# Fuzzy complex

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[[File:Sic1.png|thumb|upright|[NMR](/source/Nuclear_magnetic_resonance) structure of the [cyclin-dependent kinase inhibitor](/source/cyclin-dependent_kinase_inhibitor_protein) [Sic1](/source/Sic1) with the [ubiquitin ligase](/source/ubiquitin_ligase) [Cdc4](/source/Cell_division_control_protein_4) (grey). Out of the nine [phosphorylation](/source/phosphorylation) sites of Sic 1 (spheres) the contacts with T45 and S76 are shown (orange and blue).]]
[[File:Ubx.png|thumb|300px|The fuzzy linker region (shown by dotted line) of the [Ultrabithorax](/source/Ultrabithorax) [transcription factor](/source/transcription_factor) (orange) connects the [homeodomain](/source/homeodomain_fold) with the [Extradenticle](/source/PBX1) [homeodomain](/source/homeodomain_fold) (blue) (PDB code 1bi). [Alternative splicing](/source/Alternative_splicing) modulates the length of the fuzzy region and thus its DNA (grey) [binding affinity](/source/binding_affinity). Other regulatory fuzzy regions of Ultrabithorax are also shown by dotted lines.]]

'''Fuzzy complexes''' are [protein complexes](/source/Multiprotein_complexes), where [structural](/source/protein_structure) [ambiguity](/source/ambiguity) or [multiplicity](/source/multiplicity_(mathematics)) exists and is required for biological [function](/source/function_(biology)).<ref name=FC1>{{cite journal |doi=10.1016/j.tibs.2007.10.003 |pmid=18054235 |title=Fuzzy complexes: Polymorphism and structural disorder in protein–protein interactions |journal=Trends in Biochemical Sciences |volume=33 |issue=1 |pages=2–8 |year=2008 |last1=Tompa |first1=Peter |last2=Fuxreiter |first2=Monika }}</ref><ref name=FC2>Fuxreiter, M. & Tompa, P. (2011) Fuzziness: Structural Disorder in Protein Complexes Austin, New York.{{pn|date=February 2018}}</ref> Alteration, truncation or removal of [conformationally](/source/protein_structure) ambiguous regions impacts the activity of the corresponding [complex](/source/multiprotein_complexes).<ref name=FC3>{{cite journal |doi=10.1126/science.1111915 |pmid=15994560 |title=Variable Control of Ets-1 DNA Binding by Multiple Phosphates in an Unstructured Region |journal=Science |volume=309 |issue=5731 |pages=142–5 |year=2005 |last1=Pufall |first1=M. A |last2=Lee |first2=Gregory M |last3=Nelson |first3=Mary L |last4=Kang |first4=Hyun-Seo |last5=Velyvis |first5=Algirdas |last6=Kay |first6=Lewis E |last7=McIntosh |first7=Lawrence P |last8=Graves |first8=Barbara J |bibcode=2005Sci...309..142P |doi-access=free }}</ref><ref name=FC4>{{cite journal |doi=10.1126/science.1120941 |pmid=16424299 |title=The Ste5 Scaffold Allosterically Modulates Signaling Output of the Yeast Mating Pathway |journal=Science |volume=311 |issue=5762 |pages=822–6 |year=2006 |last1=Bhattacharyya |first1=R. P |last2=Reményi |first2=Attila |last3=Good |first3=Matthew C |last4=Bashor |first4=Caleb J |last5=Falick |first5=Arnold M |last6=Lim |first6=Wendell A |bibcode=2006Sci...311..822B |s2cid=13882487 |doi-access=free }}</ref><ref name=FC5>{{cite journal |doi=10.1016/j.jmb.2009.05.059 |pmid=19481089 |pmc=2739810 |title=Internal Regulatory Interactions Determine DNA Binding Specificity by a Hox Transcription Factor |journal=Journal of Molecular Biology |volume=390 |issue=4 |pages=760–74 |year=2009 |last1=Liu |first1=Ying |last2=Matthews |first2=Kathleen S |last3=Bondos |first3=Sarah E }}</ref> Fuzzy complexes are generally formed by [intrinsically disordered proteins](/source/intrinsically_unstructured_proteins).