Publications

2017

  • P. Kukic, Y. Pustovalova, C. Camilloni, S. Gianni, D. M. Korzhnev and M. Vendruscolo.
    Structural characterisation of the early events in the nucleation-condensation mechanism in a protein folding process.
    J. Am. Chem. Soc. in press.
  • G. T. Heller, F. A. Aprile and M. Vendruscolo.
    Methods of probing the interactions between small molecules and disordered proteins.
    Cell. Mol. Life Sci. in press.
  • J. Kitevski-LeBlanc, A. Fradet-Turcotte, P. Kukic, G. Portella, T. Yuwen, M. D. Wilson, S. Panier, S. Duan, M. D. Canny, H. van Ingen, C. Arrowsmith, J. L. Rubinstein, M. Vendruscolo, D. Durocher and L. E. Kay.
    RNF168 and RNF169 define a new class of ubiquitylated-histone reader involved in the response to DNA damage.
    eLife, in press.
  • G. Hultqvist, E. Aberg, C. Camilloni, G. Sundell, E. Andersson, J. Dogan, M. Vendruscolo and P. Jemth.
    Emergence and evolution of an interaction between intrinsically disordered proteins.
    eLife, in press.
  • Y. Yoshimura, M. A. Holmberg, P. Kukic, C. B. Andersen, A. Mata-Cabana, M. Vendruscolo, E. A.A. Nollen and F. A.A. Mulder.
    MOAG-4 promotes the aggregation of alpha-synuclein by competing with self-protective electrostatic interactions.
    J. Biol. Chem. in press.
  • P. Ciryam, I. Lambert-Smith, D. M. Bean, R. Freer, F. Cid, G. G. Tartaglia, D. N. Saunders, M. R. Wilson, S. G. Oliver, R. I. Morimoto, C. M. Dobson, M. Vendruscolo, G. Favrin and J. J. Yerbury.
    Spinal motor neuron protein supersaturation patterns are associated with inclusion body formation in ALS.
    Proc. Natl. Acad. Sci. USA, in press.
  • F. A. Aprile, P. Arosio, G. Fusco, S. W. Chen, J. R Kumita, A. Dhulesia, P. Tortora, T. P. J. Knowles, M. Vendruscolo, C. M. Dobson and N. Cremades.
    Inhibition of alpha-synuclein fibril elongation by Hsp70 is governed by a kinetic binding competition between alpha-synuclein species.
    Biochemistry, in press.
  • O. Sin, T. de Jong, A. Mata-Cabana, M. Kudron, R. Seinstra, A. Zaini, F. A. Aprile, R. Seinstra, E. Stroo, R. Willinge Prins, C. Martineau, H. H. Wang, W. Hogewerf, A. Steinhof, E. E. Wanker, M. Vendruscolo, C. F. Calkhoven, V. Reinke, V. Guryev and E. A. A. Nollen.
    Identification of a small non-coding RNA Pol III-associated regulator linked with disease-associated protein aggregation.
    Mol. Cell, in press.
  • M. J. Holliday, C. Camilloni, G. S. Armstrong, M. Vendruscolo and E. Z. Eisenmesser.
    Networks of dynamic allostery control enzyme function.
    Structure 25, 276-286 (2017).
  • P. Sormanni, D. Piovesan, G. T. Heller, M. Bonomi, P. Kukic, C. Camilloni, M. Fuxreiter, Z. Dosztanyi, R. Pappu, M. M. Babu, S. Longhi, P. Tompa, A. K. Dunker, V. N. Uversky, S. C. E. Tosatto and M. Vendruscolo.
    Simultaneous quantification of order and disorder in proteins.
    Nat. Chem. Biol. 13, 339-342 (2017). [PDF]
  • M. Bonomi, G. T. Heller, C. Camilloni and M. Vendruscolo.
    Principles of protein structural ensemble determination.
    Curr. Op. Struct. Biol. 42, 106-116 (2017). [PDF]
  • A. N. Borkar, P. Vallurupalli, C. Camilloni, L. E. Kay, and M. Vendruscolo.
    Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop.
    Phys. Chem. Chem. Phys. in press.
  • M. Perni, C. Galvagnion, A. S. Maltsev, G. Meisl, M. B. D. Muller, P. K. Challa, J. B. Kirkegaard, P. Flagmeier, S. I. A. Cohen, R. Cascella, S. W. Chen, R. Limbocker, P. Sormanni, G. T. Heller, F. A. Aprile, N. Cremades, C. Cecchi, F. Chiti, E. A. A. Nollen, T. P. J. Knowles, M. Vendruscolo, A. Bax, M. Zasloff, C. M. Dobson
    A natural product inhibits the initiation of alpha-synuclein aggregation by displacing it from lipid membranes and suppresses its toxicity.
    Proc. Natl. Acad. Sci. USA, early edition. [PDF]
  • J. Habchi, S. Chia, R. Limbocker, B. Mannini, M. Ahn, M. Perni, O. Hansson, P. Arosio, J. R. Kumita, P. K. Challa, S. I. A. Cohen, S. Linse, C. M. Dobson, T. P. J. Knowles and M. Vendruscolo.
    Systematic development of small molecules to inhibit specific microscopic steps of Abeta42 aggregation in Alzheimer's disease.
    Proc. Natl. Acad. Sci. USA, early edition. [PDF]

2016

  • J. W. P. Brown, A. K. Buell, T. C. T. Michaels, G. Meisl, J. Carozza, P. Flagmeier, M. Vendruscolo, T. P. J. Knowles, Christopher M. Dobson, C. Galvagnion.
    beta-synuclein suppresses both the initiation and amplification steps of alpha-synuclein aggregation via competitive binding to surfaces.
    Sci. Rep. 6, 36010 (2016). [PDF]
  • P. Flagmeier, G. Meisl, M. Vendruscolo, T. P. J. Knowles, C. M. Dobson, A. K. Buell and C. Galvagnion.
    Mutations associated with familial Parkinson's disease alter the initiation and amplification steps of alpha-synuclein aggregation.
    Proc. Natl. Acad. Sci. USA, 113, 10328-10333 (2016). [PDF]
  • G. Fusco, T. Pape, P. Mahou, P. Arosio, A. Rita Costa, G. Kaminski-Schierle, M. Vendruscolo, G. Veglia, C. M. Dobson and A. De Simone.
    Structural basis of synaptic vesicle assembly promoted by alpha-synuclein.
    Nat. Comm. 7, 12563 (2016). [PDF]
  • R. Freer, P. Sormanni, G. Vecchi, P. Ciryam, C. M. Dobson and M. Vendruscolo.
    A protein homeostasis signature in healthy brains recapitulates tissue vulnerability to Alzheimer's disease.
    Sci. Adv. 2, e1600947 (2016). [PDF] [The Guardian]
  • M. Bonomi, C. Camilloni and M. Vendruscolo.
    Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics.
    Sci. Rep. 6, 31232 (2016). [PDF]
  • C. Galvagnion, J. Brown, M. M. Ouberai, P. Flagmeier, M. Vendruscolo, A. K. Buell, E. Sparr and C. M. Dobson.
    Chemical properties of lipids strongly affect the kinetics of the membrane-induced aggregation of alpha-synuclein.
    Proc. Natl. Acad. Sci. USA, 113, 7065-7070 (2016). [PDF]
  • G. Fusco, A. De Simone, P. Arosio, M. Vendruscolo, G. Veglia, C. M. Dobson.
    Structural ensembles of the membrane-bound alpha-synuclein reveal the molecular determinants of synaptic vesicle affinity.
    Sci. Rep. 6, 27125 (2016). [PDF]
  • C. Camilloni, D. Bonetti, A. Morrone, R. Giri, C. M. Dobson, M. Brunori, S. Gianni and M. Vendruscolo.
    Towards a structural biology of the hydrophobic effect in protein folding.
    Sci. Rep. 6, 28285, (2016). [PDF]
  • A. N. Borkar, M. F. Bardaro, C. Camilloni, F. A. Aprile, G. Varani and M. Vendruscolo.
    Structure of a low-population binding intermediate in protein-RNA recognition.
    Proc. Natl. Acad. Sci. USA, 113, 7171-7176 (2016). [PDF]
  • F. El-Turk, F. Newby, E. J. de Genst, T. Guilliams, T. Sprules, A. Mittermaier, C. M. Dobson and M. Vendruscolo.
    Structural effects of two camelid nanobodies directed to distinct C-terminal epitopes on alpha-synuclein.
    Biochemistry, 55, 3116-3122 (2016). [PDF]
  • C. Camilloni, B. M. Sala, P. Sormanni, R. Porcari, A. Corazza, M. De Rosa, S. Zanini, A. Barbiroli, G. Esposito, M. Bolognesi, V. Bellotti, M. Vendruscolo and S. Ricagno.
    Rational design of mutations that change the aggregation rate of a protein while maintaining its native structure and stability.
    Sci. Rep. 6, 25559 (2016). [PDF]
  • T. Muller, P. Arosio, L. Rajah, S. I. A. Cohen, E. V. Yates, M. Vendruscolo, C. M. Dobson and T. P. J. Knowles.
    Particle-based Monte-Carlo simulations of steady-state mass transport at intermediate Peclet numbers.
    Int. J. Nonlinear Sci. Numer. Simul. 17, 175-183 (2016). [PDF]
  • D. Bonetti, C. Camilloni, L. Visconti, S. Longhi, M. Brunori, M. Vendruscolo and S. Gianni.
    Identification and structural characterization of an intermediate in the folding of the measles virus X domain.
    J. Biol. Chem. 291, 10886-10892 (2016). [PDF]
  • P. Ciryam, R. Kundra, R. Freer, R. I. Morimoto, C. M. Dobson and M. Vendruscolo.
    A transcriptional signature of Alzheimer's disease is associated with a metastable subproteome at risk of aggregation.
    Proc. Natl. Acad. Sci. USA, 113, 4753-4758 (2016). [PDF]
  • A. Deckert, C. A. Waudby, T. Wlodarski, A. S. Wentink, X. Wang, J. F. S. Paton, C. Camilloni, P. Kukic, C. M. Dobson, M. Vendruscolo, L. D. Cabrita and J. Christodoulou.
    Structural characterization of the interaction of alpha-synuclein nascent chains with the ribosomal surface and trigger factor.
    Proc. Natl. Acad. Sci. USA, 113, 5012-5017 (2016). [PDF]
  • P. Joshi, S. Chia, J. Habchi, T. P. J. Knowles, C. M. Dobson and M. Vendruscolo.
    A fragment-based method of generating small molecule libraries to target the aggregation of intrinsically disordered proteins.
    ACS Comb. Sci. 18, 144-153 (2016). [PDF] [Cover]
  • P. Arosio, T. C. T. Michaels, S. Linse, C. Mansson, C. Emanuelsson, J. Presto, J. Johansson, M. Vendruscolo, C. M. Dobson and T. P. J. Knowles.
    Kinetic analysis reveals the diversity of microscopic mechanisms through which molecular chaperones suppress amyloid formation.
    Nat. Comm. 7, 10948 (2016). [PDF]
  • A. Toto, C. Camilloni, R. Giri, M. Brunori, M. Vendruscolo and S. Gianni.
    Molecular recognition by templated folding of an intrinsically disordered protein.
    Sci. Rep. 6, 21994 (2016). [PDF]
  • J. Habchi, P. Arosio, M. Perni, A. R. Costa, M. Yagi-Utsumi, P. Joshi, S. Chia, S. I. A. Cohen, M. B. D. Muller, S. Linse, E. A. A. Nollen, C. M. Dobson, T. P. J. Knowles and M. Vendruscolo.
    An anti-cancer drug suppresses the primary nucleation reaction that initiates the formation of toxic Abeta aggregates linked with Alzheimer's disease.
    Sci. Adv. 2, e1501244 (2016). [PDF] [BBC News]
  • L. D. Cabrita, A. M.E. Cassaignau, H. M.M. Launay, C. A. Waudby, C. Camilloni, A. L. Robertson, X. Wang, T. Wlodarski, A. S. Wentink, C. A. Woolhead, M. Vendruscolo, C. M. Dobson and J. Christodoulou.
    A structural ensemble of a ribosome-nascent chain complex during in vivo co-translational protein folding.
    Nat. Struct. Mol. Biol. 23, 278-285 (2016). [PDF]
  • P. Arosio, T. Muller, L. Rajah, E. V. Yates, F. A. Aprile, Y. Zhang, S. I. A. Cohen, D. A. White, T. Herling, E. De Genst, S. Linse, M. Vendruscolo, C. M. Dobson, and Tuomas P. J. Knowles.
    Microfluidic diffusion analysis of sizes and interactions of protein solutions under native conditions.
    ACS Nano, 10, 333-341 (2016). [PDF]
  • P. Kukic, P. Lundstrom, C. Camilloni, J. Evenas, M. Akke and M. Vendruscolo.
    Structural insights into the calcium-mediated allosteric transition in the C-terminal domain of calmodulin from NMR measurements.
    Biochemistry, 55, 19-28 (2016). [PDF]
  • M. Bonomi, C. Camilloni, A. Cavalli and M. Vendruscolo.
    Metainference: A Bayesian inference method for heterogeneous systems.
    Sci. Adv. 2, e1501177 (2016). [PDF]
  • T. C. T. Michaels, S. I. A. Cohen, M. Vendruscolo, C. M. Dobson and T. P. J. Knowles.
    Hamiltonian dynamics of protein filament formation.
    Phys. Rev. Lett. 116, 038101 (2016). [PDF]
  • G. Meisl, J. B. Kirkegaard, M. Vendruscolo, C. M. Dobson, S. Linse and T. P. J. Knowles.
    Molecular mechanisms of protein aggregation from global fitting of kinetic models.
    Nat. Protoc. 11, 252-272 (2016). [PDF]
  • I. Ivani, P. D. Dans, A. Noy, A. Perez, I. Faustino, A. Hospital, J. Walther, P. Andrio, R. Goni, A. Balaceanu, G. Portella, F. Battistini, J. L. Gelpi, C. Gonzalez, M. Vendruscolo, C. A. Laughton, S. A. Harris, D. A. Case and M. Orozco.
    PARMBSC1: A refined force field for DNA simulations.
    Nat. Meth. 13, 55-58 (2016) [PDF]

