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Publications
How proteins sense their cellular environment.
Fuxreiter M
Nat Rev Mol Cell Biol. 2024 Nov 28. doi: 10.1038/s41580-024-00812-1. Online ahead of print. PMID: 39609649
Arc mediates intercellular tau transmission via extracellular vesicles.
Tyagi M, Chadha R, de Hoog E, Sullivan KR, Walker AC, Northrop A, Fabian B, Fuxreiter M, Hyman BT, Shepherd JD.
bioRxiv [Preprint]. 2024 Oct 22:2024.10.22.619703. doi: 10.1101/2024.10.22.619703. PMID: 39484489
FuzDrop: Sequence-Based Prediction of the Propensity of Proteins for Liquid-Liquid Phase Separation and Aggregation.
Vendruscolo M, Fuxreiter M
Nature Protocols under review. 2024
Towards universal models for collective interactions in biomolecular condensates.
Milanetti E, Manjunatha KKH, Ruocco GC, Maritan A, Fuxreiter M
Biophysics Reviews 2024. doi: 10.1101/2024.10.17.618883
Fuzzy protein-DNA interactions and beyond: A common theme in transcription?
Komives E, Sanchez-Rodriguez R, Taghavi H, Fuxreiter M
Curr Opin Struct Biol. 2024 Dec;89:102941. doi: 10.1016/j.sbi.2024.102941. Epub 2024 Oct 17. PMID: 39423710
A scale-invariant log-normal droplet size distribution below the critical concentration for protein phase separation.
Amico T, Dada ST, Lazzari A, Brezinova M, Trovato A, Vendruscolo M, Fuxreiter M, Maritan A
Elife. 2024 Nov 18;13:RP94214. doi: 10.7554/eLife.94214. PMID: 39556435
Context-dependent, fuzzy protein interactions: Towards sequence-based insights.
Fuxreiter M
Curr Opin Struct Biol. 2024 Aug;87:102834. doi: 10.1016/j.sbi.2024.102834. Epub 2024 May 16. PMID: 3875929
Multiomic prediction of therapeutic targets for human diseases associated with protein phase separation.
Lim CM, González Díaz A, Fuxreiter M, Pun FW, Zhavoronkov A, Vendruscolo M
Proc Natl Acad Sci U S A. 2023 Oct 3;120(40):e2300215120. doi: 10.1073/pnas.2300215120. Epub 2023 Sep 29. PMID: 37774095
Towards sequence-based principles for protein phase separation predictions.
Vendruscolo M, Fuxreiter M.
Curr Opin Chem Biol. 2023 May 17;75:102317. doi: 10.1016/j.cbpa.2023.102317. Online ahead of print. PMID: 37207400
FuzPred: a web server for the sequence-based prediction of the context-dependent binding modes of proteins.
Hatos A, Teixeira JM, Barrera-Vilarmau S, Horvath A, Tosatto SCE, Vendruscolo M, Fuxreiter M.
Nucleic Acids Res. 2023 Mar 29:gkad214. doi: 10.1093/nar/gkad214. Online ahead of print. PMID: 36987846
Alternatively spliced exon regulates context-dependent MEF2D higher-order assembly during myogenesis.
Gönczi M, Teixeira JMC, Barrera-Vilarmau S, Mediani L, Antoniani F, Nagy TM, Fehér K, Ráduly Z, Ambrus V, Tőzsér J, Barta E, Kövér KE, Csernoch L, Carra S, Fuxreiter M.
Nat Commun. 2023 Mar 10;14(1):1329. doi: 10.1038/s41467-023-37017-7. PMID: 36898987
Protein condensation diseases: therapeutic opportunities.
Vendruscolo M, Fuxreiter M.
Nat Commun. 2022 Sep 22;13(1):5550. doi: 10.1038/s41467-022-32940-7. PMID: 36138006
Sequence-based Prediction of the Cellular Toxicity Associated with Amyloid Aggregation within Protein Condensates.
Horvath A, Vendruscolo M, Fuxreiter M.
Biochemistry. 2022 Nov 15;61(22):2461-2469. doi: 10.1021/acs.biochem.2c00499. Epub 2022 Nov 7. PMID: 36341999
Protein interactions: anything new?
