Michele Vendruscolo

In vitro and in silico assessment of the developability of a designed monoclonal antibody library.

Self-consistent determination of the transition state for protein folding: application to a fibronectin type III domain.

Analysis of the distributed computing approach applied to the folding of a small beta peptide.

Calculation of mutational free energy changes in transition states for protein folding.

Structures and relative free energies of partially folded states of proteins.

Comparison of sequence-based and structure-based energy functions for the reversible folding of a peptide.

A glimpse at the organization of the protein universe.

Determination of the folding transition states of barnase by using PhiI-value-restrained simulations validated by double mutant PhiIJ-values.

Determination of an ensemble of structures representing the intermediate state of the bacterial immunity protein Im7.

Structural comparison of the two alternative transition states for folding of TI I27.

A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank.

BPPred: a Web-based computational tool for predicting biophysical parameters of proteins.

A PDZ domain recapitulates a unifying mechanism for protein folding.

Similarities in the thermodynamics and kinetics of aggregation of disease-related Abeta(1-40) peptides.

The distribution of residues in a polypeptide sequence is a determinant of aggregation optimized by evolution.

Structural reorganisation and potential toxicity of oligomeric species formed during the assembly of amyloid fibrils.

Systematic in vivo analysis of the intrinsic determinants of amyloid Beta pathogenicity.

Characterisation of transition state structures for protein folding using 'high', 'medium' and 'low' {Phi}-values.

Molecular determinants of the aggregation behavior of alpha- and beta-synuclein.

Biological function in a non-native partially folded state of a protein.

A coupled equilibrium shift mechanism in calmodulin-mediated signal transduction.

Calculation of the free energy barriers in the oligomerisation of Abeta peptide fragments.

Prediction of aggregation-prone regions in structured proteins.

Mapping of two networks of residues that exhibit structural and dynamical changes upon binding in a PDZ domain protein.

The Zyggregator method for predicting protein aggregation propensities.

Protein dynamics under light control.

Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms.

Mutational analysis of the aggregation-prone and disaggregation-prone regions of acylphosphatase.

Inhibition of alpha-synuclein fibrillization by dopamine is mediated by interactions with five C-terminal residues and with E83 in the NAC region.

Structure determination of protein-protein complexes using NMR chemical shifts: case of an endonuclease colicin-immunity protein complex.

A generic mechanism of emergence of amyloid protofilaments from disordered oligomeric aggregates.

Comparison of successive transition states for folding reveals alternative early folding pathways of two homologous proteins.

Determination of protein structures in the solid state from NMR chemical shifts.

The mechanism of folding of Im7 reveals competition between functional and kinetic evolutionary constraints.

A relationship between mRNA expression levels and protein solubility in E. coli.

Toward an accurate determination of free energy landscapes in solution states of proteins.

Stochastic reconstruction of protein structures from effective connectivity profiles.

Competition between intramolecular and intermolecular interactions in an amyloid-forming protein.

Towards quantitative predictions in cell biology using chemical properties of proteins.

Position-dependent electrostatic protection against protein aggregation.

Folding of small proteins by Monte Carlo simulations with chemical shift restraints without the use of molecular fragment replacement or structural homology.

Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins.

On the mechanism of nonspecific inhibitors of protein aggregation: dissecting the interactions of alpha-synuclein with Congo red and lacmoid.

A condensation-ordering mechanism in nanoparticle-catalyzed peptide aggregation.

Fast and accurate predictions of protein NMR chemical shifts from interatomic distances.

Correlation between mRNA expression levels and protein aggregation propensities in subcellular localisations.

Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins.

Analysis of sub-tauc and supra-tauc motions in protein Gbeta1 using molecular dynamics simulations.

An analytical solution to the kinetics of breakable filament assembly.

Determination of the free energy landscape of alpha-synuclein using spin label nuclear magnetic resonance measurements.

Quantitative approaches to defining normal and aberrant protein homeostasis.

Time averaging of NMR chemical shifts in the MLF peptide in the solid state.

Intrinsic determinants of neurotoxic aggregate formation by the amyloid beta peptide.

Physicochemical determinants of chaperone requirements.

Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins.

Proteome-level interplay between folding and aggregation propensities of proteins.

Enzymatic activity in disordered states of proteins.

Derivation of a solubility condition for proteins from an analysis of the competition between folding and aggregation.

Translationally optimal codons associate with aggregation-prone sites in proteins.

