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Intrinsically Disordered Proteins logoLink to Intrinsically Disordered Proteins
. 2017 Oct 16;5(1):e1327757. doi: 10.1080/21690707.2017.1327757

Paradoxes and wonders of intrinsic disorder: Stability of instability

Vladimir N Uversky a,b,
PMCID: PMC6149434  PMID: 30250771

ABSTRACT

This article continues a series of short comments on the paradoxes and wonders of the protein intrinsic disorder phenomenon by introducing the “stability of instability” paradox. Intrinsically disordered proteins (IDPs) are characterized by the lack of stable 3D-structure, and, as a result, have an exceptional ability to sustain exposure to extremely harsh environmental conditions (an illustration of the “you cannot break what is already broken” principle). Extended IDPs are known to possess extreme thermal and acid stability and are able either to keep their functionality under these extreme conditions or to rapidly regain their functionality after returning to the normal conditions. Furthermore, sturdiness of intrinsic disorder and its capability to “ignore” harsh conditions provides some interesting and important advantages to its carriers, at the molecular (e.g., the cell wall-anchored accumulation-associated protein playing a crucial role in intercellular adhesion within the biofilm of Staphylococcus epidermidis), supramolecular (e.g., protein complexes, biologic liquid-liquid phase transitions, and proteinaceous membrane-less organelles), and organismal levels (e.g., the recently popularized case of the microscopic animals, tardigrades, or water bears, that use intrinsically disordered proteins to survive desiccation).

KEYWORDS: conformational stability, intrinsically disordered protein, liquid-liquid phase transition, membrane-less organelle, protein-protein interaction

Introduction

Recent years clearly witnessed increased penetrance of the intrinsic disorder concept into the different branches of protein science.1-7 Because of their lack of stable structures, exceptional spatiotemporal heterogeneity, outstanding conformational plasticity, ability to be precisely controlled and regulated, and capability to conduct and juggle multiple jobs, intrinsically disordered proteins (IDPs) and hybrid proteins possessing ordered domains and intrinsically disordered protein regions (IDPRs)8 are specialized in unique biologic functions,1-7,9-38 which are extending far beyond mostly catalytic activities traditionally assigned to the proteins within the “one gene – one structure – one function” paradigm.1,3,10-12,18,39-41 In fact, among intrinsic disorder-based biologic functions are regulation of various cellular pathways, binding promiscuity, involvement in diverse signaling processes, and participation in cell protection, protein protection, controlled cell death, and cellular homeostasis.1-7,10-41 Several recent studies (mostly of computational nature) revealed that IDPs are very common in various proteomes, with the proteome content of IDPs being typically an indicator of both evolution and adaptation to the environment.1,18,42-46 In fact, the percentage of IDPs in proteomes is increasing from bacteria and archaebacteria, to fungi, and to eukaryotic organisms, thereby reflecting the evolutionary importance of intrinsic disorder.42,44-46 On the other hand, the role of disorder in adaptation to the environment can be illustrated by the fact that the salt, pH, and/or temperature-tolerant bacteria and Achaea typically contain more IDPs than their mesophilic and salt/pH-sensitive counterparts.31,47

Many aspects related to the structure, conformational behavior and functionality of IDPs look rather strange from the viewpoint of “traditional” ordered proteins.48,49 To give a brief outlook of various paradoxes and wonders of intrinsic disorder, a series of short comments on different unusual features of IDPs was started in the Intrinsically Disordered Proteins journal. The first comment in this series was dedicated to the introduction of the “prevalence of exceptionality” paradox, where a progression was shown in understanding of the natural abundance of IDPs from the early days, when they were taken as rare exceptions, to the current days, when the prevalence of IDPs/IDPRs in various proteomes and biological processes is well accepted.50 In the second comment, the “complexity of simplicity” paradox was introduced to indicate how the multilevel simplicity of IDPs ranging from the reduced amino acid αbet and simplified sequences containing multiple sequence repeats to their structural primitivity and inability to spontaneously fold into the ordered structures is translated into the exceptional structural and functional complexity of disorder carrying proteins.51 This article continues the aforementioned series by introducing the “stability of instability” paradox.

Intrinsic disorder from the traditional viewpoint of protein conformational stability

A set of specific non-covalent interactions (conformational forces) of different nature, such as hydrogen bonds, hydrophobic interactions, electrostatic interactions, van der Waals interactions, etc., is responsible for the ability of a typical globular/ordered protein to have a unique 3-D structure For ordered proteins, the presence of the “protein folding” code was proposed, where, under the physiological conditions, the correct folding of a globular protein into its unique biologically active structure is determined by its amino acid sequence.52 The presence of unique and stable structure in ordered proteins implies that it can be cooperatively unfolded into a random coil-like conformation under the variety of conditions.53-56 Such unfolding process of a small, single domain, globular protein is typically described by a sharp sigmoidal curve representing a case of the all-or-none transition, where a cooperatively unfoldable unit includes the whole protein molecule; i.e., no intermediate states can be observed in the transition region. In fact, based on the analysis of the urea- or guanidinium chloride-induced unfolding transitions in ordered globular proteins it has been concluded that the steepness of the corresponding unfolding curves (that can be expressed as the difference in the numbers of denaturant molecules ‘bound’ to the initial and final states in the denaturant-induced transitions, Δνeff) depends strongly on whether a given protein has a rigid tertiary structure (i.e., it is ordered) and undergoes the O→U transition from ordered (O) to unfolded (U) state or exists as a molten globule (MG) and undergoes the MG→U transition.57,58 For example, for a protein with the molecular mass of 30 kDa, ΔνeffO→U = 23.1, whereas ΔνeffMG→U = 8.2.59

Inasmuch the ability of an ordered protein to fold into unique 3D-structure is encoded in its sequence, the lack of rigid globular structures in IDPs/IDPRs is also encoded in the specific features of their amino acid sequences, such as enrichment in the disorder-promoting residues (Pro, Arg, Gly, Gln, Ser, Glu, Lys, and Ala) and depletion in the order-promoting amino acids, such as Cys, Trp, Tyr, Phe Ile, Leu, Val, and Asn.18,60-66 Obviously, due to their highly biased amino acid sequences IDPs/IDPRs might possess some unusual conformational responses to changes in their environment. Although the denaturant-induced unfolding of a native molten globule is a low cooperativity transition that can be described by a shallow sigmoidal curve,59,67 due the low content of the residual structure in native pre-molten globules or native coils their denaturant-induced structural changes are typically non-cooperative and seen as monotonous feature-less curves.59 In other words, from the traditional view of protein conformational stability, IDPs/IDPRs are characterized by low structural stability, which is reflected in low steepness of their unfolding transitions induced by strong denaturants or even in the complete lack of the sigmodal shape of these unfolding curves.59 This structural instability is supported by the well-known fact of high sensitivity of IDPs/IDPRs to proteolytic degradation.68-77

High resilience of intrinsic disorder

Although lacking stable structure, possessing non-cooperative unfolding behavior, and showing high sensitivity to proteolysis, one of the most intriguing biophysical properties ascribed to highly disordered proteins is their extraordinary resilience, where an IDP can sustain exposure to the extremely harsh environmental conditions, being able either to keep its functionality under these extreme conditions or to rapidly regain it after returning to normal conditions.48,49 An illustrative example of such behavior is given by a “funny protein” prothymosin α,48 which triggered my interest to the intrinsically disordered proteins by its unusual ability to be unharmed by the prolonged exposure to harsh conditions (activity of the protein was not affected by boiling for a few days). Because of its highly biased amino acid composition (no aromatic or cysteine residues and overall low hydrophobicity level compensated by extremely high (∼60%) content of charged residues), prothymosin α behaved as a highly disordered coil-like chain, thereby providing illustration of the “one cannot break what is already broken” concept.78

Prothymosin α is not an exception, and several other extended IDPs, such as p21, p27, α-synuclein, and phosphodiesterase γ subunit, were shown to possess high resistance toward heat denaturation and aggregation, being virtually unaltered by heating to 90°C.78-88 Curiously, this resistance to thermal aggregation has been used for purification of these proteins,83,89-92 and the indifference to heat treatment was proposed as an analytical tool for evaluation of the abundance of extended IDPs in various proteomes.93,94

Furthermore, extended IDPs, being characterized by high percentages of charged residues and low overall hydrophobicity, do not undergo large-scale structural changes at low pH95 and remain soluble under these extreme conditions.78,96 Furthermore, a careful analysis of proteins which do not precipitate during perchloric acid (PCA) or trichloroacetic acid (TCA) treatment of cell extracts revealed that many of these proteins are totally unstructured.97

In contrast to this remarkable pH resistance of IDPs, ordered proteins commonly undergo denaturation or unfolding in solution with extreme pH.98-101 Since ordered proteins contain high fractions of hydrophobic residues, their pH-denatured or unfolded conformations contain numerous solvent exposed hydrophobic residues, which are normally buried inside the folded structures. This exposure of hydrophobic residues defines the “stickiness” of the partially folded pH-induced conformations of globular proteins, leading to their aggregation and precipitation. Based on these observations it has been suggested that indifference to acid treatment represents one of the characteristic properties of extended IDPs that can be used for the isolation of extended IDPs. In fact, it was shown that substantial enrichment of IDPs in the soluble fraction can be achieved after the acid treatment, and, therefore, such PCA/TCA pretreatment can be exploited to develop standard protocols for isolating and studying IDPs on a proteomic scale.97

Besides being highly resistant to the exposure to harsh environmental conditions (high temperature or extreme pH values), extended IDPs are also characterized by the “turned out” conformational response to the changes in their environment, where they gain some structure under conditions resulting in denaturation or even unfolding of ordered proteins, such as heat, extreme pH, and desiccation.18,48,59 For example, the temperature-induced formation of secondary structure (and not partial unfolding, which is typical of ordered globular proteins) was reported for α-synuclein,102 636–771 fragment of caldesmon,88 γ-subunit of phosphodiesterase,103 the extracellular domain of nerve growth factor,104 αs-casein,105 and many other IDPs. Furthermore, complete reversibility and independence on protein concentration was reported for these heat-induced partial folding of IDPs, indicating the intramolecular nature of this structural transition. These structure-forming potential of elevated temperatures was attributed to the peculiarities of the amino acid compositions of the extended IDPs (namely, their overall low level of hydrophobicity) leading to their “turned out” response to heating: higher temperatures caused the increase in strength of the hydrophobic interaction, leading to a stronger hydrophobic attraction, which is the major driving force for protein folding.48,49,102

Similar “turned out” response to changes in pH was reported for several extended IDPs, such as prothymosin α,78 α-synuclein,102 pig calpastatin domain I,106 histidine rich protein II,107 naturally occurring human peptide LL-37,108 and several other extended IDPs. Here, partial folding of extended IDPs (which are characterized by the high net charge at neutral pH) in solutions with extremely high or low pH values can be attributed to the minimization of the overall net charge, thereby decreasing charge-charge intramolecular repulsion and permitting hydrophobic-driven collapse to the partially-folded conformation.48,49

Some biological uses of the “stability of instability” of intrinsic disorder

There are multiple way of how Nature is using stability of instability paradox introduced in this article. Sections below provide description of several cases where sturdiness of intrinsic disorder provides remarkable benefits to individual proteins (bacterial accumulation-associated protein, Aap), as well as serves as means for the mechanical regulation of the macroscopic properties of the networks formed by the neurofilament proteins, assembly of stable complexes (e.g., elastin), liquid-liquid phase transitions residing at the core of the formation of various membrane-less organelles, and defines desiccation stability of organisms.