Barrera-Vilarmau S, Teixeira JMC, Fuxreiter M.
Essays Biochem. 2022 Dec 16;66(7):821-830. doi: 10.1042/EBC20220044. PMID: 36416856
Electrostatics tunes protein interactions to context.
Fuxreiter M.
Proc Natl Acad Sci U S A. 2022 Aug 2;119(31):e2209201119. doi: 10.1073/pnas.2209201119. Epub 2022 Jul 15.PMID: 35858387 Free PMC article. No abstract available.
Are casein micelles extracellular condensates formed by liquid-liquid phase separation?
Horvath A, Fuxreiter M, Vendruscolo M, Holt C, Carver JA.
FEBS Lett. 2022 Aug;596(16):2072-2085. doi: 10.1002/1873-3468.14449. Epub 2022 Jul 18.PMID: 35815989 Review.
Editorial: Fuzzy Interactions: Many Facets of Protein Binding.
Piovesan D, Arbesú M, Fuxreiter M, Pons M.
Front Mol Biosci. 2022 Jun 20;9:947215. doi: 10.3389/fmolb.2022.947215. eCollection 2022.PMID: 35795824 Free PMC article. No abstract available.
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid-liquid phase separation and aggregation of proteins.
Hatos A, Tosatto SCE, Vendruscolo M, Fuxreiter M.
Nucleic Acids Res. 2022 May 24;50(W1):W337-44. doi: 10.1093/nar/gkac386. Online ahead of print.PMID: 35610022 Free PMC article.
Proteome-wide landscape of solubility limits in a bacterial cell.
Györkei Á, Daruka L, Balogh D, Őszi E, Magyar Z, Szappanos B, Fekete G, Fuxreiter M, Horváth P, Pál C, Kintses B, Papp B.
Sci Rep. 2022 Apr 21;12(1):6547. doi: 10.1038/s41598-022-10427-1.
Adventures on the Routes of Protein Evolution-In Memoriam Dan Salah Tawfik (1955-2021).
Jackson C, Toth-Petroczy A, Kolodny R, Hollfelder F, Fuxreiter M, Kamerlin SCL, Tokuriki N.
J Mol Biol. 2022 Apr 15;434(7):167462. doi: 10.1016/j.jmb.2022.167462. Epub 2022 Jan 29.
Protein interactions in liquid-liquid phase separation.
Fuxreiter M.
J Mol Biol. 2022 Jan 15;434(1):167388. doi: 10.1016/j.jmb.2021.167388. Epub 2021 Dec 3.
Sequence Determinants of the Aggregation of Proteins Within Condensates Generated by Liquid-liquid Phase Separation.
Vendruscolo M, Fuxreiter M.
J Mol Biol. 2022 Jan 15;434(1):167201. doi: 10.1016/j.jmb.2021.167201. Epub 2021 Aug 12.
FuzDB: a new phase in understanding fuzzy interactions.
Hatos A, Monzon AM, Tosatto SCE, Piovesan D, Fuxreiter M.
Nucleic Acids Res. 2022 Jan 7;50(D1):D509-D517. doi: 10.1093/nar/gkab1060.
Molecular Determinants of Selectivity in Disordered Complexes May Shed Light on Specificity in Protein Condensates.
Monzon AM, Piovesan D, Fuxreiter M.
Biomolecules. 2022 Jan 6;12(1):92. doi: 10.3390/biom12010092.
Observation of an α-synuclein liquid droplet state and its maturation into Lewy body-like assemblies.
Hardenberg MC, Sinnige T, Casford S, Dada ST, Poudel C, Robinson EA, Fuxreiter M, Kaminksi CF, Kaminski Schierle GS, Nollen EAA, Dobson CM, Vendruscolo M.
J Mol Cell Biol. 2021 Aug 4;13(4):282-294. doi: 10.1093/jmcb/mjaa075.
Generic nature of the condensed states of proteins.
Fuxreiter M, Vendruscolo M.
Nat Cell Biol. 2021 Jun;23(6):587-594. doi: 10.1038/s41556-021-00697-8. Epub 2021 Jun 9.