2015

  • C. Camilloni and M. Vendruscolo.
    Using pseudocontact shifts and residual dipolar couplings as exact NMR restraints for the determination of protein structural ensembles.
    Biochemistry, 54, 7470-7476 (2015). [PDF]
  • F. Newby, A. De Simone, M. Yagi-Utsumi, X. Salvatella, C. M. Dobson and M. Vendruscolo.
    Structure-free validation of RDC and PRE measurements of disordered proteins.
    Biochemistry, 54, 6876-6886 (2015). [PDF]
  • T. Murakami, S. Qamar, J. Q. Lin, G. S. Kaminski Schierle, E. Rees, A. Miyashita, A. R. Costa, R. B. Dodd, F. T. S. Chan, Claire H. Michel, D. Kronenberg-Versteeg, Y. Li, S.-P.Yang, Y. Wakutani, W. Meadows, R. R. Ferry, L. Dong, G. G. Tartaglia, G. Favrin, W.-L. Lin, D. W. Dickson, M. Zhen, D. Ron, G. Schmitt-Ulms, P. E. Fraser, N. A. Shneider, C. Holt, M. Vendruscolo, C. F. Kaminski and P. St George-Hyslop.
    ALS/FTD mutation-induced phase transition of FUS liquid droplets and reversible hydrogels into irreversible hydrogels impairs RNP granule function.
    Neuron, 88, 678-690 (2015). [PDF]
  • E. V. Yates, T. Muller, L. Rajah, E. J. De Genst, P. Arosio, S. Linse, M. Vendruscolo, C. M. Dobson, T. P. J. Knowles.
    Latent analysis of unmodified biomolecules and their complexes in solution with attomole detection sensitivity.
    Nat. Chem. 7, 802-809 (2015). [PDF]
  • M. A. Wright, F. A. Aprile, P. Arosio, M. Vendruscolo, C. M. Dobson and T. P. J. Knowles.
    Biophysical approaches for the study of interactions between molecular chaperones and protein aggregates.
    Chem. Comm. 51, 14425-14234 (2015). [PDF]
  • F. A. Aprile, P. Sormanni and M. Vendruscolo.
    A rational design strategy for the selective activity enhancement of a molecular chaperone towards a target substrate.
    Biochemistry, 54, 5103-5112 (2015). [PDF]
  • P. Sormanni, F. A. Aprile and M. Vendruscolo.
    Rational design of antibodies targeting specific epitopes within intrinsically disordered proteins.
    Proc. Natl. Acad. Sci. USA, 112, 9902-9907 (2015). [PDF]
  • R. Collepardo-Guevara, G. Portella, M. Vendruscolo, D. Frenkel, T. Schlick, M. Orozco.
    Chromatin unfolding by epigenetic modifications explained by dramatic impairment of internucleosome interactions: a multiscale computational study.
    J. Am. Chem. Soc. 137, 10205-10215 (2015). [PDF]
  • G. T. Heller, P. Sormanni and M. Vendruscolo.
    Targeting disordered proteins with small molecules using entropy.
    Trends Bioch. Sci. 40, 491-496 (2015). [PDF]
  • P. Kukic, A. Kannan, M. J. J. Dijkstra, S. Abeln, C. Camilloni and M. Vendruscolo.
    Mapping the protein fold universe using the CamTube force field in molecular dynamics simulations.
    PLoS Comp. Biol. 11, e1004435 (2015). [PDF]
  • Y. Pustovalova, P. Kukic, M. Vendruscolo and D. M. Korzhnev.
    Probing the residual structure of the low populated denatured state of ADA2h under folding conditions by relaxation dispersion NMR spectroscopy.
    Biochemistry, 54, 4611-4622 (2015). [PDF]
  • M. Pickhardt, T. Neumann, D. Schwizer, K. Callaway, M. Vendruscolo, D. Schenk, P. St George-Hyslop, E.-M. Mandelkow, C. M. Dobson, L. McConlogue, E. Mandelkow and G. Toth.
    Identification of small molecule inhibitors of Tau aggregation by targeting monomeric Tau as a potential therapeutic approach for Tauopathies.
    Curr. Alzheimer Res. 12, 814-828 (2015). [PDF]
  • D. Granata, F. Baftizadeh, J. Habchi, C. Galvagnion, A. De Simone, C. Camilloni, A. Laio and M. Vendruscolo.
    The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments.
    Sci. Rep. 5, 15449 (2015). [PDF]
  • C. Camilloni and M. Vendruscolo.
    Reply to Comment on 'A tensor-free method for the structural and dynamical refinement of proteins using residual dipolar couplings'.
    J. Phys. Chem. B, 119, 8225-8226 (2015). [PDF]
  • M. J. Holliday, C. Camilloni, G. Armstrong, N. G. Isern, F. Zhang, M. Vendruscolo and E. Eisenmesser.
    Structure and dynamics of GeoCyp: A thermophilic cyclophilin with a novel substrate binding mechanism that functions efficiently at low temperatures.
    Biochemistry, 54, 3207-3217 (2015). [PDF]
  • K. Brewer, T. Bacaj, A. Cavalli, C. Camilloni, N. Barlow, A. Zhou, P. Cao, J. Xu, A. B. Seven, E. A. Prinslow, R. Voleti, D. Haussinger, A. Bonvin, J. Liu, D. R. Tomchick, M. Vendruscolo, B. Graham, T. C. Sudhof, J. Rizo.
    Dynamic binding mode of a synaptotagmin-1-SNARE complex in solution
    Nat. Struct. Mol. Biol. 22, 555-564 (2015). [PDF]
  • D. M. Walther, P. Kasturi, M. Zheng, S. Pinkert, G. Vecchi, P. Ciryam, R. I. Morimoto, C. M. Dobson, M. Vendruscolo, M. Mann and F.-U. Hartl.
    Widespread proteome remodeling and aggregation in aging C. elegans.
    Cell 161, 919-932 (2015). [PDF]
  • A. Cavalli and M. Vendruscolo.
    Analysis of the performance of the CHESHIRE and YAPP methods at CASD-NMR round 3.
    J. Biomol. NMR, 62, 503-509 (2015). [PDF]
  • T. P. J. Knowles, M. Vendruscolo and C. M. Dobson.
    The physical basis of protein misfolding disorders.
    Physics Today 68, 36-41 (2015). [PDF]
  • A. De Simone, F. A. Aprile, A. Dhulesia, C. M. Dobson and M. Vendruscolo.
    Structure of a low-population intermediate state in the release of an enzyme product.
    eLife 4, e02777 (2015). [PDF] [Podcast]
  • S. I. A. Cohen, P. Arosio, J. Presto, F. R. Kurudenkandy, H. Biverstal, L. Dolfe, C. Dunning, X. Yang, B. Frohm, M. Vendruscolo, J. Johansonn, C. M. Dobson, A. Fisahn, T. P. J. Knowles and S. Linse.
    A molecular chaperone breaks the catalytic cycle that generates toxic Abeta oligomers.
    Nat. Struct. Mol. Biol. 22, 207-213 (2015). [PDF] [N&V] [Press]
  • C. Galvagnion, A. K. Buell, G. Meisl, T. C. T. Michaels, M. Vendruscolo, T. P. J. Knowles and C. M. Dobson.
    Lipid vesicles trigger alpha-synuclein aggregation by stimulating primary nucleation.
    Nat. Chem. Biol. 11, 229-234 (2015). [PDF] [N&V] [Press]
  • P. Sormanni, C. Camilloni, P. Fariselli and M. Vendruscolo.
    The s2D method: Simultaneous sequence-based prediction of the statistical populations of ordered and disordered regions in proteins.
    J. Mol. Biol. 427, 982-996 (2015). [PDF] [s2D web server]
  • P. Ciryam, R. Kundra, R. I. Morimoto, C. M. Dobson and M. Vendruscolo.
    Supersaturation is a major driving force for protein aggregation in neurodegenerative diseases.
    Trends Pharmacol. Sci. 36, 72-77 (2015). [PDF]
  • R. Porcari, C. Proukakis, C. A. Waudby, B. Bolognesi, P. P. Mangione, J. F. S. Paton, S. Mullin, L. D. Cabrita, A. Penco, A. Relini, G. Verona, M. Vendruscolo, M. Stoppini, G. G. Tartaglia, C. Camilloni, J. Christodoulou, A. H. V. Schapira and V. Bellotti.
    The H50Q mutation induces a tenfold decrease in the solubility of alpha-synuclein.
    J. Biol. Chem. 290, 2395-2404 (2015). [PDF]
  • P. Kukic, H. T. K. Leung, F. Bemporad, F. A. Aprile, J. R. Kumita, A. De Simone, C. Camilloni, M. Vendruscolo.
    The structure and dynamics of the integrin LFA-1 I-domain in the inactive state underlie its inside-out/outside-in signalling and allosteric mechanism.
    Structure, 23, 745-753 (2015). [PDF]
  • S. Kumar, M. Vendruscolo, A. Singh, D. Kumar and A. Samal.
    Analysis of the hierarchical structure of the B. subtilis transcriptional regulatory network.
    Mol. BioSys. 11, 930-941 (2015). [PDF]
  • H. Takahashi, N. Adachi, T. Shirafuji, S. Danno, T. Ueyama, M. Vendruscolo, A. N. Shuvaev, T. Sugimoto, T. Seki, D. Hamada, K. Irie, H. Hirai, N. Sakai and N. Saito.
    Identification and characterization of PKCgamma, a kinase implicated in SCA14, as an amyloidogenic protein.
    Hum. Mol. Gen. 24, 525-539 (2015). [PDF]
  • P. Sormanni, F. A. Aprile and M. Vendruscolo.
    The CamSol method of rational design of protein mutants with enhanced solubility.
    J. Mol. Biol. 427, 478-490 (2015). [PDF] [CamSol web server (academic)] [CamSol web server (non-academic)]
  • C. Camilloni and M. Vendruscolo.
    A tensor-free method for the structural and dynamical refinement of proteins using residual dipolar couplings.
    J. Phys. Chem. B 19, 653-661 (2015). [PDF]

