Selected Publications

M. Miskei, A Horvath, M. Vendruscolo, M Fuxreiter (2020) Sequence-based determinants and predictions of fuzzy interactions in protein complexes. J. Mol. Biol. abstract

F. Zsolyomi, V. Ambrus, M. Fuxreiter (2020) Patterns of dynamics comprise a conserved evolutionary trait J. Mol. Biol 432, 497-507. abstract

N. Kubatova, D. J. Pyper, H. R. A. Jonker, K. Saxena, L. Remmel, C. Richter, S. Brantl E. Evguenieva-Hackenberg,W. R. Hess, G. Klug, A. Marchfelder, J. Soppa, W. Streit, M. Mayzel, V. Y. Orekhov, M. Fuxreiter, R.A. Schmitz,  andHarald Schwalbe (2019) Rapid biophysical characterization and NMR structural analysis of small proteins from bacteria and archaea. ChemBioChem doi: 10.1002/cbic.201900677. abstract

A. Panchenko and Fuxreiter M. (2019) Dynamic protein interactions – from complexes to molecular machines. Current Opinion in Structural Biology, 56, vi-viii . abstract

B. Tuu-Szabo, G. Hoffka, N. Duro, Fuxreiter M. (2019) Altered dynamics may drift pathological fibrillization in membraneless organelles. BBA Proteins and Proteomics, 1867, 988-998. abstract

Sharma R, Demény M, Ambrus V, Király SB, Kurtán T, Gatti-Lafranconi P, Fuxreiter M. (2019) Specific and Fuzzy Interactions Cooperate in Modulating Protein Half-Life. J. Mol. Biol. 431, 1700-1707. abstract

Troilo F, Bignon C, Gianni S, Fuxreiter M, Longhi S. (2018) Experimental Characterization of Fuzzy Protein Assemblies: Interactions of Paramyxoviral NTAILDomains With Their Functional Partners. Methods Enzymol. 611, 137-192. abstract

Fuxreiter M (2018) Towards a stochastic paradigm: from fuzzy ensembles to cellular functions. Molecules 23, E3008. doi: 10.3390/molecules23113008 abstract

Fuxreiter M (2018) Fold or not to fold upon binding – does it really matter? Curr Opin. Struct Biol. 54, 19-25. abstract

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. (2018) Protein phase separation: a new phase in cell biology. Trends Cell Biol. 28, 420-435. abstract

Fuxreiter M.(2018) Fuzziness in protein interactions – a historical perspective. J Mol Biol. doi: 10.1016/j.jmb.2018.02.015. abstract

Tüű-Szabó B, Kóczy L, Fuxreiter M. (2018) Simulations of higher-order protein assemblies using a fuzzy framework. BioRxivdoi: 10.1101/248062. abstract

Miskei M, Gregus A, Sharma R, Duro N, Zsolyomi F, Fuxreiter M. (2017) Fuzziness enables context dependence of protein interactions. FEBS Lett. 591 :2682-2695. abstract

Marton Miskei, Csaba Antal and Monika Fuxreiter (2017)
FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies. Nucleic Acids Research 45, D228-D235 abstract

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. (2017) Simultaneous quantification of protein order and disorder Nat Chem Biol. 13, 339-342 abstract

Nnamani MC, Ganguly S, Erkenbrack EM, Lynch VJ, Mizoue LS, Tong Y, Darling HL, Fuxreiter M, Meiler J, Wagner GP. (2016) A Derived Allosteric Switch Underlies the Evolution of Conditional Cooperativity between HOXA11 and FOXO1. Cell Rep. 15(10):2097-2108. abstract

Wu H, Fuxreiter M. (2016) The Structure and Dynamics of Higher-Order Assemblies: Amyloids, Signalosomes, and Granules. Cell. 165(5):1055-1066. abstract

Gruet A, Dosnon M, Blocquel D, Brunel J, Gerlier D, Das RK, Bonetti D, Gianni S, Fuxreiter M, Longhi S, Bignon C. (2015) Fuzzy regions in an intrinsically disordered protein impair protein-protein interactions. FEBS J. 283, 576-594. abstract

Duro N, Miskei M, Fuxreiter M. (2015) Fuzziness endows viral motif-mimicry. Mol Biosyst., 11, 2821-29. abstract

Sharma R, Raduly Z, Miskei M, Fuxreiter M. (2015) Fuzzy complexes: Specific binding without complete folding. FEBS Lett. 589, 2533-42. abstract