Die-hard proline-rich extended stalk of the bacterial accumulation-associated protein

Since IDPs and IDPRs possess specific and rather unusual (from the viewpoint of ordered proteins) structural properties,48,49 it is not too surprising to find that they are uniquely suitable for orchestrating some surprising (again, from the viewpoint of ordered proteins) functions.109-111 One of the illustrative examples of such atypical function is given by an intrinsically disordered C-terminal portion of the cell wall-anchored (CWA) accumulation-associated protein (Aap) that plays a crucial role in the intercellular adhesion within the biofilm of Staphylococcus epidermidis.112 Aap is one several staphylococcal CWAs that are anchored to the peptidoglycans located at the surface of bacterial cell.113 This multifunctional protein contributes to both the primary attachment phase and the establishment of intercellular connections by forming fibrils on the cell surface.112 Structurally, Aap consists of multiple repetitive blocks. For example, besides the globular lectin domain, the N-terminally located A-domain of Aap contains 11 short (16-residue-long) A-repeats. This A-domain is responsible for the initiation of the biofilm and is proteolytically removed to promote biofilm accumulation and growth.112 The B-repeat superdomain, which follows the A-domain, contains 5–17 nearly identical 128-residue-long B-repeats that are used in the Zn2 +-mediated antiparallel self-assembly responsible for the intercellular adhesion.114,115 Finally, the C-terminal tail of Aap includes a 135-residue-long proline/glycine-rich region (PGR) containing a set of 18 nearly identical AEPGKP repeats followed by the LPXTG motif that is used for the sortase A-mediated covalent linkage of Aap to the peptidoglycan layer of the bacterial cell wall.116 Recent comprehensive multilevel biophysical analysis of the structural properties and conformational behavior of the PGR domain of Aap revealed that this intrinsically disordered region is highly extended (e.g., in SDS-PAGE experiments, PGR migrated as a species with an apparent molecular mass more than 10-fold higher than predicted, and in SEC and SLS experiments, this domain also showed very large Rh values (37.06 ± 1.1 Å and 38.39 ± 0.9 Å according to SEC and DLS analyses, respectively) that were noticeably exceeding those expected for native coil of the molecular mass of 13.2 kDa (30.2 Å) consistent with a highly elongated shape), likely due to the very high content of the polyproline type II (PPII) helical structure.117 Importantly and rather unexpectedly, PGR showed remarkable sturdiness and was able to resist temperature-induced compaction and solvent-induced α-helix formation.117 It was hypothesized that this ability of the PGR to keep an extended state irrespectively of the environmental conditions helps this region in fulfilling its biologic function as an extended stalk that pushes Aap out and away from the bacterial cell wall.117

Phosphorylation controllable expansion and collapse of the neurofilament network

Neurofilaments are the crucial constituents of the neuronal cytoskeleton that play several pivotal roles in supporting the axon structure and controlling its diameter.118 Morphologically, neurofilaments are 10 nm wide bottlebrush-like filaments assembled from the 3 intermediate filament proteins, the light or lowest (∼70kDa), the medium or middle (∼150kDa), the heavy or highest chains/subunits (∼210kDa) and designated as NF-L, NF-M, and NF-H, respectively.119,120 The neurofilament backbone is assembled from the N-terminal head and rod domains of NF-L, NF-M, and NF-H that are ∼100 and ∼300 residue long respectively and are rather similar among the NF-L, NF-M, and NF-H proteins. The C-terminal tails of these proteins are highly disordered and serve as entropic bristles protruding outwards the neurofilament body, providing means for the bottlebrush topology of the neurofilaments, and mediating the inter-filament interactions and controlling the neuronal cytoskeletal organization.121-123 These tails of the neurofilament proteins differ from each other by their length and amino acid composition. For example human NF-L, NF-M, and NF-H proteins contain 147, 504 and 613 residues, respectively.

The C-tails of NF-M and NF-H undergo extensive phosphorylation mostly at the serine residues located within the Lys-Ser-Pro (KSP) repeat motifs that results in the dramatic changes of their charge distributions (e.g., dephosphorylated NF-M and NF-H C-tails have total charges of −46 and −7, whereas, total charge of their completely phosphorylated forms are −87 and −97, respectively).124,125 It was expected that charge alterations induced by phosphorylation of these C-tails could play a role on controlling changes in the inter-filament spacing, the axonal caliber, and protein transport.122,126-129 This is because phosphorylation would increase electrostatic repulsion between the excess charges thereby promoting lateral extension of neurofilament tails. This hypothesis was proven to be wrong by a recent comprehensive analysis of physico-chemical and mechanical properties of phosphorylated and dephosphorylated composite filaments containing NF-L assembled with either NF-M (NF-LM), NF-H (NF-LH), or both (NF-LMH).125 Although, the macroscopic properties of the networks formed by the neurofilament proteins, such as expansion, orientation, and stress response, were shown to be dramatically modulated by phosphorylation, the structural and mechanical modifications caused by phosphorylation were strongly neurofilament composition-dependent, with phosphorylation being able to lead to either neurofilament network expansion or collapse.125 The found expanding-collapsing effects of phosphorylation on the neurofilament network were caused by the dual nature of the phosphorylation-introduced interactions, which depend on the protein sequence and could be repulsive or attractive.125 Therefore, the actual consequences of the extensive phosphorylation could be more complex than the naïve expectations of the increased electrostatic repulsion due to the phosphorylation introduced excess negative charges. Instead, there is a possibility of the phosphorylation-driven electrostatic attraction between the highly disordered regions that could graft unexpected structural and mechanical properties to the assemblies of intrinsically disordered proteins.125

Making sturdy complexes

One of the illustrative examples is given by utilization of intrinsic disorder in assembly of large multiprotein complexes, where highly flexible IDPs/IDPRs serve as assemblers130 or molecular glue cementing protein complexes.131 In fact, mutual folding of intrinsically disordered protomers is crucial for the formation of so-called 2-state protein complexes, where the protomers are intrinsically disordered in their unbound forms and undergo the binding-induced folding at the complex formation.132-135

Structurally, the protomers of protein complexes formed via the 2-state mechanism, where binding and folding occur concomitantly, are characterized by very large per-residue interface and surface areas.134 As a result, protomers in such complexes do not have a simple globular structure (i.e., structure that defines the smallest accessible area), but possess very unusual, mostly non-globular shapes.136,137 Resulting complexes are characterized by sophisticated, highly intertwined structures, where different parts of one protomer penetrate to the multiple binding pockets of different protomers. Therefore, IDPs participating in the formation of the 2-state proteins can be considered as a molecular glue or cement that becomes rigid once the complex forms and thereby serves as a crucial means for stable complex formation.131 The idea of using flexible disorder for making sturdy complexes is illustrated by elastin, which is a self-assembling intrinsically disordered protein of elastic fibers found in the extracellular matrix and constituting an essential part of different elastic tissues in animals (e.g., connective and vascular tissue, lungs, and skin).138 The major biological function of elastin relies on its ability to elastically extend and contract in repetitive motion when hydrated.139-143 Although monomers of elastin are highly disordered, random coil-like polypeptides,138,144-147 because of the formation of the elastic supramolecular complexes, this protein has been shown to be one of the longest lasting proteins in the body, possessing a half-life of about 74 y.148

Liquid-liquid phase transitions and membrane-less organelles

Eukaryotic cells contain numerous proteinaceous membrane-less organelles (PMLOs) that are commonly found in cytoplasm and nucleus of eukaryotic cells and represent an intricate solution of the cellular need to facilitate and regulate molecular interactions by chemically isolating target molecules in specialized compartments in a reversible and controllable way.149-151 PMLOs are also known as ribonucleoprotein (RNP) granules/bodies, or RNP droplets since they typically contain both RNAs and proteins.152 PMLOs are observed as spherical micron-sized droplets,153 structural integrity of which is not supported by encapsulation in the membrane. They are just slightly denser than the rest of the cytoplasm or nucleoplasm,154,155 exhibit liquid-like behavior, such as dripping, relaxation to spherical structures upon fusion, and wetting,156-159 and, therefore, are classified as liquid-droplet phases of the nucleoplasm/cytoplasm.156-161 These organelles have unique morphologies, are characterized by specific distribution patterns, and have specific sets of resident proteins. Importantly, the biogenesis of PMLOs is entirely controlled and mediated by protein–protein, protein–RNA, and/or protein–DNA interactions.162 The list of currently known cytoplasmic PMLOs includes centrosomes,163 germline P-granules (germ cell granules or nuage),156,164 neuronal RNA granules,165 processing bodies or P-bodies,166 and stress granules.159 The nuclear PMLOs are more numerous and include Cajal bodies (CBs),167 chromatin,168 cleavage bodies,169 histone locus bodies (HLBs),170 nuclear gems (Gemini of coiled of Cajal bodies),171,172 nuclear pores,173 nuclear speckles or interchromatin granule clusters,174 nuclear stress bodies (nSBs),175,176 nucleoli,177 Oct1/PTF/ transcription (OPT) domains,178 paraspeckles,179 PcG bodies (polycomb bodies containing polycomb group proteins),180 perinucleolar compartment (PNC),181 promyelocytic leukemia nuclear bodies (PML nuclear bodies) or nuclear dots (PODs),182 and the Sam68 nuclear body (SNB).181

