Functional roles of transiently and intrinsically disordered regions within proteins

Proteins are structurally heterogeneous and comprise folded regions with variable conformational stabilities and intrinsically disordered protein regions that do not have well‐folded structures. Even small, well‐folded single‐domain proteins are structurally heterogeneous and contain multiple foldon units with different conformational stability. Although the ability of many intrinsically disordered protein regions to undergo at least partial folding at interaction with specific binding partners is a well‐established fact, recent studies have revealed that functions of some ordered proteins rely on the decrease in the amount of their ordered structure and require local or even global functional unfolding. This functional unfolding is induced by transient alterations in protein environment or by modification of protein structure and can be reversed as soon as the environment is restored or the modification is removed. Therefore, the important features of these conditionally disordered protein regions (or unfoldons) are the induced nature and the transient character of their disorder. In other words, structurally any protein can be described as a modular assembly of foldons, inducible foldons, semi‐foldons, nonfoldons and unfoldons. Obviously, differently ordered/disordered proteins and protein regions can possess very different functional repertoires. This review represents some of the key functions of transiently and intrinsically disordered protein regions.

[1]  Michail Yu. Lobanov,et al.  Library of Disordered Patterns in 3D Protein Structures , 2010, PLoS Comput. Biol..

[2]  P. Tompa Intrinsically disordered proteins: a 10-year recap. , 2012, Trends in biochemical sciences.

[3]  H. Dyson,et al.  Coupling of folding and binding for unstructured proteins. , 2002, Current opinion in structural biology.

[4]  Christopher J. Oldfield,et al.  Intrinsically disordered protein. , 2001, Journal of molecular graphics & modelling.

[5]  A. Mohan MoRFs A Dataset of Molecular Recognition Features , 2006 .

[6]  A. Keith Dunker,et al.  Mining α-Helix-Forming Molecular Recognition Features with Cross Species Sequence Alignments† , 2007 .

[7]  R. Pappu,et al.  An intrinsically disordered linker plays a critical role in bacterial cell division. , 2015, Seminars in cell & developmental biology.

[8]  P. Tompa Intrinsically unstructured proteins. , 2002, Trends in biochemical sciences.

[9]  J. Forman-Kay,et al.  Regulatory R region of the CFTR chloride channel is a dynamic integrator of phospho-dependent intra- and intermolecular interactions , 2013, Proceedings of the National Academy of Sciences.

[10]  J. Richardson,et al.  Multiscale conformational heterogeneity in staphylococcal protein a: possible determinant of functional plasticity. , 2014, Structure.

[11]  L. Mayne,et al.  The nature of protein folding pathways , 2014, Proceedings of the National Academy of Sciences.

[12]  V. Uversky,et al.  Why are “natively unfolded” proteins unstructured under physiologic conditions? , 2000, Proteins.

[13]  S. Englander,et al.  A unified mechanism for protein folding: Predetermined pathways with optional errors , 2007, Protein science : a publication of the Protein Society.

[14]  Vladimir N. Uversky,et al.  Conditionally and transiently disordered proteins: awakening cryptic disorder to regulate protein function. , 2014, Chemical reviews.

[15]  H. Pospiech,et al.  The intrinsically disordered amino-terminal region of human RecQL4: multiple DNA-binding domains confer annealing, strand exchange and G4 DNA binding , 2014, Nucleic acids research.

[16]  H. Chan,et al.  Polyelectrostatic interactions of disordered ligands suggest a physical basis for ultrasensitivity , 2007, Proceedings of the National Academy of Sciences.

[17]  L. Hengst,et al.  p27 binds cyclin–CDK complexes through a sequential mechanism involving binding-induced protein folding , 2004, Nature Structural &Molecular Biology.

[18]  S Walter Englander,et al.  Protein folding: the stepwise assembly of foldon units. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[19]  G. Siuzdak,et al.  Molecular basis for the specificity of p27 toward cyclin-dependent kinases that regulate cell division. , 2005, Journal of molecular biology.

[20]  V. Uversky,et al.  Apo‐parvalbumin as an intrinsically disordered protein , 2008, Proteins.

[21]  D. Koshland Application of a Theory of Enzyme Specificity to Protein Synthesis. , 1958, Proceedings of the National Academy of Sciences of the United States of America.

[22]  H. Vogel The Merck Frosst Award Lecture 1994. Calmodulin: a versatile calcium mediator protein. , 1994, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[23]  V. Uversky Multitude of binding modes attainable by intrinsically disordered proteins: a portrait gallery of disorder-based complexes. , 2011, Chemical Society reviews.

[24]  S Walter Englander,et al.  Protein folding: Independent unrelated pathways or predetermined pathway with optional errors , 2008, Proceedings of the National Academy of Sciences.

