Editing Protein quaternary structure

{{short description|Number and arrangement of multiple folded protein subunits in a multi-subunit complex}}
{{Protein structure}}
{{about|quaternary structure in protein|the article about quaternary structure in nucleic acid|Nucleic acid quaternary structure}}

{{Use dmy dates|date=December 2016}}

'''Protein quaternary structure'''{{efn|Here ''[[wikt:quaternary|quaternary]]'' means "''fourth-level'' structure", not "''four-way'' interaction". Etymologically ''[[wikt:quartary|quartary]]'' is correct: ''quaternary'' is derived from Latin [[distributive number]]s, and follows ''binary'' and ''ternary''; while ''quartary'' is derived from Latin [[ordinal number]]s, and follows ''secondary'' and ''tertiary''. However, ''quaternary'' is standard in biology.}} is the fourth (and highest) classification level of [[protein structure]]. Protein quaternary structure refers to the structure of proteins which are themselves composed of two or more smaller protein chains (also referred to as subunits). Protein quaternary structure describes the number and arrangement of multiple [[protein folding|folded]] [[protein subunit]]s in a [[Multiprotein complex|multi-subunit complex]]. It includes organizations from simple [[protein dimer|dimers]] to large [[homooligomer]]s and [[multiprotein complex|complexes]] with defined or variable numbers of subunits.<ref>{{cite book| vauthors = Berg JM, Tymoczko JL, Stryer L |title=Biochemistry|date=2002|publisher=W. H. Freeman|location=New York, NY [u.a.]|isbn=0-7167-3051-0|edition=5. ed., 4. print.|url=https://archive.org/details/biochemistrychap00jere|chapter=Section 3.5Quaternary Structure: Polypeptide Chains Can Assemble Into Multisubunit Structures|chapter-url=https://www.ncbi.nlm.nih.gov/books/NBK22550/|url-access=registration}}</ref> In contrast to the first three levels of protein structure, not all proteins will have a quaternary structure since some proteins function as single units. Protein quaternary structure can also refer to [[biomolecular complex]]es of proteins with [[nucleic acid]]s and other [[Cofactor (biochemistry)|cofactors]].

==Description and examples==
 
Many proteins are actually assemblies of multiple [[polypeptide]] chains. The quaternary structure refers to the number and arrangement of the [[protein subunit]]s with respect to one another.<ref name="Predicting protein quaternary struc">{{cite journal | vauthors = Chou KC, Cai YD | title = Predicting protein quaternary structure by pseudo amino acid composition | journal = Proteins | volume = 53 | issue = 2 | pages = 282–289 | date = November 2003 | pmid = 14517979 | doi = 10.1002/prot.10500 | s2cid = 23979933 }}</ref> Examples of proteins with quaternary structure include [[hemoglobin]], [[DNA polymerase]], [[ribosome]]s, [[Antibody|antibodies]], and [[ion channel]]s.

[[Enzyme]]s composed of subunits with diverse functions are sometimes called [[holoenzyme]]s, in which some parts may be known as regulatory subunits and the functional core is known as the catalytic subunit. Other assemblies referred to instead as [[multiprotein complex]]es also possess quaternary structure. Examples include [[nucleosome]]s and [[microtubule]]s. Changes in quaternary structure can occur through [[Protein conformation|conformational changes]] within individual subunits or through reorientation of the subunits relative to each other. It is through such changes, which underlie [[cooperative binding|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 complex]]es.

==Nomenclature==
[[File:1axc tricolor.png|thumb|The quaternary structure of this protein complex would be described as a homo-trimer because it is composed of three identical smaller protein subunits (also designated as monomers or protomers).]]
The number of subunits in an [[oligomer]]ic complex is described using names that end in -mer (Greek for "part, subunit").  Formal and 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.

{| border="1"
|-----
| valign="top" |
* 1 = [[protein subunit|monomer]]
* 2 = [[protein dimer|dimer]]
* 3 = [[protein trimer|trimer]]
* 4 = [[tetramer protein|tetramer]]
* 5 = [[Pentameric protein|pentamer]]
* 6 = hexamer
| valign="top" |
* 7 = heptamer     
* 8 = [[octamer]]  
* 9 = nonamer
* 10 = decamer
* 11 = undecamer
* 12 = [[dodecamer]]
| valign="top" |
* 13 = tridecamer
* 14 = tetradecamer
* 15 = pentadecamer*
* 16 = hexadecamer
* 17 = heptadecamer*
* 18 = octadecamer
| valign="top" |
* 19 = nonadecamer
* 20 = [[eicosamer]]
* 21 = 21-mer
* 22 = 22-mer
* 23 = 23-mer*
* etc.
|}

:<nowiki>*</nowiki>''No known examples''
The smallest unit forming a homo-oligomer, i.e. one protein chain or [[protein subunit|subunit]], is designated as a monomer, subunit or [[Protomer (structural biology)|protomer]]. The  latter term was originally devised to specify the smallest unit of hetero-oligomeric proteins, but is also applied to homo-oligomeric proteins in current literature. The subunits usually arrange in [[cyclic symmetry]] to form closed [[point group]] [[symmetries]].