PMLOs are believed to be generated as a result of biologic liquid-liquid phase transitions (LLPTs), which is one of several forms of protein condensation (crystallization, liquid-liquid phase separation, aggregation, or gelation). Although crystallization, aggregation, and gelation are typically irreversible processes, PMLOs are formed as a result of reversible LLPTs under the physiologic conditions of living cells. It was shown experimentally for some PMLOs, such as nuages,153 P-granules,183 nucleolus,184 and RNA granules,185 computationally validated for several nuclear and cytoplasmic PMLOs,186 other “assemblages,”187,188 and generalized for all PMLOs and complex biological coacervates that their formation might be critically dependent on specific IDPs.149-151

Mechanistically (besides the obvious prerequisite to be present in high enough concentrations), the most important properties of the constituents capable of successful liquid-liquid phase separation are their flexibility (fluidity) and multivalency, which are the characteristic features of RNA/DNA (which are commonly found in PMLOs) and IDPs or hybrid proteins containing ordered domains and IDPRs. In fact, nucleic acid binding is one of the disorder-specific functions of proteins, and some IDPs are known to possess mosaic structure with alternating regions of opposite charges. Furthermore, many IDPs and IDPRs are highly charged, have highly repetitive sequences, contain multiple low complexity regions, and often possess disorder-based interaction motifs such as molecular recognition features (MoRFs),22,189,190 AIBSs (binding sites identified by ANCHOR algorithm),191,192 or short linear motifs (SLiMs)193 that can be used by IDPs in formation of various complexes and assemblages. All this suggests that IDPs or hybrid proteins containing IDPRs can serve as potential players in liquid-liquid phase separation causing formation of PMLOs.149-151

Sturdy IDPs to the rescue! intrinsic disorder and organismal desiccation resistance

In line with the idea that sturdy IDPs characterized by remarkable conformational stability could have crucial importance for the sturdiness at the organismal level is a recently popularized thought-provoking case of the microscopic animals, tardigrades that use IDPs to survive complete desiccation.194 Tardigrades (which are also known as water bears, space bears, pudgy wudgies, or moss piglets) are water-dwelling, 8-legged, segmented micro-animals characterized by the prodigious desiccation tolerance and the ability to survive a vast array of environmental extremes (e.g., exposure the vacuum and solar radiation of outer space for 10 full days).195 They also can remain in the dehydrated state for up to 20 y and resume normal life, when external conditions become favorable again.196 Being discovered more than 250 years, this micro-animals and the molecular mechanisms of their exceptional die-hardiness remained an enigma till recently, when it has been revealed that at the molecular level, the exceptional desiccation tolerance of tardigrades is attributed not to certain saccharides (e.g., trehalose) typically found in many anhydrobiotic organisms, but to the high contents of a set of tardigrade-specific IDPs (TDPs), which are either constitutively expressed at high levels or dramatically upregulated by desiccation.194 These TDPs are found in multiple tardigrade species, and, being heterologously expressed in both prokaryotic and eukaryotic systems, are sufficient to promote desiccation tolerance in these heterologous systems. The protective role of TDPs in the tardigrade desiccation was attributed to the ability of these proteins to vitrify; i.e., to form a glass-like matrix that physically prevents denaturation and aggregation of other cellular proteins and also preclude membrane fusion.194

The finding that TDPs are crucial for the ability of the members of the animal kingdom to survive during extreme desiccation concur with the previous work on the plant desiccation resistance that was shown to be critically dependent on several specific IDPs, such as late embryogenesis abundant (LEA) proteins and dehydrins (which are members of the Group II LEA proteins).197-199 However, the protective role of LEA proteins (which in addition to plants can be found in bacteria, nematodes, and shrimps) was attributed to their ability to suppress desiccation-induced protein aggregation via formation of a ‘molecular shield’, a physical barrier, between the neighboring proteins. Therefore, the ability of TDPs to vitrify represents a novel intrinsic disorder-based molecular mechanism of protection of biologic material from desiccation.194

Disclosure of potential conflicts of interest

No potential conflicts of interest were disclosed.