2014

  • D. Sanfelice, A. De Simone, A. Cavalli, S. Faggiano, M. Vendruscolo, A. Pastore.
    Characterisation of the conformational fluctuations in the Josephin domain of ataxin-3.
    Bioph. J. 107, 2923-2931 (2014). [PDF]
  • J. R. Allison, R. C. Rivers, J. C. Christodoulou, M. Vendruscolo and C. M. Dobson.
    A relationship between the transient structure in the monomeric state and the aggregation propensities of alpha-synuclein and beta-synuclein.
    Biochemistry, 53, 7170-7183 (2014). [PDF]
  • H. T. K. Leung, P. Kukic, C. Camilloni, F. Bemporad, A. De Simone, F. A. Aprile, J. Kumita and M. Vendruscolo.
    NMR characterisation of the conformational fluctuations of the human lymphocyte function associated antigen-1 I domain.
    Protein Sci. 23, 1596-1606 (2014) [PDF]
  • S. Gianni, C. Camilloni, R. Giri, A. Toto, D. Bonetti, A. Morrone, P. Sormanni, M. Brunori and M. Vendruscolo
    Understanding the frustration arising from the competition between function, misfolding and aggregation in a globular protein.
    Proc. Natl. Acad. Sci. USA 111, 14141-14146 (2014). [PDF]
  • W. Boomsma, P. Tian, J. Frellsen, J. Ferkinghoff-Borg, T. Hamelryck, K. Lindorff-Larsen and M. Vendruscolo.
    Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts.
    Proc. Natl. Acad. Sci. USA 111, 13852-13857 (2014). [PDF]
  • C. Camilloni, A. B. Sahakyan, M. Holliday, N. G. Isern, F. Zhang, E. Z. Eisenmesser and M. Vendruscolo.
    Cyclophilin A catalyses proline isomerization by an electrostatic handle mechanism.
    Proc. Natl. Acad. Sci. USA 111, 10203-10208 (2014). [PDF]
  • C. Camilloni and M. Vendruscolo.
    Statistical mechanics of the denatured state of a protein using replica-averaged metadynamics.
    J. Am. Chem. Soc. 136, 8982-8991 (2014). [PDF]
  • F. Blombach, H. Launay, A. P. Snijders, V. Zorraquino-Salvo, H. Wu, B. de Koning, S. J. Brouns, T. Ettema, C. Camilloni, A. Cavalli, M. Vendruscolo, M. J. Dickman, L. D. Cabrita, A. La Teana, D. Benelli, P. Londei, J. Christodoulou, J. van der Oost.
    Archaeal MBF1 binds to 30S and 70S ribosomes via its helix-turn-helix domain.
    Biochem. J. 462, 373-384 (2014). [PDF]
  • T. P. J. Knowles, M. Vendruscolo and C. M. Dobson.
    The amyloid state and its association with protein misfolding diseases.
    Nature Rev. Mol. Cell Biol. 15, 384-396 (2014). [PDF]
  • P. Ciryam, M. Vendruscolo, C. M. Dobson and E. P. O'Brien.
    Understanding the influence of codon translation rates on cotranslational protein folding.
    Acc. Chem. Res. 47, 1536-1544 (2014). [PDF]
  • A. K. Buell, C. Galvagnion, R. Gaspar, E. Sparr, M. Vendruscolo, T. P. J. Knowles, S. Linse and C. M. Dobson.
    Solution conditions determine the relative importance of nucleation and growth processes in alpha-synuclein aggregation.
    Proc. Natl. Acad. Sci. USA, 111, 7671-7676 (2014). [PDF]
  • G. Fusco, A. De Simone, G. Tata, V. Vostrikov, M. Vendruscolo, C. M. Dobson, G. Veglia.
    Direct observation of the three regions in alpha-synuclein that determine its membrane-bound behaviour.
    Nature Comm. 5, 3827 (2014). [PDF]
  • B. Fu, A. B. Sahakyan, C. Camilloni, G. G. Tartaglia, E. Paci, A. Caflisch, M. Vendruscolo and A. Cavalli.
    ALMOST: An all atom molecular simulation toolkit for protein structure determination.
    J. Comp. Chem. 35, 1101-1105 (2014). [PDF]
  • P. Kukic, C. Camilloni, A. Cavalli and M. Vendruscolo.
    Determination of the individual roles of the linker residues in the interdomain motions of calmodulin using NMR chemical shifts.
    J. Mol. Biol. 426, 1826-1838 (2014). [PDF]
  • A. A. Kendrick, M. J. Holliday, N. G. Isern, F. Zhang, C. Camilloni, C. Huynh, M. Vendruscolo, G. Armstrong and E. Z. Eisenmesser.
    The dynamics of interleukin-8 and its interaction with human CXC receptor I peptide.
    Protein Sci. 23, 464-480 (2014). [PDF]
  • R. W. Montalvao, C. Camilloni, A. De Simone and M. Vendruscolo.
    New opportunities for tensor-free calculations of residual dipolar couplings for the study of protein dynamics.
    J. Biolmol. NMR, 58, 233-238 (2014). [PDF]
  • A. Kannan, C. Camilloni, A. B. Sahakyan, A. Cavalli and M. Vendruscolo.
    A conformational ensemble derived using NMR methyl chemical shifts reveals a mechanical clamping transition that gates the binding of the HU protein to DNA.
    J. Am. Chem. Soc. 136, 2204-2207 (2014). [PDF]
  • P. Arosio, M. Vendruscolo, C. M. Dobson and T. P. J. Knowles.
    Chemical kinetics for drug discovery against protein aggregation.
    Trends Pharmacol. Sci. 35, 127-135 (2014). [PDF]
  • S. I. A. Cohen, L. Rajah, C. Yoon, A. K. Buell, D. A. White, R. A. Sperling, M. Vendruscolo, E. M. Terentjev, C. M. Dobson, D. A. Weitz and T. P. J. Knowles.
    Spatial propagation of protein polymerisation.
    Phys. Rev. Lett. 112, 098101 (2014). [PDF]
  • G. Toth, S. Gardai, W. Zago, C. W. Bertoncini, N. Cremades, S. L. Roy, M. A. Tambe, J.-C. Rochet, C. Galvaignon, G. Skibinski, S. Finkbeiner, M. Bova, K. Regnstrom, S. Chiou, J. Johnston, K. Callaway, J. P. Anderson, M. F. Jobling, A. K. Buell, T. A. Yednock, T. P. J. Knowles, M. Vendruscolo, J. Christodoulou, C. M. Dobson, D. Schenk, L. McConlogue.
    Targeting the intrinsically disordered structural ensemble of alpha-synuclein by small molecules as a potential therapeutic strategy for Parkinson's disease.
    PLoS One, 9, e87133 (2014). [PDF]
  • E. P. O'Brien, M. Vendruscolo and C. M. Dobson.
    Kinetic modeling indicates fast translating codons can coordinate cotranslational protein folding by avoiding misfolded intermediates.
    Nature Comm. 5, 2988 (2014). [PDF]
  • S. Abeln, M. Vendruscolo, C. M. Dobson, D. Frenkel.
    A simple lattice model that captures protein folding, aggregation and amyloid formation.
    PLoS One, 9, e85185 (2014). [PDF]
  • M. Varadi, S. Kosol, P. Lebrun, E. Valentini, M. Blackledge, A. K. Dunker, I. C. Felli, J. D. Forman-Kay, R. W. Kriwacki, J. Sussman, D. I. Svergun, V. N. Uversky, M. Vendruscolo, D. Wishart, P. E. Wright, P. Tompa.
    pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins.
    Nucl. Acids Res. 42, D326-D335 (2014). [PDF]