<ref name=FC6>{{cite journal |pmid=9697202 |url=http://psb.stanford.edu/psb-online/proceedings/psb98/abstracts/p437.html |year=1998 |last1=Romero |first1=P |title=Thousands of proteins likely to have long disordered regions |journal=Pacific Symposium on Biocomputing |pages=437–48 |last2=Obradovic |first2=Z |last3=Kissinger |first3=C. R |last4=Villafranca |first4=J. E |last5=Garner |first5=E |last6=Guilliot |first6=S |last7=Dunker |first7=A. K }}</ref><ref name=FC7>{{cite journal |doi=10.1006/jmbi.1999.3110 |pmid=10550212 |title=Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm |journal=Journal of Molecular Biology |volume=293 |issue=2 |pages=321–31 |year=1999 |last1=Wright |first1=Peter E |author-link2=Jane Dyson|last2=Dyson |first2=H. Jane }}</ref> Structural multiplicity usually underlies functional multiplicity of protein complexes <ref name=FC8>{{cite journal |doi=10.1016/j.jmb.2007.12.016 |pmid=18177895 |pmc=2350195 |title=Role of Intrinsic Flexibility in Signal Transduction Mediated by the Cell Cycle Regulator, p27Kip1 |journal=Journal of Molecular Biology |volume=376 |issue=3 |pages=827–38 |year=2008 |last1=Galea |first1=Charles A |last2=Nourse |first2=Amanda |last3=Wang |first3=Yuefeng |last4=Sivakolundu |first4=Sivashankar G |last5=Heller |first5=William T |last6=Kriwacki |first6=Richard W }}</ref><ref name=FC9>{{cite journal |doi=10.1038/nchembio.127 |pmid=19008886 |pmc=2921704 |title=Malleable machines take shape in eukaryotic transcriptional regulation |journal=Nature Chemical Biology |volume=4 |issue=12 |pages=728–37 |year=2008 |last1=Fuxreiter |first1=Monika |last2=Tompa |first2=Peter |last3=Simon |first3=István |last4=Uversky |first4=Vladimir N |last5=Hansen |first5=Jeffrey C |last6=Asturias |first6=Francisco J }}</ref><ref name=FC10>{{cite journal |doi=10.1038/nchembio.536 |pmid=21358637 |pmc=3124363 |title=Intrinsic disorder mediates the diverse regulatory functions of the Cdk inhibitor p21 |journal=Nature Chemical Biology |volume=7 |issue=4 |pages=214–21 |year=2011 |last1=Wang |first1=Yuefeng |last2=Fisher |first2=John C |last3=Mathew |first3=Rose |last4=Ou |first4=Li |last5=Otieno |first5=Steve |last6=Sublet |first6=Jack |last7=Xiao |first7=Limin |last8=Chen |first8=Jianhan |last9=Roussel |first9=Martine F |last10=Kriwacki |first10=Richard W }}</ref> following a [fuzzy logic](/source/fuzzy_logic). Distinct binding modes of the [nucleosome](/source/nucleosome) are also regarded as a special case of fuzziness.<ref name=FC11>{{cite journal |doi=10.1371/journal.pone.0012984 |pmid=20886052 |pmc=2945322 |title=Weakly Positioned Nucleosomes Enhance the Transcriptional Competency of Chromatin |journal=PLOS ONE |volume=5 |issue=9 |article-number=e12984 |year=2010 |last1=Belch |first1=Yaakov |last2=Yang |first2=Jingyi |last3=Liu |first3=Yang |last4=Malkaram |first4=Sridhar A |last5=Liu |first5=Rong |last6=Riethoven |first6=Jean-Jack M |last7=Ladunga |first7=Istvan |bibcode=2010PLoSO...512984B |doi-access=free }}</ref><ref name=FC12>{{cite journal |doi=10.1128/MCB.05276-11 |pmid=21896781 |pmc=3209338 |title=Evolution of Nucleosome Occupancy: Conservation of Global Properties and Divergence of Gene-Specific Patterns |journal=Molecular and Cellular Biology |volume=31 |issue=21 |pages=4348–55 |year=2011 |last1=Tsui |first1=K |last2=Dubuis |first2=S |last3=Gebbia |first3=M |last4=Morse |first4=R. H |last5=Barkai |first5=N |last6=Tirosh |first6=I |last7=Nislow |first7=C }}</ref>

== Historical background ==