Transient tertiary structure formation within the ribosome exit port.

New scenarios of protein folding can occur on the ribosome.

Protein dynamics: Moore's law in molecular biology.

Detection of early locomotor abnormalities in a Drosophila model of Alzheimer's disease.

Using chemical shifts to determine structural changes in proteins upon complex formation.

¹H, ¹³C and ¹⁵N resonance assignments of human muscle acylphosphatase.

Metastability of native proteins and the phenomenon of amyloid formation.

The iFly tracking system for an automated locomotor and behavioural analysis of Drosophila melanogaster.

The A53T mutation is key in defining the differences in the aggregation kinetics of human and mouse α-synuclein.

Structure-based prediction of methyl chemical shifts in proteins.

Protein solubility and protein homeostasis: a generic view of protein misfolding disorders.

Nucleated polymerization with secondary pathways. I. Time evolution of the principal moments.

Nucleated polymerization with secondary pathways. II. Determination of self-consistent solutions to growth processes described by non-linear master equations.

Nucleated polymerization with secondary pathways. III. Equilibrium behavior and oligomer populations.

Using side-chain aromatic proton chemical shifts for a quantitative analysis of protein structures.

ALS mutations in FUS cause neuronal dysfunction and death in Caenorhabditis elegans by a dominant gain-of-function mechanism.

Nucleated polymerisation in the presence of pre-formed seed filaments.

Inversion of the balance between hydrophobic and hydrogen bonding interactions in protein folding and aggregation.

Experimental free energy surfaces reveal the mechanisms of maintenance of protein solubility.

Determination of Conformational Equilibria in Proteins Using Residual Dipolar Couplings.

Proteome folding and aggregation.

Characterization of the conformational equilibrium between the two major substates of RNase A using NMR chemical shifts.

Blind testing of routine, fully automated determination of protein structures from NMR data.

Determination of secondary structure populations in disordered states of proteins using nuclear magnetic resonance chemical shifts.

From macroscopic measurements to microscopic mechanisms of protein aggregation.

Protein structure validation using side-chain chemical shifts.

Prediction of variable translation rate effects on cotranslational protein folding.

Trigger factor slows co-translational folding through kinetic trapping while sterically protecting the nascent chain from aberrant cytosolic interactions.

Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings.

ADP ribosylation adapts an ER chaperone response to short-term fluctuations in unfolded protein load.

Twisting transition between crystalline and fibrillar phases of aggregated peptides.

In vivo translation rates can substantially delay the cotranslational folding of the Escherichia coli cytosolic proteome.

Assessment of the use of NMR chemical shifts as replica-averaged structural restraints in molecular dynamics simulations to characterize the dynamics of proteins.

Analysis of the contributions of ring current and electric field effects to the chemical shifts of RNA bases.

Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle.

Atomic structure and hierarchical assembly of a cross-β amyloid fibril.

Nanobodies raised against monomeric α-synuclein distinguish between fibrils at different maturation stages.

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics.

Proliferation of amyloid-β42 aggregates occurs through a secondary nucleation mechanism.

A method of determining RNA conformational ensembles using structure-based calculations of residual dipolar couplings.

Single-molecule measurements of transient biomolecular complexes through microfluidic dilution.

A geometrical parametrization of C1'-C5' RNA ribose chemical shifts calculated by density functional theory.

Identification of small-molecule binding pockets in the soluble monomeric form of the Aβ42 peptide.

A relationship between the aggregation rates of α-synuclein variants and the β-sheet populations in their monomeric forms.

Characterization of the interdomain motions in hen lysozyme using residual dipolar couplings as replica-averaged structural restraints in molecular dynamics simulations.

Structures of the excited states of phospholamban and shifts in their populations upon phosphorylation.

In-cell NMR characterization of the secondary structure populations of a disordered conformation of α-synuclein within E. coli cells.

Subdomain architecture and stability of a giant repeat protein.

pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins.

Widespread aggregation and neurodegenerative diseases are associated with supersaturated proteins.

Higher order amyloid fibril structure by MAS NMR and DNP spectroscopy.

A clear view of polymorphism, twist, and chirality in amyloid fibril formation.

Kinetic modelling indicates that fast-translating codons can coordinate cotranslational protein folding by avoiding misfolded intermediates.

A simple lattice model that captures protein folding, aggregation and amyloid formation.

