Protein complex

Image:Barnase-barstar-1brs.png ribonuclease barnase (colored) and its inhibitor (blue) in a complex]]

Protein complex formation can activate or inhibit one or more of the complex members and in this way, protein complex formation can be similar to phosphorylation. Individual proteins can participate in a variety of protein complexes. Different complexes perform different functions, and the same complex can perform multiple functions depending on various factors. Factors include:

• Cell compartment location
• Cell cycle stage
• Cell nutritional status{{citation needed|date=April 2019}}

Many protein complexes are well understood, particularly in the model organism Saccharomyces cerevisiae (yeast). For this relatively simple organism, the study of protein complexes is now genome wide and the elucidation of most of its protein complexes is ongoing.{{citation needed|date=June 2019}} In 2021, researchers used deep learning software RoseTTAFold along with AlphaFold to solve the structures of 712 eukaryote complexes. They compared 6000 yeast proteins to those from 2026 other fungi and 4325 other eukaryotes.{{Cite web|title=AI cracks the code of protein complexes—providing a road map for new drug targets|url=https://www.science.org/content/article/ai-cracks-code-protein-complexes-providing-road-map-new-drug-targets|access-date=2021-11-14|website=www.science.org|language=en}}

If a protein can form a stable well-folded structure on its own (without any other associated protein) in vivo, then the complexes formed by such proteins are termed "non-obligate protein complexes". However, some proteins can't be found to create a stable well-folded structure alone, but can be found as a part of a protein complex which stabilizes the constituent proteins. Such protein complexes are called "obligate protein complexes".{{ cite book |vauthors=Amoutzias G, Van de Peer Y | year = 2010 | chapter = Single-Gene and Whole-Genome Duplications and the Evolution of Protein–Protein Interaction Networks. Evolutionary genomics and systems biology | pages = 413–429 | doi = 10.1002/9780470570418.ch19 | title=Evolutionary Genomics|editor-first=Gustavo|editor-last=Caetano-Anolles}}

Transient protein complexes form and break down transiently in vivo, whereas permanent complexes have a relatively long half-life. Typically, the obligate interactions (protein–protein interactions in an obligate complex) are permanent, whereas non-obligate interactions have been found to be either permanent or transient. Note that there is no clear distinction between obligate and non-obligate interaction, rather there exist a continuum between them which depends on various conditions e.g. pH, protein concentration etc.{{cite journal |vauthors=Nooren IM, Thornton JM | title = Diversity of protein interactions | journal = EMBO J. | volume = 22 | issue = 14 | pages = 3486–92 |date=July 2003 | pmid = 12853464 | pmc = 165629 | doi = 10.1093/emboj/cdg359 }} However, there are important distinctions between the properties of transient and permanent/stable interactions: stable interactions are highly conserved but transient interactions are far less conserved, interacting proteins on the two sides of a stable interaction have more tendency of being co-expressed than those of a transient interaction (in fact, co-expression probability between two transiently interacting proteins is not higher than two random proteins), and transient interactions are much less co-localized than stable interactions.{{cite journal |vauthors=Brown KR, Jurisica I | title = Unequal evolutionary conservation of human protein interactions in interologous networks | journal = Genome Biol. | volume = 8 | issue = 5 | pages = R95 | year = 2007 | pmid = 17535438 | pmc = 1929159 | doi = 10.1186/gb-2007-8-5-r95 | doi-access = free }} Though, transient by nature, transient interactions are very important for cell biology: the human interactome is enriched in such interactions, these interactions are the dominating players of gene regulation and signal transduction, and proteins with intrinsically disordered regions (IDR: regions in protein that show dynamic inter-converting structures in the native state) are found to be enriched in transient regulatory and signaling interactions.