2013

  • G. T. Debelouchina, M. J. Bayro, A. W. Fitzpatrick, V. Ladizhansky, M. T. Colvin, M. A. Caporini, C. P. Jaroniec, V. S. Bajaj, M. Rosay, C. E. MacPhee, M. Vendruscolo, W. E. Maas, C. M. Dobson, R. G. Griffin.
    Higher order amyloid fibril structure by MAS NMR and DNP spectroscopy.
    J. Am. Chem. Soc. 135, 19237-19247 (2013). [PDF]
  • L. Volpatti, M. Vendruscolo, C. M. Dobson and T. P. J. Knowles.
    A clear view of polymorphism, twist and chirality in amyloid fibril formation.
    ACS Nano, 7, 10443-10448 (2013). [PDF]
  • C. Camilloni, A. Cavalli and M. Vendruscolo.
    Replica-averaged metadynamics.
    J. Chem. Theor. Comput. 9, 5610-5617 (2013). [PDF]
  • P. Ciryam, G. G. Tartaglia, R. I. Morimoto, C. M. Dobson and M. Vendruscolo.
    Widespread aggregation and neurodegenerative diseases are associated with supersaturated proteins.
    Cell Rep. 5, 781-790 (2013). [PDF]
  • F. Biedermann, M. Vendruscolo, O. A. Scherman, A. De Simone, W. M. Nau.
    Cucurbit[8]uril and blue-box: High-energy water release overwhelms electrostatic interactions.
    J. Am. Chem. Soc. 135, 14879-14888 (2013). [PDF]
  • A. De Simone, M. Gustavsson, R. W. Montalvao, L. Shi, G. Veglia and M. Vendruscolo.
    Structures of the excited states of phospholamban and shifts in their populations upon phosphorylation.
    Biochemistry, 52, 6684-6694 (2013). [PDF]
  • A. De Simone, R. W. Montalvao, C. M. Dobson and M. Vendruscolo.
    Characterisation of the interdomain motions in hen lysozyme using residual dipolar couplings as replica-averaged structural restraints in molecular dynamics simulations.
    Biochemistry, 52, 6480-6486 (2013). [PDF]
  • C. Camilloni and M. Vendruscolo.
    A relationship between the aggregation rates of alpha-synuclein variants and the beta-sheet populations in their monomeric forms.
    J. Phys. Chem. B, 117, 10737-10741 (2013). [PDF]
  • M. Tsytlonok, P. Sormanni, P. J. E. Rowling, M. Vendruscolo and L. S. Itzhaki.
    Subdomain architecture and stability of a giant repeat protein.
    J. Phys. Chem. B, 117, 13029-13037 (2013). [PDF]
  • C. A. Waudby, C. Camilloni, A. W. P. Fitzpatrick, L. Cabrita, C. M. Dobson, M. Vendruscolo and J. Christodoulou.
    In-cell NMR characterization of the secondary structure populations of a disordered conformation of alpha-synuclein within E. coli cells.
    PLoS One, 8, e72286 (2013). [PDF]
  • M. H. Horrocks, L. Rajah, P. Jonsson, M. Kjaergaard, M. Vendruscolo, T. P. J. Knowles and D. Klenerman.
    Single-molecule measurements of transient biomolecular complexes through microfluidic dilution.
    Anal. Chem. 85, 6855-6859 (2013). [PDF]
  • R. Suardiaz, A. B. Sahakyan and M. Vendruscolo.
    A geometrical parametrisation of C1'- C5' RNA ribose chemical shifts calculated by density functional theory.
    J. Chem. Phys. 139, 034101 (2013). [PDF]
  • M. Zhu, A. De Simone, D. Schenk, G. Toth, C. M. Dobson and M. Vendruscolo.
    Identification of small-molecule binding pockets in the soluble monomeric form of the Abeta42 peptide.
    J. Chem. Phys. 139, 035101 (2013). [PDF]
  • A. Borkar, A. De Simone, R. W. Montalvao and M. Vendruscolo.
    A method of determining RNA conformational ensembles using structure-based calculations of residual dipolar couplings.
    J. Chem. Phys. 138, 215103 (2013). [PDF]
  • T. W. Herling, T. M. Muller, L. Rajah, J. N. Skepper, M. Vendruscolo, and T. P. J. Knowles.
    Integration and characterization of solid wall electrodes in microfluidic devices fabricated in a single photolithography step.
    App. Phys. Lett. 102, 184102 (2013). [PDF]
  • S. I. A. Cohen, S. Linse, L. M. Luheshi, E. Hellstrand, D. A. White, L. Rajah, D. E. Otzen, M. Vendruscolo, C. M. Dobson and T. P. J. Knowles.
    Proliferation of amyloid-beta42 aggregates occurs through a secondary nucleation mechanism.
    Proc. Natl. Acad. Sci. USA, 110, 9758-9763 (2013). [PDF]
  • L. Caniparoli, M. Marsili and M. Vendruscolo.
    The Codon Information Index: A quantitative measure of the information provided by the codon bias.
    J. Stat. Mech. P04031 (2013). [PDF]
  • D. Granata, C. Camilloni, M. Vendruscolo and A. Laio.
    Characterization of the free energy landscapes of proteins by NMR-guided metadynamics.
    Proc. Natl. Acad. Sci. USA, 110, 6817-6822 (2013). [PDF]
  • A. W. P. Fitzpatrick, G. T. Debelouchina, M. J. Bayro, D. K. Clare, M. A. Caporini, V. S. Bajaj, C. P. Jaroniec, L. Wang, V. Ladizhansky, S. A. Muller, C. E. MacPhee, C. A. Waudby, H. R. Mott, A. De Simone, T. P. J. Knowles, H. R. Saibil, M. Vendruscolo, E. Orlova, R. G. Griffin and C. M. Dobson.
    Atomic structure and hierarchical self-assembly of a cross-beta amyloid fibril.
    Proc. Natl. Acad. Sci. USA, 110, 5468-5473 (2013). [PDF]
  • T. Guilliams, F. El-Turk, A. K. Buell, E. M. O'Day, F. A. Aprile, E. K. Esbjorner, M. Vendruscolo, N. Cremades, E. Pardon, W. Lode, M. E. Welland, J. Steyaert, J. Christodoulou, C. M. Dobson and E. De Genst.
    Nanobodies raised against monomeric alpha-synuclein distinguish between fibrils at different maturation stages.
    J. Mol. Biol. 425, 2397-2411 (2013). [PDF]
  • M. Vendruscolo and C. M. Dobson
    Protein self-assembly intermediates.
    Nature Chem. Biol. 9, 216-217 (2013). [PDF]
  • A. Cavalli, C. Camilloni and M. Vendruscolo.
    Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle.
    J. Chem. Phys. 138, 094112 (2013) [PDF]
  • A. B. Sahakyan and M. Vendruscolo.
    Analysis of ring current and electric field effects on the chemical shifts of RNA bases.
    J. Phys. Chem. B, 117, 1989-1998 (2013). [PDF]
  • C. Camilloni, A. Cavalli and M. Vendruscolo.
    Assessment of the use chemical shifts as replica-averaged structural restraints in molecular dynamics simulations to characterise the dynamics of proteins.
    J. Phys. Chem. B, 117, 1838-1843 (2013). [PDF]
  • P. Ciryam, R. I. Morimoto, M. Vendruscolo, C. M. Dobson and E. P. O'Brien.
    In vivo translation rates can substantially delay the co-translational folding of the Escherichia coli cytosolic proteome.
    Proc. Natl. Acad. Sci. USA, 110, E132-E140 (2013). [PDF]

2012

  • C. Roodveldt, A. Andersson, E. J. De Genst, A. Labrador-Garrido, A. K. Buell, C. M. Dobson, G. G. Tartaglia and M. Vendruscolo.
    A rationally-designed six-residue swap generates comparability in the aggregation behaviour of alpha-synuclein and beta-synuclein.
    Biochemistry, 51, 8771-8778 (2012). [PDF]
  • T. P. Knowles, A. De Simone, A. W. Fitzpatrick, A. Baldwin, S. Meehan, L. Rajah, M. Vendruscolo, M. E. Welland, C. M. Dobson, E. M. Terentjev.
    Twisting transition between crystalline and fibrillar phases of aggregated peptides.
    Phys. Rev. Lett. 109, 158101 (2012). [PDF]
  • R. W. Montalvao, A. De Simone and M. Vendruscolo.
    Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings.
    J. Biomol. NMR, 53, 281-292 (2012). [PDF]
  • J. E. Chambers, K. Petrova, G. Tomba, M. Vendruscolo and D. Ron.
    ADP ribosylation adapts an endoplasmic reticulum chaperone response to short-term fluctuations in unfolded protein load.
    J. Cell Biol. 198, 371-385 (2012). [PDF]
  • E. P. O'Brien, M. Vendruscolo and C. M. Dobson.
    Prediction of variable translation rate effects on cotranslational protein folding.
    Nature Comm. 3, 868 (2012). [PDF]
  • A. B. Sahakyan, A. Cavalli, W. F. Vranken and M. Vendruscolo.
    Protein structure validation using side-chain chemical shifts.
    J. Phys. Chem. B, 116, 4754-4759 (2012). [PDF]
  • E. P. O'Brien, J. Christodoulou, M. Vendruscolo and C. M. Dobson.
    Trigger factor slows co-translational folding through kinetic trapping while sterically protecting the nascent chain from aberrant cytosolic interactions.
    J. Am. Chem. Soc. 134, 10920-10932 (2012). [PDF]
  • J. Chen, H. Yagi, P. Sormanni, M. Vendruscolo, K. Makabe, T. Nakamura, Y. Goto, K. Kuwajima.
    Fibrillogenic propensity of the GroEL apical domain: a Janus-faced minichaperone.
    FEBS Lett. 586, 1120-1127 (2012). [PDF]
  • C. Camilloni, A. De Simone, W. F. Vranken and M. Vendruscolo.
    Determination of secondary structure populations in disordered states of proteins using NMR chemical shifts.
    Biochemistry, 51, 2224-2231 (2012). [PDF] [d2D web server]
  • S. I. A. Cohen, M. Vendruscolo, C. M. Dobson, T. P. J. Knowles.
    From macroscopic measurements to microscopic mechanisms of protein aggregation.
    J. Mol. Biol. 421, 160-171 (2012). [PDF]
  • P. Neudecker, P. Robustelli, A. Cavalli, P. Walsh, P. Lundstrom, A. Zarrine-Afsar, S. Sharpe, M. Vendruscolo, L. E. Kay.
    Structure of an intermediate state in protein folding and aggregation.
    Science, 336, 362-366 (2012). [PDF]
  • C. Camilloni, P. Robustelli, A. De Simone, A. Cavalli and M. Vendruscolo.
    Characterisation of the conformational equilibrium between the two major substates of RNase A using NMR chemical shifts.
    J. Am. Chem. Soc. 134, 3968-3971 (2012). [PDF]
  • H. T. A. Leung, B. Ochoa Montano, T. L. Blundell, M. Vendruscolo and R. W. Montalvao.
    Arabesque: A tool for protein structural comparison using differential geometry and knot theory.
    Wor. Res. J. Pep. Prot. 1, 33-40 (2012). [PDF]
  • M. Vendruscolo.
    Proteome folding and aggregation.
    Curr. Op. Struct. Biol. 22, 138-143 (2012). [PDF]
  • F. Agostini, M. Vendruscolo, G. G. Tartaglia.
    Sequence-based prediction of protein solubility.
    J. Mol. Biol. 421, 237-241 (2012). [PDF]
  • G. Fusco, A. De Simone, S.-T. D. Hsu, F. Bemporad, M. Vendruscolo, F. Chiti, C. M. Dobson.
    1H, 13C and 15N resonance assignments of human muscle acylphosphatase.
    Biomol. NMR. Assign. 6, 27-29 (2012). [PDF]
  • A. Rosato, J. Aramini, C. Arrowsmith, A. Bagaria, D. Baker, A. Cavalli, J. F. Doreleijers, A. Eletsky, A. Giachetti, P. Guerry, A. Gutmanas, P. Guntert, Y.-F. He, T. Herrmann, Y. J. Huang, V. Jaravine, H. R.A. Jonker, M. A. Kennedy, O. F. Lange, G. Liu, T. E. Malliavin, R. Mani, B. Mao, G. T. Montelione, M. Nilges, P. Rossi, G. van der Schot, H. Schwalbe, T. Szyperski, M. Vendruscolo, R. Vernon, W. F. Vranken, S. de Vries, G. W. Vuister, B. Wu, Y. Yang and A. M.J.J. Bonvin.
    Blind testing of routine, fully automated determination of protein structures from NMR data.
    Structure, 20, 227-236 (2012). [PDF]
  • T. Murakami, S.-P. Yang, L. Xie, T. Kawano, D. Fu, A. Mukai, C. Bohm, F. Chen, J. Robertson, H. Suzuki, G. G. Tartaglia, M. Vendruscolo, G. S. Schierle, F. T. Chan, A. Moloney, D. C. Crowther, C. F. Kaminski, M. Zhen and P. St George-Hyslop.
    ALS mutations in FUS causes neuronal dysfunction and death in C. elegans by a dominant gain-of-function mechanism.
    Hum. Mol. Gen. 21, 1-9 (2012). [PDF]