Although complexes higher than octamers are rarely observed for most proteins, there are some important exceptions.  [[Capsid|Viral capsids]] are often composed of multiples of 60 proteins.  Several [[molecular machine]]s 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". This may suggest that the complex might dissociate into smaller sub-complexes before dissociating into monomers. This usually implies that the complex consists of different oligomerisation interfaces. For example, a tetrameric protein may have one four-fold rotation axis, i.e. point group symmetry 4 or ''C''<sub>4</sub>. In this case the four interfaces between the subunits are identical. It may also have point group symmetry 222 or ''D''<sub>2</sub>. This tetramer has different interfaces and the tetramer can dissociate into two identical homodimers. Tetramers of 222 symmetry are "dimer of dimers". Hexamers of 32 point group symmetry are "trimer of dimers" or "dimer of trimers". Thus, the nomenclature "dimer of dimers" is used to specify the point group symmetry or arrangement of the oligomer, independent of information relating to its dissociation properties. 

Another distinction often made when referring to [[oligomer]]s is whether they are homomeric or heteromeric, referring to whether the smaller protein subunits that come together to make the protein complex are the same (homomeric) or different (heteromeric) from each other. For example, two identical protein monomers would come together to form a homo-dimer, whereas two different protein monomers would create a hetero-dimer.

==Structure Determination==

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 determine whether a protein is unfolded or has formed an oligomer.

=== Common techniques used to study protein quaternary structure ===

* Ultracentrifugation
* Surface-induced dissociation mass spectrometry<ref name = "Stiving_2019">{{cite journal | vauthors = Stiving AQ, VanAernum ZL, Busch F, Harvey SR, Sarni SH, Wysocki VH | title = Surface-Induced Dissociation: An Effective Method for Characterization of Protein Quaternary Structure | journal = Analytical Chemistry | volume = 91 | issue = 1 | pages = 190–209 | date = January 2019 | pmid = 30412666 | pmc = 6571034 | doi = 10.1021/acs.analchem.8b05071 | department = review }}</ref>
* Coimmunoprecipation<ref name = "Milligan_2005">{{cite journal | vauthors = Milligan G, Bouvier M | title = Methods to monitor the quaternary structure of G protein-coupled receptors | journal = The FEBS Journal | volume = 272 | issue = 12 | pages = 2914–2925 | date = June 2005 | pmid = 15955052 | doi = 10.1111/j.1742-4658.2005.04731.x | s2cid = 23274563 | department = review }}</ref>
* [[Förster resonance energy transfer|FRET]]<ref name = "Milligan_2005" /><ref name = "Raicu_2013">{{cite journal | vauthors = Raicu V, Singh DR | title = FRET spectrometry: a new tool for the determination of protein quaternary structure in living cells | journal = Biophysical Journal | volume = 105 | issue = 9 | pages = 1937–1945 | date = November 2013 | pmid = 24209838 | pmc = 3824708 | doi = 10.1016/j.bpj.2013.09.015 | bibcode = 2013BpJ...105.1937R | department = primary }}</ref>
* Nuclear Magnetic Resonance (NMR)<ref name="Prischi_2016">{{cite book | vauthors = Prischi F, Pastore A | title = Advanced Technologies for Protein Complex Production and Characterization | chapter = Application of Nuclear Magnetic Resonance and Hybrid Methods to Structure Determination of Complex Systems | series = Advances in Experimental Medicine and Biology | volume = 896 | pages = 351–368 | date = 2016 | pmid = 27165336 | doi = 10.1007/978-3-319-27216-0_22 | isbn = 978-3-319-27214-6 | department = review }}</ref><ref name="Wells_2018">{{cite book | vauthors = Wells JN, Marsh JA | title = Protein Complex Assembly | chapter = Experimental Characterization of Protein Complex Structure, Dynamics, and Assembly | series = Methods in Molecular Biology | volume = 1764 | pages = 3–27 | date = 2018 | pmid = 29605905 | doi = 10.1007/978-1-4939-7759-8_1 | isbn = 978-1-4939-7758-1 | quote = Section 4: Nuclear Magnetic Resonance Spectroscopy | department = review }}</ref>

===Direct mass measurement of intact complexes===

* Sedimentation-equilibrium [[analytical ultracentrifugation]] 
* [[electrospray ionization|Electrospray]] [[mass spectrometry]]
* [[Mass Spectrometric Immunoassay]] MSIA

===Direct size measurement of intact complexes===

* [[Rayleigh scattering|Static light scattering]]
* [[Size exclusion chromatography]] (requires calibration)
* [[Dual polarisation interferometry]]

===Indirect size measurement of intact complexes===

* 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]])
* [[Dual polarisation interferometry]] (measures the size and the density of the complex)

Methods that measure the mass or volume under [[Denaturation (biochemistry)|unfolding]] conditions (such as 
[[Matrix-assisted laser desorption/ionization|MALDI-TOF]] [[mass spectrometry]] and [[Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis|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-link]] reagents.

