List of works - Emanuele Paci

A mechanism for agonist activation of the glucagon-like peptide-1 (GLP-1) receptor through modelling & molecular dynamics ⬇️

scientific article published on 31 January 2018

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

scientific article

Adaptive free energy sampling in multidimensional collective variable space using boxed molecular dynamics ⬇️

scientific article published on 14 October 2016

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

scientific article

Analysis of the free-energy surface of proteins from reversible folding simulations ⬇️

scientific article

Assessment of ab initio models of protein complexes by molecular dynamics. ⬇️

scientific article

Boxed Molecular Dynamics: Decorrelation Time Scales and the Kinetic Master Equation

scientific article published on 19 April 2011

CHARMM: the biomolecular simulation program

scientific article

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

scientific article

Change of the unbinding mechanism upon a mutation: a molecular dynamics study of an antibody-hapten complex

scientific article

Characterization of long and stable de novo single alpha-helix domains provides novel insight into their stability ⬇️

scientific article published on 13 March 2017

Characterization of the flexibility of the peripheral stalk of prokaryotic rotary A-ATPases by atomistic simulations ⬇️

scientific article published on 14 May 2016

Characterization of the molten globule state of retinol-binding protein using a molecular dynamics simulation approach

scientific article

Communication: Conformation state diagram of polypeptides: a chain length induced α-β transition

scientific article published in August 2011

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

scientific article published on 4 March 2005

Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints

scientific article (publication date: 15 February 2004)

Comparison of the transition states for folding of two Ig-like proteins from different superfamilies

scientific article published in October 2004

Complex unfolding kinetics of single-domain proteins in the presence of force

scientific article

Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein ⬇️

scientific article

Correction

Defining the remarkable structural malleability of a bacterial surface protein Rib domain implicated in infection ⬇️

scientific article published on 09 December 2019

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

scholarly article

Determining How Many Ionic Interactions are Needed for the High Stability of Single Alpha Helical (SAH) Domains

Differential Effects of Hydrophobic Core Packing Residues for Thermodynamic and Mechanical Stability of a Hyperthermophilic Protein ⬇️

scientific article published on 23 June 2016

Direct evidence of the multidimensionality of the free-energy landscapes of proteins revealed by mechanical probes

scientific article published on 30 March 2010

Directed Assembly of Homopentameric Cholera Toxin B-Subunit Proteins into Higher-Order Structures Using Coiled-Coil Appendages

scientific article published on 21 March 2019

Disorder drives cooperative folding in a multidomain protein ⬇️

scientific article published on 03 October 2016

Donor-strand exchange in chaperone-assisted pilus assembly revealed in atomic detail by molecular dynamics ⬇️

scientific article published on 4 November 2007

Dynamics of the coiled-coil unfolding transition of myosin rod probed by dissipation force spectrum

scientific article published in July 2010

Effect of external pulling forces on the length distribution of peptides

scientific article published on 28 September 2014

Effects of ligand binding on the mechanical properties of ankyrin repeat protein gankyrin

scientific article

Erratum: Pulling geometry defines the mechanical resistance of a β-sheet protein

scientific article published in October 2003

Exploration of partially unfolded states of human alpha-lactalbumin by molecular dynamics simulation

scientific article

Extraction of accurate biomolecular parameters from single-molecule force spectroscopy experiments ⬇️

scientific article published on 5 February 2015

Fast protein folding on downhill energy landscape

scientific article published on August 2003

Flexibility within the rotor and stators of the vacuolar H+-ATPase ⬇️

scientific article

Fluctuation power spectra reveal dynamical heterogeneity of peptides

article published in 2010

Fluorescence lifetimes of tyrosine residues in cytochrome c'' as local probes to study protein unfolding

scientific article published in April 2009

Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations

scientific article

Forces and energetics of hapten-antibody dissociation: a biased molecular dynamics simulation study

scientific article published in November 2001

Free energy for protein folding from nonequilibrium simulations using the Jarzynski equality

scientific article published in November 2006

Free-energy landscapes of proteins in the presence and absence of force

scientific article published in December 2008

Functional dynamics of hexameric helicase probed by hydrogen exchange and simulation ⬇️

scientific article published on August 2014

Gating of TonB-dependent transporters by substrate-specific forced remodelling ⬇️

scientific article published on 21 April 2017

Growth kinetics of bacterial pili from pairwise pilin association rates

scientific article

Helical Polyampholyte Sequences Have Unique Thermodynamic Properties ⬇️

High pressure simulations of biomolecules

scientific article

High-Resolution Hydrogen–Deuterium Protection Factors from Sparse Mass Spectrometry Data Validated by Nuclear Magnetic Resonance Measurements

scientific article published in 2022

Hydrogen exchange protection factors can be extracted from sparse HDX-MS data

Induction of rare conformation of oligosaccharide by binding to calcium-dependent bacterial lectin: X-ray crystallography and modelling study

scientific article published on 18 May 2019

Internal protein dynamics shifts the distance to the mechanical transition state

scientific article published on 29 December 2006

Mechanical resistance of proteins explained using simple molecular models

scientific article

Mechanical unfolding of TNfn3: the unfolding pathway of a fnIII domain probed by protein engineering, AFM and MD simulation

scientific article published in July 2005

Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering

scientific article (publication date: 27 September 2002)