Frustration in Fuzzy Protein Complexes Leads to Interaction Versatility.
Freiberger MI, Wolynes PG, Ferreiro DU, Fuxreiter M.
J Phys Chem B. 2021 Mar 18;125(10):2513-2520. doi: 10.1021/acs.jpcb.0c11068. Epub 2021 Mar 5.
Fuzziness and Frustration in the Energy Landscape of Protein Folding, Function, and Assembly.
Gianni S, Freiberger MI, Jemth P, Ferreiro DU, Wolynes PG, Fuxreiter M.
Acc Chem Res. 2021 Mar 2;54(5):1251-1259. doi: 10.1021/acs.accounts.0c00813. Epub 2021 Feb 8.
Spot in a drop: mutations in aberrant condensates.
Fuxreiter M.
Nat Rev Mol Cell Biol. 2021 Mar;22(3):162-163. doi: 10.1038/s41580-021-00338-w.
MobiDB: intrinsically disordered proteins in 2021.
Piovesan D, Necci M, Escobedo N, Monzon AM, Hatos A, Mičetić I, Quaglia F, Paladin L, Ramasamy P, Dosztányi Z, Vranken WF, Davey NE, Parisi G, Fuxreiter M, Tosatto SCE.
Nucleic Acids Res. 2021 Jan 8;49(D1):D361-D367. doi: 10.1093/nar/gkaa1058.
Widespread occurrence of the droplet state of proteins in the human proteome.
Hardenberg M, Horvath A, Ambrus V, Fuxreiter M, Vendruscolo M.
Proc Natl Acad Sci U S A. 2020 Dec 29;117(52):33254-33262. doi: 10.1073/pnas.2007670117. Epub 2020 Dec 14.
Fuzzy protein theory for disordered proteins.
Fuxreiter M.
Biochem Soc Trans. 2020 Dec 18;48(6):2557-2564. doi: 10.1042/BST20200239.
Classifying the Binding Modes of Disordered Proteins.
Fuxreiter M.
Int J Mol Sci. 2020 Nov 16;21(22):8615. doi: 10.3390/ijms21228615.
Asymmetric dynamic coupling promotes alternative evolutionary pathways in an enzyme dimer.
Ambrus V, Hoffka G, Fuxreiter M.
Sci Rep. 2020 Nov 2;10(1):18866. doi: 10.1038/s41598-020-75772-5.
Sequence-based prediction of protein binding mode landscapes.
Horvath A, Miskei M, Ambrus V, Vendruscolo M, Fuxreiter M.
PLoS Comput Biol. 2020 May 26;16(5):e1007864. doi: 10.1371/journal.pcbi.1007864. eCollection 2020 May.
Rapid Biophysical Characterization and NMR Spectroscopy Structural Analysis of Small Proteins from Bacteria and Archaea.
Kubatova N, Pyper DJ, Jonker HRA, Saxena K, Remmel L, Richter C, Brantl S, Evguenieva-Hackenberg E, Hess WR, Klug G, Marchfelder A, Soppa J, Streit W, Mayzel M, Orekhov VY, Fuxreiter M, Schmitz RA, Schwalbe H.
Chembiochem. 2020 Apr 17;21(8):1178-1187. doi: 10.1002/cbic.201900677. Epub 2020 Jan 21.
Sequence-Based Prediction of Fuzzy Protein Interactions.
Miskei M, Horvath A, Vendruscolo M, Fuxreiter M.
J Mol Biol. 2020 Mar 27;432(7):2289-2303. doi: 10.1016/j.jmb.2020.02.017. Epub 2020 Feb 27.
Patterns of Dynamics Comprise a Conserved Evolutionary Trait.
Zsolyomi F, Ambrus V, Fuxreiter M.
J Mol Biol. 2020 Jan 17;432(2):497-507. doi: 10.1016/j.jmb.2019.11.007. Epub 2019 Nov 27.
Altered dynamics may drift pathological fibrillization in membraneless organelles.
Tüű-Szabó B, Hoffka G, Duro N, Fuxreiter M.
Biochim Biophys Acta Proteins Proteom. 2019 Oct;1867(10):988-998. doi: 10.1016/j.bbapap.2019.04.005. Epub 2019 Apr 16.
