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Michele Vendruscolo

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Daniele Granata; Carlo Camilloni; Michele Vendruscolo; Alessandro Laio
Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics.
Anthony Fitzpatrick; Robert G Griffin; Christopher Jaroniec; Tuomas P J Knowles; Vladimir Ladizhansky; Cait E MacPhee; Helen R Mott; Shirley A Müller; Elena V Orlova; Helen R Saibil; Michele Vendruscolo; Luchun Wang; Christopher Waudby; Vikram S Bajaj; Marvin J Bayro; Marc A Caporini; Daniel K Clare; Alfonso De Simone; Galia T Debelouchina; Christopher M Dobson
Atomic structure and hierarchical assembly of a cross-β amyloid fibril.
Michele Vendruscolo; Christopher M Dobson
Structural biology: Protein self-assembly intermediates.

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All Publications

2013: Daniele Granata; Carlo Camilloni; Michele Vendruscolo; Alessandro Laio
Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(17):6817-22.
2013: Anthony Fitzpatrick; Robert G Griffin; Christopher Jaroniec; Tuomas P J Knowles; Vladimir Ladizhansky; Cait E MacPhee; Helen R Mott; Shirley A Müller; Elena V Orlova; Helen R Saibil; Michele Vendruscolo; Luchun Wang; Christopher Waudby; Vikram S Bajaj; Marvin J Bayro; Marc A Caporini; Daniel K Clare; Alfonso De Simone; Galia T Debelouchina; Christopher M Dobson
Atomic structure and hierarchical assembly of a cross-β amyloid fibril.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(14):5468-73.
2013: Michele Vendruscolo; Christopher M Dobson
Structural biology: Protein self-assembly intermediates.
Nature chemical biology 2013;9(4):216-7.
2013: Andrea Cavalli; Carlo Camilloni; Michele Vendruscolo
Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle.
The Journal of chemical physics 2013;138(9):094112.
2013: Aleksandr B Sahakyan; Michele Vendruscolo
Analysis of the contributions of ring current and electric field effects to the chemical shifts of RNA bases.
The journal of physical chemistry. B 2013;117(7):1989-98.
2013: Carlo Camilloni; Andrea Cavalli; Michele Vendruscolo
Assessment of the use of NMR chemical shifts as replica-averaged structural restraints in molecular dynamics simulations to characterize the dynamics of proteins.
The journal of physical chemistry. B 2013;117(6):1838-43.
2013: Prajwal Ciryam; Christopher M Dobson; Richard I Morimoto; Michele Vendruscolo; Edward P O'Brien
In vivo translation rates can substantially delay the cotranslational folding of the Escherichia coli cytosolic proteome.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(2):E132-40.
2012: Tuomas P J Knowles; Sarah Meehan; Luke Rajah; Andrew Baldwin; Alfonso De Simone; Christopher M Dobson; Anthony Fitzpatrick; Michele Vendruscolo; Mark E Welland; Eugene M Terentjev
Twisting transition between crystalline and fibrillar phases of aggregated peptides.
Physical review letters 2012;109(15):158101.
2012: Samuel I A Cohen; Christopher M Dobson; Michele Vendruscolo; Tuomas P J Knowles
From macroscopic measurements to microscopic mechanisms of protein aggregation.
Journal of molecular biology 2012;421(2-3):160-71.
2012: Federico Agostini; Michele Vendruscolo; Gian Gaetano Tartaglia
Sequence-based prediction of protein solubility.
Journal of molecular biology 2012;421(2-3):237-41.
2012: Joseph E Chambers; Kseniya Petrova; Giulia Tomba; Michele Vendruscolo; David Ron
ADP ribosylation adapts an ER chaperone response to short-term fluctuations in unfolded protein load.
The Journal of cell biology 2012;198(3):371-85.
2012: Rinaldo W Montalvao; Alfonso De Simone; Michele Vendruscolo
Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings.
Journal of biomolecular NMR 2012;53(4):281-92.
2012: Edward P O'Brien; Michele Vendruscolo; John Christodoulou; Christopher M Dobson
Trigger factor slows co-translational folding through kinetic trapping while sterically protecting the nascent chain from aberrant cytosolic interactions.
Journal of the American Chemical Society 2012;134(26):10920-32.
2012: Jin Chen; Yuji Goto; Koki Makabe; Takashi Nakamura; Pietro Sormanni; Michele Vendruscolo; Hisashi Yagi; Kunihiro Kuwajima
Fibrillogenic propensity of the GroEL apical domain: a Janus-faced minichaperone.
FEBS letters 2012;586(8):1120-7.
2012: Philipp Neudecker; Paul Robustelli; Simon Sharpe; Michele Vendruscolo; Patrick Walsh; Arash Zarrine-Afsar; Andrea Cavalli; Patrik Lundström; Lewis E Kay
Structure of an intermediate state in protein folding and aggregation.
Science (New York, N.Y.) 2012;336(6079):362-6.
2012: Michele Vendruscolo
Proteome folding and aggregation.
Current opinion in structural biology 2012;22(2):138-43.
2012: Giuliana Fusco; Shang-Te Danny Hsu; Michele Vendruscolo; Francesco Bemporad; Fabrizio Chiti; Alfonso De Simone; Christopher M Dobson
¹H, ¹³C and ¹⁵N resonance assignments of human muscle acylphosphatase.
