Multiprotein complex

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Bacillus amyloliquefaciens proteins in a complex

A multiprotein complex (or protein complex) is a group of two or more associated polypeptide chains. If the different polypeptide chains contain different protein domain, the resulting multiprotein complex can have multiple catalytic functions. This is distinct from a multienzyme polypeptide, in which multiple catalytic domains are found in a single polypeptide chain.1

Protein complexes are a form of quaternary structure. Proteins in a protein complex are linked by non-covalent protein–protein interactions, and different protein complexes have different degrees of stability over time. These complexes are a cornerstone of many (if not most) biological processes and together they form various types of molecular machinery that perform a vast array of biological functions. Increasingly, scientists view the cell as composed of modular supramolecular complexes, each of which performs an independent, discrete biological function.2

Through proximity, the speed and selectivity of binding interactions between enzymatic complex and substrates can be vastly improved, leading to higher cellular efficiency. Unfortunately, many of the techniques used to break open cells and isolate proteins are inherently disruptive to such large complexes, so their protein complexes within the cell may be even more widespread than can be detected. Examples include the proteasome for molecular degradation, the metabolon for oxidative energy generation, and the ribosome for protein synthesis. In stable complexes, large hydrophobic interfaces between proteins typically bury surface areas larger than 2500 square angstroms.3

Function

Protein complex formation sometimes serves to 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 the formation of a variety of different protein complexes. Different complexes perform different functions, and the same complex can perform very different functions that depend on a variety of factors. Some of these factors are:

  • Which cellular compartment the complex exists in when it is contained
  • Which stage in the cell cycle the complexes are present
  • The nutritional status of the cell
  • Others

Many protein complexes are well understood, particularly in the model organism Saccharomyces cerevisiae (a strain of yeast). For this relatively simple organism, the study of protein complexes is now being performed genome wide and the elucidation of most protein complexes of the yeast is undergoing.

Types of protein complexes

Obligate vs non-obligate protein complex

If a protein can form stable crystal structure of its own (without any other associated protein) in vivo, then the complexes formed by such proteins are called "non-obligate protein complex". On the other hand, some proteins can't be found to create a crystal structure alone, but can be found as a part of a protein complex which creates a stable crystal structure. Such protein complexes are called "obligate protein complex".4

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.4 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.5 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.6 Though, transient by nature, transient interactions are very important for cell biology: 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.4

Fuzzy complex

Fuzzy protein complexes have more than one structural forms or dynamic structural disorder in the bound state.7 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.8 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.9

Essential proteins in protein complexes

Essential proteins in yeast complexes occur much less randomly than expected by chance. Modified after Ryan et al. 201310

Although some early studies11 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).1213 However, the correlation is robust for networks of stable cocomplex interactions. In fact, a disproportionate number of essential genes belong to protein complexes.14 This led to the conclusion that essentiality is a property of molecular machines (i.e. complexes) rather than individual components.14 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 cocomplex interaction degree.15 Ryan et al. (2013) referred to the observation that entire complexes appear essential as "modular essentiality".10 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.10

In humans, genes whose protein products belong to the same complex are more likely to result in the same disease phenotype.161718

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 are homomultimeric.19 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.

Structure determination

The molecular structure of protein complexes can be determined by experimental techniques such as X-ray crystallography 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 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 Forster 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.20