2011

  • A. De Simone, A. Dhulesia, G. Soldi, M. Vendruscolo, S.-T. D. Hsu, F. Chiti and C. M. Dobson.
    Experimental energy surfaces reveal the mechanisms of maintenance of protein solubility
    Proc. Natl. Acad. Sci. USA, 108, 21057-21062 (2011). [PDF]
  • M. Vendruscolo, T. P. J. Knowles and C. M. Dobson.
    Protein solubility and protein homeostasis: A generic view of protein misfolding disorders.
    Cold Spring Harb Perspect. Biol. 3, a010454 (2011). [PDF]
  • K. Wolff, M. Vendruscolo and M. Porto.
    A coarse-grained model for protein folding based on structural profiles.
    Phys. Rev. E, 84, 041934 (2011). [PDF]
  • A. De Simone, R. W. Montalvao and M. Vendruscolo.
    Determination of dynamic equilibria in proteins using residual dipolar couplings.
    J. Chem. Theor. Comp. 7, 4189-4195 (2011). [PDF]
  • S. I. A. Cohen, M. Vendruscolo, C. M. Dobson, T. P. J. Knowles.
    Nucleated polymerisation in the presence of pre-formed seed filaments.
    Int. J. Mol. Sci. 12, 5844-5852 (2011). [PDF]
  • M. Vendruscolo.
    Excited-state control of protein activity.
    J. Mol. Biol. 412, 153-154 (2011). [PDF]
  • A. W. Fitzpatrick, T. P. J. Knowles, C. A. Waudby, M. Vendruscolo and C. M. Dobson.
    Inversion of the balance of hydrophobicity and hydrogen bonding between protein folding and aggregation.
    PLoS Comp. Biol. 7, e1002169 (2011). [PDF]
  • L. Kang, K.-P. Wu, M. Vendruscolo and J. Baum.
    The A53T mutation is key in defining the differences in the aggregation kinetics of human and mouse alpha-synuclein.
    J. Am. Chem. Soc. 133, 13465-13470 (2011). [PDF]
  • A. B. Sahakyan, W. F. Vranken, A. Cavalli and M. Vendruscolo.
    Using side-chain aromatic proton chemical shifts for a quantitative analysis of protein structures.
    Angew. Chem. Intl. Ed. 50, 9620-9623 (2011). [PDF] [ArShift web server]
  • S. I. A. Cohen, M. Vendruscolo, M. E. Welland, C. M. Dobson, E. M. Terentjev and T. P. J. Knowles.
    Nucleated polymerization with secondary pathways I. Time evolution of the principal moments.
    J. Chem. Phys. 135, 065105 (2011). [PDF]
  • S. I. A. Cohen, M. Vendruscolo, C. M. Dobson and T. P. J. Knowles.
    Nucleated polymerization with secondary pathways II. Determination of self-consistent solutions to growth processes described by non-linear master equations.
    J. Chem. Phys. 135, 065106 (2011). [PDF]
  • S. I. A. Cohen, M. Vendruscolo, C. M. Dobson and T. P. J. Knowles.
    Nucleated polymerization with secondary pathways III. Equilibrium behavior, filament length distribution and oligomer populations.
    J. Chem. Phys. 135, 065107 (2011). [PDF]
  • A. J. Baldwin, T. P. J. Knowles, G. G. Tartaglia, A. W. Fitzpatrick, G. L. Devlin, S. Shammas, C. A. Waudby, M. F. Mossuto, S. Meehan, S. L. Gras, J. Christodoulou, S. J. Anthony-Cahill, P. D. Barker, M. Vendruscolo, C. M. Dobson.
    Metastability of native proteins and the phenomenon of amyloid formation.
    J. Am. Chem. Soc. 133, 14160-14163 (2011). [PDF]
  • A. Cavalli, R. W. Montalvao and M. Vendruscolo.
    Using chemical shifts to determine structural changes in proteins upon complex formation.
    J. Phys. Chem. B, 115, 9491-9494 (2011). [PDF]
  • M. Vendruscolo.
    Protein regulation: The statitical theory of allostery.
    Nature Chem. Biol. 7, 411-412 (2011). [PDF]
  • A. B. Sahakyan, W. F. Vranken, A. Cavalli and M. Vendruscolo.
    Structure-based prediction of methyl chemical shifts in proteins.
    J. Biomol. NMR, 50, 331-346 (2011). [PDF] [CH3Shift web server]
  • K. Wolff, M. Vendruscolo and M. Porto.
    Asymmetric folding pathways and transient misfolding in a coarse-grained model of proteins.
    Europhys. Lett. 94, 48005 (2011). [PDF]
  • T. R. Jahn, K. J. Kohlhoff, M. Scott, G. G. Tartaglia, D. A. Lomas, C. M. Dobson, M. Vendruscolo and D. C. Crowther.
    Detection of early locomotor abnormalities in a Drosophila model of Alzheimer's disease by a three-dimensional tracking system.
    J. Neurosci. Meth. 197, 186-189 (2011). [PDF]
  • K. J. Kohlhoff, T. R. Jahn, D. A. Lomas, C. M. Dobsom, C. D. Crowther and M. Vendruscolo.
    The iFly tracking system for an automated locomotor and behavioural analysis of Drosophila melanogaster.
    Integrative Biology, 3, 755-760 (2011). [PDF]
  • S. Raimondi, F. Guglielmi, S. Giorgetti, S. Di Gaetano, A. Arciello, D. M. Monti, A. Relini, D. Nichino, S. M. Doglia, A. Natalello, P. Pucci, P. Mangione, L. Obici, G. Merlini, M. Stoppini, P. Robustelli, G. G. Tartaglia, M. Vendruscolo, C. M. Dobson, R. Piccoli, V. Bellotti.
    Effects of the known pathogenic mutations on the aggregation pathways of the amyloidogenic peptide of human apolipoprotein A-I.
    J. Mol. Biol. 407, 465-476 (2011). [PDF]
  • E. O'Brien, J. Christodoulou, M. Vendruscolo, C. M. Dobson.
    New scenarios of protein folding can occur on the ribosome.
    J. Am. Chem. Soc. 132, 16928-16937 (2011). [PDF]
  • O. Szczepankiewicz, C. Cabaleiro-Lago, G. G. Tartaglia, M. Vendruscolo, T. Hunter, G. J. Hunter, H. Nilsson, E. Thulin and S. Linse.
    Interactions in the native state of monellin, which play a protective role against aggregation.
    Mol. BioSys. 7, 521-532 (2011). [PDF]
  • L. Masino, G. Nicastro, L. Calder, M. Vendruscolo and A. Pastore.
    Functional interactions as a survival strategy against abnormal aggregation.
    FEBS J. 25, 45-54 (2011). [PDF]
  • M. Vendruscolo and C. M. Dobson.
    Protein dynamics: Moore's law in molecular biology.
    Current Biology, 21, R68-R70 (2011). [PDF]
  • H. Olzscha, S. M. Schermann, A. C. Worner, S. Pinkert, M. H. Hecht, G. G. Tartaglia, M. Vendruscolo, M. Hayer-Hartl, F. U. Hartl and R. M. Vabulas.
    Amyloid-like aggregates sequester numerous metastable proteins with essential cellular functions.
    Cell, 144, 67-78 (2011). [PDF]

2010

  • S. Gianni, Y. Ivarsson, A. De Simone, C. Travaglini-Allocatelli, M. Brunori and M. Vendruscolo.
    Characterization of the structure of a misfolded intermediate populated during the folding process of a PDZ domain.
    Nature Struct. Mol. Biol. 17, 1431-1437 (2010). [PDF]
  • M. Vendruscolo.
    Enzymatic activity in disordered states of proteins.
    Curr. Op. Chem. Biol. 14, 671-675 (2010). [PDF]
  • E. P. O'Brien, S. -T. D Hsu, J. Christodoulou, M. Vendruscolo, and C. M. Dobson.
    Transient tertiary structure formation within the ribosome exit port.
    J. Am. Chem. Soc. 132, 16928-16937 (2010). [PDF]
  • M. A. Caporini, V. S. Bajaj, M. Veshtort, A. Fitzpatrick, C. E. MacPhee, M. Vendruscolo, C. M. Dobson, and R. G. Griffin.
    Accurate determination of interstrand distances and alignment in amyloid fibrils by magic angle spinning NMR.
    J. Phys. Chem. B, 114, 13555-13561 (2010). [PDF]
  • S. Pechmann and M. Vendruscolo.
    Derivation of a solubility condition for proteins from an analysis of the competition between folding and aggregation.
    Mol. BioSys. 6, 2490-2497 (2010). [PDF]
  • G. G. Tartaglia and M. Vendruscolo.
    Proteome-level relationship between folding and aggregation propensities of proteins.
    J. Mol. Biol. 402, 919-928 (2010). [PDF]
  • Y. Lee, T. Zhou, G. G. Tartaglia, M. Vendruscolo and C. O. Wilke.
    Translationally optimal codons associate with aggregation-prone sites in proteins.
    Proteomics, 10, 4163-4171 (2010). [PDF]
  • P. Robustelli, K. J. Kohlhoff, A. Cavalli and M. Vendruscolo.
    Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins.
    Structure, 18, 923-933 (2010). [PDF]
  • G. G. Tartaglia, C. M. Dobson, F. U. Hartl and M. Vendruscolo.
    Physico-chemical determinants of chaperone requirements.
    J. Mol. Biol. 400, 579-588 (2010). [PDF]
  • I. De Gortari, G. Portella, X. Salvatella, V. S. Bajaj, P. van der Wel, J. R. Yates, M. D. Segall, C. J. Pickard, M. C. Payne and M. Vendruscolo.
    Time averaging of NMR chemical shifts in the MLF peptide in the solid state.
    J. Am. Chem. Soc. 132, 5993-6000, 2010. [PDF]
  • A.-C. Brorsson, B. Bolognesi, G. G. Tartaglia, S. L. Shammas, G. Favrin, I. Watson, D. A. Lomas, F. Chiti, M. Vendruscolo, C. M. Dobson, D. C. Crowther and L. M. Luheshi.
    Intrinsic determinants of neurotoxic aggregate formation by the amyloid beta peptide.
    Bioph. J. 98, 1677-1684, 2010. [PDF]
  • K. Wolff, M. Vendruscolo and M. Porto.
    Efficient identification of near-native conformations in ab initio protein structure prediction using structural profiles.
    Proteins, 78, 249-258 (2010). [PDF]

2009

    J. R. Allison, P. Varnai, C. M. Dobson and M. Vendruscolo.
    Determination of the free energy landscape of alpha-synuclein using spin-label nuclear magnetic resonance measurements
    J. Am. Chem. Soc. 131, 18314-18326 (2009). [PDF]

    T. P. J. Knowles, C. A. Waudby, G. L. Devlin, S. I. A. Cohen, A. Aguzzi, M. Vendruscolo, E. M. Terentjev, M. E. Welland, C. M. Dobson.
    An analytical solution to the kinetics of breakable filament assembly.
    Science, 326, 1533-1537 (2009). [PDF]