For almost 50 years [molecular biology](/source/molecular_biology) was based on two dogmas: (i) equating biological function of the protein with a unique three-dimensional [structure](/source/protein_structure) and (ii) assuming exquisite specificity in protein [complexes](/source/multiprotein_complexes). Specificity/selectivity is ensured by unambiguous set of [interactions](/source/protein-protein_interaction) formed between the protein and its ligand (another [protein](/source/protein), [DNA](/source/DNA), [RNA](/source/RNA) or [small molecule](/source/small_molecule)). Many [protein complexes](/source/multiprotein_complexes) however, contain functionally important/critical regions, which remain highly dynamic in the complex or adopt different [conformations](/source/protein_structure).<ref name=FC13>{{cite journal |doi=10.1039/c1mb05234a |pmid=21927770 |title=Fuzziness: Linking regulation to protein dynamics |journal=Molecular BioSystems |volume=8 |issue=1 |pages=168–77 |year=2012 |last1=Fuxreiter |first1=Monika |hdl=2437/124519 |hdl-access=free }}</ref> This phenomenon is defined fuzziness. The most pertinent example is the [cyclin-dependent kinase inhibitor](/source/cyclin-dependent_kinase_inhibitor_protein) [Sic1](/source/Sic1), which binds to the SCF subunit of [Cdc4](/source/Cell_division_control_protein_4) in a [phosphorylation](/source/phosphorylation) dependent manner.<ref name=FC14>{{cite journal |doi=10.1038/35107009 |pmid=11734846 |title=Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication |journal=Nature |volume=414 |issue=6863 |pages=514–21 |year=2001 |last1=Nash |first1=Piers |last2=Tang |first2=Xiaojing |last3=Orlicky |first3=Stephen |last4=Chen |first4=Qinghua |last5=Gertler |first5=Frank B |last6=Mendenhall |first6=Michael D |last7=Sicheri |first7=Frank |last8=Pawson |first8=Tony |last9=Tyers |first9=Mike |bibcode=2001Natur.414..514N |s2cid=16924667 }}</ref> No regular [secondary structures](/source/secondary_structures) are gained upon [phosphorylation](/source/phosphorylation) and the different phosphorylation sites interchange in the complex.<ref name=FC15>{{cite journal |doi=10.1073/pnas.0809222105 |jstor=25465359 |pmid=19008353 |pmc=2582940 |title=Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor |journal=Proceedings of the National Academy of Sciences |volume=105 |issue=46 |pages=17772–7 |year=2008 |last1=Mittag |first1=T |last2=Orlicky |first2=S |last3=Choy |first3=W.-Y |last4=Tang |first4=X |last5=Lin |first5=H |last6=Sicheri |first6=F |last7=Kay |first7=L. E |last8=Tyers |first8=M |last9=Forman-Kay |first9=J. D |bibcode=2008PNAS..10517772M |doi-access=free }}</ref>

== Classification of fuzzy complexes ==
Structural ambiguity in protein complexes covers a wide spectrum.<ref name=FC1 /> In a polymorphic complex, the protein adopts two or more different conformations upon binding to the same partner, and these conformations can be resolved.<ref name=FC16>{{cite journal |doi=10.1038/emboj.2011.461 |pmid=22193718 |pmc=3280557 |title=How a single residue in individual β-thymosin/WH2 domains controls their functions in actin assembly |journal=The EMBO Journal |volume=31 |issue=4 |pages=1000–13 |year=2012 |last1=Didry |first1=Dominique |last2=Cantrelle |first2=Francois-Xavier |last3=Husson |first3=Clotilde |last4=Roblin |first4=Pierre |last5=Moorthy |first5=Anna M Eswara |last6=Perez |first6=Javier |last7=Le Clainche |first7=Christophe |last8=Hertzog |first8=Maud |last9=Guittet |first9=Eric |last10=Carlier |first10=Marie-France |last11=Van Heijenoort |first11=Carine |last12=Renault |first12=Louis }}</ref> Clamp,<ref name=FC17>{{cite journal |doi=10.1006/jmbi.2000.3642 |pmid=10764582 |title=Structural basis of recognition of monopartite and bipartite nuclear localization sequences by mammalian importin-α |journal=Journal of Molecular Biology |volume=297 |issue=5 |pages=1183–94 |year=2000 |last1=Fontes |first1=Marcos R.M |last2=Teh |first2=Trazel |last3=Kobe |first3=Bostjan }}</ref> flanking <ref name=FC18>{{cite journal |doi=10.1074/jbc.M207361200 |pmid=12196545 |title=Roles of Phosphorylation and Helix Propensity in the Binding of the KIX Domain of CREB-binding Protein by Constitutive (c-Myb) and Inducible (CREB) Activators |journal=Journal of Biological Chemistry |volume=277 |issue=44 |pages=42241–8 |year=2002 |last1=Zor |first1=Tsaffrir |last2=Mayr |first2=Bernhard M |last3=Dyson |first3=H. Jane |last4=Montminy |first4=Marc R |last5=Wright |first5=Peter E |doi-access=free }}</ref><ref name=FC19>{{cite journal |doi=10.1016/S1097-2765(03)00115-1 |pmid=12718882 |title=Structural Basis for the Molecular Recognition between Human Splicing Factors U2AF65 and SF1/mBBP |journal=Molecular Cell |volume=11 |issue=4 |pages=965–76 |year=2003 |last1=Selenko |first1=Philipp |last2=Gregorovic |first2=Goran |last3=Sprangers |first3=Remco |last4=Stier |first4=Gunter |last5=Rhani |first5=Zakaria |last6=Krämer |first6=Angela |last7=Sattler |first7=Michael |doi-access=free }}</ref> and random complexes<ref name=FC20>{{cite journal |doi=10.1074/jbc.M310948200 |pmid=14625282 |title=Quantitative Observation of Backbone Disorder in Native Elastin |journal=Journal of Biological Chemistry |volume=279 |issue=9 |pages=7982–7 |year=2004 |last1=Pometun |first1=Maxim S |last2=Chekmenev |first2=Eduard Y |last3=Wittebort |first3=Richard J |doi-access=free }}</ref><ref name=FC21>{{cite journal |doi=10.1021/bi035900h |pmid=14967045 |title=Homooligomerization of the Cytoplasmic Domain of the T Cell Receptor ζ Chain and of Other Proteins Containing the Immunoreceptor Tyrosine-Based Activation Motif |journal=Biochemistry |volume=43 |issue=7 |pages=2049–61 |year=2004 |last1=Sigalov |first1=Alexander |last2=Aivazian |first2=Dikran |last3=Stern |first3=Lawrence }}</ref> are dynamic, where ambiguous conformations interchange with each other and cannot be resolved. [Interactions](/source/protein-protein_interactions) in fuzzy complexes are usually mediated by [short motifs](/source/short_linear_motif).<ref name=FC22>{{cite journal |doi=10.1016/j.tibs.2010.10.002 |pmid=21146412 |title=How viruses hijack cell regulation |journal=Trends in Biochemical Sciences |volume=36 |issue=3 |pages=159–69 |year=2011 |last1=Davey |first1=Norman E |last2=Travé |first2=Gilles |last3=Gibson |first3=Toby J }}</ref> Flanking regions are tolerant to sequence changes as long as the [amino acid](/source/amino_acid) composition is maintained, for example in case of linker [histone](/source/histone) C-terminal domains <ref name=FC24>{{cite journal |doi=10.1021/bi801636y |pmid=19072710 |pmc=2644900 |title=Chromatin Condensing Functions of the Linker Histone C-Terminal Domain Are Mediated by Specific Amino Acid Composition and Intrinsic Protein Disorder |journal=Biochemistry |volume=48 |issue=1 |pages=164–72 |year=2009 |last1=Lu |first1=Xu |last2=Hamkalo |first2=Barbara |last3=Parseghian |first3=Missag H |last4=Hansen |first4=Jeffrey C }}</ref> and H4 [histone](/source/histone) N-terminal domains.<ref name=FC25>{{cite journal |doi=10.1074/jbc.M109.011288 |pmid=19395382 |pmc=2719306 |title=Determinants of Histone H4 N-terminal Domain Function during Nucleosomal Array Oligomerization |journal=Journal of Biological Chemistry |volume=284 |issue=25 |pages=16716–22 |year=2009 |last1=McBryant |first1=Steven J |last2=Klonoski |first2=Joshua |last3=Sorensen |first3=Troy C |last4=Norskog |first4=Sarah S |last5=Williams |first5=Sere |last6=Resch |first6=Michael G |last7=Toombs |first7=James A |last8=Hobdey |first8=Sarah E |last9=Hansen |first9=Jeffrey C |doi-access=free }}</ref>