Editorial overview: Dynamic protein interactions - from complexes to molecular machines.
Fuxreiter M, Panchenko A.
Curr Opin Struct Biol. 2019 Jun;56:vi-viii. doi: 10.1016/j.sbi.2019.06.006.
Specific and Fuzzy Interactions Cooperate in Modulating Protein Half-Life.
Sharma R, Demény M, Ambrus V, Király SB, Kurtán T, Gatti-Lafranconi P, Fuxreiter M.
J Mol Biol. 2019 Apr 5;431(8):1700-1707. doi: 10.1016/j.jmb.2019.02.006. Epub 2019 Feb 18.
Fold or not to fold upon binding - does it really matter?
Fuxreiter M.
Curr Opin Struct Biol. 2019 Feb;54:19-25. doi: 10.1016/j.sbi.2018.09.008. Epub 2018 Oct 16.
Towards a Stochastic Paradigm: From Fuzzy Ensembles to Cellular Functions.
Fuxreiter M.
Molecules. 2018 Nov 17;23(11):3008. doi: 10.3390/molecules23113008.
Fuzziness in Protein Interactions-A Historical Perspective.
Fuxreiter M.
J Mol Biol. 2018 Aug 3;430(16):2278-2287. doi: 10.1016/j.jmb.2018.02.015. Epub 2018 Feb 23.
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.
Experimental Characterization of Fuzzy Protein Assemblies: Interactions of Paramyxoviral NTAIL Domains With Their Functional Partners.
Troilo F, Bignon C, Gianni S, Fuxreiter M, Longhi S.
Methods Enzymol. 2018;611:137-192. doi: 10.1016/bs.mie.2018.08.006. Epub 2018 Oct 5.
Fuzziness enables context dependence of protein interactions.
Miskei M, Gregus A, Sharma R, Duro N, Zsolyomi F, Fuxreiter M.
FEBS Lett. 2017 Sep;591(17):2682-2695. doi: 10.1002/1873-3468.12762. Epub 2017 Aug 20.
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.
Genomic variants reveal differential evolutionary constraints on human transglutaminases and point towards unrecognized significance of transglutaminase 2.
Thangaraju K, Király R, Demény MA, András Mótyán J, Fuxreiter M, Fésüs L.
PLoS One. 2017 Mar 1;12(3):e0172189. doi: 10.1371/journal.pone.0172189. eCollection 2017.
Computational analyses of the effect of novel amino acid clusters of human transglutaminase 2 on its structure and function.
Thangaraju K, Király R, Mótyán JA, Ambrus VA, Fuxreiter M, Fésüs L.
Amino Acids. 2017 Mar;49(3):605-614. doi: 10.1007/s00726-016-2330-0. Epub 2016 Sep 14.
FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies.
Miskei M, Antal C, Fuxreiter M.
Nucleic Acids Res. 2017 Jan 4;45(D1):D228-D235. doi: 10.1093/nar/gkw1019. Epub 2016 Oct 28.
A Derived Allosteric Switch Underlies the Evolution of Conditional Cooperativity between HOXA11 and FOXO1.
Nnamani MC, Ganguly S, Erkenbrack EM, Lynch VJ, Mizoue LS, Tong Y, Darling HL, Fuxreiter M, Meiler J, Wagner GP.
Cell Rep. 2016 Jun 7;15(10):2097-2108. doi: 10.1016/j.celrep.2016.04.088. Epub 2016 May 26.
The Structure and Dynamics of Higher-Order Assemblies: Amyloids, Signalosomes, and Granules.
Wu H, Fuxreiter M.
Cell. 2016 May 19;165(5):1055-1066. doi: 10.1016/j.cell.2016.05.004.
Fuzzy regions in an intrinsically disordered protein impair protein-protein interactions.
Gruet A, Dosnon M, Blocquel D, Brunel J, Gerlier D, Das RK, Bonetti D, Gianni S, Fuxreiter M, Longhi S, Bignon C.
FEBS J. 2016 Feb;283(4):576-94. doi: 10.1111/febs.13631. Epub 2016 Jan 12.
Fuzziness endows viral motif-mimicry.
