In various protein complexes, disordered protomers have large per-residue surface areas and area of protein-, DNA- and RNA-binding interfaces.

Abstract:

:We provide first large scale analysis of the peculiarities of surface areas of 5658 dissimilar (below 50% sequence similarity) proteins with known 3D-structures that bind to proteins, DNA or RNAs. We show here that area of the protein surface is highly correlated with the protein length. The size of the interface surface is only modestly correlated with the protein size, except for RNA-binding proteins where larger proteins are characterized by larger interfaces. Disordered proteins with disordered interfaces are characterized by significantly larger per-residue areas of their surfaces and interfaces when compared to the structured proteins. These result are applicable for proteins involved in interaction with DNA, RNA, and proteins and suggest that disordered proteins and binding regions are less compact and more likely to assume extended shape. We demonstrate that disordered protein binding residues in the interfaces of disordered proteins drive the increase in the per residue area of these interfaces. Our results can be used to predict in silico whether a given protomer from the DNA, RNA or protein complex is likely to be disordered in its unbound form.

journal_name

FEBS Lett

journal_title

FEBS letters

authors

Wu Z,Hu G,Yang J,Peng Z,Uversky VN,Kurgan L

doi

10.1016/j.febslet.2015.08.014

subject

Has Abstract

pub_date

2015-09-14 00:00:00

pages

2561-9

issue

19 Pt A

eissn

0014-5793

issn

1873-3468

pii

S0014-5793(15)00713-9

journal_volume

589

pub_type

杂志文章
  • Evolution of visual pigments in geckos.

    abstract::Most geckos are nocturnal forms and possess rod retinas, but some diurnal genera have pure-cone retinas. We isolated cDNAs encoding the diurnal gecko opsins, dg1 and dg2, similar to nocturnal gecko P521 and P467, respectively. Despite the large morphological differences between the diurnal and nocturnal gecko photorec...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(99)00089-7

    authors: Taniguchi Y,Hisatomi O,Yoshida M,Tokunaga F

    更新日期:1999-02-19 00:00:00

  • The KDEL receptor: new functions for an old protein.

    abstract::The KDEL receptor is a seven-transmembrane-domain protein that was first described about 20 years ago. Its well-known function is to retrotransport chaperones from the Golgi complex to the endoplasmic reticulum. Recent studies, however, have suggested that the KDEL receptor has additional functions. Indeed, we have de...

    journal_title:FEBS letters

    pub_type: 杂志文章,评审

    doi:10.1016/j.febslet.2009.10.053

    authors: Capitani M,Sallese M

    更新日期:2009-12-03 00:00:00

  • Esmolol is antiarrhythmic in doxorubicin-induced arrhythmia in cultured cardiomyocytes - determination by novel rapid cardiomyocyte assay.

    abstract::Cardiac toxicity is an uncommon but potentially serious complication of cancer therapy, especially with anthracyclines. One of the most effective anticancer drugs is doxorubicin, but its value is limited by the risk of developing cardiomyopathy and ventricular arrhythmia. When applied to a network of periodically cont...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(03)00743-9

    authors: Gorelik J,Vodyanoy I,Shevchuk AI,Diakonov IA,Lab MJ,Korchev YE

    更新日期:2003-07-31 00:00:00

  • Inhibitors of phosphoprotein phosphatases 1 and 2A cause activation of a 53 kDa protein kinase accompanying the apoptotic response of breast cancer cells.

    abstract::Treatment of MCF-7 breast cancer cells with 50 nM okadaic acid triggers an apoptotic response which is accompanied by a 7-fold increase in the activity of a protein kinase with a relative molecular mass of 53 kDa. The activity of the kinase was stimulated by cell treatment with inhibitors of phosphoprotein phosphatase...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(97)00659-5

    authors: Rossini GP,Pinna C,Viviani R

    更新日期:1997-06-30 00:00:00

  • Translation of tobacco chloroplast rps14 mRNA depends on a Shine-Dalgarno-like sequence in the 5'-untranslated region but not on internal RNA editing in the coding region.

    abstract::The role of Shine-Dalgarno-like sequences in mRNAs from higher plant chloroplasts has not been analyzed experimentally so far. In vitro translation analysis has revealed that the Shine-Dalgarno-like sequence is essential for translation of tobacco chloroplast rps14 mRNA. Two RNA editing sites have been identified in t...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(98)00673-5

    authors: Hirose T,Kusumegi T,Sugiura M

    更新日期:1998-07-03 00:00:00

  • Cloning and functional expression of a tetrabenazine sensitive vesicular monoamine transporter from bovine chromaffin granules.

    abstract::Using oligonucleotide primers derived from the vesicular monoamine transporters sequences, a cDNA predicted to encode the bovine chromaffin granule amine transporter has been cloned (b-VMAT2). Surprisingly, its structure is more similar to the rat brain transporter (VMAT2), than to the rat adrenal counterpart (VMAT1)....

