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Items: 1 to 50 of 206

1.

Specific Conformational Dynamics and Expansion Underpin a Multi-Step Mechanism for Specific Binding of p27 with Cdk2/Cyclin A.

Tsytlonok M, Hemmen K, Hamilton G, Kolimi N, Felekyan S, Seidel CAM, Tompa P, Sanabria H.

J Mol Biol. 2020 Feb 20. pii: S0022-2836(20)30160-1. doi: 10.1016/j.jmb.2020.02.010. [Epub ahead of print]

2.

A guide to regulation of the formation of biomolecular condensates.

Bratek-Skicki A, Pancsa R, Meszaros B, Van Lindt J, Tompa P.

FEBS J. 2020 Feb 20. doi: 10.1111/febs.15254. [Epub ahead of print] Review.

PMID:
32080961
3.

Learning of Signaling Networks: Molecular Mechanisms.

Csermely P, Kunsic N, Mendik P, Kerestély M, Faragó T, Veres DV, Tompa P.

Trends Biochem Sci. 2020 Apr;45(4):284-294. doi: 10.1016/j.tibs.2019.12.005. Epub 2020 Jan 30. Review.

4.

Dehydrin ERD14 activates glutathione transferase Phi9 in Arabidopsis thaliana under osmotic stress.

Nguyen PN, Tossounian MA, Kovacs DS, Thu TT, Stijlemans B, Vertommen D, Pauwels J, Gevaert K, Angenon G, Messens J, Tompa P.

Biochim Biophys Acta Gen Subj. 2020 Mar;1864(3):129506. doi: 10.1016/j.bbagen.2019.129506. Epub 2019 Dec 20.

PMID:
31870857
5.

An intrinsically disordered proteins community for ELIXIR.

Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, Jeffries CM, Le Mercier P, Mészáros B, Necci M, Notredame C, Orchard S, Ouzounis CA, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Promponas VJ, Ruch P, Rustici G, Romero P, Sarntivijai S, Saunders G, Schuler B, Sharan M, Shields DC, Sussman JL, Tedds JA, Tompa P, Turewicz M, Vondrasek J, Vranken WF, Wallace BA, Wichapong K, Tosatto SCE.

F1000Res. 2019 Oct 15;8. pii: ELIXIR-1753. doi: 10.12688/f1000research.20136.1. eCollection 2019.

6.

DisProt: intrinsic protein disorder annotation in 2020.

Hatos A, Hajdu-Soltész B, Monzon AM, Palopoli N, Álvarez L, Aykac-Fas B, Bassot C, Benítez GI, Bevilacqua M, Chasapi A, Chemes L, Davey NE, Davidović R, Dunker AK, Elofsson A, Gobeill J, Foutel NSG, Sudha G, Guharoy M, Horvath T, Iglesias V, Kajava AV, Kovacs OP, Lamb J, Lambrughi M, Lazar T, Leclercq JY, Leonardi E, Macedo-Ribeiro S, Macossay-Castillo M, Maiani E, Manso JA, Marino-Buslje C, Martínez-Pérez E, Mészáros B, Mičetić I, Minervini G, Murvai N, Necci M, Ouzounis CA, Pajkos M, Paladin L, Pancsa R, Papaleo E, Parisi G, Pasche E, Barbosa Pereira PJ, Promponas VJ, Pujols J, Quaglia F, Ruch P, Salvatore M, Schad E, Szabo B, Szaniszló T, Tamana S, Tantos A, Veljkovic N, Ventura S, Vranken W, Dosztányi Z, Tompa P, Tosatto SCE, Piovesan D.

Nucleic Acids Res. 2020 Jan 8;48(D1):D269-D276. doi: 10.1093/nar/gkz975.

PMID:
31713636
7.

PhaSePro: the database of proteins driving liquid-liquid phase separation.

Mészáros B, Erdős G, Szabó B, Schád É, Tantos Á, Abukhairan R, Horváth T, Murvai N, Kovács OP, Kovács M, Tosatto SCE, Tompa P, Dosztányi Z, Pancsa R.

