A protein complex or multiprotein complex is a group of two or more associated
polypeptide chain
Peptides (, ) are short chains of amino acids linked by peptide bonds. Long chains of amino acids are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides.
...
s. Protein complexes are distinct from
multienzyme complex Multienzyme complex contains several copies of one or several enzymes ( polypeptide chains) packed into one assembly. Multienzyme complex carries out a single or a series of biochemical reactions taking place in the cells. It allows to segregate cer ...
es, in which multiple
catalytic domains are found in a single polypeptide chain.
Protein complexes are a form of
quaternary structure. Protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
s in a protein complex are linked by
non-covalent
In chemistry, a non-covalent interaction differs from a covalent bond in that it does not involve the sharing of electrons, but rather involves more dispersed variations of electromagnetic interactions between molecules or within a molecule. The ...
protein–protein interaction
Protein–protein interactions (PPIs) are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding and th ...
s. These complexes are a cornerstone of many (if not most) biological processes. The cell is seen to be composed of modular supramolecular complexes, each of which performs an independent, discrete biological function.
Through proximity, the speed and selectivity of binding interactions between enzymatic complex and substrates can be vastly improved, leading to higher cellular efficiency. Many of the techniques used to enter cells and isolate proteins are inherently disruptive to such large complexes, complicating the task of determining the components of a complex.
Examples of protein complexes include the
proteasome
Proteasomes are protein complexes which degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds. Enzymes that help such reactions are called proteases.
Proteasomes are part of a major mechanism by w ...
for molecular degradation and most
RNA polymerase
In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that synthesizes RNA from a DNA template.
Using the enzyme helicase, RNAP locally opens the ...
s. In stable complexes, large hydrophobic interfaces between proteins typically bury surface areas larger than 2500 square
Ås.
Function
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
In chemistry, phosphorylation is the attachment of a phosphate group to a molecule or an ion. This process and its inverse, dephosphorylation, are common in biology and could be driven by natural selection. Text was copied from this source, wh ...
. 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
Many protein complexes are well understood, particularly in the model organism ''
Saccharomyces cerevisiae
''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungus microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have been o ...
'' (yeast). For this relatively simple organism, the study of protein complexes is now
genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...
wide and the elucidation of most of its protein complexes is ongoing. In 2021, researchers used
deep learning software RoseTTAFold along with
AlphaFold
AlphaFold is an artificial intelligence (AI) program developed by DeepMind, a subsidiary of Alphabet, which performs predictions of protein structure. The program is designed as a deep learning system.
AlphaFold AI software has had two major ve ...
to solve the structures of 712
eukaryote complexes. They compared 6000 yeast proteins to those from 2026 other fungi and 4325 other eukaryotes.
Types of protein complexes
Obligate vs non-obligate protein complex
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".
Transient vs permanent/stable protein complex
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.
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.
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 complex
Fuzzy protein complexes have more than one structural form or dynamic structural disorder in the bound state.
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 ensemble of structures result in different (even opposite) biological functions.
Post-translational modifications, protein interactions or alternative splicing modulate the
conformational ensembles
In computational chemistry, conformational ensembles, also known as structural ensembles, are experimentally constrained computational models describing the structure of intrinsically unstructured proteins. Such proteins are flexible in nature, ...
of fuzzy complexes, to fine-tune affinity or specificity of interactions. These mechanisms are often used for regulation within the
eukaryotic transcription
Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of transportable complementary RNA replica. Gene transcription occurs in both eukaryotic and prokaryotic cells. ...
machinery.
Essential proteins in protein complexes
Although some early studies
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
Two-hybrid screening (originally known as yeast two-hybrid system or Y2H) is a molecular biology technique used to discover protein–protein interactions (PPIs) and protein–DNA interactions by testing for physical interactions (such as bind ...
).
However, the correlation is robust for networks of stable co-complex interactions. In fact, a disproportionate number of
essential genes
Essential genes are indispensable genes for organisms to grow and reproduce offspring under certain environment. However, being ''essential'' is highly dependent on the circumstances in which an organism lives. For instance, a gene required to dige ...
belong to protein complexes.
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.
Ryan et al. (2013) referred to the observation that entire complexes appear essential as "modular essentiality".
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.
Homomultimeric and heteromultimeric proteins
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
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cry ...
are homomultimeric.
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
Voltage-gated potassium channels (VGKCs) are transmembrane channels specific for potassium and sensitive to voltage changes in the cell's membrane potential. During action potentials, they play a crucial role in returning the depolarized ce ...
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.