Fuzzy protein complexes have more than one structural form or dynamic structural disorder in the bound state.{{cite journal |vauthors=Tompa P, Fuxreiter M | title = Fuzzy complexes: polymorphism and structural disorder in protein–protein interactions | journal = Trends Biochem. Sci. | volume = 33 | issue = 1 | pages = 2–8 |date=January 2008 | pmid = 18054235 | doi = 10.1016/j.tibs.2007.10.003 }} This means that proteins may not fold completely in either transient or permanent complexes. Consequently, specific complexes can have ambiguous interactions, which vary according to the environmental signals. Hence different ensembles of structures result in different (even opposite) biological functions.{{cite journal | author = Fuxreiter M | title = Fuzziness: linking regulation to protein dynamics | journal = Mol Biosyst | volume = 8 | issue = 1 | pages = 168–77 |date=January 2012 | pmid = 21927770 | doi = 10.1039/c1mb05234a }} Post-translational modifications, protein interactions or alternative splicing modulate the conformational ensembles of fuzzy complexes, to fine-tune affinity or specificity of interactions. These mechanisms are often used for regulation within the eukaryotic transcription machinery.{{cite journal |vauthors=Fuxreiter M, Simon I, Bondos S | title = Dynamic protein–DNA recognition: beyond what can be seen | journal = Trends Biochem. Sci. | volume = 36 | issue = 8 | pages = 415–23 |date=August 2011 | pmid = 21620710 | doi = 10.1016/j.tibs.2011.04.006 }}

Image:Essential proteins in yeast complexes.png

Although some early studies{{Cite journal

| pmid = 11333967

| year = 2001

| last1 = Jeong

| first1 = H

| title = Lethality and centrality in protein networks

| journal = Nature

| volume = 411

| issue = 6833

| pages = 41–2

| last2 = Mason

| first2 = S. P.

| last3 = Barabási

| first3 = A. L.

| last4 = Oltvai

| first4 = Z. N.

| doi = 10.1038/35075138

| arxiv = cond-mat/0105306

| bibcode = 2001Natur.411...41J

| s2cid = 258942

}} suggested a strong correlation between essentiality and protein interaction degree (the "centrality-lethality" rule) subsequent analyses have shown that this correlation is weak for binary or transient interactions (e.g., yeast two-hybrid).{{Cite journal

| pmid = 18719252

| year = 2008

| last1 = Yu

| first1 = H

| title = High-quality binary protein interaction map of the yeast interactome network

| journal = Science

| volume = 322

| issue = 5898

| pages = 104–10

| last2 = Braun

| first2 = P

| last3 = Yildirim

| first3 = M. A.

| last4 = Lemmens

| first4 = I

| last5 = Venkatesan

| first5 = K

| last6 = Sahalie

| first6 = J

| last7 = Hirozane-Kishikawa

| first7 = T

| last8 = Gebreab

| first8 = F

| last9 = Li

| first9 = N

| last10 = Simonis

| first10 = N

| last11 = Hao

| first11 = T

| last12 = Rual

| first12 = J. F.

| last13 = Dricot

| first13 = A

| last14 = Vazquez

| first14 = A

| last15 = Murray

| first15 = R. R.

| last16 = Simon

| first16 = C

| last17 = Tardivo

| first17 = L

| last18 = Tam

| first18 = S

| last19 = Svrzikapa

| first19 = N

| last20 = Fan

| first20 = C

| last21 = De Smet

| first21 = A. S.

| last22 = Motyl

| first22 = A

| last23 = Hudson

| first23 = M. E.

| last24 = Park

| first24 = J

| last25 = Xin

| first25 = X

| last26 = Cusick

| first26 = M. E.

| last27 = Moore

| first27 = T

| last28 = Boone

| first28 = C

| last29 = Snyder

| first29 = M

| last30 = Roth

| first30 = F. P.

| doi = 10.1126/science.1158684

| pmc = 2746753

| bibcode = 2008Sci...322..104Y

}}{{Cite journal

| pmid = 18670624

| year = 2008

| last1 = Zotenko

| first1 = E

| title = Why do hubs in the yeast protein interaction network tend to be essential: Reexamining the connection between the network topology and essentiality

| journal = PLOS Computational Biology

| volume = 4

| issue = 8

| pages = e1000140

| last2 = Mestre

| first2 = J

| last3 = O'Leary

| first3 = D. P. | author3-link = Dianne P. O'Leary

| last4 = Przytycka

| first4 = T. M. | author4-link = Teresa Przytycka

| doi = 10.1371/journal.pcbi.1000140

| pmc = 2467474

| bibcode = 2008PLSCB...4E0140Z

| doi-access = free

}} However, the correlation is robust for networks of stable co-complex interactions. In fact, a disproportionate number of essential genes belong to protein complexes.{{Cite journal

| pmid = 17605818

| year = 2007

| last1 = Hart

| first1 = G. T.