    A. De Simone, A. Cavalli, S.-T. D. Hsu, W. Vranken and M. Vendruscolo.
    Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins.
    J. Am. Chem. Soc. 131, 16332-16333 (2009). [PDF] [CamCoil web server]

    K. J. Kohlhoff, P. Robustelli, A. Cavalli, X. Salvatella and M. Vendruscolo
    Fast and accurate predictions of protein NMR chemical shifts from interatomic distances
    J. Am. Chem. Soc. 131, 13894-13895 (2009). [PDF] [CamShift web server]

    G. G. Tartaglia and M. Vendruscolo.
    Correlation between mRNA expression levels and protein aggregation propensities in subcellular localisations.
    Mol. BioSys. 5, 1873-1876 (2009). [PDF]

    C. Lendel, C. W. Bertoncini, N. Cremades, C. A. Waudby, M. Vendruscolo, C. M. Dobson, D. Schenk, J. Christodoulou, G. Toth.
    On the mechanism of non-specific inhibitors of protein aggregation: dissecting the interactions of alpha-synuclein with Congo red and Lacmoid.
    Biochemistry, 48, 8322-8334 (2009). [PDF]

    J. M. Bui, J. Gsponer, M. Vendruscolo and C. M. Dobson.
    Correlation functions exhibit sub-tau_c and supra-tau_c motions in protein Gbeta1.
    Bioph. J. 97, 2513-2520 (2009). [PDF]

    M. Porto, H. E. Roman and M. Vendruscolo.
    Physical principles of protein behavior in the cell.
    J. Proteome Res. 8, 2615 (2009) [PDF]

    M. Vendruscolo and C. M. Dobson.
    Quantitative approaches to defining normal and aberrant protein homeostasis.
    Faraday Discussions, 143, 277-291 (2009). [PDF]

    K. E. Routledge, G. G. Tartaglia, G. W. Platt, M. Vendruscolo and S. E. Radford.
    Competition between intra-molecular and inter-molecular interactions in an amyloid forming protein.
    J. Mol. Biol. 389, 776-786 (2009). [PDF]

    S. Auer, A. Trovato and M. Vendruscolo
    A condensation-ordering mechanism in nanoparticle-catalyzed peptide aggregation.
    PLoS Comp. Biol. 5, e1000458 (2009). [PDF]

    S. Pechmann, E. D. Levy, G. G. Tartaglia and M. Vendruscolo.
    Physico-chemical principles that regulate the competition between functional and dysfunctional association of proteins.
    Proc. Natl. Acad. Sci. USA, 106, 10159-10164 (2009) [PDF]

    P. Robustelli, A. Cavalli, C. M. Dobson, M. Vendruscolo and X. Salvatella.
    Folding of small proteins with chemical shift restrained Monte Carlo simulations without the use of molecular fragment replacement or structural homology.
    J. Phys. Chem. B, 113, 7890-7896 (2009).

    A. K. Buell, N. R. Birkett, G. G. Tartaglia, M. Vendruscolo, X. Salvatella, M. E. Welland, C. M. Dobson and T. P. J. Knowles.
    Position dependent electrostatic protection against protein aggregation.
    ChemBioChem, 10, 1309-1312 (2009).

    G. G. Tartaglia, S. Pechmann, C. M. Dobson and M. Vendruscolo.
    A relationship between mRNA expression levels and protein solubility in E. coli.
    J. Mol. Biol. 388, 381-389 (2009). [PDF]

    M. Calamai, G. G. Tartaglia, M. Vendruscolo, F. Chiti and C. M. Dobson.
    Mutational and computational analysis of the aggregation-prone and disaggregation-prone regions of AcP.
    J. Mol. Biol. 387, 965-974 (2009). [PDF]

    A. De Simone, B. Richter, X. Salvatella and M. Vendruscolo.
    Toward an accurate determination of free energy landscapes in solution states of proteins.
    J. Am. Chem. Soc. 131, 3810-3811 (2009). [PDF]

    C. T. Friel, D. A. Smith, M. Vendruscolo, J. Gsponer, S. E. Radford.
    The mechanism of formation of a folding intermediate reveals the competition between functional and kinetic evolutionary constraints.
    Nature Struct. Mol. Biol. 16, 318-324 (2009). [PDF]

    X. Periole, A. Rampioni, M. Vendruscolo and A. Mark.
    Molecular dynamics simulations of a cross-beta filament of the GNNQQNY peptide reveal a combination of factors that determine the degree of twist of beta sheets.
    J. Phys. Chem. B, 113, 1728-1737 (2009). [PDF]

    D. Hamada, T. Tanaka, G. G. Tartaglia, A. Pawar, M. Vendruscolo, M. Kawamura, A. Tamura, N. Tanaka, and C. M. Dobson.
    Competition between folding, native state dimerisation and amyloid aggregation in beta-lactoglobulin.
    J. Mol. Biol. 386, 878-890 (2009). [PDF]

2008

    P. Robustelli, A. Cavalli and M. Vendruscolo.
    Determination of protein structures from solid-state NMR chemical shifts.
    Structure, 16, 1764-1769 (2008). [PDF]

    S. Auer, C. M. Dobson, M. Vendruscolo and A. Maritan.
    Self-templated nucleation in peptide and protein aggregation
    Phys. Rev. Lett. 101, 258101 (2008) [PDF]

    N. Calosci, C. N. Chi, B. Richter, C. Camilloni, A. Engstrom, L. Eklund, C. Travaglini-Allocatelli, S. Gianni, M. Vendruscolo and P. Jemth.
    Comparison of successive transition states for folding reveals alternative early folding pathways of two homologous three-state proteins.
    Proc. Natl. Acad. Sci. USA, 105, 19240-19245 (2008). [PDF]

    K. Wolff, M. Vendruscolo and M. Porto.
    Stochastic reconstruction of protein structures from effective connectivity profiles.
    PMC Biophy. 1, 5 (2008).

    M. Vendruscolo and G. G. Tartaglia.
    Towards quantitative predictions in cell biology using chemical properties of proteins.
    Mol. BioSys. 4, 1170-1175 (2008). [PDF]

    R. Montalvao, A. Cavalli, X. Salvatella, T. L. Blundell and M. Vendruscolo.
    Structure determination of protein-protein complexes using NMR chemical shifts: the case of an endonuclease colicin - immunity protein complex.
    J. Am. Chem. Soc. 130, 15990-15996 (2008). [PDF]

    S. Auer, F. Meersman, C. M. Dobson and M. Vendruscolo.
    Generic mechanism of emergence of amyloid protofilaments from disordered oligomeric aggregates.
    PLoS Comp. Biol. 4, e1000222 (2008). [PDF]

    F. Herrera, A. Chesi, K. E. Paleologou, A. Schmid, A. Munoz, M. Vendruscolo, S. Gustincich, H. A. Lashuel and P. Carloni.
    Inhibition of alpha-synuclein fibrillation by dopamine is mediated by its interactions with E83 and the C-terminal residues 125YEMPS129.
    PLoS One, 3, e3394 (2008).

    G. Calloni, C. Lendel, S. Campioni, S. Giannini, A. Gliozzi, A. Relini, M. Vendruscolo, C. M. Dobson, X. Salvatella, and F. Chiti.
    Structure and dynamics of a partially folded protein are decoupled from its mechanism of aggregation.
    J. Am. Chem. Soc. 130, 13040-13050 (2008).

    T. M. K. Cheng, Y.-E. Lu, M. Vendruscolo, P. Lio', T. L. Blundell.
    Prediction by graph teoretic measures of structural effects in proteins arising from non-synonimous single nucleotide polymorphism.
    PLoS Comp. Biol. 4, e1000135 (2008).

    K. Wolff, M. Vendruscolo and M. Porto.
    A stochastic method for the reconstruction of protein structures from one-dimensional structural profiles.
    Gene, 422, 47-51 (2008).

    B. Strodel, A. W. Fitzpatrick, M. Vendruscolo, C. M. Dobson and D. J. Wales.
    Characterising the first steps of amyloid formation for the ccbeta peptide.
    J. Phys. Chem. B, 32, 9998-10004 (2008).

    M. Vendruscolo.
    Protein dynamics under light control.
    Nature Chem. Biol. 4, 449-450 (2008). [PDF]

    A. Dhulesia, J. Gsponer and M. Vendruscolo.
    Mapping of two networks of residues that exhibit structural and dynamical changes upon binding in a PDZ domain protein.
    J. Am. Chem. Soc. 130, 8931-8939 (2008). [PDF]

    G. G. Tartaglia, A. Pawar, S. Campioni, F. Chiti, C. M. Dobson and M. Vendruscolo.
    Prediction of aggregation-prone regions in structured proteins.
    J. Mol. Biol. 380, 425-436 (2008). [PDF] [Zyggregator web server]

    G. G. Tartaglia and M. Vendruscolo.
    The Zyggregator method for predicting protein aggregation propensities.
    Chem. Soc. Rev. 37, 1395-1401 (2008). [PDF]

    F. Bemporad, J. Gsponer, H. I. Hopearuoho, G. Plakoutsi, G. Stati, M. Stefani, N. Taddei, M. Vendruscolo and F. Chiti.
    Biological function in a non-native partially folded state of a protein.
    EMBO J. 27, 1525-1535 (2008).

    M. Cheon, G. Favrin, I. Chang, C. M. Dobson and M. Vendruscolo.
    Calculation of the free energy barriers in the oligomerisation of Abeta peptide fragments.
    Frontiers in Bioscience, 13, 5614-5622 (2008).

    J. Gsponer, J. Christodoulou, A. Cavalli, Jennifer M. Bui, B. Richter, C. M. Dobson and M. Vendruscolo.
    A coupled equilibrium shift mechanism in calmodulin-mediated signal transduction.
    Structure, 16, 736-746 (2008). [PDF]

    R. C. Rivers, J. R. Kumita, G. G. Tartaglia, M. M. Dedmon, A. Pawar, M. Vendruscolo, C. M. Dobson, and J. Christodoulou.
    Molecular determinants of the aggregation behaviour of alpha- and beta-synuclein.
    Protein Sci. 17, 887-898 (2008).

    P. Varnai, C. M. Dobson and M. Vendruscolo.
    Determination of the transition state ensemble for folding of ubiquitin from a combination of phi and psi analyses.
    J. Mol. Biol. 377, 575-588 (2008).

    C. Geierhaas, X. Salvatella, J. Clarke and M. Vendruscolo.
    Characterisation of transition state structures for protein folding using high, medium and low phi values.
    Prot. Eng. Des. Sel. 21, 215-222 (2008).

    X. Salvatella, B. Richter and M. Vendruscolo.
    Influence of the fluctuations of the alignment tensoron the analysis of the structure and dynamics of proteins using residual dipolar couplings.
    J. Biomol. NMR, 40, 71-81 (2008).

2007

    E. Monsellier, M. Ramazzotti, P. Polverino de Laureto, G. G. Tartaglia, N. Taddei, A. Fontana, M. Vendruscolo and F. Chiti.
    The distribution of the amino acid residues in a polypeptide sequence is a determinant of the aggregation rate optimized by evolution.
    Biophys. J. 93, 4382-4391 (2007).

