    • Chemical conformation, in chemistry, is the chemical structure of a molecule. In polymer chemistry, it's the three-dimensional shape of the macromolecular chain.

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    In biochemistry, a macromolecule exhibits cooperative binding if its affinity for its ligand changes with the amount of ligand already bound.

    Cooperative binding is a special case of allostery.
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    In biochemistry, allosteric regulation is the regulation of an enzyme or protein by binding an effector molecule at the protein's allosteric site (that is, a site other than the protein's active site).
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    protein complex is a group of two or more associated proteins formed by protein-protein interaction that is stable over time. Protein complexes are a form of quaternary structure.
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    In chemistry, an oligomer consists of a finite number of monomer units (ολιγος, or oligos, is Greek for "a few"), in contrast to a polymer which, at least in principle, consists of an unbounded number of monomers.
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    A monomer (from Greek mono "one" and meros "part") is a small molecule that may become chemically bonded to other monomers to form a polymer.

    Examples of monomers are hydrocarbons such as the alkene and arene homologous series.
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    dimer refers to a molecule composed of two identical subunits or monomers linked together.

    Chemistry

    The molecules in a dimer are connected by covalent bonds or weaker interactions such as hydrogen bonds.
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    Trimer might refer to:
    • trimer (chemistry), a reaction product composed of three identical molecules
    • trimer (biochemistry), a compound of three macromolecules non-covalently bound
    • Trimer, a commune of the Ille-et-Vilaine département, in France

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    A tetramer is a protein with four subunits (tetrameric). There are homo-tetramers (all subunits are identical) such as glutathione S-transferase or single-strand binding protein, dimers of hetero-dimers such as haemoglobin (a dimer of an alpha/beta dimer), and hetero-tetramers,
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    In chemistry, an oligomer consists of a finite number of monomer units (ολιγος, or oligos, is Greek for "a few"), in contrast to a polymer which, at least in principle, consists of an unbounded number of monomers.
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    Dodecameric is a term pertaining to protein quaternary structure, and describes a protein complex with 12 protein subunits (protein chains). Dodecameric complexes can have a number of subunit 'topologies', but typically only a few of the theoretically possible subunit arrangements
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    Eicosameric refers to biological polymers or multimers having exactly twenty 'monomers' (or 20 repeating components).

    Protein complexes having exactly 20 subunits are referred to as eicosameric (or sometimes 20-Meric).
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    capsid is the protein shell of a virus. It consists of several oligomeric subunits made of protein. The capsid encloses the genetic material of the virus.

    Capsids are broadly classified according to their structure.
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    A molecular machine has been defined as a discrete number of molecular components that have been designed to perform mechanical-like movements (output) in response to specific stimuli (input).
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    Proteasomes are large protein complexes inside all eukaryotes and archaea, as well as in some bacteria. In eukaryotes, they are located in the nucleus and the cytoplasm.[1]
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    The spliceosome is a complex of RNA and protein subunits that removes non-coding intervening sequences (introns) from precursor mRNA, a process generally referred to as splicing.
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    A ribosome is a small, dense, functional structure found in most known cells that assemble proteins and polypeptides used in cell division. It catalyses the assembly of individual amino acids into polypeptide chains by reading messenger RNAs and binding amino acids that are
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    The ultracentrifuge is a centrifuge optimized for spinning a rotor at very high speeds, capable of generating acceleration as high as 1,000,000 g (9,800 km/s²). There are two kinds of ultracentrifuges, the preparative and the analytical ultracentrifuge.
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