| title = A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality

| journal = BMC Bioinformatics

| volume = 8

| pages = 236

| last2 = Lee

| first2 = I

| last3 = Marcotte

| first3 = E. R.

| doi = 10.1186/1471-2105-8-236

| pmc = 1940025

| doi-access = free

}} This led to the conclusion that essentiality is a property of molecular machines (i.e. complexes) rather than individual components. Wang et al. (2009) noted that larger protein complexes are more likely to be essential, explaining why essential genes are more likely to have high co-complex interaction degree.{{Cite journal

| pmid = 19176519

| year = 2009

| last1 = Wang

| first1 = H

| title = A complex-based reconstruction of the Saccharomyces cerevisiae interactome

| journal = Molecular & Cellular Proteomics

| volume = 8

| issue = 6

| pages = 1361–81

| last2 = Kakaradov

| first2 = B

| last3 = Collins

| first3 = S. R.

| last4 = Karotki

| first4 = L

| last5 = Fiedler

| first5 = D

| last6 = Shales

| first6 = M

| last7 = Shokat

| first7 = K. M.

| last8 = Walther

| first8 = T. C.

| last9 = Krogan

| first9 = N. J.

| last10 = Koller

| first10 = D

| doi = 10.1074/mcp.M800490-MCP200

| doi-access = free

| pmc = 2690481

}} Ryan et al. (2013) referred to the observation that entire complexes appear essential as "modular essentiality".{{Cite journal

| pmid = 23661563

| year = 2013

| last1 = Ryan

| first1 = C. J.

| title = All or nothing: Protein complexes flip essentiality between distantly related eukaryotes

| journal = Genome Biology and Evolution

| volume = 5

| issue = 6

| pages = 1049–59

| last2 = Krogan

| first2 = N. J.

| last3 = Cunningham

| first3 = P

| last4 = Cagney

| first4 = G

| doi = 10.1093/gbe/evt074

| pmc = 3698920

}} These authors also showed that complexes tend to be composed of either essential or non-essential proteins rather than showing a random distribution (see Figure). However, this not an all or nothing phenomenon: only about 26% (105/401) of yeast complexes consist of solely essential or solely nonessential subunits.

In humans, genes whose protein products belong to the same complex are more likely to result in the same disease phenotype.{{Cite journal

| pmid = 18042286

| year = 2007

| last1 = Fraser

| first1 = H. B.

| title = Using protein complexes to predict phenotypic effects of gene mutation

| journal = Genome Biology

| volume = 8

| issue = 11

| pages = R252

| last2 = Plotkin

| first2 = J. B.

| doi = 10.1186/gb-2007-8-11-r252

| pmc = 2258176

| doi-access = free

}}{{Cite journal

| pmid = 17344885

| year = 2007

| last1 = Lage

| first1 = K

| title = A human phenome-interactome network of protein complexes implicated in genetic disorders

| journal = Nature Biotechnology

| volume = 25

| issue = 3

| pages = 309–16

| last2 = Karlberg

| first2 = E. O.

| last3 = Størling

| first3 = Z. M.

| last4 = Olason

| first4 = P. I.

| last5 = Pedersen

| first5 = A. G.

| last6 = Rigina

| first6 = O

| last7 = Hinsby

| first7 = A. M.

| last8 = Tümer

| first8 = Z

| last9 = Pociot

| first9 = F

| last10 = Tommerup

| first10 = N

| last11 = Moreau

| first11 = Y

| last12 = Brunak

| first12 = S

| doi = 10.1038/nbt1295

| s2cid = 5691546

| url = https://lirias.kuleuven.be/handle/123456789/74164

}}{{Cite journal

| pmid = 17204041

| year = 2007

| last1 = Oti

| first1 = M

| title = The modular nature of genetic diseases

| journal = Clinical Genetics

| volume = 71

| issue = 1

| pages = 1–11

| last2 = Brunner

| first2 = H. G.