Kanchan K, Fuxreiter M, Fésüs L. (2015) Physiological, pathological, and structural implications of non-enzymatic protein-protein interactions of the multifunctional human transglutaminase 2. Cell Mol Life Sci., 72(16),3009-35. abstract

van der Lee R, Lang B, Kruse K, Gsponer J, Sánchez de Groot N., Huynen MA, Matouschek A, Fuxreiter M and Babu MM (2014) Intrinsically disordered segments affect protein half-life in the cell and during evolution. Cell Reports 8, 1-12. abstract

van der Lee R, M. Buljan, B. Lang, RJ. Weatheritt, GW. Daughdrill, AK. Dunker, M. Fuxreiter, J. Gough, J. Gsponer, DT. Jones, PM. Kim, RW. Kriwacki, CJ. Oldfield, RV. Pappu, P. Tompa, VN. Uversky, PE. Wright, MM. Babu (2014) Classification of intrinsically disordered regions and proteins. Chem Rev. 114(13):6589-631. abstract

M. Fuxreiter, L. Mones (2014) The role of reorganization energy in rational enzyme design. Curr Opin Chem Biol. 21C:34-41  abstract

M. Fuxreiter, A. Tóth-Petróczy, DA. Kraut, AT. Matouschek , RY. Lim, B. Xue, L. Kurgan, VN. Uversky (2014) Disordered proteinaceous machines. Chem Rev. 114(13):6806-43. abstract

Kanchan K, Ergülen E, Király R, Simon Vecsei Z, Fuxreiter M, Fésüs L. (2013) Identification of specific one amino acid change in recombinant human transglutaminase 2 in regulating its activity and calcium sensitivity. Biochem Jabstract

Buljan M, Chalancon G, Dunker AK, Bateman A, Balaji S, Fuxreiter M, Babu MM. (2013) Alternative splicing of intrinsically disordered regions and rewiring of protein interactions Curr Opin Struct Biol. 23, 443-50. abstract

Dunker A.K., Babu M., Barbar E., Blackledge M., Bondos S.E., Dosztányi Z., Dyson H.J., Forman-Kay J., Fuxreiter M., Gsponer J., Han K.-H., Jones D.T., Longhi S., Metallo S.J., Nishikawa K., Nussinov R., Obradovic Z., Pappu R., Rost B., Selenko P., Subramaniam V., Sussman J.L., Tompa P., Uversky V.N. (2013) What’s in a name? Why these proteins are intrinsically disordered. Intrinsically Disordered Proteins. 1 (1) e24157.

M. Buljan, G. Chalancon, S. Eustermann, G. Wagner, M. Fuxreiter, A. Bateman, M.M. Babu (2012) Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. Mol Cell 46, 871-883. abstract

R. Pancsa, M. Fuxreiter (2012) Interactions via intrinsically disordered regions: what kind of motifs? IUBMB Life 64, 513-520. abstract

N Bernstein, C Várnai, I Solt, SA Winfield, MC Payne, I Simon, M Fuxreiter, G. Csányi  (2012) QM/MM simulation of liquid water with an adaptive quantum region Phys. Chem. Chem. Phys. 14, 646-656. abstract

M Fuxreiter (2012) Fuzziness: linking regulation to protein dynamics. Mol Biosystems  8, 168-177. abstract

M.Fuxreiter*, I. Simon, S. Bondos (2011) Dynamic protein-DNA recognition: beyond what can be seen. Trends in Biochem Sci 36, 415-423. abstract

ML Di Paolo, M Lunelli, M Fuxreiter, A Rigo, I Simon, M Scarpa  (2011) Active site involvement in monoamine or diamine oxidation catalyzed by pea seedling amine oxidase. FEBS J 278, 1232-43. abstract

A Toth-Petroczy, I Simon M Fuxreiter, Y Levy (2009) Disordered tails of homeodomains facilitate DNA recognition by providing a trade-off between folding and specific binding. J Am Chem Soc 131, 15084-85. abstract

V Pingoud, W Wende, P Friedhoff, M Reuter, J Alves, A Jeltsch, L Mones, M Fuxreiter, A. Pingoud (2009) On the divalent ion dependence of DNA cleavage by restriction endonucleases of the EcoRI  family. J Mol Biol 393, 140-60. abstract

L Mones, P Kulhanek, I Simon, A Laio and M Fuxreiter* (2009) Egap as a universal coordinate for simulating chemical reactions. J Phys Chem B 113, 7867-73.  abstract