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(94)80108-8

    authors: Howell M,Shirvan A,Stern-Bach Y,Steiner-Mordoch S,Strasser JE,Dean GE,Schuldiner S

    更新日期:1994-01-24 00:00:00

  • Potentiation of the antagonistic effect of ACTH11-24 on steroidogenesis by synthesis of covalent dimeric conjugates.

    abstract::Covalent dimerization of the adrenocorticotropin fragment ACTH11-24 increases its antagonistic potency on the ACTH-induced steroidogenesis in isolated bovine fasciculata/reticularis cells by 3 orders of magnitude when the C-termini are linked via a 10 A long spacer. This strong potentiation, probably mediated by cross...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(85)80794-8

    authors: Fauchère JL,Rossier M,Capponi A,Vallotton MB

    更新日期:1985-04-22 00:00:00

  • Vapor-phase modification of sulfhydryl groups in proteins.

    abstract::Proteins and peptides are readily and specifically modified at their sulfhydryl groups by the vapors of a mixture of 4-vinylpyridine and tributylphosphine. The phenylthiohydantoin derivative of S-beta-(4-pyridylethyl)cysteine formed during sequence analysis is easily detectable in current identification systems. ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(87)81558-2

    authors: Amons R

    更新日期:1987-02-09 00:00:00

  • Calcium mobilization and Na+/H+ antiport activation by endothelin in human skin fibroblasts.

    abstract::Endothelin (ET-1) has been shown to exert vasoconstrictor activity in vivo and mobilize Ca2+ in vascular smooth muscle cells in culture. In this paper we show that the human skin fibroblast exhibits specific receptors to ET-1 and that activation of these receptors results in increased intracellular Ca2+ (Ca2+i) and ac...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(89)81713-2

    authors: Gardner JP,Maher E,Aviv A

    更新日期:1989-10-09 00:00:00

  • A unified framework for unraveling the functional interaction structure of a biomolecular network based on stimulus-response experimental data.

    abstract::We propose a unified framework for the identification of functional interaction structures of biomolecular networks in a way that leads to a new experimental design procedure. In developing our approach, we have built upon previous work. Thus we begin by pointing out some of the restrictions associated with existing s...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2005.07.025

    authors: Cho KH,Choo SM,Wellstead P,Wolkenhauer O

    更新日期:2005-08-15 00:00:00

  • Guinea pig copeptin. The glycopeptide domain of the vasopressin precursor.

    abstract::The vasopressin precursor is composed of 3 domains in line, namely vasopressin, MSEL-neurophysin and a glycopeptide referred to as copeptin, which are separated during the processing. In guinea pig neurohypophysis, the precursor is partially processed so that a two-domain fragment, MSEL-neurophysin--copeptin, can be f...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(86)80320-9

    authors: Chauvet MT,Chauvet J,Acher R

    更新日期:1986-03-03 00:00:00

  • On the biosynthesis of free and covalently bound PQQ. Glutamic acid decarboxylase from Escherichia coli is a pyridoxo-quinoprotein.

    abstract::Analysis of glutamic acid decarboxylase (GDC) (EC 4.1.1.15) from Escherichia coli ATCC 11246 revealed the presence of six pyridoxal phosphates (PLPs) as well as six covalently bound pyrroloquinoline quinones (PQQs) per hexameric enzyme molecule. This is the second example of a pyridoxo-quinoprotein, suggesting that ot...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(89)80263-7

    authors: van der Meer RA,Groen BW,Duine JA

    更新日期:1989-03-27 00:00:00

  • Stimulation of glyceraldehyde-3-phosphate dehydrogenase by oxyhemoglobin.

    abstract::Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a key glycolytic enzyme regulated by many diverse mechanisms. In this study we present evidence that GAPDH activity is stimulated in the presence of oxyhemoglobin (2.3-fold, P < 0.005). No stimulation was seen by myoglobin, and only slight stimulation (1.2-fold, not ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(97)01181-2

    authors: Brookes PS,Land JM,Clark JB,Heales SJ

    更新日期:1997-10-13 00:00:00

  • Denaturation and partial renaturation of a tightly tetramerized DsRed protein under mildly acidic conditions.