Biomolecular NMR assignments 2012;6(1):27-9.
2012: Carlo Camilloni; Alfonso De Simone; Wim Vranken; Michele Vendruscolo
Determination of secondary structure populations in disordered states of proteins using nuclear magnetic resonance chemical shifts.
Biochemistry 2012;51(11):2224-31.
2012: Carlo Camilloni; Andrea Cavalli; Paul Robustelli; Alfonso De Simone; Michele Vendruscolo
Characterization of the conformational equilibrium between the two major substates of RNase A using NMR chemical shifts.
Journal of the American Chemical Society 2012;134(9):3968-71.
2012: Edward P O'Brien; Michele Vendruscolo; Christopher M Dobson
Prediction of variable translation rate effects on cotranslational protein folding.
Nature communications 2012;3():868.
2011: Michele Vendruscolo; Tuomas P J Knowles; Christopher M Dobson
Protein solubility and protein homeostasis: a generic view of protein misfolding disorders.
Cold Spring Harbor perspectives in biology 2011;3(12):.
2011: Aleksandr B Sahakyan; Andrea Cavalli; Wim Vranken; Michele Vendruscolo
Using side-chain aromatic proton chemical shifts for a quantitative analysis of protein structures.
Angewandte Chemie (International ed. in English) 2011;50(41):9620-3.
2011: Anthony Fitzpatrick; Tuomas P J Knowles; Michele Vendruscolo; Christopher Waudby; Christopher M Dobson
Inversion of the balance between hydrophobic and hydrogen bonding interactions in protein folding and aggregation.
PLoS computational biology 2011;7(10):e1002169.
2011: Michele Vendruscolo
Excited-state control of protein activity.
Journal of molecular biology 2011;412(2):153-4.
2011: Andrew Baldwin; Paul D Barker; John Christodoulou; Glyn L Devlin; Spencer J Anthony-Cahill; Anthony Fitzpatrick; Sally L Gras; Tuomas P J Knowles; Sarah Meehan; Maria F Mossuto; Sarah Lucy Shammas; Gian Gaetano Tartaglia; Michele Vendruscolo; Christopher Waudby; Christopher M Dobson
Metastability of native proteins and the phenomenon of amyloid formation.
Journal of the American Chemical Society 2011;133(36):14160-3.
2011: Lijuan Kang; Michele Vendruscolo; Kuen-Phon Wu; Jean Baum
The A53T mutation is key in defining the differences in the aggregation kinetics of human and mouse α-synuclein.
Journal of the American Chemical Society 2011;133(34):13465-70.
2011: Samuel I A Cohen; Christopher M Dobson; Michele Vendruscolo; Tuomas P J Knowles
Nucleated polymerization with secondary pathways. III. Equilibrium behavior and oligomer populations.
The Journal of chemical physics 2011;135(6):065107.
2011: Samuel I A Cohen; Christopher M Dobson; Michele Vendruscolo; Tuomas P J Knowles
Nucleated polymerization with secondary pathways. II. Determination of self-consistent solutions to growth processes described by non-linear master equations.
The Journal of chemical physics 2011;135(6):065106.
2011: Samuel I A Cohen; Christopher M Dobson; Eugene M Terentjev; Michele Vendruscolo; Mark E Welland; Tuomas P J Knowles
Nucleated polymerization with secondary pathways. I. Time evolution of the principal moments.
The Journal of chemical physics 2011;135(6):065105.
2011: Andrea Cavalli; Rinaldo W Montalvao; Michele Vendruscolo
Using chemical shifts to determine structural changes in proteins upon complex formation.
The journal of physical chemistry. B 2011;115(30):9491-4.
2011: Kai J Kohlhoff; David A Lomas; Damian C Crowther; Christopher M Dobson; Thomas R Jahn; Michele Vendruscolo
The iFly tracking system for an automated locomotor and behavioural analysis of Drosophila melanogaster.
Integrative biology : quantitative biosciences from nano to macro 2011;3(7):755-60.
2011: Michele Vendruscolo
Protein regulation: the statistical theory of allostery.
Nature chemical biology 2011;7(7):411-2.
2011: Thomas R Jahn; Kai J Kohlhoff; Michael Scott; Gian Gaetano Tartaglia; David A Lomas; Christopher M Dobson; Michele Vendruscolo; Damian C Crowther
Detection of early locomotor abnormalities in a Drosophila model of Alzheimer's disease.
Journal of neuroscience methods 2011;197(1):186-9.
2011: Sara Raimondi; Fulvio Guglielmi; Sofia Giorgetti; Angela Arciello; Daria M Monti; Annalisa Relini; Daniela Nichino; Silvia M Doglia; Antonino Natalello; Piero Pucci; Palma Mangione; Laura Obici; Giampaolo Merlini; Monica Stoppini; Paul Robustelli; Gian Gaetano Tartaglia; Michele Vendruscolo; Christopher M Dobson; Renata Piccoli; Sonia Di Gaetano; Vittorio Bellotti
Effects of the known pathogenic mutations on the aggregation pathway of the amyloidogenic peptide of apolipoprotein A-I.
Journal of molecular biology 2011;407(3):465-76.
2011: Olga Szczepankiewicz; Celia Cabaleiro-Lago; Gian Gaetano Tartaglia; Michele Vendruscolo; Thérèse Hunter; Gary J Hunter; Hanna Nilsson; Eva Thulin; Sara Linse
Interactions in the native state of monellin, which play a protective role against aggregation.