[25]  E. Fischer Einfluss der Configuration auf die Wirkung der Enzyme , 1894 .

[26]  Veerendra Kumar,et al.  Linkers in the structural biology of protein–protein interactions , 2013, Protein science : a publication of the Protein Society.

[27]  R. Perham,et al.  Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. , 2000, Annual review of biochemistry.

[28]  K. Bessonov,et al.  The Effects of Threonine Phosphorylation on the Stability and Dynamics of the Central Molecular Switch Region of 18.5-kDa Myelin Basic Protein , 2013, PloS one.

[29]  P E Wright,et al.  Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2-bound state: conformational disorder mediates binding diversity. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[30]  S Walter Englander,et al.  Protein folding and misfolding: mechanism and principles , 2007, Quarterly Reviews of Biophysics.

[31]  J. Evans,et al.  AP7, a partially disordered pseudo C-RING protein, is capable of forming stabilized aragonite in vitro. , 2009, Biochemistry.

[32]  Sarel J. Fleishman,et al.  Intrinsically disordered C-terminal segments of voltage-activated potassium channels: a possible fishing rod-like mechanism for channel binding to scaffold proteins , 2006, Bioinform..

[33]  B. Ramakrishnan,et al.  Structure and Function of -1,4-Galactosyltransferase , 2008 .

[34]  Hans J. Vogel,et al.  Calmodulin: a versatile calcium mediator protein , 1994 .

[35]  H. Dyson,et al.  Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. , 1999, Journal of molecular biology.

[36]  S. Englander,et al.  How cytochrome c folds, and why: submolecular foldon units and their stepwise sequential stabilization. , 2004, Journal of molecular biology.

[37]  C. Brown,et al.  Intrinsic protein disorder in complete genomes. , 2000, Genome informatics. Workshop on Genome Informatics.

[38]  P. Tompa,et al.  Introducing protein intrinsic disorder. , 2014, Chemical reviews.

[39]  S. Ciurli,et al.  The conformational response to Zn(II) and Ni(II) binding of Sporosarcina pasteurii UreG, an intrinsically disordered GTPase , 2014, JBIC Journal of Biological Inorganic Chemistry.

[40]  R. Lemieux,et al.  How Emil Fischer was led to the lock and key concept for enzyme specificity. , 1994, Advances in carbohydrate chemistry and biochemistry.

[41]  V. Uversky,et al.  Intrinsic disorder in S100 proteins. , 2011, Molecular bioSystems.

[42]  A. Dunker,et al.  Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life , 2012, Journal of biomolecular structure & dynamics.

[43]  A Keith Dunker,et al.  Intrinsic disorder in scaffold proteins: getting more from less. , 2008, Progress in biophysics and molecular biology.

[44]  Wei-Chiang Shen,et al.  Fusion protein linkers: property, design and functionality. , 2013, Advanced drug delivery reviews.

[45]  A. Kidera,et al.  Disorder-to-order transition of an intrinsically disordered region of sortase revealed by multiscale enhanced sampling. , 2012, Journal of the American Chemical Society.

[46]  M. Oliveberg,et al.  Malleability of protein folding pathways: a simple reason for complex behaviour. , 2007, Current opinion in structural biology.

[47]  A Keith Dunker,et al.  Intrinsically disordered proteins and intrinsically disordered protein regions. , 2014, Annual review of biochemistry.

[48]  Claudio Luchinat,et al.  Insights into Domain–Domain Motions in Proteins and RNA from Solution NMR , 2014, Accounts of chemical research.

[49]  R. Tu,et al.  Engineering of an environmentally responsive beta roll peptide for use as a calcium-dependent cross-linking domain for peptide hydrogel formation. , 2012, Biomacromolecules.

[50]  Susan S. Taylor,et al.  Allosteric linkers in cAMP signalling. , 2014, Biochemical Society transactions.

[51]  Marc S. Cortese,et al.  Coupled folding and binding with α-helix-forming molecular recognition elements , 2005 .

[52]  M. Periasamy,et al.  The C‐terminal calcium‐sensitive disordered motifs regulate isoform‐specific polymerization characteristics of calsequestrin , 2015, Biopolymers.

[53]  Olga Abian,et al.  NS3 Protease from Hepatitis C Virus: Biophysical Studies on an Intrinsically Disordered Protein Domain , 2013, International journal of molecular sciences.

[54]  J. Evans,et al.  A pearl protein self-assembles to form protein complexes that amplify mineralization. , 2013, Biochemistry.

[55]  A Keith Dunker,et al.  Mining alpha-helix-forming molecular recognition features with cross species sequence alignments. , 2007, Biochemistry.