A conformational ensemble derived using NMR methyl chemical shifts reveals a mechanical clamping transition that gates the binding of the HU protein to DNA.

Determination of the individual roles of the linker residues in the interdomain motions of calmodulin using NMR chemical shifts.

Targeting the intrinsically disordered structural ensemble of α-synuclein by small molecules as a potential therapeutic strategy for Parkinson's disease.

Chemical kinetics for drug discovery to combat protein aggregation diseases.

ALMOST: an all atom molecular simulation toolkit for protein structure determination.

Understanding the influence of codon translation rates on cotranslational protein folding.

Solution conditions determine the relative importance of nucleation and growth processes in α-synuclein aggregation.

A tensor-free method for the structural and dynamical refinement of proteins using residual dipolar couplings.

Archaeal MBF1 binds to 30S and 70S ribosomes via its helix-turn-helix domain.

The amyloid state and its association with protein misfolding diseases.

Direct observation of the three regions in α-synuclein that determine its membrane-bound behaviour.

Statistical mechanics of the denatured state of a protein using replica-averaged metadynamics.

Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism.

NMR characterization of the conformational fluctuations of the human lymphocyte function-associated antigen-1 I-domain.

Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts.

Identification and characterization of PKCγ, a kinase associated with SCA14, as an amyloidogenic protein.

Understanding the frustration arising from the competition between function, misfolding, and aggregation in a globular protein.

A relationship between the transient structure in the monomeric state and the aggregation propensities of α-synuclein and β-synuclein.

The CamSol method of rational design of protein mutants with enhanced solubility.

The H50Q mutation induces a 10-fold decrease in the solubility of α-synuclein.

Characterization of the conformational fluctuations in the Josephin domain of ataxin-3.

The s2D method: simultaneous sequence-based prediction of the statistical populations of ordered and disordered regions in proteins.

Structure of a low-population intermediate state in the release of an enzyme product.

Supersaturation is a major driving force for protein aggregation in neurodegenerative diseases.

Lipid vesicles trigger α-synuclein aggregation by stimulating primary nucleation.

A molecular chaperone breaks the catalytic cycle that generates toxic Aβ oligomers.

Structure and dynamics of the integrin LFA-1 I-domain in the inactive state underlie its inside-out/outside-in signaling and allosteric mechanisms.

Structure and Dynamics of GeoCyp: A Thermophilic Cyclophilin with a Novel Substrate Binding Mechanism That Functions Efficiently at Low Temperatures.

Widespread Proteome Remodeling and Aggregation in Aging C. elegans.

Analysis of the performance of the CHESHIRE and YAPP methods at CASD-NMR round 3.

Dynamic binding mode of a Synaptotagmin-1-SNARE complex in solution.

Probing the Residual Structure of the Low Populated Denatured State of ADA2h under Folding Conditions by Relaxation Dispersion Nuclear Magnetic Resonance Spectroscopy.

A Rational Design Strategy for the Selective Activity Enhancement of a Molecular Chaperone toward a Target Substrate.

Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study.

Rational design of antibodies targeting specific epitopes within intrinsically disordered proteins.

Targeting disordered proteins with small molecules using entropy.

Biophysical approaches for the study of interactions between molecular chaperones and protein aggregates.

Structure and Dynamics of Intrinsically Disordered Proteins.

Druggability of Intrinsically Disordered Proteins.

Latent analysis of unmodified biomolecules and their complexes in solution with attomole detection sensitivity.

Structure-Free Validation of Residual Dipolar Coupling and Paramagnetic Relaxation Enhancement Measurements of Disordered Proteins.

The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments.

Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.

Identification of Small Molecule Inhibitors of Tau Aggregation by Targeting Monomeric Tau As a Potential Therapeutic Approach for Tauopathies.

ALS/FTD Mutation-Induced Phase Transition of FUS Liquid Droplets and Reversible Hydrogels into Irreversible Hydrogels Impairs RNP Granule Function.

Parmbsc1: a refined force field for DNA simulations.

Replica-Averaged Metadynamics.

Structural Insights into the Calcium-Mediated Allosteric Transition in the C-Terminal Domain of Calmodulin from Nuclear Magnetic Resonance Measurements.

Using Pseudocontact Shifts and Residual Dipolar Couplings as Exact NMR Restraints for the Determination of Protein Structural Ensembles.

Microfluidic Diffusion Analysis of the Sizes and Interactions of Proteins under Native Solution Conditions.

