Editing Protein complex (section)

==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".<ref name = "Amoutzias_2010">{{ 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}}</ref>

=== 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.<ref name = "Amoutzias_2010"/> 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.<ref name="pmid12853464">{{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 }}</ref> 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.<ref name="pmid17535438">{{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 }}</ref> 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.<ref name = "Amoutzias_2010"/>

=== Fuzzy complex ===
[[Fuzzy complex|Fuzzy protein complexes]] have more than one structural form or dynamic structural disorder in the bound state.<ref name="pmid18054235">{{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 }}</ref> 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.<ref name="pmid21927770">{{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 }}</ref> 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.<ref name="pmid21620710">{{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 }}</ref>