See also

References

  1. ^ Price NC, Stevens L (1999). Fundamentals of enzymology: The cell and molecular biology of catalytic protein. Oxford ; New York: Oxford University Press. ISBN 0-19-850229-X. 
  2. ^ Hartwell LH, Hopfield JJ, Leibler S, Murray AW (December 1999). "From molecular to modular cell biology". Nature 402 (6761 Suppl): C47–52. doi:10.1038/35011540. PMID 10591225. 
  3. ^ Pereira-Leal JB, Levy ED, Teichmann SA (March 2006). "The origins and evolution of functional modules: lessons from protein complexes". Philos. Trans. R. Soc. Lond., B, Biol. Sci. 361 (1467): 507–17. doi:10.1098/rstb.2005.1807. PMC 1609335. PMID 16524839. 
  4. ^ a b c Amoutzias G, Van de Peer Y (2010). Single-Gene and Whole-Genome Duplications and the Evolution of Protein–Protein Interaction Networks. Evolutionary genomics and systems biology. pp. 413–429. doi:10.1002/9780470570418.ch19. 
  5. ^ Nooren IM, Thornton JM (July 2003). "Diversity of protein-protein interactions". EMBO J. 22 (14): 3486–92. doi:10.1093/emboj/cdg359. PMC 165629. PMID 12853464. 
  6. ^ Brown KR, Jurisica I (2007). "Unequal evolutionary conservation of human protein interactions in interologous networks". Genome Biol. 8 (5): R95. doi:10.1186/gb-2007-8-5-r95. PMC 1929159. PMID 17535438. 
  7. ^ Tompa P, Fuxreiter M (January 2008). "Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions". Trends Biochem. Sci. 33 (1): 2–8. doi:10.1016/j.tibs.2007.10.003. PMID 18054235. 
  8. ^ Fuxreiter M (January 2012). "Fuzziness: linking regulation to protein dynamics". Mol Biosyst 8 (1): 168–77. doi:10.1039/c1mb05234a. PMID 21927770. 
  9. ^ Fuxreiter M, Simon I, Bondos S (August 2011). "Dynamic protein-DNA recognition: beyond what can be seen". Trends Biochem. Sci. 36 (8): 415–23. doi:10.1016/j.tibs.2011.04.006. PMID 21620710. 
  10. ^ a b c Ryan, C. J.; Krogan, N. J.; Cunningham, P; Cagney, G (2013). "All or nothing: Protein complexes flip essentiality between distantly related eukaryotes". Genome Biology and Evolution 5 (6): 1049–59. doi:10.1093/gbe/evt074. PMC 3698920. PMID 23661563.  
  11. ^ Jeong, H; Mason, S. P.; Barabási, A. L.; Oltvai, Z. N. (2001). "Lethality and centrality in protein networks". Nature 411 (6833): 41–2. doi:10.1038/35075138. PMID 11333967.  
  12. ^ Yu, H; Braun, P; Yildirim, M. A.; Lemmens, I; Venkatesan, K; Sahalie, J; Hirozane-Kishikawa, T; Gebreab, F; Li, N; Simonis, N; Hao, T; Rual, J. F.; Dricot, A; Vazquez, A; Murray, R. R.; Simon, C; Tardivo, L; Tam, S; Svrzikapa, N; Fan, C; De Smet, A. S.; Motyl, A; Hudson, M. E.; Park, J; Xin, X; Cusick, M. E.; Moore, T; Boone, C; Snyder, M; Roth, F. P. (2008). "High-quality binary protein interaction map of the yeast interactome network". Science 322 (5898): 104–10. doi:10.1126/science.1158684. PMC 2746753. PMID 18719252.  
  13. ^ Zotenko, E; Mestre, J; O'Leary, D. P.; Przytycka, T. M. (2008). "Why do hubs in the yeast protein interaction network tend to be essential: Reexamining the connection between the network topology and essentiality". PLoS Computational Biology 4 (8): e1000140. doi:10.1371/journal.pcbi.1000140. PMC 2467474. PMID 18670624.  
  14. ^ a b Hart, G. T.; Lee, I; Marcotte, E. R. (2007). "A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality". BMC Bioinformatics 8: 236. doi:10.1186/1471-2105-8-236. PMC 1940025. PMID 17605818.  
  15. ^ Wang, H; Kakaradov, B; Collins, S. R.; Karotki, L; Fiedler, D; Shales, M; Shokat, K. M.; Walther, T. C.; Krogan, N. J.; Koller, D (2009). "A complex-based reconstruction of the Saccharomyces cerevisiae interactome". Molecular & Cellular Proteomics 8 (6): 1361–81. doi:10.1074/mcp.M800490-MCP200. PMC 2690481. PMID 19176519.  
  16. ^ Fraser, H. B.; Plotkin, J. B. (2007). "Using protein complexes to predict phenotypic effects of gene mutation". Genome Biology 8 (11): R252. doi:10.1186/gb-2007-8-11-r252. PMC 2258176. PMID 18042286.  
  17. ^ Lage, K; Karlberg, E. O.; Størling, Z. M.; Olason, P. I.; Pedersen, A. G.; Rigina, O; Hinsby, A. M.; Tümer, Z; Pociot, F; Tommerup, N; Moreau, Y; Brunak, S (2007). "A human phenome-interactome network of protein complexes implicated in genetic disorders". Nature Biotechnology 25 (3): 309–16. doi:10.1038/nbt1295. PMID 17344885.  
  18. ^ Oti, M; Brunner, H. G. (2007). "The modular nature of genetic diseases". Clinical Genetics 71 (1): 1–11. doi:10.1111/j.1399-0004.2006.00708.x. PMID 17204041.  
  19. ^ Hashimoto K, Nishi H, Bryant S, Panchenko AR (June 2011). "Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization". Phys Biol 8 (3): 035007. doi:10.1088/1478-3975/8/3/035007. PMC 3148176. PMID 21572178. 
  20. ^ Raicu V, Stoneman MR, Fung R, Melnichuk M, Jansma DB, Pisterzi LF, Rath S, Fox, M, Wells, JW, Saldin DK (2008). "Determination of supramolecular structure and spatial distribution of protein complexes in living cells.". Nature Photonics 3: 107–113. doi:10.1038/nphoton.2008.291. 

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