    T. P. Knowles, A. W. Fitzpatrick, H. Mott, S. Meehan, M. Vendruscolo, C. M. Dobson and M. E. Welland.
    Self-assembling protein fibrils represent a novel class of high performance nanoscale biomaterials.
    Science, 318, 1900-1903 (2007).

    S. Auer, M. Miller, S. V. Krivov, C. M. Dobson, M. Karplus and M. Vendruscolo.
    Importance of metastable states in the free energy landscapes of polypeptide chains.
    Phys. Rev. Lett. 99, 178104 (2007). [PDF]

    L. M. Luheshi, G. G. Tartaglia, A.-C. Brorsson, A. P. Pawar, I. E. Watson, F. Chiti, M. Vendruscolo, D. A. Lomas, C. M. Dobson and D. C. Crowther.
    Systematic in vivo analysis of the intrinsic determinants of Amyloid beta pathogenicity.
    PLoS Biol. 5, 2493-2500 (2007). [PDF]

    M. Cheon, I. Chang, S. Mohanty, L. M. Luheshi, C. M. Dobson, M. Vendruscolo and G. Favrin.
    Structural reorganisation and potential toxicity of oligomeric species formed during the assembly of amyloid fibrils.
    PLoS Comp. Biol. 3, 1727-1738 (2007). [PDF]

    X. Periole, M. Vendruscolo and A. Mark.
    Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain.
    Proteins, 69, 536-550 (2007). [PDF]

    S. Meehan, A. J. Baldwin, T. P. J. Knowles, J. F. Smith, A. M. Squires, P. Clements, T. M. Treweek, H. Ecroyd, G. G. Tartaglia, M. Vendruscolo, C. E. MacPhee, C. M. Dobson and J. A. Carver.
    Characterisation of amyloid fibril formation by small heat-shock chaperone proteins, human alphaA-, alphaB- and R120G alphaB-crystallin.
    J. Mol. Biol. 372, 470-484 (2007).

    J. Meinhardt, G. G. Tartaglia, A. P. Pawar, T. Christopeit, P. Hortschansky, V. Schroeckh, C. M. Dobson, M. Vendruscolo and M. Fandrich.
    Similarities in the thermodynamics and kinetics of aggregation of disease-related Abeta(1-40) peptides.
    Protein Science, 16, 1214-1222 (2007).

    S. Auer, C. M. Dobson and M. Vendruscolo.
    Revealing the nucleation barriers for protein aggregation and amyloid formation.
    HFSP J. 1, 137-146 (2007). [PDF]

    M. Vendruscolo and C. M. Dobson.
    More charges against aggregation.
    Nature, 449, 555, 2007. [PDF]

    A. Cavalli, X. Salvatella, C. M. Dobson and M. Vendruscolo.
    Protein structure determination from NMR chemical shifts.
    Proc. Natl. Acad. Sci. USA, 104, 9615-9620, 2007. [PDF]

    G. G. Tartaglia, S. Pechmann, C. M. Dobson and M. Vendruscolo.
    Life on the edge: A link between gene expression levels and aggregation rates of human proteins.
    Trends Biochem. Sci. 32, 204-206 (2007). [PDF]

    M. Vendruscolo.
    Structure determination of highly heterogenous states of proteins.
    Curr. Op. Struct. Biol. 17, 15-20 (2007). [PDF]

    G. G. Tartaglia, A. Cavalli and M. Vendruscolo.
    Prediction of local structural stabilities of proteins from their amino acid sequences.
    Structure, 15, 139-143 (2007). [PDF]

    B. Richter, J. Gsponer, P. Varnai, X. Salvatella, and M. Vendruscolo.
    The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins.
    J. Biomol. NMR, 37, 117-135 (2007). [PDF]

    C. Geierhaas, A. A. Nickson, K. Lindorff-Larsen, J. Clarke and M. Vendruscolo.
    BPPred: A web-based computational tool for predicting biophysical parameters of proteins.
    Protein Sci. 16, 125-134 (2007).

    S. Gianni, C. D. Geierhaas, N. Calosci, P. Jemth, G. W. Vuister, C. Travaglini-Allocatelli, M. Vendruscolo and M. Brunori.
    A PDZ domain recapitulates a unifying mechanism for protein folding.
    Proc. Natl. Acad. Sci. USA, 104, 128-133 (2007). [PDF]

2006

    J. Gsponer, H. Hopeauroho, A. Cavalli, C. M. Dobson and M. Vendruscolo.
    Geometry, energetics and dynamics of hydrogen bonds in proteins: Structural information derived from NMR scalar couplings.
    J. Am. Chem. Soc. 128, 15127-15135 (2006). [PDF]

    M. Vendruscolo and C. M. Dobson.
    Dynamic visions of enzymatic reactions.
    Science, 313, 1586-1587 (2006). [PDF]

    C. J. Francis, K. Lindorff-Larsen, R. B. Best and M. Vendruscolo.
    Characterization of the residual structure in the unfolded state of the Delta131Delta fragment of staphylococcal nuclease.
    Proteins, 65, 145-152 (2006).

    U. Bastolla, M. Porto, H. E. Roman and M. Vendruscolo.
    A protein evolution model with independent sites that reproduce site-specific amino acid distributions from the Protein Data Bank
    BMC Evol. Biol. 6, 43 (2006).

    R. B. Best, K. Lindorff-Larsen, M. A. De Pristo and M. Vendruscolo.
    Relation between native ensembles and experimental structures of proteins
    Proc. Natl. Acad. Sci. USA, 103, 10901-10906 (2006). [PDF]

    C. Geierhaas, R. B. Best, E. Paci, M. Vendruscolo and J. Clarke.
    Structural comparison betwen the two alternative transition states for folding of TI I27.
    Bioph. J. 91, 263-295 (2006).

    R. B. Best and M. Vendruscolo.
    Structural interpretation of equilibrium hydrogen exchange protection factors in proteins: Characterisation of the large conformational fluctuations in the native state of CI2.
    Structure, 14, 97-106 (2006).

    J. Gsponer, H. I. Hopearuoho, S. B.-M.Whittaker, G. M. Spence, G. R. Moore, E. Paci, S. E. Radford and M. Vendruscolo.
    Determination of an ensemble of structures representing the exchange-competent intermediate state of the bacterial immunity protein Im7.
    Proc. Natl. Acad. Sci. USA, 103, 99-104 (2006). [PDF]

    J. Gsponer and M. Vendruscolo.
    Theoretical approaches to protein aggregation.
    Protein Pep. Lett. 13, 287-293 (2006). [PDF]

2005

    G. Salvi, P. De Los Rios and M. Vendruscolo.
    Effective interactions between chaotropic agents and proteins.
    Proteins, 61, 492-499 (2005).

    K. Lindorff-Larsen, R. B. Best and M. Vendruscolo.
    Interpreting dynamically-averaged scalar couplings in proteins.
    J. Biomol. NMR, 32, 273-280 (2005).

    E. Paci, K. Lindorff-Larsen, C. M. Dobson, M. Karplus and M. Vendruscolo.
    Transition state contact orders correlate with protein folding rates.
    J. Mol. Biol. 352, 495-500 (2005).

    D. Marenduzzo, T.~X. Hoang, F. Seno, M. Vendruscolo and A. Maritan.
    Form of growing strings.
    Phys. Rev. Lett. 95, 098103 (2005).

    X. Salvatella, C. M. Dobson, A. R. Fersht and M. Vendruscolo.
    Determination of the folding transition states of barnase by Phi_I-value-restrained simulations and validation by double-mutant Phi_IJ-values.
    Proc. Natl. Acad. Sci. USA, 102, 12389-12394 (2005).

    A. P. Pawar, K. F. DuBay, J. Zurdo, F. Chiti, M. Vendruscolo and C. M. Dobson.
    Prediction of aggregation-prone and aggregation-susceptible regions in proteins associated with neurodegenerative diseases.
    J. Mol. Biol. 350, 379-392 (2005). [PDF] [Zyggregator web server]

    E. Paci and M. Vendruscolo.
    Detection of non-native hydrophobic interactions in the denatured state of lysozyme by molecular dynamics simulations.
    J. Phys. Cond. Matt. 17, S1617-S1626 (2005).

    A. Cavalli, M. Vendruscolo and E. Paci.
    Comparison of sequence-based and structure-based energy functions for the reversible folding of a peptide.
    Bioph. J. 88, 3158-3166 (2005).

    M. Vendruscolo and C. M. Dobson.
    A glimpse at the organization of the protein universe.
    Proc. Natl. Acad. Sci. USA, 102, 5641-5642 (2005).

    S. Kristjansdottir, K. Lindorff-Larsen, W. Fieber, C. M. Dobson, M. Vendruscolo and F. M. Poulsen.
    Formation of native and non-native interactions in ensembles of denatured ACBP molecules from paramagnetic relaxation enhancement studies.
    J. Mol. Biol. 347, 1053-1062 (2005).

    U. Bastolla, M. Porto, H. E. Roman and M. Vendruscolo.
    Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles.
    Gene, 347, 219-230 (2005).

    M. Porto, H. E. Roman, M. Vendruscolo and U. Bastolla.
    Prediction of site-specific amino acid distributions from a model of neutral evolution.
    Mol. Biol. Evol. 22, 630-638 (2005).

    M. Vendruscolo and C. M. Dobson
    Towards complete descriptions of free energy landscapes of proteins.
    Phil. Trans. R. Soc. A, 363, 433-452 (2005). [PDF]

    M. M. Dedmon, K. Lindorff-Larsen, J. Christodoulou, M. Vendruscolo and C. M. Dobson.
    Mapping residual contacts in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations.
    J. Am. Chem. Soc. 127, 476-477 (2005). [PDF]

    K. Lindorff-Larsen, R. B. Best. M. A. De Pristo, C. M. Dobson and M. Vendruscolo.
    Simultaneous determination of protein structure and dynamics.
    Nature, 433, 128-132 (2005). [PDF]

    K. Lindorff-Larsen, P. Rogen, E. Paci, M. Vendruscolo and C. M. Dobson.
    Protein folding and the organization of the protein topology universe.
    Trends Bioch. Sci. 30, 13-19 (2005).

    U. Bastolla, M. Porto, H. E. Roman and M. Vendruscolo.
    The principal eigenvector of contact matrices and hydrophobicity profiles in proteins.
    Proteins, 58, 22-30 (2005).

2004

    C. Geierhaas, E. Paci, M. Vendruscolo and J. Clarke.
    Comparison of the transition states for folding of two Ig-like proteins from different superfamilies.
    J. Mol. Biol. 343, 1111-1123 (2004).

    K. F. DuBay, A. P. Pawar, F. Chiti, J. Zurdo, C. M. Dobson and M. Vendruscolo.
    Prediction of the absolute aggregation rates of amyloidogenic polypeptide chains.
    J. Mol. Biol. 341, 1317-1326 (2004). [PDF]

    D. M. Korzhnev, X. Salvatella, M. Vendruscolo, A. Di Nardo, A. R. Davidson, C. M. Dobson and L. E. Kay.
    Low-populated folding intermediates of Fyn SH3 characterized by relaxation-disperison NMR.
    Nature, 430, 586-590 (2004).