Duro N, Miskei M, Fuxreiter M.
Mol Biosyst. 2015 Oct;11(10):2821-9. doi: 10.1039/c5mb00301f.
Fuzzy complexes: Specific binding without complete folding.
Sharma R, Raduly Z, Miskei M, Fuxreiter M.
FEBS Lett. 2015 Sep 14;589(19 Pt A):2533-42. doi: 10.1016/j.febslet.2015.07.022. Epub 2015 Jul 27.
Physiological, pathological, and structural implications of non-enzymatic protein-protein interactions of the multifunctional human transglutaminase 2.
Kanchan K, Fuxreiter M, Fésüs L.
Cell Mol Life Sci. 2015 Aug;72(16):3009-35. doi: 10.1007/s00018-015-1909-z. Epub 2015 May 6.
Correction to disordered proteinaceous machines.
Fuxreiter M, Tóth-Petróczy Á, Kraut DA, Matouschek A, Lim RY, Xue B, Kurgan L, Uversky VN.
Chem Rev. 2015 Apr 8;115(7):2780. doi: 10.1021/acs.chemrev.5b00150. Epub 2015 Mar 26.
Intrinsically disordered segments affect protein half-life in the cell and during evolution.
van der Lee R, Lang B, Kruse K, Gsponer J, Sánchez de Groot N, Huynen MA, Matouschek A, Fuxreiter M, Babu MM.
Cell Rep. 2014 Sep 25;8(6):1832-1844. doi: 10.1016/j.celrep.2014.07.055. Epub 2014 Sep 15.
The role of reorganization energy in rational enzyme design.
Fuxreiter M, Mones L.
Curr Opin Chem Biol. 2014 Aug;21:34-41. doi: 10.1016/j.cbpa.2014.03.011. Epub 2014 Apr 24.
PMID: 24769299 Free article. Review.
Classification of intrinsically disordered regions and proteins.
van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones DT, Kim PM, Kriwacki RW, Oldfield CJ, Pappu RV, Tompa P, Uversky VN, Wright PE, Babu MM.
Chem Rev. 2014 Jul 9;114(13):6589-631. doi: 10.1021/cr400525m. Epub 2014 Apr 29.
Disordered proteinaceous machines.
Fuxreiter M, Tóth-Petróczy Á, Kraut DA, Matouschek A, Lim RY, Xue B, Kurgan L, Uversky VN.
Chem Rev. 2014 Jul 9;114(13):6806-43. doi: 10.1021/cr4007329. Epub 2014 Apr 4.
Identification of a specific one amino acid change in recombinant human transglutaminase 2 that regulates its activity and calcium sensitivity.
Kanchan K, Ergülen E, Király R, Simon-Vecsei Z, Fuxreiter M, Fésüs L.
Biochem J. 2013 Nov 1;455(3):261-72. doi: 10.1042/BJ20130696.
Alternative splicing of intrinsically disordered regions and rewiring of protein interactions.
Buljan M, Chalancon G, Dunker AK, Bateman A, Balaji S, Fuxreiter M, Babu MM.
Curr Opin Struct Biol. 2013 Jun;23(3):443-50. doi: 10.1016/j.sbi.2013.03.006. Epub 2013 May 22.
Optimization of reorganization energy drives evolution of the designed Kemp eliminase KE07.
Labas A, Szabo E, Mones L, Fuxreiter M.
Biochim Biophys Acta. 2013 May;1834(5):908-17. doi: 10.1016/j.bbapap.2013.01.005. Epub 2013 Feb 1.
What's in a name? Why these proteins are intrinsically disordered: Why these proteins are intrinsically disordered.
Dunker AK, Babu MM, Barbar E, Blackledge M, Bondos SE, Dosztányi Z, Dyson HJ, Forman-Kay J, Fuxreiter M, Gsponer J, Han KH, Jones DT, Longhi S, Metallo SJ, Nishikawa K, Nussinov R, Obradovic Z, Pappu RV, Rost B, Selenko P, Subramaniam V, Sussman JL, Tompa P, Uversky VN.
Intrinsically Disord Proteins. 2013 Apr 1;1(1):e24157. doi: 10.4161/idp.24157. eCollection 2013 Jan-Dec.
Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks.
Buljan M, Chalancon G, Eustermann S, Wagner GP, Fuxreiter M, Bateman A, Babu MM.
Mol Cell. 2012 Jun 29;46(6):871-83. doi: 10.1016/j.molcel.2012.05.039.
Interactions via intrinsically disordered regions: what kind of motifs?
Pancsa R, Fuxreiter M.
IUBMB Life. 2012 Jun;64(6):513-20. doi: 10.1002/iub.1034. Epub 2012 Apr 25.
QM/MM simulation of liquid water with an adaptive quantum region.
Bernstein N, Várnai C, Solt I, Winfield SA, Payne MC, Simon I, Fuxreiter M, Csányi G.
Phys Chem Chem Phys. 2012 Jan 14;14(2):646-56. doi: 10.1039/c1cp22600b. Epub 2011 Nov 16.
"Fuzziness" in the celular interactome: a historical perspective.
Welch GR.
Adv Exp Med Biol. 2012;725:184-90. doi: 10.1007/978-1-4614-0659-4_11.
The approach here builds on a generalized principle of "fuzziness" in protein behavior, proposed by Tompa and Fuxreiter.(1) Recent controversies in the analysis and interpretation of the interactome studies are rationalized historically under the auspices of this concept. …
Fuzzy complexes: a more stochastic view of protein function.
Fuxreiter M, Tompa P.
Adv Exp Med Biol. 2012;725:1-14. doi: 10.1007/978-1-4614-0659-4_1.
Fuzziness: linking regulation to protein dynamics.
Fuxreiter M.
Mol Biosyst. 2012 Jan;8(1):168-77. doi: 10.1039/c1mb05234a. Epub 2011 Sep 19.
Dynamic protein-DNA recognition: beyond what can be seen.
Fuxreiter M, Simon I, Bondos S.
Trends Biochem Sci. 2011 Aug;36(8):415-23. doi: 10.1016/j.tibs.2011.04.006. Epub 2011 May 27.
Active site residue involvement in monoamine or diamine oxidation catalysed by pea seedling amine oxidase.
Di Paolo ML, Lunelli M, Fuxreiter M, Rigo A, Simon I, Scarpa M.
FEBS J. 2011 Apr;278(8):1232-43. doi: 10.1111/j.1742-4658.2011.08044.x. Epub 2011 Mar 1.
Disordered tails of homeodomains facilitate DNA recognition by providing a trade-off between folding and specific binding.
Tóth-Petróczy A, Simon I, Fuxreiter M, Levy Y.
J Am Chem Soc. 2009 Oct 28;131(42):15084-5. doi: 10.1021/ja9052784.
On the divalent metal ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family.
Pingoud V, Wende W, Friedhoff P, Reuter M, Alves J, Jeltsch A, Mones L, Fuxreiter M, Pingoud A.
J Mol Biol. 2009 Oct 16;393(1):140-60. doi: 10.1016/j.jmb.2009.08.011. Epub 2009 Aug 13.
The energy gap as a universal reaction coordinate for the simulation of chemical reactions.
Mones L, Kulhánek P, Simon I, Laio A, Fuxreiter M.
J Phys Chem B. 2009 Jun 4;113(22):7867-73. doi: 10.1021/jp9000576.
Evaluating boundary dependent errors in QM/MM simulations.
Solt I, Kulhánek P, Simon I, Winfield S, Payne MC, Csányi G, Fuxreiter M.
J Phys Chem B. 2009 Apr 30;113(17):5728-35. doi: 10.1021/jp807277r.
Close encounters of the third kind: disordered domains and the interactions of proteins.
Tompa P, Fuxreiter M, Oldfield CJ, Simon I, Dunker AK, Uversky VN.
Bioessays. 2009 Mar;31(3):328-35. doi: 10.1002/bies.200800151.
Interoperability services in the MPOWER Ambient Assisted Living platform.
Mikalsen M, Hanke S, Fuxreiter T, Walderhaug S, Wienhofen L.
Stud Health Technol Inform. 2009;150:366-70.
Malleable machines in transcription regulation: the mediator complex.