References

  • [1].Dunker AK, Lawson JD, Brown CJ, Williams RM, Romero P, Oh JS, Oldfield CJ, Campen AM, Ratliff CM, Hipps KW, et al.. Intrinsically disordered protein. J Mol Graph Model 2001; 19:26-59; PMID:11381529; https://doi.org/ 10.1016/S1093-3263(00)00138-8 [DOI] [PubMed] [Google Scholar]
  • [2].Uversky VN, Gillespie JR, Fink AL. Why are “natively unfolded” proteins unstructured under physiologic conditions? Proteins 2000; 41:415-27; PMID:11025552; https://doi.org/ 10.1002/1097-0134(20001115)41:3%3c415::AID-PROT130%3e3.0.CO;2-7 [DOI] [PubMed] [Google Scholar]
  • [3].Wright PE, Dyson HJ. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol 1999; 293:321-31; PMID:10550212; https://doi.org/ 10.1006/jmbi.1999.3110 [DOI] [PubMed] [Google Scholar]
  • [4].Tompa P. Intrinsically unstructured proteins. Trends Biochem Sci 2002; 27:527-33; PMID:12368089; https://doi.org/ 10.1016/S0968-0004(02)02169-2 [DOI] [PubMed] [Google Scholar]
  • [5].Tompa P. Unstructural biology coming of age. Curr Opin Struct Biol 2011; 21:419-25; PMID:21514142; https://doi.org/ 10.1016/j.sbi.2011.03.012 [DOI] [PubMed] [Google Scholar]
  • [6].Tompa P. Intrinsically disordered proteins: a 10-year recap. Trends Biochem Sci 2012; 37:509-16; PMID:22989858; https://doi.org/ 10.1016/j.tibs.2012.08.004 [DOI] [PubMed] [Google Scholar]
  • [7].Uversky VN. A decade and a half of protein intrinsic disorder: biology still waits for physics. Protein Sci 2013; 22:693-724; PMID:23553817; https://doi.org/ 10.1002/pro.2261 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [8].Dunker AK, Babu M, Barbar E, Blackledge M, Bondos SE, Dosztányi Z, Dyson HJ, Forman-Kay J, Fuxreiter M, Gsponer J, et al.. What's in a name? Why these proteins are intrinsically disordered. Intrinsically Disord Proteins 2013; 1:e24157; https://doi.org/ 10.4161/idp.24157 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [9].Dunker AK, Brown CJ, Lawson JD, Iakoucheva LM, Obradovic Z. Intrinsic disorder and protein function. Biochemistry 2002; 41:6573-82; PMID:12022860; https://doi.org/ 10.1021/bi012159+ [DOI] [PubMed] [Google Scholar]
  • [10].Dunker AK, Brown CJ, Obradovic Z. Identification and functions of usefully disordered proteins. Adv Protein Chem 2002; 62:25-49; PMID:12418100 [DOI] [PubMed] [Google Scholar]
  • [11].Turoverov KK, Kuznetsova IM, Uversky VN. The protein kingdom extended: ordered and intrinsically disordered proteins, their folding, supramolecular complex formation, and aggregation. Prog Biophys Mol Biol 2010; 102:73-84; PMID:20097220; https://doi.org/ 10.1016/j.pbiomolbio.2010.01.003 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [12].Uversky VN. Natively unfolded proteins: a point where biology waits for physics. Protein Sci 2002; 11:739-56; PMID:11910019; https://doi.org/ 10.1110/ps.4210102 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [13].Uversky VN. What does it mean to be natively unfolded? Eur J Biochem 2002; 269:2-12; PMID:11784292; https://doi.org/ 10.1046/j.0014-2956.2001.02649.x [DOI] [PubMed] [Google Scholar]
  • [14].Dunker AK, Cortese MS, Romero P, Iakoucheva LM, Uversky VN. Flexible nets. The roles of intrinsic disorder in protein interaction networks. FEBS J 2005; 272:5129-48; PMID:16218947; https://doi.org/ 10.1111/j.1742-4658.2005.04948.x [DOI] [PubMed] [Google Scholar]
  • [15].Uversky VN. Multitude of binding modes attainable by intrinsically disordered proteins: a portrait gallery of disorder-based complexes. Chem Soc Rev 2011; 40:1623-34; PMID:21049125; https://doi.org/ 10.1039/C0CS00057D [DOI] [PubMed] [Google Scholar]
  • [16].Uversky VN. Intrinsically disordered proteins from A to Z. Int J Biochem Cell Biol 2011; 43:1090-103; PMID:21501695; https://doi.org/ 10.1016/j.biocel.2011.04.001 [DOI] [PubMed] [Google Scholar]
  • [17].Uversky VN. Intrinsic disorder-based protein interactions and their modulators. Curr Pharm Des 2012; 19(23):4191-213:In press [DOI] [PubMed] [Google Scholar]
  • [18].Uversky VN, Dunker AK. Understanding protein non-folding. Biochim Biophys Acta 2010; 1804:1231-64; PMID:20117254; https://doi.org/ 10.1016/j.bbapap.2010.01.017 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [19].Uversky VN, Oldfield CJ, Dunker AK. Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling. J Mol Recognit 2005; 18:343-84; PMID:16094605; https://doi.org/ 10.1002/jmr.747 [DOI] [PubMed] [Google Scholar]
  • [20].Cortese MS, Uversky VN, Dunker AK. Intrinsic disorder in scaffold proteins: getting more from less. Prog Biophys Mol Biol 2008; 98:85-106; PMID:18619997; https://doi.org/ 10.1016/j.pbiomolbio.2008.05.007 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [21].Fuxreiter M, Tompa P. Fuzzy complexes: a more stochastic view of protein function. Adv Exp Med Biol 2012; 725:1-14; PMID:22399315 [DOI] [PubMed] [Google Scholar]
  • [22].Oldfield CJ, Cheng Y, Cortese MS, Romero P, Uversky VN, Dunker AK. Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry 2005; 44:12454-70; PMID:16156658; https://doi.org/ 10.1021/bi047993o [DOI] [PubMed] [Google Scholar]
  • [23].Oldfield CJ, Meng J, Yang JY, Yang MQ, Uversky VN, Dunker AK. Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners. BMC Genomics 2008; 9(Suppl 1):S1; https://doi.org/ 10.1186/1471-2164-9-S1-S1 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [24].Pejaver V, Hsu WL, Xin F, Dunker AK, Uversky VN, Radivojac P. The structural and functional signatures of proteins that undergo multiple events of post-translational modification. Protein Sci 2014; 23:1077-93; PMID:24888500; https://doi.org/ 10.1002/pro.2494 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [25].Romero PR, Zaidi S, Fang YY, Uversky VN, Radivojac P, Oldfield CJ, Cortese MS, Sickmeier M, LeGall T, Obradovic Z, et al.. Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. Proc Natl Acad Sci U S A 2006; 103:8390-5; PMID:16717195; https://doi.org/ 10.1073/pnas.0507916103 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [26].Santner AA, Croy CH, Vasanwala FH, Uversky VN, Van YY, Dunker AK. Sweeping away protein aggregation with entropic bristles: intrinsically disordered protein fusions enhance soluble expression. Biochemistry 2012; 51:7250-62; PMID:22924672; https://doi.org/ 10.1021/bi300653m [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [27].Vucetic S, Xie H, Iakoucheva LM, Oldfield CJ, Dunker AK, Obradovic Z, Uversky VN. Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions. J Proteome Res 2007; 6:1899-916; PMID:17391015; https://doi.org/ 10.1021/pr060393m [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [28].Wright PE, Dyson HJ. Linking folding and binding. Curr Opin Struct Biol 2009; 19:31-8; PMID:19157855; https://doi.org/ 10.1016/j.sbi.2008.12.003 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [29].Xie H, Vucetic S, Iakoucheva LM, Oldfield CJ, Dunker AK, Obradovic Z, Uversky VN. Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins. J Proteome Res 2007; 6:1917-32; PMID:17391016; https://doi.org/ 10.1021/pr060392u [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [30].Xie H, Vucetic S, Iakoucheva LM, Oldfield CJ, Dunker AK, Uversky VN, Obradovic Z. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J Proteome Res 2007; 6:1882-98; PMID:17391014; https://doi.org/ 10.1021/pr060392u [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [31].Xue B, Dunker AK, Uversky VN. The roles of intrinsic disorder in orchestrating the Wnt-pathway. J Biomol Struct Dyn 2012; 29:843-61; PMID:22292947; https://doi.org/ 10.1080/073911012010525024 [DOI] [PubMed] [Google Scholar]
  • [32].van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones DT, et al.. Classification of intrinsically disordered regions and proteins. Chem Rev 2014; 114:6589-631; PMID:24773235; https://doi.org/ 10.1021/cr400525m [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [33].DeForte S, Uversky VN. Order, Disorder, and Everything in Between. Molecules 2016; 21:pii: E1090; PMID:27548131; https://doi.org/ 10.3390/molecules21081090 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [34].Uversky VN. Functional roles of transiently and intrinsically disordered regions within proteins. FEBS J 2015; 282:1182-9; PMID:25631540; https://doi.org/ 10.1111/febs.13202 [DOI] [PubMed] [Google Scholar]
  • [35].Uversky VN. Proteins without unique 3D structures: biotechnological applications of intrinsically unstable/disordered proteins. Biotechnol J 2015; 10:356-66; PMID:25287424; https://doi.org/ 10.1002/biot.201400374 [DOI] [PubMed] [Google Scholar]
  • [36].Habchi J, Tompa P, Longhi S, Uversky VN. Introducing protein intrinsic disorder. Chem Rev 2014; 114:6561-88; PMID:24739139; https://doi.org/ 10.1021/cr400514h [DOI] [PubMed] [Google Scholar]
  • [37].Fuxreiter M, Toth-Petroczy A, Kraut DA, Matouschek A, Lim RY, Xue B, Kurgan L, Uversky VN. Disordered proteinaceous machines. Chem Rev 2014; 114:6806-43; PMID:24702702; https://doi.org/ 10.1021/cr4007329 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [38].Uversky VN. Intrinsic disorder-based protein interactions and their modulators. Curr Pharm Des 2013; 19:4191-213; PMID:23170892; https://doi.org/ 10.2174/1381612811319230005 [DOI] [PubMed] [Google Scholar]
  • [39].Dunker AK, Silman I, Uversky VN, Sussman JL. Function and structure of inherently disordered proteins. Curr Opin Struct Biol 2008; 18:756-64; PMID:18952168; https://doi.org/ 10.1016/j.sbi.2008.10.002 [DOI] [PubMed] [Google Scholar]
  • [40].Jakob U, Kriwacki R, Uversky VN. Conditionally and transiently disordered proteins: awakening cryptic disorder to regulate protein function. Chem Rev 2014; 114:6779-805; PMID:24502763; https://doi.org/ 10.1021/cr400459c [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [41].Uversky VN. The most important thing is the tail: multitudinous functionalities of intrinsically disordered protein termini. FEBS Lett 2013; 587:1891-901; PMID:23665034; https://doi.org/ 10.1016/j.febslet.2013.04.042 [DOI] [PubMed] [Google Scholar]
  • [42].Dunker AK, Obradovic Z, Romero P, Garner EC, Brown CJ. Intrinsic protein disorder in complete genomes. Genome Inform Ser Workshop Genome Inform 2000; 11:161-71; PMID:11700597 [PubMed] [Google Scholar]
  • [43].Uversky VN. The mysterious unfoldome: structureless, underappreciated, yet vital part of any given proteome. J Biomed Biotechnol 2010; 2010:568068; PMID:20011072; https://doi.org/ 10.1155/2010/568068 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [44].Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 2004; 337:635-45; PMID:15019783; https://doi.org/ 10.1016/j.jmb.2004.02.002 [DOI] [PubMed] [Google Scholar]