Molecular bioSystems 2011;7(2):521-32.
2011: Edward P O'Brien; Michele Vendruscolo; John Christodoulou; Christopher M Dobson
New scenarios of protein folding can occur on the ribosome.
Journal of the American Chemical Society 2011;133(3):513-26.
2011: Michele Vendruscolo; Christopher M Dobson
Protein dynamics: Moore's law in molecular biology.
Current biology : CB 2011;21(2):R68-70.
2011: Heidi Olzscha; Sonya M Schermann; Andreas C Woerner; Stefan Pinkert; Michael H Hecht; Gian G Tartaglia; Michele Vendruscolo; Manajit Hayer-Hartl; F Ulrich Hartl; Ramunas M Vabulas
Amyloid-like aggregates sequester numerous metastable proteins with essential cellular functions.
Cell 2011;144(1):67-78.
2011: Samuel I A Cohen; Christopher M Dobson; Michele Vendruscolo; Tuomas P J Knowles
Nucleated polymerisation in the presence of pre-formed seed filaments.
International journal of molecular sciences 2011;12(9):5844-52.
2010: Stefano Gianni; ylva ivarsson; Alfonso De Simone; Carlo Travaglini-Allocatelli; Maurizio Brunori; Michele Vendruscolo
Structural characterization of a misfolded intermediate populated during the folding process of a PDZ domain.
Nature structural & molecular biology 2010;17(12):1431-7.
2010: Edward P O'Brien; Shang-Te Danny Hsu; John Christodoulou; Michele Vendruscolo; Christopher M Dobson
Transient tertiary structure formation within the ribosome exit port.
Journal of the American Chemical Society 2010;132(47):16928-37.
2010: Yaelim Lee; Tong Zhou; Gian Gaetano Tartaglia; Michele Vendruscolo; Claus O Wilke
Translationally optimal codons associate with aggregation-prone sites in proteins.
Proteomics 2010;10(23):4163-71.
2010: Sebastian Pechmann; Michele Vendruscolo
Derivation of a solubility condition for proteins from an analysis of the competition between folding and aggregation.
Molecular bioSystems 2010;6(12):2490-7.
2010: Marc A Caporini; Vikram S Bajaj; Mikhail Veshtort; Anthony Fitzpatrick; Cait E MacPhee; Michele Vendruscolo; Christopher M Dobson; Robert G Griffin
Accurate determination of interstrand distances and alignment in amyloid fibrils by magic angle spinning NMR.
The journal of physical chemistry. B 2010;114(42):13555-61.
2010: Michele Vendruscolo
Enzymatic activity in disordered states of proteins.
Current opinion in chemical biology 2010;14(5):671-5.
2010: Paul Robustelli; Kai Kohlhoff; Andrea Cavalli; Michele Vendruscolo
Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins.
Structure (London, England : 1993) 2010;18(8):923-33.
2010: Gian Gaetano Tartaglia; Christopher M Dobson; F Ulrich Hartl; Michele Vendruscolo
Physicochemical determinants of chaperone requirements.
Journal of molecular biology 2010;400(3):579-88.
2010: Itzam De Gortari; Guillem Portella; Xavier Salvatella; Vikram S Bajaj; Patrick van der Wel; Jonathan R Yates; MD Segall; Chris J Pickard; Mike C Payne; Michele Vendruscolo
Time averaging of NMR chemical shifts in the MLF peptide in the solid state.
Journal of the American Chemical Society 2010;132(17):5993-6000.
2010: Katrin Wolff; Michele Vendruscolo; Markus Porto
Efficient identification of near-native conformations in ab initio protein structure prediction using structural profiles.
Proteins 2010;78(2):249-58.
2009: Jane R Allison; Péter Várnai; Christopher M Dobson; Michele Vendruscolo
Determination of the free energy landscape of alpha-synuclein using spin label nuclear magnetic resonance measurements.
Journal of the American Chemical Society 2009;131(51):18314-26.
2009: Tuomas P J Knowles; Christopher Waudby; Glyn L Devlin; Samuel I A Cohen; Adriano Aguzzi; Michele Vendruscolo; Eugene M Terentjev; Mark E Welland; Christopher M Dobson
An analytical solution to the kinetics of breakable filament assembly.
Science (New York, N.Y.) 2009;326(5959):1533-7.
2009: Gian Gaetano Tartaglia; Michele Vendruscolo
Correlation between mRNA expression levels and protein aggregation propensities in subcellular localisations.
Molecular bioSystems 2009;5(12):1873-6.
2009: Alfonso De Simone; Andrea Cavalli; Shang-Te Danny Hsu; Wim Vranken; Michele Vendruscolo
Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins.
Journal of the American Chemical Society 2009;131(45):16332-3.
2009: Jennifer M Bui; Joerg Gsponer; Michele Vendruscolo; Christopher M Dobson
Analysis of sub-tauc and supra-tauc motions in protein Gbeta1 using molecular dynamics simulations.
Biophysical journal 2009;97(9):2513-20.
2009: Kai J Kohlhoff; Paul Robustelli; Andrea Cavalli; Xavier Salvatella; Michele Vendruscolo
Fast and accurate predictions of protein NMR chemical shifts from interatomic distances.
Journal of the American Chemical Society 2009;131(39):13894-5.