Mechanical unfolding of an ankyrin repeat protein

scientific article

Mechanical unfolding revisited through a simple but realistic model

scientific article published in April 2006

Mechanically unfolding the small, topologically simple protein L.

scientific article published on 29 April 2005

Modulation of a protein free-energy landscape by circular permutation ⬇️

scientific article published on 23 October 2013

Molecular dynamics simulation of dextran extension by constant force in single molecule AFM.

scientific article

Molecular dynamics studies of the process of amyloid aggregation of peptide fragments of transthyretin

scientific article published in July 2004

Myosin tails and single α-helical domains ⬇️

scientific article published on February 2015

New dynamical window onto the landscape for forced protein unfolding

scientific article published on 12 December 2008

Non-native interactions are critical for mechanical strength in PKD domains

scientific article published on December 2009

Nonexponential Kinetics of Loop Formation in Proteins and Peptides: A Signature of Rugged Free Energy Landscapes? ⬇️

scientific article published on 26 September 2017

Optimal reaction coordinate as a biomarker for the dynamics of recovery from kidney transplant ⬇️

scientific article

Orientational averaging of dye molecules attached to proteins in Förster resonance energy transfer measurements: insights from a simulation study

scientific article published in August 2009

Peptide kinetics from picoseconds to microseconds using boxed molecular dynamics: power law rate coefficients in cyclisation reactions

scientific article

Prediction of stability changes upon mutation in an icosahedral capsid ⬇️

scientific article published on 14 July 2015

Prediction of the translocation kinetics of a protein from its mechanical properties

scientific article published on 30 June 2006

Protein folding and the organization of the protein topology universe.

scientific article

Protein folding: bringing theory and experiment closer together

scientific article

Prying open single GroES ring complexes by force reveals cooperativity across domains

scientific article published in April 2012

Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules

scientific article published on 6 February 2008

Pulling geometry defines the mechanical resistance of a beta-sheet protein

scientific article

Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange

scientific article published in December 2003

Rate of loop formation in peptides: a simulation study

scientific article

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

scientific article

Single-molecule folding mechanism of an EF-hand neuronal calcium sensor

article by Pétur O Heidarsson et al published 8 October 2013 in Structure

Small-world view of the amino acids that play a key role in protein folding

scientific article published on 25 June 2002

Stable single α-helices are constant force springs in proteins ⬇️

scientific article

Structural Dynamics in the Myosin 7A Single α-Helix Domain

article

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

scientific article

Structural determinants of polymerization reactivity of the P pilus adaptor subunit PapF

scientific article

Structures and relative free energies of partially folded states of proteins

scientific article

Terahertz time-domain spectroscopy of lysozyme and mouse urinary protein single crystals ⬇️

The effect of increasing the stability of non-native interactions on the folding landscape of the bacterial immunity protein Im9.

scientific article published on 10 May 2007

The remarkable mechanical strength of polycystin-1 supports a direct role in mechanotransduction

scientific article published in June 2005

The role of high-dimensional diffusive search, stabilization, and frustration in protein folding ⬇️

scientific article published on April 2014

The structure of a folding intermediate provides insight into differences in immunoglobulin amyloidogenicity

scientific article

The structure of neuronal calcium sensor-1 in solution revealed by molecular dynamics simulations

scientific article

Three key residues form a critical contact network in a protein folding transition state

scientific article

Transition state contact orders correlate with protein folding rates

scientific article published in September 2005

Transition states for protein folding have native topologies despite high structural variability

scientific article

Tuning protein mechanics through an ionic cluster graft from an extremophilic protein ⬇️

scientific article published on 26 January 2016

Understanding the apparent stator-rotor connections in the rotary ATPase family using coarse-grained computer modeling ⬇️

scientific article published on 11 November 2014

Unfolding proteins by external forces and temperature: the importance of topology and energetics

scientific article published on June 2000

Unraveling the molecular basis of subunit specificity in P pilus assembly by mass spectrometry ⬇️

scholarly article

Unravelling the Properties of Single α-Helical Domains in Myosin and other Proteins

Using Models to Design New Bioinspired Materials ⬇️

scientific article published on November 7, 2012

Validity of Gō models: comparison with a solvent-shielded empirical energy decomposition

scientific article

List of works by Emanuele Paci

A mechanism for agonist activation of the glucagon-like peptide-1 (GLP-1) receptor through modelling & molecular dynamics ⬇️

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

Adaptive free energy sampling in multidimensional collective variable space using boxed molecular dynamics ⬇️

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

Analysis of the free-energy surface of proteins from reversible folding simulations ⬇️

Assessment of ab initio models of protein complexes by molecular dynamics. ⬇️

Boxed Molecular Dynamics: Decorrelation Time Scales and the Kinetic Master Equation