  • [45].Xue B, Dunker AK, Uversky VN. Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life. J Biomol Struct Dyn 2012; 30:137-49; PMID:22702725; https://doi.org/ 10.1080/07391102.2012.675145 [DOI] [PubMed] [Google Scholar]
  • [46].Peng Z, Yan J, Fan X, Mizianty MJ, Xue B, Wang K, Hu G, Uversky VN, Kurgan L. Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life. Cell Mol Life Sci 2015; 72:137-51; PMID:24939692; https://doi.org/ 10.1007/s00018-014-1661-9 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [47].Xue B, Williams RW, Oldfield CJ, Dunker AK, Uversky VN. Archaic chaos: intrinsically disordered proteins in Archaea. BMC Syst Biol 2010; 4(Suppl 1):S1; PMID:20522251; https://doi.org/ 10.1186/1752-0509-4-S1-S1 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [48].Uversky VN. Unusual biophysics of intrinsically disordered proteins. Biochim Biophys Acta 2013; 1834:932-51; PMID:23269364; https://doi.org/ 10.1016/j.bbapap.2012.12.008 [DOI] [PubMed] [Google Scholar]
  • [49].Uversky VN. Dancing protein clouds: the strange biology and chaotic physics of intrinsically disordered proteins. J Biol Chem 2016; 291:6681-8; PMID:26851286; https://doi.org/ 10.1074/jbc.R115.685859 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [50].Uversky VN. Paradoxes and wonders of intrinsic disorder: Prevalence of exceptionality. Intrinsically Disord Proteins 2015; 3:e1065029; PMID:28232891; https://doi.org/ 10.1080/21690707.2015.1027032 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [51].Uversky VN. Paradoxes and wonders of intrinsic disorder: Complexity of simplicity. Intrinsically Disord Proteins 2016; 4:e1135015; PMID:28232895; https://doi.org/ 10.1080/21690707.2015.1135015 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [52].Anfinsen CB, Haber E, Sela M, White FH Jr.. The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proc Natl Acad Sci U S A 1961; 47:1309-14; PMID:13683522; https://doi.org/ 10.1073/pnas.47.9.1309 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [53].Anson ML, Mirsky AE. The effect of denaturation on the viscosity of protein systems. J Gen Physiol 1932; 15:341-50; PMID:19872650; https://doi.org/ 10.1085/jgp.15.3.341 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [54].Mirsky AE, Pauling L. On the structure of native, denatured and coagulated proteins. Proc Natl Acad Sci U S A 1936; 22:439-47; PMID:16577722; https://doi.org/ 10.1073/pnas.22.2.147 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [55].Neurath H, Greenstein JP, Putnam FW, Erickson JO. The chemistry of protein denaturation. Chem Rew 1944; 34:157-265; https://doi.org/ 10.1021/cr60108a003 [DOI] [Google Scholar]
  • [56].Tanford C. Protein denaturation. Adv Protein Chem 1968; 23:121-282; PMID:4882248 [DOI] [PubMed] [Google Scholar]
  • [57].Ptitsyn OB, Uversky VN. The molten globule is a third thermodynamical state of protein molecules. FEBS Lett 1994; 341:15-8; PMID:8137915; https://doi.org/ 10.1016/0014-5793(94)80231-9 [DOI] [PubMed] [Google Scholar]
  • [58].Uversky VN, Ptitsyn OB. All-or-none solvent-induced transitions between native, molten globule and unfolded states in globular proteins. Fold Des 1996; 1:117-22; PMID:9079371; https://doi.org/ 10.1016/S1359-0278(96)00020-X [DOI] [PubMed] [Google Scholar]
  • [59].Uversky VN. Intrinsically disordered proteins and their environment: effects of strong denaturants, temperature, pH, counter ions, membranes, binding partners, osmolytes, and macromolecular crowding. Protein J 2009; 28:305-25; PMID:19768526; https://doi.org/ 10.1007/s10930-009-9201-4 [DOI] [PubMed] [Google Scholar]
  • [60].Williams RM, Obradovi Z, Mathura V, Braun W, Garner EC, Young J, Takayama S, Brown CJ, Dunker AK. The protein non-folding problem: amino acid determinants of intrinsic order and disorder. Pac Symp Biocomput 2001:89-100; PMID:11262981 [DOI] [PubMed] [Google Scholar]
  • [61].Romero P, Obradovic Z, Li X, Garner EC, Brown CJ, Dunker AK. Sequence complexity of disordered protein. Proteins 2001; 42:38-48; PMID:11093259; https://doi.org/ 10.1002/1097-0134(20010101)42:1%3c38::AID-PROT50%3e3.0.CO;2-3 [DOI] [PubMed] [Google Scholar]
  • [62].Radivojac P, Iakoucheva LM, Oldfield CJ, Obradovic Z, Uversky VN, Dunker AK. Intrinsic disorder and functional proteomics. Biophys J 2007; 92(5):1439-56; PMID:17158572; https://doi.org/ 10.1529/biophysj.106.094045 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [63].Vacic V, Uversky VN, Dunker AK, Lonardi S. Composition Profiler: a tool for discovery and visualization of amino acid composition differences. BMC Bioinformatics 2007; 8:211; PMID:17578581; https://doi.org/ 10.1186/1471-2105-8-211 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [64].Dunker AK, Garner E, Guilliot S, Romero P, Albrecht K, Hart J, Obradovic Z, Kissinger C, Villafranca JE. Protein disorder and the evolution of molecular recognition: theory, predictions and observations. Pac Symp Biocomput 1998:473-84; PMID:9697205 [PubMed] [Google Scholar]
  • [65].Garner E, Cannon P, Romero P, Obradovic Z, Dunker AK. Predicting disordered regions from amino acid sequence: common themes despite differing structural characterization. Genome Inform Ser Workshop Genome Inform 1998; 9:201-13; PMID:11072336 [PubMed] [Google Scholar]
  • [66].Campen A, Williams RM, Brown CJ, Meng J, Uversky VN, Dunker AK. TOP-IDP-scale: a new amino acid scale measuring propensity for intrinsic disorder. Protein Pept Lett 2008; 15:956-63; PMID:18991772; https://doi.org/ 10.2174/092986608785849164 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [67].Neyroz P, Zambelli B, Ciurli S. Intrinsically disordered structure of Bacillus pasteurii UreG as revealed by steady-state and time-resolved fluorescence spectroscopy. Biochemistry 2006; 45:8918-30; PMID:16846235; https://doi.org/ 10.1021/bi060227s [DOI] [PubMed] [Google Scholar]
  • [68].Fontana A, de Laureto PP, Spolaore B, Frare E, Picotti P, Zambonin M. Probing protein structure by limited proteolysis. Acta Biochim Pol 2004; 51:299-321; PMID:15218531 [PubMed] [Google Scholar]
  • [69].Iakoucheva LM, Kimzey AL, Masselon CD, Bruce JE, Garner EC, Brown CJ, Dunker AK, Smith RD, Ackerman EJ. Identification of intrinsic order and disorder in the DNA repair protein XPA. Protein Sci 2001; 10:560-71; PMID:11344324; https://doi.org/ 10.1110/ps.29401 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [70].Balazs A, Csizmok V, Buday L, Rakacs M, Kiss R, Bokor M, Udupa R, Tompa K, Tompa P. High levels of structural disorder in scaffold proteins as exemplified by a novel neuronal protein, CASK-interactive protein1. FEBS J 2009; 276:3744-56; PMID:19523119; https://doi.org/ 10.1111/j.1742-4658.2009.07090.x [DOI] [PubMed] [Google Scholar]
  • [71].Brocca S, Samalikova M, Uversky VN, Lotti M, Vanoni M, Alberghina L, Grandori R. Order propensity of an intrinsically disordered protein, the cyclin-dependent-kinase inhibitor Sic1. Proteins 2009; 76:731-46; PMID:19280601; https://doi.org/ 10.1002/prot.22385 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [72].Nocula-Lugowska M, Rymarczyk G, Lisowski M, Ozyhar A. Isoform-specific variation in the intrinsic disorder of the ecdysteroid receptor N-terminal domain. Proteins 2009; 76:291-308; PMID:19156821; https://doi.org/ 10.1002/prot.22342 [DOI] [PubMed] [Google Scholar]
  • [73].Suskiewicz MJ, Sussman JL, Silman I, Shaul Y. Context-dependent resistance to proteolysis of intrinsically disordered proteins. Protein Sci 2011; 20:1285-97; PMID:21574196; https://doi.org/ 10.1002/pro.657 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [74].Johnson DE, Xue B, Sickmeier MD, Meng J, Cortese MS, Oldfield CJ, Le Gall T, Dunker AK, Uversky VN. High-throughput characterization of intrinsic disorder in proteins from the Protein Structure Initiative. J Struct Biol 2012; 180:201-15; PMID:22651963; https://doi.org/ 10.1016/j.jsb.2012.05.013 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [75].Tsvetkov P, Myers N, Moscovitz O, Sharon M, Prilusky J, Shaul Y. Thermo-resistant intrinsically disordered proteins are efficient 20S proteasome substrates. Mol Biosyst 2012; 8:368-73; PMID:22027891; https://doi.org/ 10.1039/C1MB05283G [DOI] [PubMed] [Google Scholar]
  • [76].Gardner KA, Moore DA, Erickson HP. The C-terminal linker of Escherichia coli FtsZ functions as an intrinsically disordered peptide. Mol Microbiol 2013; 89:264-75; PMID:23714328; https://doi.org/ 10.1111/mmi.12279 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [77].Minde DP, Radli M, Forneris F, Maurice MM, Rudiger SG. Large extent of disorder in Adenomatous Polyposis Coli offers a strategy to guard Wnt signalling against point mutations. PLoS One 2013; 8:e77257; PMID:24130866; https://doi.org/ 10.1371/journal.pone.0077257 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [78].Uversky VN, Gillespie JR, Millett IS, Khodyakova AV, Vasiliev AM, Chernovskaya TV, Vasilenko RN, Kozlovskaya GD, Dolgikh DA, Fink AL, et al.. Natively unfolded human prothymosin alpha adopts partially folded collapsed conformation at acidic pH. Biochemistry 1999; 38:15009-16; PMID:10555983; https://doi.org/ 10.1021/bi990752+ [DOI] [PubMed] [Google Scholar]
  • [79].Kriwacki RW, Hengst L, Tennant L, Reed SI, Wright PE. Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2-bound state: conformational disorder mediates binding diversity. Proc Natl Acad Sci U S A 1996; 93:11504-9; PMID:8876165; https://doi.org/ 10.1073/pnas.93.21.11504 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [80].Lacy ER, Filippov I, Lewis WS, Otieno S, Xiao L, Weiss S, Hengst L, Kriwacki RW. p27 binds cyclin-CDK complexes through a sequential mechanism involving binding-induced protein folding. Nat Struct Mol Biol 2004; 11:358-64; PMID:15024385; https://doi.org/ 10.1038/nsmb746 [DOI] [PubMed] [Google Scholar]
  • [81].Bienkiewicz EA, Adkins JN, Lumb KJ. Functional consequences of preorganized helical structure in the intrinsically disordered cell-cycle inhibitor p27(Kip1). Biochemistry 2002; 41:752-9; PMID:11790096; https://doi.org/ 10.1021/bi015763t [DOI] [PubMed] [Google Scholar]