| doi = 10.1111/j.1399-0004.2006.00708.x

| s2cid = 24615025

| doi-access = free

}}

The subunits of a multimeric protein may be identical as in a homomultimeric (homooligomeric) protein or different as in a heteromultimeric protein. Many soluble and membrane proteins form homomultimeric complexes in a cell, majority of proteins in the Protein Data Bank are homomultimeric.{{cite journal |vauthors=Hashimoto K, Nishi H, Bryant S, Panchenko AR | title = Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization | journal = Phys Biol | volume = 8 | issue = 3 | pages = 035007 |date=June 2011 | pmid = 21572178 | pmc = 3148176 | doi = 10.1088/1478-3975/8/3/035007 | bibcode = 2011PhBio...8c5007H }} Homooligomers are responsible for the diversity and specificity of many pathways, may mediate and regulate gene expression, activity of enzymes, ion channels, receptors, and cell adhesion processes.

The voltage-gated potassium channels in the plasma membrane of a neuron are heteromultimeric proteins composed of four of forty known alpha subunits. Subunits must be of the same subfamily to form the multimeric protein channel. The tertiary structure of the channel allows ions to flow through the hydrophobic plasma membrane. Connexons are an example of a homomultimeric protein composed of six identical connexins. A cluster of connexons forms the gap-junction in two neurons that transmit signals through an electrical synapse.

When multiple copies of a polypeptide encoded by a gene form a complex, this protein structure is referred to as a multimer. When a multimer is formed from polypeptides produced by two different mutant alleles 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 intragenic complementation (also called inter-allelic complementation). Intragenic complementation has been demonstrated 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 bacteriophage T4,{{cite journal |last1=Bernstein |first1=H |last2=Edgar |first2=RS |last3=Denhardt |first3=GH |title=Intragenic Complementation among Temperature Sensitive Mutants of Bacteriophage T4D |journal=Genetics |date=June 1965 |volume=51 |issue=6 |pages=987–1002 |doi=10.1093/genetics/51.6.987 |pmid=14337770 |pmc=1210828}} an RNA virusSmallwood S, Cevik B, Moyer SA. Intragenic complementation and oligomerization of the L subunit of the sendai virus RNA polymerase. Virology. 2002;304(2):235-245. {{doi|10.1006/viro.2002.1720}} and humans.Rodríguez-Pombo P, Pérez-Cerdá C, Pérez B, Desviat LR, Sánchez-Pulido L, Ugarte M. Towards a model to explain the intragenic complementation in the heteromultimeric protein propionyl-CoA carboxylase. Biochim Biophys Acta. 2005;1740(3):489-498. {{doi|10.1016/j.bbadis.2004.10.009}} In such studies, numerous mutations defective in the same gene were often isolated and mapped in a linear order on the basis of recombination frequencies to form a genetic map of the gene. Separately, the mutants were tested in pairwise combinations to measure complementation. An analysis of the results from such studies led to the conclusion that intragenic complementation, in general, arises from the interaction of differently defective polypeptide monomers to form a multimer.Crick FH, Orgel LE. The theory of inter-allelic complementation. J Mol Biol. 1964 Jan;8:161-5. {{doi|10.1016/s0022-2836(64)80156-x}}. PMID 14149958 Genes that encode multimer-forming polypeptides appear to be common. One interpretation of the data is that polypeptide monomers are often aligned in the multimer in such a way that mutant polypeptides defective at nearby sites in the genetic map tend to form a mixed multimer that functions poorly, whereas mutant polypeptides defective at distant sites tend to form a mixed multimer that functions more effectively. The intermolecular forces likely responsible for self-recognition and multimer formation were discussed by Jehle.Jehle H. Intermolecular forces and biological specificity. Proc Natl Acad Sci U S A. 1963;50(3):516-524. {{doi|10.1073/pnas.50.3.516}}