Nucleic Acids Res. 2020 Jan 8;48(D1):D360-D367. doi: 10.1093/nar/gkz848.

PMID:
31612960
8.

Intrinsically Disordered Linkers Impart Processivity on Enzymes by Spatial Confinement of Binding Domains.

Szabo B, Horvath T, Schad E, Murvai N, Tantos A, Kalmar L, Chemes LB, Han KH, Tompa P.

Int J Mol Sci. 2019 Apr 29;20(9). pii: E2119. doi: 10.3390/ijms20092119.

9.

Dynamic anticipation by Cdk2/Cyclin A-bound p27 mediates signal integration in cell cycle regulation.

Tsytlonok M, Sanabria H, Wang Y, Felekyan S, Hemmen K, Phillips AH, Yun MK, Waddell MB, Park CG, Vaithiyalingam S, Iconaru L, White SW, Tompa P, Seidel CAM, Kriwacki R.

Nat Commun. 2019 Apr 11;10(1):1676. doi: 10.1038/s41467-019-09446-w.

10.

Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties.

Boeynaems S, Holehouse AS, Weinhardt V, Kovacs D, Van Lindt J, Larabell C, Van Den Bosch L, Das R, Tompa PS, Pappu RV, Gitler AD.

Proc Natl Acad Sci U S A. 2019 Apr 16;116(16):7889-7898. doi: 10.1073/pnas.1821038116. Epub 2019 Mar 29.

11.

The Balancing Act of Intrinsically Disordered Proteins: Enabling Functional Diversity while Minimizing Promiscuity.

Macossay-Castillo M, Marvelli G, Guharoy M, Jain A, Kihara D, Tompa P, Wodak SJ.

J Mol Biol. 2019 Apr 5;431(8):1650-1670. doi: 10.1016/j.jmb.2019.03.008. Epub 2019 Mar 13.

12.

Emergent functions of proteins in non-stoichiometric supramolecular assemblies.

Pancsa R, Schad E, Tantos A, Tompa P.

Biochim Biophys Acta Proteins Proteom. 2019 Oct;1867(10):970-979. doi: 10.1016/j.bbapap.2019.02.007. Epub 2019 Feb 28. Review.

PMID:
30826453
13.

Calpain Purification Through Calpastatin and Calcium: Strategy and Procedures.

Nguyen HH, Tompa P, Pauwels K.

Methods Mol Biol. 2019;1929:233-244. doi: 10.1007/978-1-4939-9030-6_15.

PMID:
30710277
14.

Misprediction of Structural Disorder in Halophiles.

Pancsa R, Kovacs D, Tompa P.

Molecules. 2019 Jan 29;24(3). pii: E479. doi: 10.3390/molecules24030479.

15.

Does Intrinsic Disorder in Proteins Favor Their Interaction with Lipids?

Deryusheva E, Nemashkalova E, Galloux M, Richard CA, Eléouët JF, Kovacs D, Van Belle K, Tompa P, Uversky V, Permyakov S.

Proteomics. 2019 Mar;19(6):e1800098. doi: 10.1002/pmic.201800098. Epub 2019 Jan 25.

PMID:
30592560
16.

Challenges in the Structural-Functional Characterization of Multidomain, Partially Disordered Proteins CBP and p300: Preparing Native Proteins and Developing Nanobody Tools.

Bekesi A, Abdellaoui S, Holroyd N, Van Delm W, Pardon E, Pauwels J, Gevaert K, Steyaert J, Derveaux S, Borysik A, Tompa P.

Methods Enzymol. 2018;611:607-675. doi: 10.1016/bs.mie.2018.09.032. Epub 2018 Nov 3.

PMID:
30471702
17.

The Melting Diagram of Protein Solutions and Its Thermodynamic Interpretation.

Tompa K, Bokor M, Tompa P.

Int J Mol Sci. 2018 Nov 12;19(11). pii: E3571. doi: 10.3390/ijms19113571.

18.

Co-Evolution of Intrinsically Disordered Proteins with Folded Partners Witnessed by Evolutionary Couplings.

Pancsa R, Zsolyomi F, Tompa P.