  • [82].Hengst L, Dulic V, Slingerland JM, Lees E, Reed SI. A cell cycle-regulated inhibitor of cyclin-dependent kinases. Proc Natl Acad Sci U S A 1994; 91:5291-5; PMID:8202483; https://doi.org/ 10.1073/pnas.91.12.5291 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [83].Weinreb PH, Zhen W, Poon AW, Conway KA, Lansbury PT Jr.. NACP, a protein implicated in Alzheimer's disease and learning, is natively unfolded. Biochemistry 1996; 35:13709-15; PMID:8901511; https://doi.org/ 10.1021/bi961799n [DOI] [PubMed] [Google Scholar]
  • [84].Uversky VN, Li J, Fink AL. Evidence for a partially folded intermediate in alpha-synuclein fibril formation. J Biol Chem 2001; 276:10737-44; PMID:11152691; https://doi.org/ 10.1074/jbc.M105343200 [DOI] [PubMed] [Google Scholar]
  • [85].Li J, Uversky VN, Fink AL. Effect of familial Parkinson's disease point mutations A30P and A53T on the structural properties, aggregation, and fibrillation of human alpha-synuclein. Biochemistry 2001; 40:11604-13; PMID:11560511; https://doi.org/ 10.1021/bi002785r [DOI] [PubMed] [Google Scholar]
  • [86].Uversky VN, Permyakov SE, Zagranichny VE, Rodionov IL, Fink AL, Cherskaya AM, Wasserman LA, Permyakov EA. Effect of zinc and temperature on the conformation of the gamma subunit of retinal phosphodiesterase: a natively unfolded protein. J Proteome Res 2002; 1:149-59; PMID:12643535; https://doi.org/ 10.1021/pr0155127 [DOI] [PubMed] [Google Scholar]
  • [87].Uversky VN, Li J, Souillac P, Millett IS, Doniach S, Jakes R, Goedert M, Fink AL. Biophysical properties of the synucleins and their propensities to fibrillate: inhibition of alpha-synuclein assembly by beta- and gamma-synucleins. J Biol Chem 2002; 277:11970-8; PMID:11812782; https://doi.org/ 10.1074/jbc.M109541200 [DOI] [PubMed] [Google Scholar]
  • [88].Permyakov SE, Millett IS, Doniach S, Permyakov EA, Uversky VN. Natively unfolded C-terminal domain of caldesmon remains substantially unstructured after the effective binding to calmodulin. Proteins 2003; 53:855-62; PMID:14635127; https://doi.org/ 10.1002/prot.10481 [DOI] [PubMed] [Google Scholar]
  • [89].Hackel M, Konno T, Hinz H. A new alternative method to quantify residual structure in ‘unfolded’ proteins. Biochim Biophys Acta 2000; 1479:155-65; PMID:11004537; https://doi.org/ 10.1016/S0167-4838(00)00051-0 [DOI] [PubMed] [Google Scholar]
  • [90].Belmont LD, Mitchison TJ. Identification of a protein that interacts with tubulin dimers and increases the catastrophe rate of microtubules. Cell 1996; 84:623-31; PMID:8598048; https://doi.org/ 10.1016/S0092-8674(00)81037-5 [DOI] [PubMed] [Google Scholar]
  • [91].Hernandez MA, Avila J, Andreu JM. Physicochemical characterization of the heat-stable microtubule-associated protein MAP2. Eur J Biochem 1986; 154:41-8; PMID:3943524; https://doi.org/ 10.1111/j.1432-1033.1986.tb09356.x [DOI] [PubMed] [Google Scholar]
  • [92].Kalthoff C. A novel strategy for the purification of recombinantly expressed unstructured protein domains. J Chromatogr B Analyt Technol Biomed Life Sci 2003; 786:247-54; PMID:12651021; https://doi.org/ 10.1016/S1570-0232(02)00908-X [DOI] [PubMed] [Google Scholar]
  • [93].Oldfield CJ, Cheng Y, Cortese MS, Brown CJ, Uversky VN, Dunker AK. Comparing and combining predictors of mostly disordered proteins. Biochemistry 2005; 44:1989-2000; PMID:15697224; https://doi.org/ 10.1021/bi047993o [DOI] [PubMed] [Google Scholar]
  • [94].Galea CA, Pagala VR, Obenauer JC, Park CG, Slaughter CA, Kriwacki RW. Proteomic studies of the intrinsically unstructured mammalian proteome. J Proteome Res 2006; 5:2839-48; PMID:17022655; https://doi.org/ 10.1021/pr060328c [DOI] [PubMed] [Google Scholar]
  • [95].Uversky VN. Intrinsically disordered proteins and their environment: Effects of strong denaturants, temperature, ph, counter ions, membranes, binding partners, osmolytes, and macromolecular crowding. Protein J 2009; 28(7-8):305-25:In press; PMID:19768526; https://doi.org/ 10.1007/s10930-009-9201-4 [DOI] [PubMed] [Google Scholar]
  • [96].Uversky VN. A protein-chameleon: conformational plasticity of alpha-synuclein, a disordered protein involved in neurodegenerative disorders. J Biomol Struct Dyn 2003; 21:211-34; PMID:12956606; https://doi.org/ 10.1080/07391102.2003.10506918 [DOI] [PubMed] [Google Scholar]
  • [97].Cortese MS, Baird JP, Uversky VN, Dunker AK. Uncovering the unfoldome: enriching cell extracts for unstructured proteins by Acid treatment. J Proteome Res 2005; 4:1610-8; PMID:16212413; https://doi.org/ 10.1021/pr050119c [DOI] [PubMed] [Google Scholar]
  • [98].Goto Y, Calciano LJ, Fink AL. Acid-induced folding of proteins. Proc Natl Acad Sci U S A 1990; 87:573-7; PMID:2153957; https://doi.org/ 10.1073/pnas.87.2.573 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [99].Goto Y, Fink AL. Phase diagram for acidic conformational states of apomyoglobin. J Mol Biol 1990; 214:803-5; PMID:2388268; https://doi.org/ 10.1016/0022-2836(90)90334-I [DOI] [PubMed] [Google Scholar]
  • [100].Goto Y, Takahashi N, Fink AL. Mechanism of acid-induced folding of proteins. Biochemistry 1990; 29:3480-8; PMID:2162192; https://doi.org/ 10.1021/bi00466a009 [DOI] [PubMed] [Google Scholar]
  • [101].Fink AL, Calciano LJ, Goto Y, Kurotsu T, Palleros DR. Classification of acid denaturation of proteins: intermediates and unfolded states. Biochemistry 1994; 33:12504-11; PMID:7918473; https://doi.org/ 10.1021/bi00207a018 [DOI] [PubMed] [Google Scholar]
  • [102].Uversky VN, Li J, Fink AL. Evidence for a partially folded intermediate in alpha-synuclein fibril formation. J Biol Chem 2001; 276:10737-44; PMID:11152691; https://doi.org/ 10.1074/jbc.M105343200 [DOI] [PubMed] [Google Scholar]
  • [103].Uversky VN, Permyakov SE, Zagranichny VE, Rodionov IL, Fink AL, Cherskaya AM, Wasserman LA, Permyakov EA. Effect of zinc and temperature on the conformation of the gamma subunit of retinal phosphodiesterase: a natively unfolded protein. J Proteome Res 2002; 1:149-59; PMID:12643535; https://doi.org/ 10.1021/pr0155127 [DOI] [PubMed] [Google Scholar]
  • [104].Timm DE, Vissavajjhala P, Ross AH, Neet KE. Spectroscopic and chemical studies of the interaction between nerve growth factor (NGF) and the extracellular domain of the low affinity NGF receptor. Protein Sci 1992; 1:1023-31; PMID:1304381; https://doi.org/ 10.1002/pro.5560010808 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [105].Kim TD, Ryu HJ, Cho HI, Yang CH, Kim J. Thermal behavior of proteins: heat-resistant proteins and their heat-induced secondary structural changes. Biochemistry 2000; 39:14839-46; PMID:11101300; https://doi.org/ 10.1021/bi001441y [DOI] [PubMed] [Google Scholar]
  • [106].Konno T, Tanaka N, Kataoka M, Takano E, Maki M. A circular dichroism study of preferential hydration and alcohol effects on a denatured protein, pig calpastatin domain I. Biochim Biophys Acta 1997; 1342:73-82; PMID:9366272; https://doi.org/ 10.1016/S0167-4838(97)00092-7 [DOI] [PubMed] [Google Scholar]
  • [107].Lynn A, Chandra S, Malhotra P, Chauhan VS. Heme binding and polymerization by Plasmodium falciparum histidine rich protein II: influence of pH on activity and conformation. FEBS Lett 1999; 459:267-71; PMID:10518033; https://doi.org/ 10.1016/S0014-5793(99)01260-0 [DOI] [PubMed] [Google Scholar]
  • [108].Johansson J, Gudmundsson GH, Rottenberg ME, Berndt KD, Agerberth B. Conformation-dependent antibacterial activity of the naturally occurring human peptide LL-37. J Biol Chem 1998; 273:3718-24; PMID:9452503; https://doi.org/ 10.1074/jbc.273.45.29816 [DOI] [PubMed] [Google Scholar]
  • [109].Tompa P. The interplay between structure and function in intrinsically unstructured proteins. FEBS Lett 2005; 579:3346-54; PMID:15943980; https://doi.org/ 10.1016/j.febslet.2005.03.072 [DOI] [PubMed] [Google Scholar]
  • [110].Oldfield CJ, Dunker AK. Intrinsically disordered proteins and intrinsically disordered protein regions. Annu Rev Biochem 2014; 83:553-84; PMID:24606139; https://doi.org/ 10.1146/annurev-biochem-072711-164947 [DOI] [PubMed] [Google Scholar]
  • [111].Berlow RB, Dyson HJ, Wright PE. Functional advantages of dynamic protein disorder. FEBS Lett 2015; 589:2433-40; PMID:26073260; https://doi.org/ 10.1016/j.febslet.2015.06.003 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [112].Speziale P, Pietrocola G, Foster TJ, Geoghegan JA. Protein-based biofilm matrices in Staphylococci. Front Cell Infect Microbiol 2014; 4:171; PMID:25540773; https://doi.org/ 10.3389/fcimb.2014.00171 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [113].Foster TJ, Geoghegan JA, Ganesh VK, Hook M. Adhesion, invasion and evasion: the many functions of the surface proteins of Staphylococcus aureus. Nat Rev Microbiol 2014; 12:49-62; PMID:24336184; https://doi.org/ 10.1038/nrmicro3161 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [114].Conrady DG, Brescia CC, Horii K, Weiss AA, Hassett DJ, Herr AB. A zinc-dependent adhesion module is responsible for intercellular adhesion in staphylococcal biofilms. Proc Natl Acad Sci U S A 2008; 105:19456-61; PMID:19047636; https://doi.org/ 10.1073/pnas.0807717105 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [115].Conrady DG, Wilson JJ, Herr AB. Structural basis for Zn2+-dependent intercellular adhesion in staphylococcal biofilms. Proc Natl Acad Sci U S A 2013; 110:E202-11; PMID:23277549; https://doi.org/ 10.1073/pnas.1208134110 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [116].Marraffini LA, Dedent AC, Schneewind O. Sortases and the art of anchoring proteins to the envelopes of gram-positive bacteria. Microbiol Mol Biol Rev 2006; 70:192-221; PMID:16524923; https://doi.org/ 10.1128/MMBR.70.1.192-221.2006 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [117].Yarawsky AE, English LR, Whitten ST, Herr AB. The proline/glycine-rich region of the biofilm adhesion protein aap forms an extended stalk that resists compaction. J Mol Biol 2017; 429:261-79; PMID:27890783; https://doi.org/ 10.1016/j.jmb.2016.11.017 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [118].Hirokawa N, Glicksman MA, Willard MB. Organization of mammalian neurofilament polypeptides within the neuronal cytoskeleton. J Cell Biol 1984; 98:1523-36; PMID:6425303; https://doi.org/ 10.1083/jcb.98.4.1523 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [119].Yuan A, Rao MV, Veeranna  , Nixon RA. Neurofilaments at a glance. J Cell Sci 2012; 125:3257-63; PMID:22956720; https://doi.org/ 10.1242/jcs.104729 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [120].Laser-Azogui A, Kornreich M, Malka-Gibor E, Beck R. Neurofilament assembly and function during neuronal development. Curr Opin Cell Biol 2015; 32:92-101; PMID:25635910; https://doi.org/ 10.1016/j.ceb.2015.01.003 [DOI] [PubMed] [Google Scholar]