    abstract::The red fluorescent protein, DsRed, recently cloned from coral Discosoma sp. has one of the longest fluorescence waves and one of the most complex absorbance spectra among the family of fluorescent proteins. In this work we found that with time DsRed fluorescence decreases under mildly acidic conditions (pH 4.0-4.8) i...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(00)02344-9

    authors: Vrzheshch PV,Akovbian NA,Varfolomeyev SD,Verkhusha VV

    更新日期:2000-12-29 00:00:00

  • HIV-1 envelope protein, gp120, has no effects on inositol phosphate production and metabolism in the Jurkat T-cell line either in the presence or absence of receptor stimulation.

    abstract::We have used HPLC techniques to investigate the effects of gp120 upon inositol phosphate turnover in Jurkat E6-1 CD4+ T-cells, to pursue previous reports that this viral coat protein: (a) inhibits receptor-activated inositol phosphate release; (b) stimulates basal inositol phosphate release; (c) inhibits inositol poly...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(97)00880-6

    authors: Sumner MT,Shears SB

    更新日期:1997-08-11 00:00:00

  • Observation of the pre-steady state process in thermolysin catalysis with a fluorescent displacement probe at low pH.

    abstract::The pre-steady state process in the thermolysin-catalyzed hydrolysis of Cbz-Gly-Phe-Ala was observed at pH 4.5 by fluorescence stopped-flow method using Dns-Phe as a displacement probe. After the confirmation of the pre-equilibrium hypothesis for the binary interaction, the nonlinear substrate concentration dependence...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(95)00242-2

    authors: Kunugi S,Yokoyama M,Sakamoto A

    更新日期:1995-04-03 00:00:00

  • Characterization of Arabidopsis decapping proteins AtDCP1 and AtDCP2, which are essential for post-embryonic development.

    abstract::Although decapping is an important process in eukaryotic mRNA turnover, little is known about this process in plants. Here, we identified Arabidopsis thaliana decapping proteins AtDCP1 and AtDCP2 and showed that (I) AtDCP2 is an active decapping enzyme, (II) AtDCP1 interacts with itself, (III) AtDCP1 and AtDCP2 are lo...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2007.04.051

    authors: Iwasaki S,Takeda A,Motose H,Watanabe Y

    更新日期:2007-05-29 00:00:00

  • Purification of Escherichia coli 50 S ribosomal proteins by high performance liquid chromatography.

    abstract::The 50 S subunit proteins from the Escherichia coli ribosome were purified by size-exclusion, ion-exchange or reversed phase high performance liquid chromatography (HPLC) avoiding any precipitation or desalting procedures during isolation. Best resolution of this complex protein mixture was achieved by reversed phase ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(84)80832-7

    authors: Kamp RM,Wittmann-Liebold B

    更新日期:1984-02-13 00:00:00

  • Localization of leptin receptor mRNA and the long form splice variant (Ob-Rb) in mouse hypothalamus and adjacent brain regions by in situ hybridization.

    abstract::Expression of the leptin receptor gene has been examined in mouse hypothalamus and other brain regions by in situ hybridization. With a probe recognizing all the known splice variants, receptor mRNA was evident in several brain regions (cortex, hippocampus, thalamus), with strong expression in the hypothalamus (arcuat...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(96)00473-5

    authors: Mercer JG,Hoggard N,Williams LM,Lawrence CB,Hannah LT,Trayhurn P

    更新日期:1996-06-03 00:00:00

  • Mitogen-stimulated events in nuclei of Swiss 3T3 cells. Evidence for a direct link between changes of inositol lipids, protein kinase C requirement and the onset of DNA synthesis.

    abstract::Two different clones of Swiss 3T3 cells belonging to the same original cell line have been obtained, one of which was unresponsive to mitogenic stimulation (e.g. insulin-like growth factor-I, bombesin, insulin-like growth factor-I + bombesin), while the other clone showed a very high rate of DNA synthesis under identi...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(91)80598-w

    authors: Martelli AM,Gilmour RS,Neri LM,Manzoli L,Corps AN,Cocco L

    更新日期:1991-06-03 00:00:00

  • A novel human UDP-N-acetyl-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase, GalNAc-T7, with specificity for partial GalNAc-glycosylated acceptor substrates.

    abstract::A novel member of the human UDP-N-acetyl-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase gene family, designated GalNAc-T7, was cloned and expressed. GalNAc-T7 exhibited different properties compared to other characterized members of this gene family, in showing apparent exclusive specificity for partial...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(99)01268-5

    authors: Bennett EP,Hassan H,Hollingsworth MA,Clausen H

    更新日期:1999-10-29 00:00:00

  • RNA/DNA hybrid duplexes with identical nearest-neighbor base-pairs have identical stability.