2009: Christofer Lendel; CARLOS WALTER BERTONCINI; Nunilo Cremades; Christopher Waudby; Michele Vendruscolo; Christopher M Dobson; Dale Schenk; John Christodoulou; Gergely Toth
On the mechanism of nonspecific inhibitors of protein aggregation: dissecting the interactions of alpha-synuclein with Congo red and lacmoid.
Biochemistry 2009;48(35):8322-34.
2009: Stefan Auer; Antonio Trovato; Michele Vendruscolo
A condensation-ordering mechanism in nanoparticle-catalyzed peptide aggregation.
PLoS computational biology 2009;5(8):e1000458.
2009: Sebastian Pechmann; emmanuel levy; Gian Gaetano Tartaglia; Michele Vendruscolo
Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(25):10159-64.
2009: Katy E Routledge; Gian Gaetano Tartaglia; Geoffrey W Platt; Michele Vendruscolo; Sheena E Radford
Competition between intramolecular and intermolecular interactions in an amyloid-forming protein.
Journal of molecular biology 2009;389(4):776-86.
2009: Paul Robustelli; Andrea Cavalli; Christopher M Dobson; Michele Vendruscolo; Xavier Salvatella
Folding of small proteins by Monte Carlo simulations with chemical shift restraints without the use of molecular fragment replacement or structural homology.
The journal of physical chemistry. B 2009;113(22):7890-6.
2009: Markus Porto; H Eduardo Roman; Michele Vendruscolo
Physical principles of protein behavior in the cell.
Journal of proteome research 2009;8(6):2615.
2009: Alexander K Buell; Gian Gaetano Tartaglia; Neil R Birkett; Christopher Waudby; Michele Vendruscolo; Xavier Salvatella; Mark E Welland; Christopher M Dobson; Tuomas P J Knowles
Position-dependent electrostatic protection against protein aggregation.
Chembiochem : a European journal of chemical biology 2009;10(8):1309-12.
2009: Gian Gaetano Tartaglia; Sebastian Pechmann; Christopher M Dobson; Michele Vendruscolo
A relationship between mRNA expression levels and protein solubility in E. coli.
Journal of molecular biology 2009;388(2):381-9.
2009: Martino Calamai; Gian Gaetano Tartaglia; Michele Vendruscolo; Fabrizio Chiti; Christopher M Dobson
Mutational analysis of the aggregation-prone and disaggregation-prone regions of acylphosphatase.
Journal of molecular biology 2009;387(4):965-74.
2009: Alfonso De Simone; Barbara Richter; Xavier Salvatella; Michele Vendruscolo
Toward an accurate determination of free energy landscapes in solution states of proteins.
Journal of the American Chemical Society 2009;131(11):3810-1.
2009: Claire T Friel; D Alastair Smith; Michele Vendruscolo; Joerg Gsponer; Sheena E Radford
The mechanism of folding of Im7 reveals competition between functional and kinetic evolutionary constraints.
Nature structural & molecular biology 2009;16(3):318-24.
2009: Daizo Hamada; Toshiki Tanaka; Gian Gaetano Tartaglia; Amol Pawar; Michele Vendruscolo; Mei Kawamura; Atsuo Tamura; Naoki Tanaka; Christopher M Dobson
Competition between folding, native-state dimerisation and amyloid aggregation in beta-lactoglobulin.
Journal of molecular biology 2009;386(3):878-90.
2009: Xavier Periole; Aldo Rampioni; Michele Vendruscolo; Alan E Mark
Factors that affect the degree of twist in beta-sheet structures: a molecular dynamics simulation study of a cross-beta filament of the GNNQQNY peptide.
The journal of physical chemistry. B 2009;113(6):1728-37.
2009: Michele Vendruscolo; Christopher M Dobson
Quantitative approaches to defining normal and aberrant protein homeostasis.
Faraday discussions 2009;143():277-91; discussion 359-72.
2008: Stefan Auer; Christopher M Dobson; Michele Vendruscolo; Amos Maritan
Self-templated nucleation in peptide and protein aggregation.
Physical review letters 2008;101(25):258101.
2008: Nicoletta Calosci; Celestine N Chi; Barbara Richter; Carlo Camilloni; Ake Engström; Lars Eklund; Carlo Travaglini-Allocatelli; Stefano Gianni; Michele Vendruscolo; Per Jemth
Comparison of successive transition states for folding reveals alternative early folding pathways of two homologous proteins.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(49):19241-6.
2008: Michele Vendruscolo; Gian Gaetano Tartaglia
Towards quantitative predictions in cell biology using chemical properties of proteins.
Molecular bioSystems 2008;4(12):1170-5.
2008: Rinaldo W Montalvao; Andrea Cavalli; Xavier Salvatella; Tom L Blundell; Michele Vendruscolo
Structure determination of protein-protein complexes using NMR chemical shifts: case of an endonuclease colicin-immunity protein complex.
Journal of the American Chemical Society 2008;130(47):15990-6.
2008: Stefan Auer; Filip Meersman; Christopher M Dobson; Michele Vendruscolo
A generic mechanism of emergence of amyloid protofilaments from disordered oligomeric aggregates.
PLoS computational biology 2008;4(11):e1000222.