  • [121].Safinya CR, Deek J, Beck R, Jones JB, Li YL. Assembly of biological nanostructures: isotropic and liquid crystalline phases of neurofilament hydrogels. Ann Rev Condensed Matter Phys 2015; 6:113-36; https://doi.org/ 10.1146/annurev-conmatphys-031214-014623 [DOI] [Google Scholar]
  • [122].Sihag RK, Inagaki M, Yamaguchi T, Shea TB, Pant HC. Role of phosphorylation on the structural dynamics and function of types III and IV intermediate filaments. Exp Cell Res 2007; 313:2098-109; PMID:17498690; https://doi.org/ 10.1016/j.yexcr.2007.04.010 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [123].Hoh JH. Functional protein domains from the thermally driven motion of polypeptide chains: A proposal. Proteins 1998; 32:223-8; https://doi.org/ 10.1002/(SICI)1097-0134(19980801)32:2%3c223::AID-PROT8%3e3.0.CO;2-L [DOI] [PubMed] [Google Scholar]
  • [124].Trimpin S, Mixon AE, Stapels MD, Kim MY, Spencer PS, Deinzer ML. Identification of endogenous phosphorylation sites of bovine medium and low molecular weight neurofilament proteins by tandem mass spectrometry. Biochemistry 2004; 43:2091-105; PMID:14967049; https://doi.org/ 10.1021/bi030196q [DOI] [PubMed] [Google Scholar]
  • [125].Malka-Gibor E, Kornreich M, Laser-Azogui A, Doron O, Zingerman-Koladko I, Harapin J, Medalia O, Beck R. Phosphorylation-Induced Mechanical Regulation of Intrinsically Disordered Neurofilament Proteins. Biophys J 2017; 112:892-900; PMID:28297648; https://doi.org/ 10.1016/j.bpj.2016.12.050 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [126].Kriz J, Zhu Q, Julien JP, Padjen AL. Electrophysiological properties of axons in mice lacking neurofilament subunit genes: disparity between conduction velocity and axon diameter in absence of NF-H. Brain Res 2000; 885:32-44 PMID:11121527; https://doi.org/ 10.1016/S0006-8993(00)02899-7 [DOI] [PubMed] [Google Scholar]
  • [127].Ackerley S, Thornhill P, Grierson AJ, Brownlees J, Anderton BH, Leigh PN, Shaw CE, Miller CC. Neurofilament heavy chain side arm phosphorylation regulates axonal transport of neurofilaments. J Cell Biol 2003; 161:489-95; PMID:12743103; https://doi.org/ 10.1083/jcb.200303138 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [128].Shea TB, Jung C, Pant HC. Does neurofilament phosphorylation regulate axonal transport? Trends Neurosci 2003; 26:397-400; PMID:12900166; https://doi.org/ 10.1016/S0166-2236(03)00199-1 [DOI] [PubMed] [Google Scholar]
  • [129].Dale JM, Garcia ML. Neurofilament phosphorylation during development and disease: which came first, the phosphorylation or the accumulation? J Amino Acids 2012; 2012:382107; PMID:22570767; https://doi.org/ 10.1155/2012/382107 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [130].Tompa P. The interplay between structure and function in intrinsically unstructured proteins. FEBS Lett 2005; 579:3346-54; PMID:15943980; https://doi.org/ 10.1016/j.febslet.2005.03.072 [DOI] [PubMed] [Google Scholar]
  • [131].Uversky VN. The multifaceted roles of intrinsic disorder in protein complexes. FEBS Lett 2015; 589:2498-506; PMID:26073257; https://doi.org/ 10.1016/j.febslet.2015.06.004 [DOI] [PubMed] [Google Scholar]
  • [132].Teschke CM, King J. Folding and assembly of oligomeric proteins in Escherichia coli. Curr Opin Biotechnol 1992; 3:468-73; PMID:1368931; https://doi.org/ 10.1016/0958-1669(92)90073-R [DOI] [PubMed] [Google Scholar]
  • [133].Xu D, Tsai CJ, Nussinov R. Mechanism and evolution of protein dimerization. Protein Sci 1998; 7:533-44; PMID:9541384; https://doi.org/ 10.1002/pro.5560070117 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [134].Gunasekaran K, Tsai CJ, Nussinov R. Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers. J Mol Biol 2004; 341:1327-41; PMID:15321724; https://doi.org/ 10.1016/j.jmb.2004.07.002 [DOI] [PubMed] [Google Scholar]
  • [135].Fuxreiter M, Toth-Petroczy A, Kraut DA, Matouschek AT, Lim RY, Xue B, Kurgan L, Uversky VN. Disordered proteinaceous machines. Chem Rev 2014; 114:6806-43; PMID:24702702; https://doi.org/ 10.1021/cr4007329 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [136].Peng Z, Oldfield CJ, Xue B, Mizianty MJ, Dunker AK, Kurgan L, Uversky VN. A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome. Cell Mol Life Sci 2014; 71:1477-504; PMID:23942625; https://doi.org/ 10.1007/s00018-013-1446-6 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [137].Peng Z, Mizianty MJ, Xue B, Kurgan L, Uversky VN. More than just tails: intrinsic disorder in histone proteins. Mol Biosyst 2012; 8:1886-901; PMID:22543956; https://doi.org/ 10.1039/c2mb25286d [DOI] [PubMed] [Google Scholar]
  • [138].Muiznieks LD, Weiss AS, Keeley FW. Structural disorder and dynamics of elastin. Biochem Cell Biol 2010; 88:239-50; PMID:20453927; https://doi.org/ 10.1139/O09-161 [DOI] [PubMed] [Google Scholar]
  • [139].Rosenbloom J, Abrams WR, Mecham R. Extracellular matrix 4: the elastic fiber. FASEB J 1993; 7:1208-18; PMID:8405806 [PubMed] [Google Scholar]
  • [140].Visconti RP, Barth JL, Keeley FW, Little CD. Codistribution analysis of elastin and related fibrillar proteins in early vertebrate development. Matrix Biol 2003; 22:109-21; PMID:12782138; https://doi.org/ 10.1016/S0945-053X(03)00014-3 [DOI] [PubMed] [Google Scholar]
  • [141].Mithieux SM, Weiss AS. Elastin. Adv Protein Chem 2005; 70:437-61; PMID:15837523 [DOI] [PubMed] [Google Scholar]
  • [142].Pepe A, Bochicchio B, Tamburro AM. Supramolecular organization of elastin and elastin-related nanostructured biopolymers. Nanomedicine (Lond) 2007; 2:203-18; PMID:17716121; https://doi.org/ 10.2217/17435889.2.2.203 [DOI] [PubMed] [Google Scholar]
  • [143].Tamburro AM. A never-ending love story with elastin: a scientific autobiography. Nanomedicine (Lond) 2009; 4:469-87; PMID:19505248; https://doi.org/ 10.2217/nnm.09.18 [DOI] [PubMed] [Google Scholar]
  • [144].Torchia DA, Piez KA. Mobility of elastin chains as determined by 13C nuclear magnetic resonance. J Mol Biol 1973; 76:419-24; PMID:4738731; https://doi.org/ 10.1016/0022-2836(73)90514-7 [DOI] [PubMed] [Google Scholar]
  • [145].Lyerla JR Jr, Torchia DA. Molecular mobility and structure of elastin deduced from the solvent and temperature dependence of 13C magnetic resonance relaxation data. Biochemistry 1975; 14:5175-83; PMID:1191633; https://doi.org/ 10.1021/bi00694a024 [DOI] [PubMed] [Google Scholar]
  • [146].Perry A, Stypa MP, Foster JA, Kumashiro KK. Observation of the glycines in elastin using (13)C and (15)N solid-state NMR spectroscopy and isotopic labeling. J Am Chem Soc 2002; 124:6832-3; PMID:12059197; https://doi.org/ 10.1021/ja017711x [DOI] [PubMed] [Google Scholar]
  • [147].Pometun MS, Chekmenev EY, Wittebort RJ. Quantitative observation of backbone disorder in native elastin. J Biol Chem 2004; 279:7982-7; PMID:14625282; https://doi.org/ 10.1074/jbc.M310948200 [DOI] [PubMed] [Google Scholar]
  • [148].Shapiro SD, Endicott SK, Province MA, Pierce JA, Campbell EJ. Marked longevity of human lung parenchymal elastic fibers deduced from prevalence of D-aspartate and nuclear weapons-related radiocarbon. J Clin Invest 1991; 87:1828-34; PMID:2022748; https://doi.org/ 10.1172/JCI115204 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [149].Uversky VN. Protein intrinsic disorder-based liquid-liquid phase transitions in biological systems: Complex coacervates and membrane-less organelles. Adv Colloid Interface Sci 2017; 239:97-114; PMID:27291647; https://doi.org/ 10.1016/j.cis.2016.05.012 [DOI] [PubMed] [Google Scholar]
  • [150].Uversky VN. Intrinsically disordered proteins in overcrowded milieu: Membrane-less organelles, phase separation, and intrinsic disorder. Curr Opin Struct Biol 2016; 44:18-30; PMID:27838525; https://doi.org/ 10.1016/j.sbi.2016.10.015 [DOI] [PubMed] [Google Scholar]
  • [151].Uversky VN, Kuznetsova IM, Turoverov KK, Zaslavsky B. Intrinsically disordered proteins as crucial constituents of cellular aqueous two phase systems and coacervates. FEBS Lett 2015; 589:15-22; PMID:25436423; https://doi.org/ 10.1016/j.febslet.2015.06.004 [DOI] [PubMed] [Google Scholar]
  • [152].Brangwynne CP. Phase transitions and size scaling of membrane-less organelles. J Cell Biol 2013; 203:875-81; PMID:24368804; https://doi.org/ 10.1083/jcb.201308087 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [153].Nott TJ, Petsalaki E, Farber P, Jervis D, Fussner E, Plochowietz A, Craggs TD, Bazett-Jones DP, Pawson T, Forman-Kay JD, et al.. Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles. Mol Cell 2015; 57:936-47; PMID:25747659; https://doi.org/ 10.1016/j.molcel.2015.01.013 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [154].Handwerger KE, Cordero JA, Gall JG. Cajal bodies, nucleoli, and speckles in the Xenopus oocyte nucleus have a low-density, sponge-like structure. Mol Biol Cell 2005; 16:202-11; PMID:15509651; https://doi.org/ 10.1091/mbc.E04-08-0742 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [155].Updike DL, Hachey SJ, Kreher J, Strome S. P granules extend the nuclear pore complex environment in the C. elegans germ line. J Cell Biol 2011; 192:939-48; PMID:21402789; https://doi.org/ 10.1083/jcb.201010104 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [156].Brangwynne CP, Eckmann CR, Courson DS, Rybarska A, Hoege C, Gharakhani J, Julicher F, Hyman AA. Germline P granules are liquid droplets that localize by controlled dissolution/condensation. Science 2009; 324:1729-32; PMID:19460965; https://doi.org/ 10.1126/science.1172046 [DOI] [PubMed] [Google Scholar]
  • [157].Brangwynne CP, Mitchison TJ, Hyman AA. Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes. Proc Natl Acad Sci U S A 2011; 108:4334-9; PMID:21368180; https://doi.org/ 10.1073/pnas.1017150108 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [158].Feric M, Brangwynne CP. A nuclear F-actin scaffold stabilizes ribonucleoprotein droplets against gravity in large cells. Nat Cell Biol 2013; 15:1253-9; PMID:23995731; https://doi.org/ 10.1038/ncb2830 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [159].Wippich F, Bodenmiller B, Trajkovska MG, Wanka S, Aebersold R, Pelkmans L. Dual specificity kinase DYRK3 couples stress granule condensation/dissolution to mTORC1 signaling. Cell 2013; 152:791-805; PMID:23415227; https://doi.org/ 10.1016/j.cell.2013.01.033 [DOI] [PubMed] [Google Scholar]