Connexon
In biology, a connexon, also known as a connexin hemichannel, is an assembly of six proteins called connexins that form the pore for a gap junction between the cytoplasm of two adjacent cells. This channel allows for bidirectional flow of ions and ...
s are an example of a homomultimeric protein composed of six identical
connexin
Connexins (Cx)TC# 1.A.24, or gap junction proteins, are structurally related transmembrane proteins that assemble to form vertebrate gap junctions. An entirely different family of proteins, the innexins, form gap junctions in invertebrates. Ea ...
s. A cluster of connexons forms the gap-junction in two neurons that transmit signals through an electrical synapse.
Intragenic complementation
When multiple copies of a polypeptide encoded by a
gene
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
form a complex, this protein structure is referred to as a multimer. When a multimer is formed from polypeptides produced by two different
mutant
In biology, and especially in genetics, a mutant is an organism or a new genetic character arising or resulting from an instance of mutation, which is generally an alteration of the DNA sequence of the genome or chromosome of an organism. It ...
allele
An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is a variation of the same sequence of nucleotides at the same place on a long DNA molecule, as described in leading textbooks on genetics and evolution.
::"The chro ...
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
intragenic complementation
Epistasis is a phenomenon in genetics in which the effect of a gene mutation is dependent on the presence or absence of mutations in one or more other genes, respectively termed modifier genes. In other words, the effect of the mutation is dep ...
(also called inter-allelic complementation). Intragenic complementation has been demonstrated in many different genes in a variety of organisms including the fungi ''
Neurospora crassa
''Neurospora crassa'' is a type of red bread mold of the phylum Ascomycota. The genus name, meaning "nerve spore" in Greek, refers to the characteristic striations on the spores. The first published account of this fungus was from an infestation ...
'', ''
Saccharomyces cerevisiae
''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungus microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have been o ...
'' and ''
Schizosaccharomyces pombe
''Schizosaccharomyces pombe'', also called "fission yeast", is a species of yeast used in traditional brewing and as a model organism in molecular and cell biology. It is a unicellular eukaryote, whose cells are rod-shaped. Cells typically measur ...
''; the bacterium ''
Salmonella typhimurium''; the virus
bacteriophage T4
Escherichia virus T4 is a species of bacteriophages that infect ''Escherichia coli'' bacteria. It is a double-stranded DNA virus in the subfamily '' Tevenvirinae'' from the family Myoviridae. T4 is capable of undergoing only a lytic lifecycle ...
, an RNA virus and humans. In such studies, numerous
mutation
In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, mi ...
s 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. 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.
Structure determination
The
molecular structure
Molecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that deter ...
of protein complexes can be determined by experimental techniques such as
X-ray crystallography
X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles ...
,
Single particle analysis
Single particle analysis is a group of related computerized image processing techniques used to analyze images from transmission electron microscopy (TEM). These methods were developed to improve and extend the information obtainable from TEM imag ...
or
nuclear magnetic resonance
Nuclear magnetic resonance (NMR) is a physical phenomenon in which nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field (in the near field) and respond by producing an electromagnetic signal with a ...
. Increasingly the theoretical option of
protein–protein docking is also becoming available. One method that is commonly used for identifying the meomplexes 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
Förster resonance energy transfer (FRET), fluorescence resonance energy transfer, resonance energy transfer (RET) or electronic energy transfer (EET) is a mechanism describing energy transfer between two light-sensitive molecules (chromophores). ...
(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.
Assembly
Proper assembly of multiprotein complexes is important, since misassembly can lead to disastrous consequences. 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.
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.
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.
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.
Evolutionary significance of multiprotein complex assembly
In homomultimeric complexes, the
homomeric
Something that is composed of one repeating subunit, the antonym of heteromeric. It is often used to describe proteins made up of multiple identical repeating polypeptide chains e.g. beta galactosidase
β-Galactosidase (EC 3.2.1.23, lactase, ...
proteins assemble in a way that mimics evolution. That is, an intermediate in the assembly process is present in the complex's evolutionary history.
The opposite phenomenon is observed in heteromultimeric complexes, where gene fusion occurs in a manner that preserves the original assembly pathway.
See also
*
Heterotetramer
A tetrameric protein is a protein with a quaternary structure of four subunits (tetrameric). Homotetramers have four identical subunits (such as glutathione S-transferase), and heterotetramers are complexes of different subunits. A tetramer ca ...
*
Biomolecular complex
A biomolecule or biological molecule is a loosely used term for molecules present in organisms that are essential to one or more typically biological processes, such as cell division, morphogenesis, or development. Biomolecules include large ...
*
Protein subunit
In structural biology, a protein subunit is a polypeptide chain or single protein molecule that assembles (or "''coassembles''") with others to form a protein complex.
Large assemblies of proteins such as viruses often use a small number of ty ...
References
External links
*
{{Multienzyme complexes
*