==Structure Prediction==
Some bioinformatics methods have been developed for predicting the quaternary structural attributes of proteins based on their sequence information by using various modes of [[pseudo amino acid composition]].<ref name="Predicting protein quaternary struc"/><ref>{{cite journal | vauthors = Zhang SW, Chen W, Yang F, Pan Q | title = Using Chou's pseudo amino acid composition to predict protein quaternary structure: a sequence-segmented PseAAC approach | journal = Amino Acids | volume = 35 | issue = 3 | pages = 591–598 | date = October 2008 | pmid = 18427713 | doi = 10.1007/s00726-008-0086-x | s2cid = 689955 }}</ref><ref>{{cite journal | vauthors = Xiao X, Wang P, Chou KC |year=2009 |title=Predicting protein quaternary structural attribute by hybridizing functional domain composition and pseudo amino acid composition |journal=Journal of Applied Crystallography |volume=42 |pages=169–173 |doi=10.1107/S0021889809002751 }}</ref>

Protein folding prediction programs used to predict protein tertiary structure have also been expanding to better predict protein quaternary structure. One such development is AlphaFold-Multimer<ref>{{Cite journal| vauthors = Evans R, O'Neill M, Pritzel A, Antropova N, Senior AW, Green T, Žídek A, Bates R, Blackwell S, Yim J, Ronneberger O | display-authors = 6 |date=2021-10-04|title=Protein complex prediction with AlphaFold-Multimer | journal = bioRxiv|url=https://www.biorxiv.org/content/10.1101/2021.10.04.463034v1 |language=en |pages=2021.10.04.463034 |doi=10.1101/2021.10.04.463034| s2cid = 238413014 }}</ref> built upon the [[AlphaFold]] model for predicting protein tertiary structure.

== Role in Cell Signaling ==
Protein quaternary structure also plays an important role in certain cell signaling pathways. The G-protein coupled receptor pathway involves a heterotrimeric protein known as a G-protein. G-proteins contain three distinct subunits known as the G-alpha, G-beta, and G-gamma subunits. When the G-protein is activated, it binds to the G-protein coupled receptor protein and the cell signaling pathway is initiated. Another example is the receptor tyrosine kinase (RTK) pathway, which is initiated by the dimerization of two receptor tyrosine kinase monomers. When the dimer is formed, the two kinases can phosphorylate each other and initiate a cell signaling pathway.<ref>{{cite journal | vauthors = Heldin CH | title = Dimerization of cell surface receptors in signal transduction | journal = Cell | volume = 80 | issue = 2 | pages = 213–223 | date = January 1995 | pmid = 7834741 | doi = 10.1016/0092-8674(95)90404-2 | s2cid = 18925209 | doi-access = free }}</ref>

==Protein–protein interactions==
{{main|Protein–protein interaction}}
Proteins are capable of forming very tight but also only transient 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 domain]]s) or proline-rich segments ([[SH3 domain]]s). Protein–protein interactions can be engineered to favor certain oligomerization states.<ref>{{cite journal | vauthors = Ardejani MS, Chok XL, Foo CJ, Orner BP | title = Complete shift of ferritin oligomerization toward nanocage assembly via engineered protein-protein interactions | journal = Chemical Communications | volume = 49 | issue = 34 | pages = 3528–3530 | date = May 2013 | pmid = 23511498 | doi = 10.1039/C3CC40886H }}</ref>