I Solt, P Kulhanek, I Simon, S Winfield, MC Payne, G Csanyi and M Fuxreiter* (2009) Evaluating Boundary dependent force errors in QM/MM simulations. J Phys Chem B 113, 5728-35. abstract

P Tompa, M Fuxreiter, CJ Oldfield, I Simon, AK Dunker, VN Uversky (2009) Close encounters of the thrid kind: disordered domains and interactions of proteins. Bioessays 31, 328-35. abstract

M Fuxreiter and P Tompa (2009) Fuzzy interactome: the limitations of models in molecular biology, Trends in Biochem Sci, 34, 3  

Á Tóth-Petróczy, CJ Oldfield, I Simon, Y Takagi, AK Dunker, VN Uversky and M. Fuxreiter* (2008) Malleable machines take shape in transcription regulation: the mediator complex  PloS Comp Biol 4, e1000243 abstract

M Fuxreiter*, P Tompa, I Simon, VN Uversky, JC Hansen, F Asturias (2008) Malleable machines take shape in eukaryotic transcription regulation. Nat Chem Biol 4, 728-737 abstract

Á Tóth-Petróczy, B. Mészáros, I Simon, AK Dunker, VN Uversky and M. Fuxreiter* (2008) Assessing conservation of disordered regions in proteins. The Open Proteomics Journal 1, 46-53.

P. Tompa and M Fuxreiter (2008) Fuzzy complexes: polymorphism and structural disorder in protein–protein interactions. Trends in Biochem. Sci 33, 2-8 abstract

L. Mones, P. Kulhanek, J. Florian, I Simon and M. Fuxreiter* (2007) Probing the two-metal ion mechanism in the restriction endonuclease BamHI Biochemistry 46, 14514-14523 abstract

I. Solt, I. Simon, A.G. Császár, M. Fuxreiter* (2007) Electrostatic vs. non-electrostatic effects in DNA sequence discrimination by divalent metal ions Mg2+ and Mn2+ . J. Phys Chem B 111, 6272-6279. abstract

M. Fuxreiter, P. Tompa, I. Simon (2007) Local structural disorder imparts plasticity on linear motifs. Bioinformatics 23, 950-956. abstract

Chuluunbaatar, T.Ivanenko-Johnston, M. Fuxreiter*, R. Meleshko, T. Rasko, I. Simon, J. Heitman and A. Kiss (2007) An EcoRI-RsrI chimeric restriction endonuclease retains parental sequence specificity. BBA Proteins & Proteomics 1174, 583-594 abstract

V. Németh-Pongrácz, O. Barabás, M. Fuxreiter, I. Simon, I. Pichová, M. Rumlová, D. Svergun, M. Petoukhov, V. Harmat, É. Klement, É. Hunyadi-Gulyás, K. F. Medzihradszky, E. Kónya and B. G. Vértessy (2007) Flexible Segments Modulate Co-folding of DUTPase and Nucleocapsid Proteins. Nucleic Acids Res.35, 495-505. abstract

L.Mones, I.Simon, M. Fuxreiter* (2007) Metal sites at the active site of BamHI can conform to a one-ion mechanism. Biol. Chem. 388 (1) 73-79 abstract

I.Solt, Cs. Magyar, I.Simon, P.Tompa, M. Fuxreiter* (2006) Phosphorylation-induced transient intrinsic structure in the kinase-inducible domain of CREB facilitates its recognition by the KIX domain of CBP. Proteins 64, 749-757. abstract

M. Fuxreiter*, M. Mezei, I. Simon, R. Osman (2005) Interfacial water as a “Hydration Fingerprint” in the noncognate complex of BamHI. Biophys. J. 89, 903-911. abstract

M. Fuxreiter, Cs. Magyar, T. Juhász , Z. Szeltner, L. Polgár, I. Simon (2005) The Dynamic Properties of the Structure of Prolyl Oligopeptidase. Implication for Catalysis. Proteins  60, 504-512. abstract

A. Pingoud, M. Fuxreiter, V. Pingoud, W. Wende (2005) Type II restriction endonucleases: structure and mechanism. Cellular and Molecular Life Sciences 62, 685-707. abstract

M. Fuxreiter, I. Simon, P. Friedrich and P. Tompa (2004) Preformed structural elements feature in partner recognition by intrinsically unstructured proteins. J. Mol. Biol. 338, 1015-1026. abstract

E. Tüdős, A. Fiser, A. Simon, Zs. Dosztányi, M. Fuxreiter, Cs. Magyar and I. Simon (2004) Non-covalent crosslinks in context with other structural and functional elements of proteins. J. Chem. Inf  Comp. Sc., 44, 347-351. abstract

M. Fuxreiter, R. Osman, I Simon (2003) Computational Approaches to Restriction Endonucleases. J. Mol. Structure, 666-667, 469-479.