The molecular structure of protein complexes can be determined by experimental techniques such as X-ray crystallography, Single particle analysis or nuclear magnetic resonance. Increasingly the theoretical option of protein–protein docking is also becoming available. One method that is commonly used for identifying the meomplexes{{Clarify|What is this term|date=May 2017}} is immunoprecipitation. Recently, Raicu and coworkers developed a method to determine the quaternary structure of protein complexes in living cells. This method is based on the determination of pixel-level Förster resonance energy transfer (FRET) efficiency in conjunction with spectrally resolved two-photon microscope. The distribution of FRET efficiencies are simulated against different models to get the geometry and stoichiometry of the complexes.{{ cite journal | author = Raicu V, Stoneman MR, Fung R, Melnichuk M, Jansma DB, Pisterzi LF, Rath S, Fox, M, Wells, JW, Saldin DK | year = 2008 | title = Determination of supramolecular structure and spatial distribution of protein complexes in living cells. | journal = Nature Photonics | volume = 3 | issue = 2 | pages = 107–113 | doi = 10.1038/nphoton.2008.291 }}

Proper assembly of multiprotein complexes is important, since misassembly can lead to disastrous consequences.{{cite journal|last1=Dobson|first1=Christopher M|title=Protein folding and misfolding|journal=Nature|date=December 2003|volume=426|issue=6968|pages=884–90|doi=10.1038/nature02261|pmid=14685248|bibcode=2003Natur.426..884D|s2cid=1036192}} In order to study pathway assembly, researchers look at intermediate steps in the pathway. One such technique that allows one to do that is electrospray mass spectrometry, which can identify different intermediate states simultaneously. This has led to the discovery that most complexes follow an ordered assembly pathway.{{cite journal |vauthors=Marsh JA, Hernández H, Hall Z, Ahnert SE, Perica T, Robinson CV, Teichmann SA | title = Protein complexes are under evolutionary selection to assemble via ordered pathways | journal = Cell | volume = 153 | issue = 2 | pages = 461–470 | date = Apr 2013 | pmid = 23582331 | doi = 10.1016/j.cell.2013.02.044 | pmc=4009401}} In the cases where disordered assembly is possible, the change from an ordered to a disordered state leads to a transition from function to dysfunction of the complex, since disordered assembly leads to aggregation.{{cite journal|last1=Sudha|first1=Govindarajan|last2=Nussinov|first2=Ruth|last3=Srinivasan|first3=Narayanaswamy|title=An overview of recent advances in structural bioinformatics of protein–protein interactions and a guide to their principles|journal=Progress in Biophysics and Molecular Biology|year=2014|volume=116|issue=2–3|pages=141–50|doi=10.1016/j.pbiomolbio.2014.07.004|pmid=25077409}}

The structure of proteins play a role in how the multiprotein complex assembles. The interfaces between proteins can be used to predict assembly pathways. The intrinsic flexibility of proteins also plays a role: more flexible proteins allow for a greater surface area available for interaction.{{cite journal|last1=Marsh|first1=Joseph|last2=Teichmann|first2=Sarah A|title=Protein flexibility facilitates quaternary structure assembly and evolution|journal=PLOS Biology|date=May 2014|volume=12|issue=5|doi=10.1371/journal.pbio.1001870|pmid=24866000|pages=e1001870|pmc=4035275 |doi-access=free }}

While assembly is a different process from disassembly, the two are reversible in both homomeric and heteromeric complexes. Thus, the overall process can be referred to as (dis)assembly.

In homomultimeric complexes, the homomeric proteins assemble in a way that mimics evolution. That is, an intermediate in the assembly process is present in the complex's evolutionary history.{{cite journal|last1=Levy|first1=Emmanuel D|last2=Boeri Erba|first2=Elisabetta|last3=Robinson|first3=Carol V|last4=Teichmann|first4=Sarah A|title=Assembly reflects evolution of protein complexes|journal=Nature|date=July 2008|volume=453|issue=7199|pages=1262–5|doi=10.1038/nature06942|pmid=18563089|pmc=2658002|bibcode=2008Natur.453.1262L}}

The opposite phenomenon is observed in heteromultimeric complexes, where gene fusion occurs in a manner that preserves the original assembly pathway.

• Heterotetramer
• Biomolecular complex
• Protein subunit

{{reflist|35em}}

• {{MeshName|Multiprotein+Complexes}}

{{Protein topics}}

{{Multienzyme complexes}}