Molecular mechanisms of protein aggregation from global fitting of kinetic models.

Metainference: A Bayesian inference method for heterogeneous systems.

Hamiltonian Dynamics of Protein Filament Formation.

Molecular Recognition by Templated Folding of an Intrinsically Disordered Protein.

A Fragment-Based Method of Creating Small-Molecule Libraries to Target the Aggregation of Intrinsically Disordered Proteins.

A structural ensemble of a ribosome-nascent chain complex during cotranslational protein folding.

An anticancer drug suppresses the primary nucleation reaction that initiates the production of the toxic Aβ42 aggregates linked with Alzheimer's disease.

Identification and Structural Characterization of an Intermediate in the Folding of the Measles Virus X Domain.

Kinetic analysis reveals the diversity of microscopic mechanisms through which molecular chaperones suppress amyloid formation.

A transcriptional signature of Alzheimer's disease is associated with a metastable subproteome at risk for aggregation.

Structural characterization of the interaction of α-synuclein nascent chains with the ribosomal surface and trigger factor.

Structural Effects of Two Camelid Nanobodies Directed to Distinct C-Terminal Epitopes on α-Synuclein.

Rational design of mutations that change the aggregation rate of a protein while maintaining its native structure and stability.

Structural Ensembles of Membrane-bound α-Synuclein Reveal the Molecular Determinants of Synaptic Vesicle Affinity.

Structure of a low-population binding intermediate in protein-RNA recognition.

Chemical properties of lipids strongly affect the kinetics of the membrane-induced aggregation of α-synuclein.

Towards a structural biology of the hydrophobic effect in protein folding.

A protein homeostasis signature in healthy brains recapitulates tissue vulnerability to Alzheimer's disease.

Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics.

Mutations associated with familial Parkinson's disease alter the initiation and amplification steps of α-synuclein aggregation.

Structural basis of synaptic vesicle assembly promoted by α-synuclein.

β-Synuclein suppresses both the initiation and amplification steps of α-synuclein aggregation via competitive binding to surfaces.

A tau homeostasis signature is linked with the cellular and regional vulnerability of excitatory neurons to tau pathology.

Systematic development of small molecules to inhibit specific microscopic steps of Aβ42 aggregation in Alzheimer's disease.

Principles of protein structural ensemble determination.

Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop.

Networks of Dynamic Allostery Regulate Enzyme Function.

A natural product inhibits the initiation of α-synuclein aggregation and suppresses its toxicity.

Inhibition of α-Synuclein Fibril Elongation by Hsp70 Is Governed by a Kinetic Binding Competition between α-Synuclein Species.

Identification of an RNA Polymerase III Regulator Linked to Disease-Associated Protein Aggregation.

Simultaneous quantification of protein order and disorder.

MOAG-4 promotes the aggregation of α-synuclein by competing with self-protective electrostatic interactions.

Spinal motor neuron protein supersaturation patterns are associated with inclusion body formation in ALS.

Emergence and evolution of an interaction between intrinsically disordered proteins.

Structural Characterization of the Early Events in the Nucleation-Condensation Mechanism in a Protein Folding Process.

The RNF168 paralog RNF169 defines a new class of ubiquitylated histone reader involved in the response to DNA damage.

Amyloid-like Fibrils from an α-Helical Transmembrane Protein.

Phage display and kinetic selection of antibodies that specifically inhibit amyloid self-replication.

Methods of probing the interactions between small molecules and disordered proteins.

Protein homeostasis of a metastable subproteome associated with Alzheimer's disease.

Nanobodies raised against monomeric ɑ-synuclein inhibit fibril formation and destabilize toxic oligomeric species.

Selective targeting of primary and secondary nucleation pathways in Aβ42 aggregation using a rational antibody scanning method.

Monomeric and fibrillar α-synuclein exert opposite effects on the catalytic cycle that promotes the proliferation of Aβ42 aggregates.

Sequence Specificity in the Entropy-Driven Binding of a Small Molecule and a Disordered Peptide.

Rapid and accurate in silico solubility screening of a monoclonal antibody library.

The molecular chaperones DNAJB6 and Hsp70 cooperate to suppress α-synuclein aggregation.

Oxetane Grafts Installed Site-Selectively on Native Disulfides to Enhance Protein Stability and Activity In Vivo.

Delivery of Native Proteins into C. elegans Using a Transduction Protocol Based on Lipid Vesicles.