    E. Paci, J. Gsponer, X. Salvatella and M. Vendruscolo.
    Molecular dynamics studies of the process of amyloid aggregation of peptide fragments of transthyretin.
    J. Mol. Biol. 340, 555-569 (2004).

    R. B. Best and M. Vendruscolo.
    Determination of protein structures consistent with NMR order parameters.
    J. Am. Chem. Soc. 126, 8090-8091 (2004).

    M. Porto, U. Bastolla, H. E. Roman and M. Vendruscolo.
    Reconstruction of protein contact maps from their principal eigenvectors.
    Phys. Rev. Lett. 92, 218101 (2004).

    K. Lindorff-Larsen, M. Vendruscolo, E. Paci and C. M. Dobson.
    Transition states for protein folding have native topologies despite high structural similarity.
    Nature Struct. Mol. Biol. 11, 443-449 (2004).

    K. Lindorff-Larsen, S. Kristjansdottir, K. Teilum, W. Fieber, C. M. Dobson, F. M. Poulsen and M. Vendruscolo.
    Determination of an ensemble of structures representing the denatured state of ACBP.
    J. Am. Chem. Soc. 126, 3291-3299 (2004).

    J. P. K. Doye, A. A. Louis and M. Vendruscolo.
    Inhibition of protein crystallization by evolutionary negative design.
    Physical Biology, 1, 9-13 (2004).

    E. Paci, C. T. Friel, K. Lindorff-Larsen, S. E. Radford, M. Karplus and M. Vendruscolo.
    Comparison of the structures in the transition state ensembles for folding of Im7 and Im9 using all-atom molecular dynamics simulations with phi value restraints.
    Proteins, 54, 513-525 (2004).

2003

    M. Vendruscolo, E. Paci, C. M. Dobson and M. Karplus.
    Rare fluctuations of native proteins sampled during equilibrium hydrogen exchange.
    J. Am. Chem. Soc. 125, 15686-15687 (2003). [PDF]

    M. Vendruscolo, E. Paci, M. Karplus and C. M. Dobson.
    Structures and relative free energies of partially folded states of proteins.
    Proc. Natl. Acad. Sci. USA, 100, 14817-14821 (2003). [PDF]

    U. Bastolla, M. Porto, H. E. Roman and M. Vendruscolo.
    Structural conservation in protein evolution and connectivity of neutral networks.
    J. Mol. Evol. 57, S103-S119 (2003).

    K. Lindorff-Larsen, E. Paci, L. Serrano, C. M. Dobson and M. Vendruscolo.
    Calculation of mutational free energy changes in the transition state for protein folding.
    Bioph. J. 85, 1207-1214 (2003).

    E. Paci, A. Cavalli, M. Vendruscolo and A. Caflisch.
    Analysis of the distributed computing approach applied to the folding of a small beta peptide.
    Proc. Natl. Acad. Sci. USA, 100, 8217-8222 (2003).

    M. Vendruscolo, J. Zurdo, C. E. MacPhee and C. M. Dobson.
    Protein folding and misfolding: A paradigm of self-assembly and regulation in complex biological systems.
    Phil. Trans. R. Soc. A, 361, 1205-1222 (2003).

    U. Bastolla, M. Porto, H. E. Roman and M. Vendruscolo.
    Connectivity of neutral networks, overdispersion and structural conservation in protein evolution.
    J. Mol. Evol. 56, 243-154 (2003).

    M. Vendruscolo and E. Paci.
    Protein folding: Bringing theory and experiment closer together.
    Curr. Op. Struct. Biol. 13, 82-87 (2003). [PDF]

    E. Paci, A. Steward, J. Clarke, M. Vendruscolo and M. Karplus.
    Self-consistent determination of the transition state for protein folding. Application to a fibronectin type III domain.
    Proc. Natl. Acad. Sci. USA, 100, 394-399 (2003).

2002

    E. Paci, M. Vendruscolo and M. Karplus.
    Validity of Go models: Comparison with a solvent-shielded empirical energy decomposition.
    Biophys. J. 83, 3032-3038 (2002).

    R. Davis, C. M. Dobson and M. Vendruscolo.
    Determination of the structures of distinct transition state ensembles for a beta-sheet peptide with parallel folding pathways.
    J. Chem. Phys. 117, 9510-9517 (2002).

    E. Paci, M. Vendruscolo, C. M. Dobson and M. Karplus.
    Determination of a transition state at atomic resolution from protein engineering data.
    J. Mol. Biol. 324, 151-163 (2002).

    U. Bastolla, M. Porto, H. E. Roman and M. Vendruscolo.
    Lack of self-averaging in neutral evolution of proteins.
    Phys. Rev. Lett. 89, 208101 (2002).

    M. Vendruscolo, N. V. Dokholyan, E. Paci and M. Karplus.
    A small-world view of the amino acids that play a key role in protein folding.
    Phys. Rev. E, 65, 061910 (2002). [PDF]

    A. Kabakciouglu, I. Kanter, M. Vendruscolo, and E. Domany.
    Statistical properties of contact vectors.
    Phys. Rev. E, 65, 041904 (2002).

    E. Paci, M. Vendruscolo and M. Karplus.
    Native and non-native interactions along protein folding and unfolding pathways.
    Proteins, 47, 379-392 (2002).

    G. Getz, M. Vendruscolo D. Sachs and E. Domany.
    Automated assignment of SCOP and CATH protein structure classifications from FSSP scores.
    Proteins, 46, 405-415 (2002).

    M. Vendruscolo.
    Energetics of enzyme stability.
    Trends in Biotech. 20, 1-2 (2002).

2001

    M. Vendruscolo.
    Assessment of the quality of energy functions for protein folding by using a criterion derived with the help of the noisy Go model.
    J. Biol. Phys. 27, 205-215 (2001).

    U. Bastolla, J. Farwer, E.W. Knapp and M. Vendruscolo.
    How to guarantee optimal stability for most representative structures in the protein data bank.
    Proteins, 43, 79-96 (2001).

    M. Vendruscolo, E. Paci, C. M. Dobson and M. Karplus.
    Three key residues form a critical contact network in a transition state for protein folding.
    Nature, 409, 641-645 (2001). [PDF]

2000

    M. Vendruscolo, L. A. Mirny, E. I. Shakhnovich and E. Domany.
    Comparison of two optimization methods to derive energy parameters for protein folding: perceptron and Z score.
    Proteins, 41, 192-201 (2000).

    K. Park, M. Vendruscolo and E. Domany.
    Towards an energy function for the contact map representation of proteins.
    Proteins, 40, 237-248 (2000).

    U. Bastolla, M. Vendruscolo and E. W. Knapp.
    A statistical mechanical method to optimize energy functions for protein folding.
    Proc. Natl. Acad. Sci. USA, 97, 3977-3981 (2000).

    U. Bastolla, H. E. Roman and M. Vendruscolo.
    Structurally constrained protein evolution: results from a lattice simulation.
    Eur. J. Phys. B, 15 385-397 (2000).

    M. Vendruscolo and E. Domany.
    Prediction of protein structure using contact maps.
    Vitamins and Hormones, 58, 171-212 (2000).

    M. Vendruscolo, R. Najmanovich and E. Domany.
    Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?
    Proteins, 38 134-148 (2000).

1999

    U. Bastolla, H. E. Roman and M. Vendruscolo.
    Neutral evolution of model proteins: diffusion in sequence space and overdispersion.
    J. Theor. Biol. 200, 49-64 (1999).

    C. Clementi, M. Vendruscolo, A. Maritan and E. Domany.
    Folding Lennard-Jones proteins by a contact potential.
    Proteins, 37, 544-553 (1999).

    M. Vendruscolo, R. Najmanovich and E. Domany.
    Protein folding in contact map space.
    Phys. Rev. Lett. 82, 656-659 (1999) .

    M. Vendruscolo.
    Hydrophobicity and unique folding of selected polymers.
    Eur. J. Phys. B, 8 323 (1999).

    M. Vendruscolo.
    An optimal derivation of a potential for protein folding.
    Physica A, 262, 35-39 (1999).

    M. Vendruscolo, B. Subramanian, I. Kanter, E. Domany and J. L. Lebowitz.
    Statistical properties of contact maps.
    Phys. Rev. E, 59, 977-984 (1999) .

1998

    M. Vendruscolo and E. Domany.
    Pairwise contact potentials are unsuitable for protein folding.
    J. Chem. Phys. 109, 11101-11108 (1998).

    M. Vendruscolo and E. Domany.
    Efficient dynamics in the space of contact maps.
    Folding & Design, 3, 329-336 (1998)

    P. De los Rios, M. Marsili and M. Vendruscolo.
    On the high dimensional Bak-Sneppen model.
    Phys. Rev. Lett. 80, 5746-5749 (1998).

    M. Vendruscolo.
    Protein stability and foldability-designability complementarity.
    Physica A, 249, 576-580 (1998).

1997

    M. Vendruscolo, E. Kussell, and E. Domany.
    Recovery of protein structure from contact maps.
    Folding & Design, 2, 295-306 (1997).

    M. Vendruscolo, A. Maritan, and J. R. Banavar.
    Stability threshold as a selection principle for protein design.
    Phys. Rev. Lett. 78, 3967-3970 (1997).

    M. Marsili and M. Vendruscolo.
    Growth with memory.
    Europhys. Lett. 37, 505-509 (1997).

    M. Vendruscolo.
    Modified configurational bias Monte Carlo method for simulation of polymer systems.
    J. Chem. Phys. 106, 2970-2976 (1997).

1996

    M. Vendruscolo, P. De Los Rios and L. Bonesi.
    A model of correlated evolution.
    Phys. Rev. E, 54, 6053-6057 (1996).

    G. Caldarelli, A. Maritan and M. Vendruscolo.
    Hot Sandpiles.
    Europhys. Lett. 35, 481-485 (1996)

    F. Seno, M. Vendruscolo, A. Maritan and J. R. Banavar.
    An optimal protein design procedure.
    Phys. Rev. Lett. 77, 1901-1904, (1996)

    M. Vendruscolo and M. Marsili.
    Diffusion in disordered media as a process with memory.
    Phys. Rev. E, 54, 1021-1024 (1996).

    M. Marsili, G. Caldarelli and M. Vendruscolo.
    Quenched disorder, memory and self-organization.
    Phys. Rev. E, 53, 13-16 (1996).

    G. Santoro, M. Vendruscolo, S. Prestipino and E. Tosatti.
    Disordered flat phase and phase diagram for restricted solid-on-solid models of FCC(110) surfaces.
    Phys. Rev. B, 53, 13169-13186 (1996).

1994

    D. Cvetko, L. Floreano, A. Morgante, M. Peloi, F. Tommasini, K. C. Prince, M. Vendruscolo and E. Tosatti.
    Evolution of the missing row deconstruction on Rh(110).
    Surf. Sci. 318 L1193-L1200 (1994)

1993

    M. Vendruscolo, A. Fasolino and M. Rovere.
    A mean field study of the temperature dependence of the layer magnetizations in a semi-infinite Ising model.
    Nuovo Cimento D, 15, 541-546 (1993)

1992

    M. Vendruscolo, M. Rovere and A. Fasolino.
    Magnetic phase transitions of Ising surfaces with modified surface-bulk coupling: a Monte Carlo study.
    Europhys. Lett. 20, 547-552 (1992)