2008: Giulia Calloni; Christofer Lendel; Silvia Campioni; Silva Giannini; Alessandra Gliozzi; Annalisa Relini; Michele Vendruscolo; Christopher M Dobson; Xavier Salvatella; Fabrizio Chiti
Structure and dynamics of a partially folded protein are decoupled from its mechanism of aggregation.
Journal of the American Chemical Society 2008;130(39):13040-50.
2008: Katrin Wolff; Michele Vendruscolo; Markus Porto
A stochastic method for the reconstruction of protein structures from one-dimensional structural profiles.
Gene 2008;422(1-2):47-51.
2008: Birgit Strodel; Anthony W Fitzpatrick; Michele Vendruscolo; Christopher M Dobson; David J Wales
Characterizing the first steps of amyloid formation for the ccbeta peptide.
The journal of physical chemistry. B 2008;112(32):9998-10004.
2008: Michele Vendruscolo
Protein dynamics under light control.
Nature chemical biology 2008;4(8):449-50.
2008: Anne Dhulesia; Joerg Gsponer; Michele Vendruscolo
Mapping of two networks of residues that exhibit structural and dynamical changes upon binding in a PDZ domain protein.
Journal of the American Chemical Society 2008;130(28):8931-9.
2008: Gian Gaetano Tartaglia; Amol P Pawar; Silvia Campioni; Christopher M Dobson; Fabrizio Chiti; Michele Vendruscolo
Prediction of aggregation-prone regions in structured proteins.
Journal of molecular biology 2008;380(2):425-36.
2008: Gian Gaetano Tartaglia; Michele Vendruscolo
The Zyggregator method for predicting protein aggregation propensities.
Chemical Society reviews 2008;37(7):1395-401.
2008: Francesco Bemporad; Joerg Gsponer; Harri I Hopearuoho; Georgia Plakoutsi; Gianmarco Stati; Massimo Stefani; Niccolò Taddei; Michele Vendruscolo; Fabrizio Chiti
Biological function in a non-native partially folded state of a protein.
The EMBO journal 2008;27(10):1525-35.
2008: Jörg Gsponer; John Christodoulou; Andrea Cavalli; Jennifer M Bui; Barbara Richter; Christopher M Dobson; Michele Vendruscolo
A coupled equilibrium shift mechanism in calmodulin-mediated signal transduction.
Structure (London, England : 1993) 2008;16(5):736-46.
2008: Robert C Rivers; Janet R Kumita; Gian Gaetano Tartaglia; Matthew M. Dedmon; Amol P Pawar; Michele Vendruscolo; Christopher M Dobson; John Christodoulou
Molecular determinants of the aggregation behavior of alpha- and beta-synuclein.
Protein science : a publication of the Protein Society 2008;17(5):887-98.
2008: Péter Várnai; Christopher M Dobson; Michele Vendruscolo
Determination of the transition state ensemble for the folding of ubiquitin from a combination of Phi and Psi analyses.
Journal of molecular biology 2008;377(2):575-88.
2008: Christian D Geierhaas; Xavier Salvatella; Jane Clarke; Michele Vendruscolo
Characterisation of transition state structures for protein folding using 'high', 'medium' and 'low' {Phi}-values.
Protein engineering, design & selection : PEDS 2008;21(3):215-22.
2008: Katrin Wolff; Michele Vendruscolo; Markus Porto
Stochastic reconstruction of protein structures from effective connectivity profiles.
PMC biophysics 2008;1(1):5.
2008: Fernando E Herrera; Alessandra Chesi; Katerina E Paleologou; Adrian Schmid; Adriana Munoz; Michele Vendruscolo; Stefano Gustincich; Hilal A Lashuel; Paolo Carloni
Inhibition of alpha-synuclein fibrillization by dopamine is mediated by interactions with five C-terminal residues and with E83 in the NAC region.
PloS one 2008;3(10):e3394.
2008: Tammy M K Cheng; Yu-En Lu; Michele Vendruscolo; Pietro Lio'; Tom L Blundell
Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms.
PLoS computational biology 2008;4(7):e1000135.
2008: Mookyung Cheon; Giorgio Favrin; Iksoo Chang; Christopher M Dobson; Michele Vendruscolo
Calculation of the free energy barriers in the oligomerisation of Abeta peptide fragments.
Frontiers in bioscience : a journal and virtual library 2008;13():5614-22.
2008: Xavier Salvatella; B Richter; Michele Vendruscolo
Influence of the fluctuations of the alignment tensor on the analysis of the structure and dynamics of proteins using residual dipolar couplings.
Journal of biomolecular NMR 2008;40(1):71-81.
2007: Tuomas P J Knowles; Anthony Fitzpatrick; Sarah Meehan; Helen R Mott; Michele Vendruscolo; Christopher M Dobson; Mark E Welland
Role of intermolecular forces in defining material properties of protein nanofibrils.
Science (New York, N.Y.) 2007;318(5858):1900-3.
2007: Elodie Monsellier; Matteo Ramazzotti; Patrizia Polverino de Laureto; Gian Gaetano Tartaglia; Niccolò Taddei; Angelo Fontana; Michele Vendruscolo; Fabrizio Chiti
The distribution of residues in a polypeptide sequence is a determinant of aggregation optimized by evolution.
Biophysical journal 2007;93(12):4382-91.
2007: Xavier Periole; Michele Vendruscolo; Alan E Mark
Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain.
Proteins 2007;69(3):536-50.