Int J Mol Sci. 2018 Oct 25;19(11). pii: E3315. doi: 10.3390/ijms19113315.

19.

Quantification of Intrinsically Disordered Proteins: A Problem Not Fully Appreciated.

Contreras-Martos S, Nguyen HH, Nguyen PN, Hristozova N, Macossay-Castillo M, Kovacs D, Bekesi A, Oemig JS, Maes D, Pauwels K, Tompa P, Lebrun P.

Front Mol Biosci. 2018 Sep 4;5:83. doi: 10.3389/fmolb.2018.00083. eCollection 2018.

20.

Unique Physicochemical Patterns of Residues in Protein-Protein Interfaces.

Lazar T, Guharoy M, Schad E, Tompa P.

J Chem Inf Model. 2018 Oct 22;58(10):2164-2173. doi: 10.1021/acs.jcim.8b00270. Epub 2018 Oct 3.

PMID:
30212197
21.

Disordered Substrates of the 20S Proteasome Link Degradation with Phase Separation.

Guharoy M, Lazar T, Tompa P.

Proteomics. 2018 Nov;18(21-22):e1800276. doi: 10.1002/pmic.201800276. Epub 2018 Aug 20.

PMID:
30070766
22.

Protein Phase Separation: A New Phase in Cell Biology.

Boeynaems S, Alberti S, Fawzi NL, Mittag T, Polymenidou M, Rousseau F, Schymkowitz J, Shorter J, Wolozin B, Van Den Bosch L, Tompa P, Fuxreiter M.

Trends Cell Biol. 2018 Jun;28(6):420-435. doi: 10.1016/j.tcb.2018.02.004. Epub 2018 Mar 27. Review.

23.

Phasing in on the cell cycle.

Boeynaems S, Tompa P, Van Den Bosch L.

Cell Div. 2018 Jan 25;13:1. doi: 10.1186/s13008-018-0034-4. eCollection 2018. Review.

24.

In vivo biotinylated calpastatin improves the affinity purification of human m-calpain.

Nguyen HH, Volkov AN, Vandenbussche G, Tompa P, Pauwels K.

Protein Expr Purif. 2018 May;145:77-84. doi: 10.1016/j.pep.2018.01.002. Epub 2018 Jan 13.

25.

Molecular Motions and Interactions in Aqueous Solutions of Thymosin-β4 , Stabilin C-Terminal Domain (CTD) and Their 1:1 Complex Studied by 1 H NMR Spectroscopy.

Bokor M, Tantos Á, Mészáros A, Jenei B, Haminda R, Tompa P, Tompa K.

Chemphyschem. 2018 Apr 5;19(7):848-856. doi: 10.1002/cphc.201701187. Epub 2018 Feb 16.

PMID:
29274195
26.

Chemical shift assignments of the partially deuterated Fyn SH2-SH3 domain.

Kieken F, Loth K, van Nuland N, Tompa P, Lenaerts T.

Biomol NMR Assign. 2018 Apr;12(1):117-122. doi: 10.1007/s12104-017-9792-1. Epub 2017 Dec 9.

PMID:
29224116
27.

MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins.

Piovesan D, Tabaro F, Paladin L, Necci M, Micetic I, Camilloni C, Davey N, Dosztányi Z, Mészáros B, Monzon AM, Parisi G, Schad E, Sormanni P, Tompa P, Vendruscolo M, Vranken WF, Tosatto SCE.

Nucleic Acids Res. 2018 Jan 4;46(D1):D471-D476. doi: 10.1093/nar/gkx1071.

28.

AmyPro: a database of proteins with validated amyloidogenic regions.

Varadi M, De Baets G, Vranken WF, Tompa P, Pancsa R.

Nucleic Acids Res. 2018 Jan 4;46(D1):D387-D392. doi: 10.1093/nar/gkx950.

29.

Fructose-1,6-bisphosphate couples glycolytic flux to activation of Ras.

Peeters K, Van Leemputte F, Fischer B, Bonini BM, Quezada H, Tsytlonok M, Haesen D, Vanthienen W, Bernardes N, Gonzalez-Blas CB, Janssens V, Tompa P, Versées W, Thevelein JM.