    abstract::Energetic behaviors of eight pairs of RNA/DNA hybrid duplexes with identical nearest neighbors have been investigated by UV melting analysis. In the pairs with identical nearest-neighbor pairs, the melting curve traces at the same strand concentration were very similar. The average difference in stabilization energy o...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(94)01098-6

    authors: Sugimoto N,Katoh M,Nakano S,Ohmichi T,Sasaki M

    更新日期:1994-10-31 00:00:00

  • A complex peptide-sorting signal, but no mRNA signal, is required for the Sec-independent transport of Ist2 from the yeast ER to the plasma membrane.

    abstract::The yeast integral plasma membrane protein Ist2 belongs to a group of membrane proteins which are synthesized from localized mRNAs. The protein reaches the plasma membrane via the ER on a route operating independently of the classical secretory pathway. We have identified a complex peptide-sorting signal located at th...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2006.12.048

    authors: Franz A,Maass K,Seedorf M

    更新日期:2007-02-06 00:00:00

  • Transient expression of botulinum neurotoxin C1 light chain differentially inhibits calcium and glucose induced insulin secretion in clonal beta-cells.

    abstract::We have investigated the effect of botulinum neurotoxin (BoNT) C1 light chain (LC) on insulin exocytosis from the clonal beta-cell line HIT-T15. In streptolysin-O permeabilized cells, the beta-cell impermeant BoNT C1 cleaved mainly syntaxin 1 and inhibited Ca2+ as well as GTPgammaS induced exocytosis. To study the eff...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(97)01411-7

    authors: Land J,Zhang H,Vaidyanathan VV,Sadoul K,Niemann H,Wollheim CB

    更新日期:1997-12-08 00:00:00

  • Inhibition of lipid peroxidation by ubiquinol in submitochondrial particles in the absence of vitamin E.

    abstract::The relationship between the antioxidant effects of reduced coenzyme Q10 (ubiquinol, UQH2) and vitamin E (alpha-tocopherol) was investigated in beef heart submitochondrial particles in which lipid peroxidation was initiated by incubation with ascorbate + ADP-Fe3+. These effects were examined after extraction of coenzy...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(91)80720-n

    authors: Forsmark P,Aberg F,Norling B,Nordenbrand K,Dallner G,Ernster L

    更新日期:1991-07-08 00:00:00

  • Two species of phospholipase C isolated from lymphocytes produce specific ratios of inositol phosphate products.

    abstract::Chromatography of the soluble porcine lymphocyte phospholipase C on cellulose phosphate resolves the activity into two species. An HPLC method is described for separating the enzyme products, Ins 1,2 greater than P and Ins 1P. Use of these methods reveals that the two iso-enzymes liberate, with a high degree of reprod...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(86)81380-1

    authors: Carter HR,Bird IM,Smith AD

    更新日期:1986-08-11 00:00:00

  • Protein-based phylogenetic analysis by using hydropathy profile of amino acids.

    abstract::So far, various approaches for phylogenetic analysis have been developed. Almost all of them put stress on analyzing nucleic acid sequences or protein primary structures. In this paper, we take the physicochemical properties of amino acids into account and introduce the hydropathy profile of amino acids into phylogene...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2006.08.086

    authors: Liu N,Wang T

    更新日期:2006-10-02 00:00:00

  • A putative internal promoter in the 16 S/23 S intergenic spacer of the rRNA operon of archaebacteria and eubacteria.

    abstract::The existence of the internal promoter Pi in the 16 S/23 S intergenic spacers of the rRNA operons of an eubacterium Escherichia coli and archaebacterium Halobacterium halobium is proposed. The possible functional significance of these promoters is discussed. ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(87)80233-8

    authors: Mankin AS,Skripkin EA,Kagramanova VK

    更新日期:1987-07-27 00:00:00

  • Impact of 9-(2-phosphonylmethoxyethyl)adenine on (deoxy)ribonucleotide metabolism and nucleic acid synthesis in tumor cells.

    abstract::Following exposure to 9-(2-phosphonylmethoxyethyl)adenine (an inhibitor of the cellular DNA polymerases alpha, delta and epsilon), human erythroleukemia K562, human T-lymphoid CEM and murine leukemia L1210 cells markedly accumulated in the S phase of the cell cycle. In contrast to DNA replication, RNA synthesis (trans...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(99)00104-0

    authors: Hatse S,De Clercq E,Balzarini J

    更新日期:1999-02-19 00:00:00

  • Seminalplasmin and caltrin are the same protein.

    abstract::The sequence of seminalplasmin, a basic antimicrobial and transcription-inhibitory protein from bovine seminal plasma, has been determined using an automated sequenator. This sequence is slightly different from that reported earlier by Theil and Scheit [(1983) EMBO J. 2, 1159-1163] and identical with that of caltrin, ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(86)80615-9

    authors: Sitaram N,Kumari VK,Bhargava PM

    更新日期:1986-06-09 00:00:00