== Regulatory pathways via fuzzy regions ==
Fuzzy regions modulate the conformational equilibrium <ref name=FC26>{{cite journal |doi=10.1021/bi0500729 |pmid=16171389 |title=Structural and Thermodynamical Characterization of the Complete p21 Gene Product of Max |journal=Biochemistry |volume=44 |issue=38 |pages=12746–58 |year=2005 |last1=Naud |first1=Jean-François |last2=McDuff |first2=François-Olivier |last3=Sauvé |first3=Simon |last4=Montagne |first4=Martin |last5=Webb |first5=Bradley A |last6=Smith |first6=Steven P |last7=Chabot |first7=Benoit |last8=Lavigne |first8=Pierre }}</ref> or flexibility <ref name=FC3 /><ref name=FC27>{{cite journal |doi=10.1016/j.jmb.2008.07.064 |pmid=18692067 |pmc=4808631 |title=The Affinity of Ets-1 for DNA is Modulated by Phosphorylation Through Transient Interactions of an Unstructured Region |journal=Journal of Molecular Biology |volume=382 |issue=4 |pages=1014–30 |year=2008 |last1=Lee |first1=Gregory M |last2=Pufall |first2=Miles A |last3=Meeker |first3=Charles A |last4=Kang |first4=Hyun-Seo |last5=Graves |first5=Barbara J |last6=McIntosh |first6=Lawrence P }}</ref> of the binding interface via [transient interactions](/source/multiprotein_complex).<ref name=FC28>{{cite journal |doi=10.1016/j.tibs.2011.04.006 |pmid=21620710 |title=Dynamic protein–DNA recognition: Beyond what can be seen |journal=Trends in Biochemical Sciences |volume=36 |issue=8 |pages=415–23 |year=2011 |last1=Fuxreiter |first1=Monika |last2=Simon |first2=Istvan |last3=Bondos |first3=Sarah |hdl=2437/124518 |hdl-access=free }}</ref> Dynamic regions can also compete with binding sites<ref name=FC29>{{cite journal |doi=10.1016/j.jmb.2007.09.075 |pmid=17988686 |title=Mapping Intramolecular Interactions between Domains in HMGB1 using a Tail-truncation Approach |journal=Journal of Molecular Biology |volume=374 |issue=5 |pages=1286–97 |year=2007 |last1=Watson |first1=Matthew |last2=Stott |first2=Katherine |last3=Thomas |first3=Jean O }}</ref> or tether them to the target.<ref name=FC30>{{cite journal |doi=10.1080/07391102.2005.10507052 |pmid=16060685 |title=Secondary Structure and Dynamics of an Intrinsically Unstructured Linker Domain |journal=Journal of Biomolecular Structure and Dynamics |volume=23 |issue=2 |pages=113–24 |year=2005 |last1=Olson |first1=Katie E |last2=Narayanaswami |first2=Pranesh |last3=Vise |first3=Pamela D |last4=Lowry |first4=David F |last5=Wold |first5=Marc S |last6=Daughdrill |first6=Gary W |s2cid=37429006 }}</ref> Modifications of fuzzy regions by further interactions,<ref name=FC8 /><ref name=FC31>{{cite journal |doi=10.1016/j.bpj.2008.10.003 |pmid=19134474 |pmc=2710047 |title=Induced Secondary Structure and Polymorphism in an Intrinsically Disordered Structural Linker of the CNS: Solid-State NMR and FTIR Spectroscopy of Myelin Basic Protein Bound to Actin |journal=Biophysical Journal |volume=96 |issue=1 |pages=180–91 |year=2009 |last1=Ahmed |first1=Mumdooh A.M |last2=Bamm |first2=Vladimir V |last3=Shi |first3=Lichi |last4=Steiner-Mosonyi |first4=Marta |last5=Dawson |first5=John F |last6=Brown |first6=Leonid |last7=Harauz |first7=George |last8=Ladizhansky |first8=Vladimir |bibcode=2009BpJ....96..180A }}</ref> or [posttranslational modifications](/source/posttranslational_modifications)<ref name=FC32>{{cite journal |doi=10.1111/j.1742-4658.2006.05165.x |pmid=16689930 |title=Gradual phosphorylation regulates PC4 coactivator function |journal=FEBS Journal |volume=273 |issue=7 |pages=1430–44 |year=2006 |last1=Jonker |first1=Hendrik R. A |last2=Wechselberger |first2=Rainer W |last3=Pinkse |first3=Martijn |last4=Kaptein |first4=Robert |last5=Folkers |first5=Gert E |hdl=1874/19762 |s2cid=38856641 |hdl-access=free }}</ref><ref name=FC33>{{cite journal |doi=10.1074/jbc.M109.001958 |pmid=19605348 |pmc=2782050 |title=Phosphorylated Intrinsically Disordered Region of FACT Masks Its Nucleosomal DNA Binding Elements |journal=Journal of Biological Chemistry |volume=284 |issue=36 |pages=24610–21 |year=2009 |last1=Tsunaka |first1=Yasuo |last2=Toga |first2=Junko |last3=Yamaguchi |first3=Hiroto |last4=Tate |first4=Shin-Ichi |last5=Hirose |first5=Susumu |last6=Morikawa |first6=Kosuke |doi-access=free }}</ref> impact [binding affinity](/source/binding_affinity) or specificity. [Alternative splicing](/source/Alternative_splicing) can modulate the length of fuzzy regions resulting in context-dependent binding (e.g. [tissue](/source/tissue_(biology))-specificity) on the complex.<ref name=FC34>{{cite journal |doi=10.1074/jbc.M212057200 |pmid=12816948 |title=Regulation of the NEDD8 Conjugation System by a Splicing Variant, NUB1L |journal=Journal of Biological Chemistry |volume=278 |issue=35 |pages=32905–13 |year=2003 |last1=Tanaka |first1=Tomoaki |last2=Kawashima |first2=Hidenori |last3=Yeh |first3=Edward T. H |last4=Kamitani |first4=Tetsu |doi-access=free }}</ref><ref name=FC35>{{cite journal |doi=10.1074/jbc.M800375200 |pmid=18508761 |pmc=2475714 |title=Multiple Intrinsically Disordered Sequences Alter DNA Binding by the Homeodomain of the ''Drosophila'' ''Hox'' Protein Ultrabithorax |journal=Journal of Biological Chemistry |volume=283 |issue=30 |pages=20874–87 |year=2008 |last1=Liu |first1=Ying |last2=Matthews |first2=Kathleen S |last3=Bondos |first3=Sarah E |doi-access=free }}</ref><ref name=FC36>{{cite journal |doi=10.1073/pnas.1100990108 |pmid=21788518 |pmc=3156161 |title=Evolution of a derived protein-protein interaction between HoxA11 and Foxo1a in mammals caused by changes in intramolecular regulation |journal=Proceedings of the National Academy of Sciences |volume=108 |issue=32 |pages=E414–20 |year=2011 |last1=Brayer |first1=K. J |last2=Lynch |first2=V. J |last3=Wagner |first3=G. P |bibcode=2011PNAS..108E.414B |doi-access=free }}</ref> [EGF](/source/Epidermal_growth_factor)/[MAPK](/source/Mitogen-activated_protein_kinase), [TGF-β](/source/transforming_growth_factor_beta) and [WNT/Wingless](/source/Wnt_signaling_pathway) [signaling pathways](/source/signal_transduction) employ tissue-specific fuzzy regions.

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== References ==
{{reflist|35em}}

Category:Protein structure
Category:Stereochemistry

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Adapted from the Wikipedia article [Fuzzy complex](https://en.wikipedia.org/wiki/Fuzzy_complex) by Wikipedia contributors ([contributor history](https://en.wikipedia.org/wiki/Fuzzy_complex?action=history)). Available under [Creative Commons Attribution-ShareAlike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/). Changes may have been made.