Tóth-Petróczy A, Oldfield CJ, Simon I, Takagi Y, Dunker AK, Uversky VN, Fuxreiter M.
PLoS Comput Biol. 2008 Dec;4(12):e1000243. doi: 10.1371/journal.pcbi.1000243. Epub 2008 Dec 19.
Malleable machines take shape in eukaryotic transcriptional regulation.
Fuxreiter M, Tompa P, Simon I, Uversky VN, Hansen JC, Asturias FJ.
Nat Chem Biol. 2008 Dec;4(12):728-37. doi: 10.1038/nchembio.127.
Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions.
Tompa P, Fuxreiter M.
Trends Biochem Sci. 2008 Jan;33(1):2-8. doi: 10.1016/j.tibs.2007.10.003. Epub 2007 Nov 28.
Probing the two-metal ion mechanism in the restriction endonuclease BamHI.
Mones L, Kulhánek P, Florián J, Simon I, Fuxreiter M.
Biochemistry. 2007 Dec 18;46(50):14514-23. doi: 10.1021/bi701630s. Epub 2007 Nov 17.
Electrostatic versus nonelectrostatic effects in DNA sequence discrimination by divalent ions Mg2+ and Mn2+.
Solt I, Simon I, Császár AG, Fuxreiter M.
J Phys Chem B. 2007 Jun 7;111(22):6272-9. doi: 10.1021/jp0668192. Epub 2007 May 12.
An EcoRI-RsrI chimeric restriction endonuclease retains parental sequence specificity.
Chuluunbaatar T, Ivanenko-Johnston T, Fuxreiter M, Meleshko R, Raskó T, Simon I, Heitman J, Kiss A.
Biochim Biophys Acta. 2007 May;1774(5):583-94. doi: 10.1016/j.bbapap.2007.02.011. Epub 2007 Mar 14.
Local structural disorder imparts plasticity on linear motifs.
Fuxreiter M, Tompa P, Simon I.
Bioinformatics. 2007 Apr 15;23(8):950-6. doi: 10.1093/bioinformatics/btm035. Epub 2007 Mar 25.
Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism.
Mones L, Simon I, Fuxreiter M.
Biol Chem. 2007 Jan;388(1):73-8. doi: 10.1515/BC.2007.009.
Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins.
Németh-Pongrácz V, Barabás O, Fuxreiter M, Simon I, Pichová I, Rumlová M, Zábranská H, Svergun D, Petoukhov M, Harmat V, Klement E, Hunyadi-Gulyás E, Medzihradszky KF, Kónya E, Vértessy BG.
Nucleic Acids Res. 2007;35(2):495-505. doi: 10.1093/nar/gkl1074. Epub 2006 Dec 14.
Phosphorylation-induced transient intrinsic structure in the kinase-inducible domain of CREB facilitates its recognition by the KIX domain of CBP.
Solt I, Magyar C, Simon I, Tompa P, Fuxreiter M.
Proteins. 2006 Aug 15;64(3):749-57. doi: 10.1002/prot.21032.
Flexibility of prolyl oligopeptidase: molecular dynamics and molecular framework analysis of the potential substrate pathways.
Fuxreiter M, Magyar C, Juhász T, Szeltner Z, Polgár L, Simon I.
Proteins. 2005 Aug 15;60(3):504-12. doi: 10.1002/prot.20508.
Interfacial water as a "hydration fingerprint" in the noncognate complex of BamHI.
Fuxreiter M, Mezei M, Simon I, Osman R.
Biophys J. 2005 Aug;89(2):903-11. doi: 10.1529/biophysj.105.063263. Epub 2005 May 13.
Type II restriction endonucleases: structure and mechanism.
Pingoud A, Fuxreiter M, Pingoud V, Wende W.
Cell Mol Life Sci. 2005 Mar;62(6):685-707. doi: 10.1007/s00018-004-4513-1.
Preformed structural elements feature in partner recognition by intrinsically unstructured proteins.
Fuxreiter M, Simon I, Friedrich P, Tompa P.
J Mol Biol. 2004 May 14;338(5):1015-26. doi: 10.1016/j.jmb.2004.03.017.
Noncovalent cross-links in context with other structural and functional elements of proteins.