2007: Leila M Luheshi; Gian Gaetano Tartaglia; Ann-Christin Brorsson; Amol P Pawar; Ian E Watson; Fabrizio Chiti; Michele Vendruscolo; David A Lomas; Christopher M Dobson; Damian C Crowther
Systematic in vivo analysis of the intrinsic determinants of amyloid Beta pathogenicity.
PLoS biology 2007;5(11):e290.
2007: Stefan Auer; Mark A Miller; Sergei V Krivov; Christopher M Dobson; Martin Karplus; Michele Vendruscolo
Importance of metastable states in the free energy landscapes of polypeptide chains.
Physical review letters 2007;99(17):178104.
2007: Michele Vendruscolo; Christopher M Dobson
Chemical biology: More charges against aggregation.
Nature 2007;449(7162):555.
2007: Sarah Meehan; Tuomas P J Knowles; Andrew Baldwin; Jeffrey F Smith; Adam M Squires; Phillip Clements; Teresa M Treweek; Heath Ecroyd; Gian Gaetano Tartaglia; Michele Vendruscolo; Cait E MacPhee; Christopher M Dobson; John A Carver
Characterisation of amyloid fibril formation by small heat-shock chaperone proteins human alphaA-, alphaB- and R120G alphaB-crystallins.
Journal of molecular biology 2007;372(2):470-84.
2007: Mookyung Cheon; Iksoo Chang; Sandipan Mohanty; Leila M Luheshi; Christopher M Dobson; Michele Vendruscolo; Giorgio Favrin
Structural reorganisation and potential toxicity of oligomeric species formed during the assembly of amyloid fibrils.
PLoS computational biology 2007;3(9):1727-38.
2007: Stefan Auer; Christopher M Dobson; Michele Vendruscolo
Characterization of the nucleation barriers for protein aggregation and amyloid formation.
HFSP journal 2007;1(2):137-46.
2007: Andrea Cavalli; Xavier Salvatella; Christopher M Dobson; Michele Vendruscolo
Protein structure determination from NMR chemical shifts.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(23):9615-20.
2007: Jessica Meinhardt; Gian Gaetano Tartaglia; Amol Pawar; Tony Christopeit; Peter Hortschansky; Volker Schroeckh; Christopher M Dobson; Michele Vendruscolo; Marcus Fändrich
Similarities in the thermodynamics and kinetics of aggregation of disease-related Abeta(1-40) peptides.
Protein science : a publication of the Protein Society 2007;16(6):1214-22.
2007: Gian Gaetano Tartaglia; Sebastian Pechmann; Christopher M Dobson; Michele Vendruscolo
Life on the edge: a link between gene expression levels and aggregation rates of human proteins.
Trends in biochemical sciences 2007;32(5):204-6.
2007: Gian Gaetano Tartaglia; Andrea Cavalli; Michele Vendruscolo
Prediction of local structural stabilities of proteins from their amino acid sequences.
Structure (London, England : 1993) 2007;15(2):139-43.
2007: Michele Vendruscolo
Determination of conformationally heterogeneous states of proteins.
Current opinion in structural biology 2007;17(1):15-20.
2007: Barbara Richter; Joerg Gsponer; Péter Várnai; Xavier Salvatella; Michele Vendruscolo
The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins.
Journal of biomolecular NMR 2007;37(2):117-35.
2007: Stefano Gianni; Christian D Geierhaas; Nicoletta Calosci; Per Jemth; Geerten W Vuister; Carlo Travaglini-Allocatelli; Michele Vendruscolo; Maurizio Brunori
A PDZ domain recapitulates a unifying mechanism for protein folding.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(1):128-33.
2007: Christian D Geierhaas; Adrian A Nickson; Kresten Lindorff-Larsen; Jane Clarke; Michele Vendruscolo
BPPred: a Web-based computational tool for predicting biophysical parameters of proteins.
Protein science : a publication of the Protein Society 2007;16(1):125-34.
2006: Joerg Gsponer; Harri Hopearuoho; Andrea Cavalli; Christopher M Dobson; Michele Vendruscolo
Geometry, energetics, and dynamics of hydrogen bonds in proteins: structural information derived from NMR scalar couplings.
Journal of the American Chemical Society 2006;128(47):15127-35.
2006: Christopher J Francis; Kresten Lindorff-Larsen; Robert B Best; Michele Vendruscolo
Characterization of the residual structure in the unfolded state of the Delta131Delta fragment of staphylococcal nuclease.
Proteins 2006;65(1):145-52.
2006: Michele Vendruscolo; Christopher M Dobson
Structural biology. Dynamic visions of enzymatic reactions.
Science (New York, N.Y.) 2006;313(5793):1586-7.
2006: Robert B Best; Kresten Lindorff-Larsen; Mark A DePristo; Michele Vendruscolo
Relation between native ensembles and experimental structures of proteins.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(29):10901-6.
2006: Christian D Geierhaas; Robert B Best; Emanuele Paci; Michele Vendruscolo; Jane Clarke
Structural comparison of the two alternative transition states for folding of TI I27.
Biophysical journal 2006;91(1):263-75.
2006: Joerg Gsponer; Harri Hopearuoho; Sara B-M Whittaker; Graham R Spence; Geoffrey R Moore; Emanuele Paci; Sheena E Radford; Michele Vendruscolo
Determination of an ensemble of structures representing the intermediate state of the bacterial immunity protein Im7.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(1):99-104.