  • [160].Li P, Banjade S, Cheng HC, Kim S, Chen B, Guo L, Llaguno M, Hollingsworth JV, King DS, Banani SF, et al.. Phase transitions in the assembly of multivalent signalling proteins. Nature 2012; 483:336-40; PMID:22398450; https://doi.org/ 10.1038/nature10879 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [161].Aggarwal S, Snaidero N, Pahler G, Frey S, Sanchez P, Zweckstetter M, Janshoff A, Schneider A, Weil MT, Schaap IA, et al.. Myelin membrane assembly is driven by a phase transition of myelin basic proteins into a cohesive protein meshwork. PLoS Biol 2013; 11:e1001577; PMID:23762018; https://doi.org/ 10.1371/journal.pbio.1001577 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [162].Dundr M, Misteli T. Biogenesis of nuclear bodies. Cold Spring Harb Perspect Biol 2010; 2:a000711; PMID:21068152; https://doi.org/ 10.1101/cshperspect.a000711 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [163].Decker M, Jaensch S, Pozniakovsky A, Zinke A, O'Connell KF, Zachariae W, Myers E, Hyman AA. Limiting amounts of centrosome material set centrosome size in C. elegans embryos. Curr Biol 2011; 21:1259-67; PMID:21802300; https://doi.org/ 10.1016/j.cub.2011.06.002 [DOI] [PubMed] [Google Scholar]
  • [164].Chuma S, Hosokawa M, Tanaka T, Nakatsuji N. Ultrastructural characterization of spermatogenesis and its evolutionary conservation in the germline: germinal granules in mammals. Mol Cell Endocrinol 2009; 306:17-23; PMID:19063939; https://doi.org/ 10.1016/j.mce.2008.11.009 [DOI] [PubMed] [Google Scholar]
  • [165].Kiebler MA, Bassell GJ. Neuronal RNA granules: movers and makers. Neuron 2006; 51:685-90; PMID:16982415; https://doi.org/ 10.1016/j.neuron.2006.08.021 [DOI] [PubMed] [Google Scholar]
  • [166].Decker CJ, Teixeira D, Parker R. Edc3p and a glutamine/asparagine-rich domain of Lsm4p function in processing body assembly in Saccharomyces cerevisiae. J Cell Biol 2007; 179:437-49; PMID:17984320; https://doi.org/ 10.1083/jcb.200704147 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [167].Strzelecka M, Trowitzsch S, Weber G, Luhrmann R, Oates AC, Neugebauer KM. Coilin-dependent snRNP assembly is essential for zebrafish embryogenesis. Nat Struct Mol Biol 2010; 17:403-9; https://doi.org/ 10.1038/nsmb.1783 [DOI] [PubMed] [Google Scholar]
  • [168].Li B, Carey M, Workman JL. The role of chromatin during transcription. Cell 2007; 128:707-19; PMID:17320508; https://doi.org/ 10.1016/j.cell.2007.01.015 [DOI] [PubMed] [Google Scholar]
  • [169].Li L, Roy K, Katyal S, Sun X, Bleoo S, Godbout R. Dynamic nature of cleavage bodies and their spatial relationship to DDX1 bodies, Cajal bodies, and gems. Mol Biol Cell 2006; 17:1126-40; PMID:16371507; https://doi.org/ 10.1091/mbc.E05-04-0333 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [170].Nizami Z, Deryusheva S, Gall JG. The Cajal body and histone locus body. Cold Spring Harb Perspect Biol 2010; 2:a000653; PMID:20504965; https://doi.org/ 10.1101/cshperspect.a000653 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [171].Matera AG, Frey MR. Coiled bodies and gems: Janus or gemini? Am J Hum Genet 1998; 63:317-21; PMID:9683623; https://doi.org/ 10.1086/301992 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [172].Gubitz AK, Feng W, Dreyfuss G. The SMN complex. Exp Cell Res 2004; 296:51-6; PMID:15120993; https://doi.org/ 10.1016/j.yexcr.2004.03.022 [DOI] [PubMed] [Google Scholar]
  • [173].Grossman E, Medalia O, Zwerger M. Functional architecture of the nuclear pore complex. Annu Rev Biophys 2012; 41:557-84; PMID:22577827; https://doi.org/ 10.1146/annurev-biophys-050511-102328 [DOI] [PubMed] [Google Scholar]
  • [174].Lamond AI, Spector DL. Nuclear speckles: a model for nuclear organelles. Nat Rev Mol Cell Biol 2003; 4:605-12; PMID:12923522; https://doi.org/ 10.1038/nrm1172 [DOI] [PubMed] [Google Scholar]
  • [175].Biamonti G, Vourc'h C. Nuclear stress bodies. Cold Spring Harb Perspect Biol 2010; 2:a000695; PMID:20516127; https://doi.org/ 10.1101/cshperspect.a000695 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [176].Biamonti G. Nuclear stress bodies: a heterochromatin affair? Nat Rev Mol Cell Biol 2004; 5:493-8; PMID:15173828; https://doi.org/ 10.1038/nrm1405 [DOI] [PubMed] [Google Scholar]
  • [177].Shav-Tal Y, Blechman J, Darzacq X, Montagna C, Dye BT, Patton JG, Singer RH, Zipori D. Dynamic sorting of nuclear components into distinct nucleolar caps during transcriptional inhibition. Mol Biol Cell 2005; 16:2395-413; PMID:15758027; https://doi.org/ 10.1091/mbc.E04-11-0992 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [178].Harrigan JA, Belotserkovskaya R, Coates J, Dimitrova DS, Polo SE, Bradshaw CR, Fraser P, Jackson SP. Replication stress induces 53BP1-containing OPT domains in G1 cells. J Cell Biol 2011; 193:97-108; PMID:21444690; https://doi.org/ 10.1083/jcb.201011083 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [179].Fox AH, Lam YW, Leung AK, Lyon CE, Andersen J, Mann M, Lamond AI. Paraspeckles: a novel nuclear domain. Curr Biol 2002; 12:13-25; PMID:11790299; https://doi.org/ 10.1016/S0960-9822(01)00632-7 [DOI] [PubMed] [Google Scholar]
  • [180].Pirrotta V, Li HB. A view of nuclear Polycomb bodies. Curr Opin Genet Dev 2012; 22:101-9; PMID:22178420; https://doi.org/ 10.1016/j.gde.2011.11.004 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [181].Huang S. Review: perinucleolar structures. J Struct Biol 2000; 129:233-40; PMID:10806073; https://doi.org/ 10.1006/jsbi.2000.4247 [DOI] [PubMed] [Google Scholar]
  • [182].Maul GG, Negorev D, Bell P, Ishov AM. Review: properties and assembly mechanisms of ND10, PML bodies, or PODs. J Struct Biol 2000; 129:278-87; PMID:10806078; https://doi.org/ 10.1006/jsbi.2000.4239 [DOI] [PubMed] [Google Scholar]
  • [183].Elbaum-Garfinkle S, Kim Y, Szczepaniak K, Chen CC, Eckmann CR, Myong S, Brangwynne CP. The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics. Proc Natl Acad Sci U S A 2015; 112:7189-94; PMID:26015579; https://doi.org/ 10.1073/pnas.1504822112 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [184].Mitrea DM, Cika JA, Guy CS, Ban D, Banerjee PR, Stanley CB, Nourse A, Deniz AA, Kriwacki RW. Nucleophosmin integrates within the nucleolus via multi-modal interactions with proteins displaying R-rich linear motifs and rRNA. Elife 2016; 5:pii: e13571; PMID:26836305; https://doi.org/ 10.7554/eLife.13571 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [185].Lin Y, Protter DS, Rosen MK, Parker R. Formation and maturation of phase-separated liquid droplets by RNA-binding proteins. Mol Cell 2015; 60:208-19; PMID:26412307; https://doi.org/ 10.1016/j.molcel.2015.08.018 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [186].Meng F, Na I, Kurgan L, Uversky VN. Compartmentalization and functionality of nuclear disorder: intrinsic disorder and protein-protein interactions in intra-nuclear compartments. Int J Mol Sci 2015; 17:pii: E24; PMID:26712748; https://doi.org/ 10.3390/ijms17010024 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [187].Toretsky JA, Wright PE. Assemblages: functional units formed by cellular phase separation. J Cell Biol 2014; 206:579-88; PMID:25179628; https://doi.org/ 10.1083/jcb.201404124 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [188].Csizmok V, Follis AV, Kriwacki RW, Forman-Kay JD. Dynamic protein interaction networks and new structural paradigms in signaling. Chem Rev 2016; 116(11):6424-62; PMID:26922996; https://doi.org/ 10.1021/acs.chemrev.5b00548 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [189].Cheng Y, Oldfield CJ, Meng J, Romero P, Uversky VN, Dunker AK. Mining alpha-helix-forming molecular recognition features with cross species sequence alignments. Biochemistry 2007; 46:13468-77; PMID:17973494; https://doi.org/ 10.1021/bi0616908 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [190].Mohan A, Oldfield CJ, Radivojac P, Vacic V, Cortese MS, Dunker AK, Uversky VN. Analysis of molecular recognition features (MoRFs). J Mol Biol 2006; 362:1043-59; PMID:16935303; https://doi.org/ 10.1016/j.jmb.2006.07.087 [DOI] [PubMed] [Google Scholar]
  • [191].Dosztanyi Z, Meszaros B, Simon I. ANCHOR: web server for predicting protein binding regions in disordered proteins. Bioinformatics 2009; 25:2745-6; PMID:19717576; https://doi.org/ 10.1093/bioinformatics/btp518 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [192].Meszaros B, Simon I, Dosztanyi Z. Prediction of protein binding regions in disordered proteins. PLoS Comput Biol 2009; 5:e1000376; PMID:19412530; https://doi.org/ 10.1371/journal.pcbi.1000376 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [193].Meszaros B, Dosztanyi Z, Simon I. Disordered binding regions and linear motifs–bridging the gap between two models of molecular recognition. PLoS One 2012; 7:e46829; PMID:23056474; https://doi.org/ 10.1371/journal.pone.0046829 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [194].Boothby TC, Tapia H, Brozena AH, Piszkiewicz S, Smith AE, Giovannini I, Rebecchi L, Pielak GJ, Koshland D, Goldstein B. Tardigrades Use Intrinsically Disordered Proteins to Survive Desiccation. Mol Cell 2017; 65:975-84 e5; PMID:28306513; https://doi.org/ 10.1016/j.molcel.2017.02.018 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [195].Jonsson KI, Rabbow E, Schill RO, Harms-Ringdahl M, Rettberg P. Tardigrades survive exposure to space in low Earth orbit. Curr Biol 2008; 18:R729-R31; PMID:18786368; https://doi.org/ 10.1016/j.cub.2008.06.048 [DOI] [PubMed] [Google Scholar]
  • [196].Goldstein B, Blaxter M. Tardigrades. Curr Biol 2002; 12:R475; PMID:12176341; https://doi.org/ 10.1016/S0960-9822(02)00959-4 [DOI] [PubMed] [Google Scholar]
  • [197].Tompa P, Kovacs D. Intrinsically disordered chaperones in plants and animals. Biochem Cell Biol 2010; 88:167-74; PMID:20453919; https://doi.org/ 10.1139/O09-163 [DOI] [PubMed] [Google Scholar]
  • [198].Hincha DK, Thalhammer A. LEA proteins: IDPs with versatile functions in cellular dehydration tolerance. Biochem Soc Trans 2012; 40:1000-3; PMID:22988854; https://doi.org/ 10.1042/BST20120109 [DOI] [PubMed] [Google Scholar]
  • [199].Graether SP, Boddington KF. Disorder and function: a review of the dehydrin protein family. Front Plant Sci 2014; 5:576; PMID:25400646; https://doi.org/ 10.3389/fpls.2014.00576 [DOI] [PMC free article] [PubMed] [Google Scholar]

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