==Intragenic complementation==

When multiple copies of a polypeptide encoded by a [[gene]] form a quaternary complex, this protein structure is referred to as a multimer.<ref>{{cite journal | vauthors = Crick FH, Orgel LE | title = The theory of inter-allelic complementation | journal = Journal of Molecular Biology | volume = 8 | pages = 161–165 | date = January 1964 | pmid = 14149958 | doi = 10.1016/s0022-2836(64)80156-x }}</ref>  When a multimer is formed from polypeptides produced by two different [[mutant]] [[allele]]s of a particular gene, the mixed multimer may exhibit greater functional activity than the unmixed multimers formed by each of the mutants alone.  In such a case, the phenomenon is referred to as [[complementation (genetics)#Intragenic complementation|intragenic complementation]] (also called inter-allelic complementation).  Intragenic complementation appears to be common and has been studied in many different genes in a variety of organisms including the fungi ''[[Neurospora crassa]]'', ''[[Saccharomyces cerevisiae]]'' and ''[[Schizosaccharomyces pombe]]''; the bacterium ''[[Salmonella]] typhimurium''; the virus [[Escherichia virus T4|bacteriophage T4]],<ref>{{cite journal | vauthors = Bernstein H, Edgar RS, Denhardt GH | title = Intragenic complementation among temperature sensitive mutants of bacteriophage T4D | journal = Genetics | volume = 51 | issue = 6 | pages = 987–1002 | date = June 1965 | pmid = 14337770 | pmc = 1210828 | doi = 10.1093/genetics/51.6.987 }}</ref> an RNA virus,<ref>{{cite journal | vauthors = Smallwood S, Cevik B, Moyer SA | title = Intragenic complementation and oligomerization of the L subunit of the sendai virus RNA polymerase | journal = Virology | volume = 304 | issue = 2 | pages = 235–245 | date = December 2002 | pmid = 12504565 | doi = 10.1006/viro.2002.1720 | doi-access = free }}</ref> and humans.<ref>{{cite journal | vauthors = Rodríguez-Pombo P, Pérez-Cerdá C, Pérez B, Desviat LR, Sánchez-Pulido L, Ugarte M | title = Towards a model to explain the intragenic complementation in the heteromultimeric protein propionyl-CoA carboxylase | journal = Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease | volume = 1740 | issue = 3 | pages = 489–498 | date = June 2005 | pmid = 15949719 | doi = 10.1016/j.bbadis.2004.10.009 | doi-access = free }}</ref>  The intermolecular forces likely responsible for self-recognition and multimer formation were discussed by Jehle.<ref>{{cite journal | vauthors = Jehle H | title = Intermolecular forces and biological specificity | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 50 | issue = 3 | pages = 516–524 | date = September 1963 | pmid = 16578546 | pmc = 221211 | doi = 10.1073/pnas.50.3.516 | bibcode = 1963PNAS...50..516J | doi-access = free }}</ref>

==Assembly==
Direct interaction of two nascent proteins emerging from nearby [[ribosome]]s appears to be a general mechanism for oligomer formation.<ref name="Bertolini_2021">{{cite journal | vauthors = Bertolini M, Fenzl K, Kats I, Wruck F, Tippmann F, Schmitt J, Auburger JJ, Tans S, Bukau B, Kramer G | display-authors = 6 | title = Interactions between nascent proteins translated by adjacent ribosomes drive homomer assembly | journal = Science | volume = 371 | issue = 6524 | pages = 57–64 | date = January 2021 | pmid = 33384371 | doi = 10.1126/science.abc7151 | pmc = 7613021 | bibcode = 2021Sci...371...57B | s2cid = 229935047 | url = https://ir.amolf.nl/pub/10361 | department = primary }}</ref>  Hundreds of protein oligomers were identified that assemble in human cells by such an interaction.<ref name="Bertolini_2021" />  The most prevalent form of interaction was between the N-terminal regions of the interacting proteins.  Dimer formation appears to be able to occur independently of dedicated assembly machines.

== See also ==

* [[Structural biology]]
* [[Nucleic acid quaternary structure]]
* [[Multiprotein complex]]
* [[Biomolecular complex]]
*[[Oligomer]]s

==Notes==
{{notelist}}

== References ==
{{reflist}}

== External links ==
* [http://www.ebi.ac.uk/msd/ The Macromolecular Structure Database] (MSD) at the [[European Bioinformatics Institute]] (EBI) – Serves a list of the Probable Quaternary Structure (PQS) for every protein in the [[Protein Data Bank]] (PDB).
* [http://pqs.ebi.ac.uk/ PQS server] – PQS has not been updated since August 2009
* [http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html PISA] – The Protein Interfaces, Surfaces and Assemblies server at the [[Macromolecular Structure Database|MSD]].
* [http://www.eppic-web.org EPPIC] – Evolutionary Protein–Protein Interface Classification: evolutionary assessment of interfaces in crystal structures
* [https://archive.today/20070124184622/http://www.mrc-lmb.cam.ac.uk/genomes/elevy/3dcomplex/Home.cgi 3D complex] – Structural classification of protein complexes 
* [[Proteopedia]] – [http://www.proteopedia.org Proteopedia Home Page] The collaborative, 3D encyclopedia of proteins and other molecules.
* [[PDBWiki]] – [http://PDBWiki.Org PDBWiki Home Page] – a website for community annotation of PDB structures.
* [[ProtCID]] – [http://dunbrack2.fccc.edu/protcid ProtCID]—a database of similar protein–protein interfaces in crystal structures of homologous proteins.

{{Protein quaternary structure}}
{{Biomolecular structure}}

[[Category:Protein structure|Protein structure 4]]
[[Category:Stereochemistry]]