2006: Ugo Bastolla; Markus Porto; H Eduardo Roman; Michele Vendruscolo
A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank.
BMC evolutionary biology 2006;6():43.
2006: Joerg Gsponer; Michele Vendruscolo
Theoretical approaches to protein aggregation.
Protein and peptide letters 2006;13(3):287-93.
2006: Robert B Best; Michele Vendruscolo
Structural interpretation of hydrogen exchange protection factors in proteins: characterization of the native state fluctuations of CI2.
Structure (London, England : 1993) 2006;14(1):97-106.
2005: Giovanni Salvi; Paolo De los Rios; Michele Vendruscolo
Effective interactions between chaotropic agents and proteins.
Proteins 2005;61(3):492-9.
2005: Emanuele Paci; Kresten Lindorff-Larsen; Christopher M Dobson; Martin Karplus; Michele Vendruscolo
Transition state contact orders correlate with protein folding rates.
Journal of molecular biology 2005;352(3):495-500.
2005: Xavier Salvatella; Christopher M Dobson; Alan Fersht; Michele Vendruscolo
Determination of the folding transition states of barnase by using PhiI-value-restrained simulations validated by double mutant PhiIJ-values.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(35):12389-94.
2005: Kresten Lindorff-Larsen; Robert B Best; Michele Vendruscolo
Interpreting dynamically-averaged scalar couplings in proteins.
Journal of biomolecular NMR 2005;32(4):273-80.
2005: Amol P Pawar; Kateri F Dubay; Jesús Zurdo; Fabrizio Chiti; Michele Vendruscolo; Christopher M Dobson
Prediction of "aggregation-prone" and "aggregation-susceptible" regions in proteins associated with neurodegenerative diseases.
Journal of molecular biology 2005;350(2):379-92.
2005: Andrea Cavalli; Michele Vendruscolo; Emanuele Paci
Comparison of sequence-based and structure-based energy functions for the reversible folding of a peptide.
Biophysical journal 2005;88(5):3158-66.
2005: Michele Vendruscolo; Christopher M Dobson
A glimpse at the organization of the protein universe.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(16):5641-2.
2005: Sigridur Kristjansdottir; Kresten Lindorff-Larsen; Wolfgang Fieber; Christopher M Dobson; Michele Vendruscolo; Flemming M Poulsen
Formation of native and non-native interactions in ensembles of denatured ACBP molecules from paramagnetic relaxation enhancement studies.
Journal of molecular biology 2005;347(5):1053-62.
2005: Ugo Bastolla; Markus Porto; H Eduardo Roman; Michele Vendruscolo
Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles.
Gene 2005;347(2):219-30.
2005: Markus Porto; H Eduardo Roman; Michele Vendruscolo; Ugo Bastolla
Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences.
Molecular biology and evolution 2005;22(3):630-8.
2005: Michele Vendruscolo; Christopher M Dobson
Towards complete descriptions of the free-energy landscapes of proteins.
Philosophical transactions. Series A, Mathematical, physical, and engineering sciences 2005;363(1827):433-50; discussion 450-2.
2005: Matthew M. Dedmon; Kresten Lindorff-Larsen; John Christodoulou; Michele Vendruscolo; Christopher M Dobson
Mapping long-range interactions in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations.
Journal of the American Chemical Society 2005;127(2):476-7.
2005: Kresten Lindorff-Larsen; Robert B Best; Mark A DePristo; Christopher M Dobson; Michele Vendruscolo
Simultaneous determination of protein structure and dynamics.
Nature 2005;433(7022):128-32.
2005: Kresten Lindorff-Larsen; Peter Røgen; Emanuele Paci; Michele Vendruscolo; Christopher M Dobson
Protein folding and the organization of the protein topology universe.
Trends in biochemical sciences 2005;30(1):13-9.
2005: Ugo Bastolla; Markus Porto; H Eduardo Roman; Michele Vendruscolo
Principal eigenvector of contact matrices and hydrophobicity profiles in proteins.
Proteins 2005;58(1):22-30.
2004: Christian D Geierhaas; Emanuele Paci; Michele Vendruscolo; Jane Clarke
Comparison of the transition states for folding of two Ig-like proteins from different superfamilies.
Journal of molecular biology 2004;343(4):1111-23.
2004: Kateri F DuBay; Amol P Pawar; Fabrizio Chiti; Jesús Zurdo; Christopher M Dobson; Michele Vendruscolo
Prediction of the absolute aggregation rates of amyloidogenic polypeptide chains.
Journal of molecular biology 2004;341(5):1317-26.
2004: Dmitry M Korzhnev; Xavier Salvatella; Michele Vendruscolo; Ariel A Di Nardo; Alan R Davidson; Christopher M Dobson; Lewis E Kay
Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR.
Nature 2004;430(6999):586-90.
2004: Emanuele Paci; Joerg Gsponer; Xavier Salvatella; Michele Vendruscolo
Molecular dynamics studies of the process of amyloid aggregation of peptide fragments of transthyretin.
Journal of molecular biology 2004;340(3):555-69.
2004: Robert B Best; Michele Vendruscolo
Determination of protein structures consistent with NMR order parameters.
Journal of the American Chemical Society 2004;126(26):8090-1.
2004: Jonathan P K Doye; Ard A Louis; Michele Vendruscolo
Inhibition of protein crystallization by evolutionary negative design.