M. Fuxreiter, N. Luo, P. Jedlovszky, I. Simon and R. Osman (2002) Role of base flipping in specific recognition of damaged DNA by repair enzymes. J. Mol. Biol. 323, 823-834. abstract

M. Fuxreiter and I. Simon (2002) Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases. Protein Sci.  11, 1978-1983. abstract

M. Fuxreiter and I. Simon (2002) Role of stabilization centers in 4 helix bundle proteins. Proteins  48, 320-326. abstract

E.L. Mehler, M. Fuxreiter, I. Simon, and B.E. Garcia-Moreno (2002) The role of hydrophobic microenvironments in modulating pKa shifts in proteins. Proteins  48, 283-292. abstract

M. Fuxreiter and R. Osman (2001) Probing the general base catalysis in the first step of BamHI action by computer simulations. Biochemistry  40, 15017-15023. abstract

U. Das, S. Chen, M. Fuxreiter, A.A.Vaguine, J. Richelle, H.M. Berman and S.J. Wodak (2001) Checking nucleic acid crystal structures. Acta Cryst.D. 57, 813-828. abstract

R. Osman, M. Fuxreiter and N. Luo (2000) Specificity of damage recognition and catalysis of DNA repair.Computers & Chemistry  24, 331-339. abstract

M. Fuxreiter, A. Warshel and R. Osman (1999) Role of active site residues in the glycosylase step of T4 Endonuclease V. Computer simulation studies on ionization states. Biochemistry  38, 9577-9589. abstract

P. Martel, C.M. Soares, A.M. Baptista, M. Fuxreiter,  G. Náray-Szabó, R.O. Louro, and M.A. Carrondo (1999) Comparative redox and pKa calculations on cytochromes c3 from  Desulfovibrio species using continuum electrostatic methods. J. Biol. Inorg. Chem.  4, 73-86. abstract

M. Fuxreiter and A Warshel (1998) On the origin of the catalytic power of acetylcholinesterase. Computer simulation studies. J. Am. Chem. Soc.  120, 183-194.

Zs. Böcskei, M. Fuxreiter, G. Náray-Szabó, E. Szabó and L. Polgár (1998) Crystallization and preliminary X-ray analysis of prolyl oligopeptidase. Acta Cryst. D.  54, 1414-1415. abstract

A. Szabó, M. Fuxreiter, A. Csámpai, K. Körmendy and J. Császár (1997) Substrate Specific Nucleophilic Amination of Nitro-substituted  4-(2-Hydroxyethyl- amino)phtalazin-1-(2H)-ones. Heterocyclic Communication  3, 555-562.

M. Fuxreiter, Zs. Böcskei, A. Szeibert, E. Szabó, G. Dallman, G. Náray-Szabó and B. Asbóth (1997) The role of electrostatics at the catalytic metal binding site in xylose isomerase action. Ca2+ inhibition and metal competence in double mutant D254E/D256E. Proteins 28, 183-193. abstract

I. Fernandez, J. Ubach, M. Fuxreiter, J.M. Andreu, D. Andreu, M. Pons (1996) Conformation and self association of a hybride peptide of cecropin-A and melittin with improved antibiotic activity. Chemistry 2,  838-846. abstract

M. Fuxreiter, Ö. Farkas and G. Náray-Szabó (1995) Molecular modelling of xylose isomerase catalysis. Protein Engineering  8 , 925-33. abstract

M. Fuxreiter, A. Csámpai and J. Császár (1994) Formation of a strained triazapentalenoindene skeleton via the rearrangement of 2,3-dihydro-7-nitro-1H-imidazo{2,1-a]phtalazin-4-ium-6-olate effected by dichloroacetic anhydride. Heterocycles  38, 1453-1457. 






Monika Fuxreiter and Peter Tompa (Eds) Fuzziness: Structural disorder in protein complexes,  Landes Bioscience/Springer, Austin, NY 2011  abstract1, abstract2