Nat Commun. 2017 Oct 13;8(1):922. doi: 10.1038/s41467-017-01019-z.

30.

A comprehensive assessment of long intrinsic protein disorder from the DisProt database.

Necci M, Piovesan D, Dosztányi Z, Tompa P, Tosatto SCE.

Bioinformatics. 2018 Feb 1;34(3):445-452. doi: 10.1093/bioinformatics/btx590.

PMID:
28968848
31.

Linking functions: an additional role for an intrinsically disordered linker domain in the transcriptional coactivator CBP.

Contreras-Martos S, Piai A, Kosol S, Varadi M, Bekesi A, Lebrun P, Volkov AN, Gevaert K, Pierattelli R, Felli IC, Tompa P.

Sci Rep. 2017 Jul 5;7(1):4676. doi: 10.1038/s41598-017-04611-x.

32.

To be disordered or not to be disordered: is that still a question for proteins in the cell?

Pauwels K, Lebrun P, Tompa P.

Cell Mol Life Sci. 2017 Sep;74(17):3185-3204. doi: 10.1007/s00018-017-2561-6. Epub 2017 Jun 13. Review.

PMID:
28612216
33.

Protein Delivery into Plant Cells: Toward In vivo Structural Biology.

Cedeño C, Pauwels K, Tompa P.

Front Plant Sci. 2017 Apr 19;8:519. doi: 10.3389/fpls.2017.00519. eCollection 2017.

34.

Simultaneous quantification of protein order and disorder.

Sormanni P, Piovesan D, Heller GT, Bonomi M, Kukic P, Camilloni C, Fuxreiter M, Dosztanyi Z, Pappu RV, Babu MM, Longhi S, Tompa P, Dunker AK, Uversky VN, Tosatto SC, Vendruscolo M.

Nat Chem Biol. 2017 Mar 22;13(4):339-342. doi: 10.1038/nchembio.2331. No abstract available.

PMID:
28328918
35.

Affinity purification of human m-calpain through an intrinsically disordered inhibitor, calpastatin.

Nguyen HH, Varadi M, Tompa P, Pauwels K.

PLoS One. 2017 Mar 20;12(3):e0174125. doi: 10.1371/journal.pone.0174125. eCollection 2017.

36.

Phase Separation of C9orf72 Dipeptide Repeats Perturbs Stress Granule Dynamics.

Boeynaems S, Bogaert E, Kovacs D, Konijnenberg A, Timmerman E, Volkov A, Guharoy M, De Decker M, Jaspers T, Ryan VH, Janke AM, Baatsen P, Vercruysse T, Kolaitis RM, Daelemans D, Taylor JP, Kedersha N, Anderson P, Impens F, Sobott F, Schymkowitz J, Rousseau F, Fawzi NL, Robberecht W, Van Damme P, Tompa P, Van Den Bosch L.

Mol Cell. 2017 Mar 16;65(6):1044-1055.e5. doi: 10.1016/j.molcel.2017.02.013.

37.

1H, 15N, 13C resonance assignment of plant dehydrin early response to dehydration 10 (ERD10).

Cedeño C, Żerko S, Tompa P, Koźmiński W.

Biomol NMR Assign. 2017 Oct;11(2):127-131. doi: 10.1007/s12104-017-9732-0. Epub 2017 Mar 8.

PMID:
28275980
38.

Hydrogen Mobility and Protein-Water Interactions in Proteins in the Solid State.

Tompa K, Bokor M, Ágner D, Iván D, Kovács D, Verebélyi T, Tompa P.

Chemphyschem. 2017 Mar 17;18(6):677-682. doi: 10.1002/cphc.201601136. Epub 2017 Feb 7.

PMID:
28066974
39.

Corrigendum: DisProt 7.0: a major update of the database of disordered proteins.

Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SC.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1123-D1124. doi: 10.1093/nar/gkw1279. Epub 2016 Dec 13. No abstract available.

40.

DisProt 7.0: a major update of the database of disordered proteins.

Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SC.

Nucleic Acids Res. 2017 Jan 4;45(D1):D219-D227. doi: 10.1093/nar/gkw1056. Epub 2016 Nov 28. Erratum in: Nucleic Acids Res. 2017 Jan 4;45(D1):D1123-D1124.

41.

Phosphorylation of MAP65-1 by Arabidopsis Aurora Kinases Is Required for Efficient Cell Cycle Progression.

Boruc J, Weimer AK, Stoppin-Mellet V, Mylle E, Kosetsu K, Cedeño C, Jaquinod M, Njo M, De Milde L, Tompa P, Gonzalez N, Inzé D, Beeckman T, Vantard M, Van Damme D.

Plant Physiol. 2017 Jan;173(1):582-599. doi: 10.1104/pp.16.01602. Epub 2016 Nov 22.

42.

Coding Regions of Intrinsic Disorder Accommodate Parallel Functions.

Pancsa R, Tompa P.

Trends Biochem Sci. 2016 Nov;41(11):898-906. doi: 10.1016/j.tibs.2016.08.009. Epub 2016 Sep 16. Review.

PMID:
27647212
43.

Essential functions linked with structural disorder in organisms of minimal genome.

Pancsa R, Tompa P.

Biol Direct. 2016 Sep 8;11:45. doi: 10.1186/s13062-016-0149-y.

44.

A Novel Method for Assessing the Chaperone Activity of Proteins.

Hristozova N, Tompa P, Kovacs D.

PLoS One. 2016 Aug 26;11(8):e0161970. doi: 10.1371/journal.pone.0161970. eCollection 2016.

45.

Computational analysis of translational readthrough proteins in Drosophila and yeast reveals parallels to alternative splicing.

Pancsa R, Macossay-Castillo M, Kosol S, Tompa P.

Sci Rep. 2016 Aug 26;6:32142. doi: 10.1038/srep32142.

46.

Molecular Mechanism of SSR128129E, an Extracellularly Acting, Small-Molecule, Allosteric Inhibitor of FGF Receptor Signaling.

Herbert C, Schieborr U, Saxena K, Juraszek J, De Smet F, Alcouffe C, Bianciotto M, Saladino G, Sibrac D, Kudlinzki D, Sreeramulu S, Brown A, Rigon P, Herault JP, Lassalle G, Blundell TL, Rousseau F, Gils A, Schymkowitz J, Tompa P, Herbert JM, Carmeliet P, Gervasio FL, Schwalbe H, Bono F.

Cancer Cell. 2016 Jul 11;30(1):176-178. doi: 10.1016/j.ccell.2016.06.015. Epub 2016 Jul 11. No abstract available.

47.

Editorial: Function and Flexibility: Friend or Foe?

Pauwels K, Tompa P.

Front Mol Biosci. 2016 Jul 7;3:31. doi: 10.3389/fmolb.2016.00031. eCollection 2016. No abstract available.

48.

Wide-line NMR and DSC studies on intrinsically disordered p53 transactivation domain and its helically pre-structured segment.

Tompa P, Han KH, Bokor M, Kamasa P, Tantos Á, Fritz B, Kim DH, Lee C, Verebélyi T, Tompa K.

BMB Rep. 2016 Sep;49(9):497-501.

49.

Numerous proteins with unique characteristics are degraded by the 26S proteasome following monoubiquitination.

Braten O, Livneh I, Ziv T, Admon A, Kehat I, Caspi LH, Gonen H, Bercovich B, Godzik A, Jahandideh S, Jaroszewski L, Sommer T, Kwon YT, Guharoy M, Tompa P, Ciechanover A.

Proc Natl Acad Sci U S A. 2016 Aug 9;113(32):E4639-47. doi: 10.1073/pnas.1608644113. Epub 2016 Jul 6.

50.

Intrinsic protein disorder in histone lysine methylation.

Lazar T, Schad E, Szabo B, Horvath T, Meszaros A, Tompa P, Tantos A.

Biol Direct. 2016 Jun 30;11:30. doi: 10.1186/s13062-016-0129-2.

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