Physical biology 2004;1(1-2):P9-13.
2004: Markus Porto; Ugo Bastolla; H Eduardo Roman; Michele Vendruscolo
Reconstruction of protein structures from a vectorial representation.
Physical review letters 2004;92(21):218101.
2004: Kresten Lindorff-Larsen; Michele Vendruscolo; Emanuele Paci; Christopher M Dobson
Transition states for protein folding have native topologies despite high structural variability.
Nature structural & molecular biology 2004;11(5):443-9.
2004: Kresten Lindorff-Larsen; Sigridur Kristjansdottir; Kaare Teilum; Wolfgang Fieber; Christopher M Dobson; Flemming M Poulsen; Michele Vendruscolo
Determination of an ensemble of structures representing the denatured state of the bovine acyl-coenzyme a binding protein.
Journal of the American Chemical Society 2004;126(10):3291-9.
2004: Emanuele Paci; Claire T Friel; Kresten Lindorff-Larsen; Sheena E Radford; Martin Karplus; Michele Vendruscolo
Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints.
Proteins 2004;54(3):513-25.
2003: Michele Vendruscolo; Emanuele Paci; Christopher M Dobson; Martin Karplus
Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange.
Journal of the American Chemical Society 2003;125(51):15686-7.
2003: Michele Vendruscolo; Emanuele Paci; Martin Karplus; Christopher M Dobson
Structures and relative free energies of partially folded states of proteins.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(25):14817-21.
2003: Kresten Lindorff-Larsen; Emanuele Paci; Luis Serrano; Christopher M Dobson; Michele Vendruscolo
Calculation of mutational free energy changes in transition states for protein folding.
Biophysical journal 2003;85(2):1207-14.
2003: Emanuele Paci; Andrea Cavalli; Michele Vendruscolo; Amedeo Caflisch
Analysis of the distributed computing approach applied to the folding of a small beta peptide.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(14):8217-22.
2003: Michele Vendruscolo; Jesús Zurdo; Cait E MacPhee; Christopher M Dobson
Protein folding and misfolding: a paradigm of self-assembly and regulation in complex biological systems.
Philosophical transactions. Series A, Mathematical, physical, and engineering sciences 2003;361(1807):1205-22.
2003: Ugo Bastolla; Markus Porto; Markus H Eduardo Roman; Michele Vendruscolo
Connectivity of neutral networks, overdispersion, and structural conservation in protein evolution.
Journal of molecular evolution 2003;56(3):243-54.
2003: Michele Vendruscolo; Emanuele Paci
Protein folding: bringing theory and experiment closer together.
Current opinion in structural biology 2003;13(1):82-7.
2003: Emanuele Paci; Jane Clarke; Annette Steward; Michele Vendruscolo; Martin Karplus
Self-consistent determination of the transition state for protein folding: application to a fibronectin type III domain.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(2):394-9.
2003: Ugo Bastolla; Markus Porto; H Eduardo Roman; Michele Vendruscolo
Statistical properties of neutral evolution.
Journal of molecular evolution 2003;57 Suppl 1():S103-19.
2002: Emanuele Paci; Michele Vendruscolo; Martin Karplus
Validity of Gō models: comparison with a solvent-shielded empirical energy decomposition.
Biophysical journal 2002;83(6):3032-8.
2002: Emanuelel Paci; Michele Vendruscolo; Christopher M Dobson; Martin Karplus
Determination of a transition state at atomic resolution from protein engineering data.
Journal of molecular biology 2002;324(1):151-63.
2002: Ugo Bastolla; Markus Porto; H Eduardo Roman; Michele Vendruscolo
Lack of self-averaging in neutral evolution of proteins.
Physical review letters 2002;89(20):208101.
2002: Emanuele Paci; Michele Vendruscolo; Martin Karplus
Native and non-native interactions along protein folding and unfolding pathways.
Proteins 2002;47(3):379-92.
2002: Gad Getz; Michele Vendruscolo; David Sachs; Eytan Domany
Automated assignment of SCOP and CATH protein structure classifications from FSSP scores.
Proteins 2002;46(4):405-15.
2002: Michele Vendruscolo
Energetics of enzyme stability.
Trends in biotechnology 2002;20(1):1-2; discussion 2-3.
2001: Ugo Bastolla; Jochen Farwer; Ernst-Walter Knapp; Michele Vendruscolo
How to guarantee optimal stability for most representative structures in the Protein Data Bank.
Proteins 2001;44(2):79-96.
2001: Michele Vendruscolo; E Paci; Christopher M Dobson; M Karplus
Three key residues form a critical contact network in a protein folding transition state.
Nature 2001;409(6820):641-5.
2000: Michele Vendruscolo; L A Mirny; E I Shakhnovich; Eytan Domany
Comparison of two optimization methods to derive energy parameters for protein folding: perceptron and Z score.
Proteins 2000;41(2):192-201.
2000: K Park; Michele Vendruscolo; Eytan Domany
Toward an energy function for the contact map representation of proteins.
Proteins 2000;40(2):237-48.
2000: Ugo Bastolla; Michele Vendruscolo; Ernst-Walter Knapp
A statistical mechanical method to optimize energy functions for protein folding.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(8):3977-81.
2000: Michele Vendruscolo; Rafael J Najmanovich; Eytan Domany
Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?
Proteins 2000;38(2):134-48.