Lista de obras - Emanuele Paci - Dominio Público Uruguay

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

artículo científico publicado en 2018

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

artículo científico publicado en 2014

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

artículo científico publicado en 2016

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

artículo científico publicado en 2003

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

artículo científico publicado en 2009

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

artículo científico publicado en 2018

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

artículo científico publicado en 2011

CHARMM: the biomolecular simulation program

artículo científico publicado en 2009

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

artículo científico publicado en 2003

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

artículo científico publicado en 2005

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

artículo científico publicado en 2017

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

artículo científico publicado en 2016

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

artículo científico publicado en 2005

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

artículo científico publicado en 2011

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

artículo científico publicado en 2005

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

artículo científico publicado en 2004

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

artículo científico publicado en 2004

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

artículo científico publicado en 2010

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

artículo científico publicado en 2015

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.

artículo científico publicado en 2005

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 ⬇️

artículo científico publicado en 2016

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

artículo científico publicado en 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 ⬇️

artículo científico publicado en 2016

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

artículo científico publicado en 2007

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

artículo científico publicado en 2010

Effect of external pulling forces on the length distribution of peptides

artículo científico publicado en 2014

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

artículo científico publicado en 2013

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

artículo científico publicado en 2003

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

artículo científico publicado en 2001

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

artículo científico publicado en 2015

Fast protein folding on downhill energy landscape

artículo científico publicado en 2003

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

artículo científico publicado en 2013

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

artículo científico publicado en 2009

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

artículo científico publicado en 1999

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

artículo científico publicado en 2001

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

artículo científico publicado en 2006

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

artículo científico publicado en 2008

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

artículo científico publicado en 2014

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

artículo científico publicado en 2017

Growth kinetics of bacterial pili from pairwise pilin association rates

artículo científico publicado en 2013

Helical Polyampholyte Sequences Have Unique Thermodynamic Properties ⬇️

High pressure simulations of biomolecules

artículo científico publicado en 2002

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

artículo científico publicado en 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

artículo científico publicado en 2019

Internal protein dynamics shifts the distance to the mechanical transition state

artículo científico publicado en 2006

Mechanical resistance of proteins explained using simple molecular models

artículo científico publicado en 2005

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

artículo científico publicado en 2005

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

artículo científico publicado en 2002

Mechanical unfolding of an ankyrin repeat protein

artículo científico publicado en 2010

Mechanical unfolding revisited through a simple but realistic model

artículo científico publicado en 2006

Mechanically unfolding the small, topologically simple protein L.

artículo científico publicado en 2005

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

artículo científico publicado en 2013

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

artículo científico publicado en 2006

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

artículo científico publicado en 2004

Myosin tails and single α-helical domains ⬇️

artículo científico publicado en 2015

New dynamical window onto the landscape for forced protein unfolding

artículo científico publicado en 2008

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

artículo científico publicado en 2009

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

artículo científico publicado en 2017

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

artículo científico publicado en 2014

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

artículo científico publicado en 2009

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

artículo científico publicado en 2012

Prediction of stability changes upon mutation in an icosahedral capsid ⬇️

artículo científico publicado en 2015

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

artículo científico publicado en 2006

Protein folding and the organization of the protein topology universe.

artículo científico publicado en 2005

Protein folding: bringing theory and experiment closer together

artículo científico publicado en 2003

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

artículo científico publicado en 2012

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

artículo científico publicado en 2008

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

artículo científico publicado en 2003

Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange

artículo científico publicado en 2003

Rate of loop formation in peptides: a simulation study

artículo científico publicado en 2008

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

artículo científico publicado en 2003

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

artículo científico publicado en 2002

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

artículo científico publicado en 2014

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

article

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

artículo científico publicado en 2006

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

artículo científico publicado en 2008

Structures and relative free energies of partially folded states of proteins

artículo científico publicado en 2003

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.

artículo científico publicado en 2007

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

artículo científico publicado en 2005

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

artículo científico publicado en 2014

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

artículo científico publicado en 2008

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

artículo científico publicado en 2013

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

artículo científico publicado en 2001

Transition state contact orders correlate with protein folding rates

artículo científico publicado en 2005

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

artículo científico publicado en 2004

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

artículo científico publicado en 2016

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

artículo científico publicado en 2014

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

artículo científico publicado en 2000

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

artículo científico publicado en 2008

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

Using Models to Design New Bioinspired Materials ⬇️

artículo científico publicado el 7 de noviembre de 2012

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

artículo científico publicado en 2002

Lista de obras de 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