CHARMM: the biomolecular simulation program

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

Change of the unbinding mechanism upon a mutation: a molecular dynamics study of an antibody-hapten complex

Characterization of long and stable de novo single alpha-helix domains provides novel insight into their stability ⬇️

Characterization of the flexibility of the peripheral stalk of prokaryotic rotary A-ATPases by atomistic simulations ⬇️

Characterization of the molten globule state of retinol-binding protein using a molecular dynamics simulation approach

Communication: Conformation state diagram of polypeptides: a chain length induced α-β transition

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

Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints

Comparison of the transition states for folding of two Ig-like proteins from different superfamilies

Complex unfolding kinetics of single-domain proteins in the presence of force

Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein ⬇️

Correction

Defining the remarkable structural malleability of a bacterial surface protein Rib domain implicated in infection ⬇️

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

Determining How Many Ionic Interactions are Needed for the High Stability of Single Alpha Helical (SAH) Domains

Differential Effects of Hydrophobic Core Packing Residues for Thermodynamic and Mechanical Stability of a Hyperthermophilic Protein ⬇️

Direct evidence of the multidimensionality of the free-energy landscapes of proteins revealed by mechanical probes

Directed Assembly of Homopentameric Cholera Toxin B-Subunit Proteins into Higher-Order Structures Using Coiled-Coil Appendages

Disorder drives cooperative folding in a multidomain protein ⬇️

Donor-strand exchange in chaperone-assisted pilus assembly revealed in atomic detail by molecular dynamics ⬇️

Dynamics of the coiled-coil unfolding transition of myosin rod probed by dissipation force spectrum

Effect of external pulling forces on the length distribution of peptides

Effects of ligand binding on the mechanical properties of ankyrin repeat protein gankyrin

Erratum: Pulling geometry defines the mechanical resistance of a β-sheet protein

Exploration of partially unfolded states of human alpha-lactalbumin by molecular dynamics simulation

Extraction of accurate biomolecular parameters from single-molecule force spectroscopy experiments ⬇️

Fast protein folding on downhill energy landscape

Flexibility within the rotor and stators of the vacuolar H+-ATPase ⬇️

Fluctuation power spectra reveal dynamical heterogeneity of peptides

Fluorescence lifetimes of tyrosine residues in cytochrome c'' as local probes to study protein unfolding

Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations

Forces and energetics of hapten-antibody dissociation: a biased molecular dynamics simulation study

Free energy for protein folding from nonequilibrium simulations using the Jarzynski equality

Free-energy landscapes of proteins in the presence and absence of force

Functional dynamics of hexameric helicase probed by hydrogen exchange and simulation ⬇️

Gating of TonB-dependent transporters by substrate-specific forced remodelling ⬇️

Growth kinetics of bacterial pili from pairwise pilin association rates

Helical Polyampholyte Sequences Have Unique Thermodynamic Properties ⬇️

High pressure simulations of biomolecules

High-Resolution Hydrogen–Deuterium Protection Factors from Sparse Mass Spectrometry Data Validated by Nuclear Magnetic Resonance Measurements

Hydrogen exchange protection factors can be extracted from sparse HDX-MS data

Induction of rare conformation of oligosaccharide by binding to calcium-dependent bacterial lectin: X-ray crystallography and modelling study

Internal protein dynamics shifts the distance to the mechanical transition state

Mechanical resistance of proteins explained using simple molecular models

Mechanical unfolding of TNfn3: the unfolding pathway of a fnIII domain probed by protein engineering, AFM and MD simulation

Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering

Mechanical unfolding of an ankyrin repeat protein

Mechanical unfolding revisited through a simple but realistic model

Mechanically unfolding the small, topologically simple protein L.

Modulation of a protein free-energy landscape by circular permutation ⬇️

Molecular dynamics simulation of dextran extension by constant force in single molecule AFM.

Molecular dynamics studies of the process of amyloid aggregation of peptide fragments of transthyretin

Myosin tails and single α-helical domains ⬇️

New dynamical window onto the landscape for forced protein unfolding

Non-native interactions are critical for mechanical strength in PKD domains

Nonexponential Kinetics of Loop Formation in Proteins and Peptides: A Signature of Rugged Free Energy Landscapes? ⬇️

Optimal reaction coordinate as a biomarker for the dynamics of recovery from kidney transplant ⬇️

Orientational averaging of dye molecules attached to proteins in Förster resonance energy transfer measurements: insights from a simulation study

Peptide kinetics from picoseconds to microseconds using boxed molecular dynamics: power law rate coefficients in cyclisation reactions

Prediction of stability changes upon mutation in an icosahedral capsid ⬇️

Prediction of the translocation kinetics of a protein from its mechanical properties

Protein folding and the organization of the protein topology universe.

Protein folding: bringing theory and experiment closer together

Prying open single GroES ring complexes by force reveals cooperativity across domains

Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules

Pulling geometry defines the mechanical resistance of a beta-sheet protein

Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange

Rate of loop formation in peptides: a simulation study

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

Single-molecule folding mechanism of an EF-hand neuronal calcium sensor

Small-world view of the amino acids that play a key role in protein folding