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

Scaling behaviour and rate-determining steps in filamentous self-assembly.

Structural basis of membrane disruption and cellular toxicity by α-synuclein oligomers.

Massively parallel C. elegans tracking provides multi-dimensional fingerprints for phenotypic discovery.

Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.

Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide.

Structural Ensemble Modulation upon Small-Molecule Binding to Disordered Proteins.

Molecular determinants of the interaction of EGCG with ordered and disordered proteins.

Exploring the role of post-translational modifications in regulating α-synuclein interactions by studying the effects of phosphorylation on nanobody binding.

Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy.

Parapred: antibody paratope prediction using convolutional and recurrent neural networks.

FUS Phase Separation Is Modulated by a Molecular Chaperone and Methylation of Arginine Cation-π Interactions.

Cholesterol catalyses Aβ42 aggregation through a heterogeneous nucleation pathway in the presence of lipid membranes.

A Rationally Designed Hsp70 Variant Rescues the Aggregation-Associated Toxicity of Human IAPP in Cultured Pancreatic Islet β-Cells.

Cooperative Assembly of Hsp70 Subdomain Clusters.

A method for partitioning the information contained in a protein sequence between its structure and function.

Reversible inhibition of the ClpP protease via an N-terminal conformational switch.

Multistep Inhibition of α-Synuclein Aggregation and Toxicity in Vitro and in Vivo by Trodusquemine.

Stabilization and Characterization of Cytotoxic Aβ Oligomers Isolated from an Aggregation Reaction in the Presence of Zinc Ions.

Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs.

Structural differences between toxic and nontoxic HypF-N oligomers.

Determination of the conformational states of strychnine in solution using NMR residual dipolar couplings in a tensor-free approach.

Author Correction: The molecular chaperones DNAJB6 and Hsp70 cooperate to suppress α-synuclein aggregation.

Systematic mapping of free energy landscapes of a growing filamin domain during biosynthesis.

Microfluidic deposition for resolving single-molecule protein architecture and heterogeneity.

SAR by kinetics for drug discovery in protein misfolding diseases.

Third generation antibody discovery methods: in silico rational design.

Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling.

Determination of Structural Ensembles of Proteins: Restraining vs Reweighting.

Determination of protein structural ensembles using cryo-electron microscopy.

A superposition free method for protein conformational ensemble analyses and local clustering based on a differential geometry representation of backbone.

Chemical and mechanistic analysis of photodynamic inhibition of Alzheimer's β-amyloid aggregation.

Trodusquemine enhances Aβ aggregation but suppresses its toxicity by displacing oligomers from cell membranes.

Atomic force microscopy for single molecule characterisation of protein aggregation.

Protein Solubility Predictions Using the CamSol Method in the Study of Protein Homeostasis.

A method of predicting the in vitro fibril formation propensity of Aβ40 mutants based on their inclusion body levels in E. coli.

The Amyloid Phenomenon and Its Significance in Biology and Medicine.

Different soluble aggregates of Aβ42 can give rise to cellular toxicity through different mechanisms.

The metastability of the proteome of spinal motor neurons underlies their selective vulnerability in ALS.

The free energy landscape of the oncogene protein E7 of human papillomavirus type 16 reveals a complex interplay between ordered and disordered regions.

Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming.

Secondary nucleation and elongation occur at different sites on Alzheimer's amyloid-β aggregates.

Intrinsically aggregation-prone proteins form amyloid-like aggregates and contribute to tissue aging in .

Probing the Origin of the Toxicity of Oligomeric Aggregates of α-Synuclein with Antibodies.

Effects of α-tubulin acetylation on microtubule structure and stability.

Common Regulatory Pathways Mediate Activity of MicroRNAs Inducing Cardiomyocyte Proliferation.

Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response.

Fast Fluorescence Lifetime Imaging Reveals the Aggregation Processes of α-Synuclein and Polyglutamine in Aging .

Differential Interactome and Innate Immune Response Activation of Two Structurally Distinct Misfolded Protein Oligomers.

Soluble aggregates present in cerebrospinal fluid change in size and mechanism of toxicity during Alzheimer's disease progression.

The Hsp70 Chaperone System Stabilizes a Thermo-sensitive Subproteome in E. coli.

A Practical Guide to the Simultaneous Determination of Protein Structure and Dynamics Using Metainference.

Enhancement of the Anti-Aggregation Activity of a Molecular Chaperone Using a Rationally Designed Post-Translational Modification.