Tüdos E, Fiser A, Simon A, Dosztányi Z, Fuxreiter M, Magyar C, Simon I.
J Chem Inf Comput Sci. 2004 Mar-Apr;44(2):347-51. doi: 10.1021/ci030409i.
Role of base flipping in specific recognition of damaged DNA by repair enzymes.
Fuxreiter M, Luo N, Jedlovszky P, Simon I, Osman R.
J Mol Biol. 2002 Nov 8;323(5):823-34. doi: 10.1016/s0022-2836(02)00999-3.
Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases.
Fuxreiter M, Simon I.
Protein Sci. 2002 Aug;11(8):1978-83. doi: 10.1110/ps.4980102.
Role of stabilization centers in 4 helix bundle proteins.
Fuxreiter M, Simon I.
Proteins. 2002 Aug 1;48(2):320-6. doi: 10.1002/prot.10167.
The role of hydrophobic microenvironments in modulating pKa shifts in proteins.
Mehler EL, Fuxreiter M, Simon I, Garcia-Moreno EB.
Proteins. 2002 Aug 1;48(2):283-92. doi: 10.1002/prot.10153.
Probing the general base catalysis in the first step of BamHI action by computer simulations.
Fuxreiter M, Osman R.
Biochemistry. 2001 Dec 11;40(49):15017-23. doi: 10.1021/bi010987x.
Checking nucleic acid crystal structures.
Das U, Chen S, Fuxreiter M, Vaguine AA, Richelle J, Berman HM, Wodak SJ.
Acta Crystallogr D Biol Crystallogr. 2001 Jun;57(Pt 6):813-28. doi: 10.1107/s0907444901003936. Epub 2001 May 25.
Specificity of damage recognition and catalysis of DNA repair.
Osman R, Fuxreiter M, Luo N.
Comput Chem. 2000 May;24(3-4):331-9. doi: 10.1016/s0097-8485(99)00073-x.
PMID: 10816003
Role of active site residues in the glycosylase step of T4 endonuclease V. Computer simulation studies on ionization states.
Fuxreiter M, Warshel A, Osman R.
Biochemistry. 1999 Jul 27;38(30):9577-89. doi: 10.1021/bi9901937.
Comparative redox and pKa calculations on cytochrome c3 from several Desulfovibrio species using continuum electrostatic methods.
Martel PJ, Soares CM, Baptista AM, Fuxreiter M, Náray-Szabó G, Louro RO, Carrondo MA.
J Biol Inorg Chem. 1999 Feb;4(1):73-86. doi: 10.1007/s007750050291.
Crystallization and preliminary X-ray analysis of porcine muscle prolyl oligopeptidase.
Böcskei Z, Fuxreiter M, Náray-Szabó G, Szabó E, Polgár L.
Acta Crystallogr D Biol Crystallogr. 1998 Nov 1;54(Pt 6 Pt 2):1414-5. doi: 10.1107/s0907444998004181.
Role of electrostatics at the catalytic metal binding site in xylose isomerase action: Ca(2+)-inhibition and metal competence in the double mutant D254E/D256E.
Fuxreiter M, Böcskei Z, Szeibert A, Szabó E, Dallmann G, Naray-Szabo G, Asboth B.
Proteins. 1997 Jun;28(2):183-93. doi: 10.1002/(sici)1097-0134(199706)28:2<183::aid-prot7>3.0.co;2-g.
Molecular modelling of xylose isomerase catalysis: the role of electrostatics and charge transfer to metals.
Fuxreiter M, Farkas O, Náray-Szabó G.
Protein Eng. 1995 Sep;8(9):925-33. doi: 10.1093/protein/8.9.925.
How perchlorate improves excitation-contraction coupling in skeletal muscle fibers.
Lüttgau HC, Gottschalk G, Kovács L, Fuxreiter M.
Biophys J. 1983 Aug;43(2):247-9. doi: 10.1016/S0006-3495(83)84346-X.
Effects of physostigmine on the excitation-contraction coupling of skeletal muscle fibres.
Szücs G, Fuxreiter M, Sirkó E, Szállási A.
Acta Physiol Hung. 1983;62(1):61-73.
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