[56]  V. Uversky Intrinsically Disordered Proteins , 2014 .

[57]  L. Kay,et al.  Protein dynamics and conformational disorder in molecular recognition , 2009, Journal of molecular recognition : JMR.

[58]  Predrag Radivojac,et al.  The structural and functional signatures of proteins that undergo multiple events of post‐translational modification , 2014, Protein science : a publication of the Protein Society.

[59]  B. Ramakrishnan,et al.  Substrate-induced conformational changes in glycosyltransferases. , 2005, Trends in biochemical sciences.

[60]  S. Englander,et al.  Functional role of a protein foldon—An Ω‐loop foldon controls the alkaline transition in ferricytochrome c , 2005, Proteins.

[61]  Marc S. Cortese,et al.  Coupled folding and binding with alpha-helix-forming molecular recognition elements. , 2005, Biochemistry.

[62]  E. Heinzle,et al.  Zinc ion-induced domain organization in metallo-beta-lactamases: a flexible "zinc arm" for rapid metal ion transfer? , 2009, The Journal of biological chemistry.

[63]  A Keith Dunker,et al.  Characterization of molecular recognition features, MoRFs, and their binding partners. , 2007, Journal of proteome research.

[64]  J. S. Sodhi,et al.  Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. , 2004, Journal of molecular biology.

[65]  R. Nussinov,et al.  Dynamic allostery: linkers are not merely flexible. , 2011, Structure.

[66]  Christopher J. Oldfield,et al.  Classification of Intrinsically Disordered Regions and Proteins , 2014, Chemical reviews.

[67]  P. Bjorkman,et al.  Design and characterization of structured protein linkers with differing flexibilities , 2014, Protein engineering, design & selection : PEDS.

[68]  Benjamin A. Shoemaker,et al.  Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[69]  Mingjie Zhang,et al.  Molecular mechanisms of calmodulin's functional versatility , 1998 .

[70]  A. Dunker,et al.  Understanding protein non-folding. , 2010, Biochimica et biophysica acta.

[71]  K. Nagata,et al.  Intrinsically disordered regions of nucleophosmin/B23 regulate its RNA binding activity through their inter- and intra-molecular association , 2013, Nucleic acids research.

[72]  L. Iakoucheva,et al.  Intrinsic disorder in cell-signaling and cancer-associated proteins. , 2002, Journal of molecular biology.

[73]  V. Uversky Unusual biophysics of intrinsically disordered proteins. , 2013, Biochimica et biophysica acta.

[74]  S. Boonen,et al.  The hinge region in androgen receptor control , 2012, Molecular and Cellular Endocrinology.

[75]  Robert Kiss,et al.  High levels of structural disorder in scaffold proteins as exemplified by a novel neuronal protein, CASK‐interactive protein1 , 2009, The FEBS journal.

[76]  A. Wand,et al.  The foldon substructure of staphylococcal nuclease. , 2008, Journal of molecular biology.

[77]  Vladimir N Uversky,et al.  The most important thing is the tail: Multitudinous functionalities of intrinsically disordered protein termini , 2013, FEBS letters.

[78]  V. Uversky A decade and a half of protein intrinsic disorder: Biology still waits for physics , 2013, Protein science : a publication of the Protein Society.

[79]  J. Fetrow Omega loops; nonregular secondary structures significant in protein function and stability , 1995, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[80]  B. Boys,et al.  Effects of zinc binding on the structure and dynamics of the intrinsically disordered protein prothymosin alpha: evidence for metalation as an entropic switch. , 2007, Biochemistry.

[81]  Marc S. Cortese,et al.  Comparing and combining predictors of mostly disordered proteins. , 2005, Biochemistry.

[82]  E. Mancini,et al.  Conformational flexibility of the oncogenic protein LMO2 primes the formation of the multi-protein transcription complex , 2014, Scientific Reports.

[83]  T. Yuan,et al.  Molecular mechanisms of calmodulin's functional versatility. , 1998, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[84]  Birgit Eisenhaber,et al.  Posttranslational modifications and subcellular localization signals: indicators of sequence regions without inherent 3D structure? , 2007, Current protein & peptide science.

[85]  Lukasz Kurgan,et al.  Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life , 2014, Cellular and Molecular Life Sciences.

[86]  Ramya Viswanathan,et al.  One small step for Mot1; one giant leap for other Swi2/Snf2 enzymes? , 2011, Biochimica et biophysica acta.

[87]  László Buday,et al.  Functional classification of scaffold proteins and related molecules , 2010, The FEBS journal.

[88]  M. Delepierre,et al.  RTX Calcium Binding Motifs Are Intrinsically Disordered in the Absence of Calcium , 2009, Journal of Biological Chemistry.