E. Paci

发表

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

J. Gsponer, E. Paci, X. Salvatella, 2004, Journal of molecular biology.

Transition state contact orders correlate with protein folding rates.

M. Karplus, C. Dobson, K. Lindorff-Larsen, 2005, Journal of molecular biology.

Protein mechanics probed using simple molecular models.

E. Paci, Matthew Batchelor, K. Papachristos, 2020, Biochimica et biophysica acta. General subjects.

Native and non‐native interactions along protein folding and unfolding pathways

Michele Vendruscolo, Emanuele Paci, Martin Karplus, 2002, Proteins.

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

S. Radford, E. Paci, M. Vendruscolo, 2006, Proceedings of the National Academy of Sciences of the United States of America.

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

M. Karplus, C. Dobson, E. Paci, 2001, Nature.

Determination of a transition state at atomic resolution from protein engineering data.

M. Karplus, C. Dobson, E. Paci, 2002, Journal of molecular biology.

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

M. Karplus, S. Radford, K. Lindorff-Larsen, 2003, Proteins.

Fast protein folding on downhill energy landscape

A. Cavalli, A. Caflisch, E. Paci, 2003, Protein science : a publication of the Protein Society.

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

A. Cavalli, A. Caflisch, E. Paci, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Functional Dynamics of Hexameric Helicase Probed by Hydrogen Exchange and Simulation

E. Paci, R. Tuma, G. Radou, 2014, Biophysical journal.

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

M Karplus, E Paci, M. Karplus, 1999, Journal of molecular biology.

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

M. Rief, E. Paci, Z. T. Yew, 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

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

Emanuele Paci, Sheena E Radford, S. Radford, 2014, Biophysical journal.

Fluctuation power spectra reveal dynamical heterogeneity of peptides.

Bhavin S. Khatri, E. Paci, T. McLeish, 2010, The Journal of chemical physics.

Molecular Dynamics Simulations to Study Protein Folding and Unfolding

A. Caflisch, E. Paci, 2008 .

Sampling of molecular conformations by molecular dynamics techniques

Giovanni Ciccotti, Emanuele Paci, Jean-Paul Ryckaert, 1993 .

Vacancy migration rates by molecular dynamics with constraints

G. Ciccotti, E. Paci, 1992 .

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

A. Bateman, E. Paci, F. Whelan, 2019, Proceedings of the National Academy of Sciences.

Construction and characterization of I 27 GKN polyprotein

E. Paci, L. Itzhaki, P. Marszalek, 2012 .

Unraveling the Factors That Control Soft Landing of Small Silyl Ions on Fluorinated Self-Assembled Monolayers

M. Alcamí, F. Martín, E. Paci, 2014 .

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

S. Auer, E. Paci, Piero Ricchiuto, 2011, The Journal of chemical physics.

Computational Modeling of Designed Ankyrin Repeat Protein Complexes with Their Targets.

A. Plückthun, E. Paci, F. Radom, 2019, Journal of molecular biology.

odeling of in Repeat Protein Their Targets eas Plückthun

E. Paci, F. Radom, 2019 .

Structures and relative free energies of partially folded states of proteins

M. Karplus, C. Dobson, E. Paci, 2003, Proceedings of the National Academy of Sciences of the United States of America.

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

M. Karplus, C. Dobson, L. J. Smith, 2001, Journal of molecular biology.

Dynamic ion pair behavior stabilizes single α-helices in proteins

E. Paci, M. Peckham, Matthew Batchelor, 2018, The Journal of Biological Chemistry.

Prediction of stability changes upon mutation in an icosahedral capsid

E. Paci, Samuel J. Hickman, J. Ross, 2015, Proteins.

ADOPT: intrinsic protein disorder prediction through deep bidirectional transformers

E. Paci, K. Tamiola, Matthew M. Heberling, 2022, bioRxiv.

Intrinsic compressibility and volume compression in solvated proteins by molecular dynamics simulation at high pressure.

E. Paci, M. Marchi, 1996, Proceedings of the National Academy of Sciences of the United States of America.

Dynamic ion pair behavior stabilizes single alpha helices in proteins.

E. Paci, M. Peckham, Matthew Batchelor, 2018 .

This is a repository copy of A mechanism for agonist activation of the glucagon-like peptide-1 (GLP-1) receptor through modelling

E. Paci, D. Donnelly, Carla Gómez Santiago, 2019 .

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

E. Paci, D. Donnelly, Carla Gómez Santiago, 2018, Biochemical and biophysical research communications.

Simulation of fluorescence resonance energy transfer experiments: effect of the dyes on protein folding

E. Paci, L. R. Allen, 2010, Journal of physics. Condensed matter : an Institute of Physics journal.

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

E. Paci, D. Woolfson, P. Knight, 2017, Scientific Reports.

Computational methods to predict the mutational landscape of the spike protein

E. Paci, J. Ross, James F. Ross, 2021, Biophysical Journal.

ADOPT: intrinsic protein disorder prediction through deep bidirectional transformers

E. Paci, K. Tamiola, Matthew M. Heberling, 2023, bioRxiv.

CHARMM: The biomolecular simulation program

Jianpeng Ma, Charles L. Brooks, Themis Lazaridis, 2009, J. Comput. Chem..

Tracking local conformational changes of ribonuclease A using picosecond time-resolved fluorescence of the six tyrosine residues.

H. Santos, E. Paci, J. C. Lima, 2007, Biophysical journal.

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

M. L. Hughes, E. Paci, Michael C Wilson, 2016, Langmuir : the ACS journal of surfaces and colloids.

Comparative proximity biotinylation implicates RAB18 in sterol mobilization and biosynthesis

Mark T. Handley, A. von Kriegsheim, E. Paci, 2019, bioRxiv.

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

M Karplus, M Vendruscolo, N V Dokholyan, 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

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

E. Paci, J. Clarke, A. Steward, 2005, Journal of molecular biology.

Optimal Reaction Coordinate as a Biomarker for the Dynamics of Recovery from Kidney Transplant

Julie Fisher, Sergei V. Krivov, Emanuele Paci, 2014, PLoS Comput. Biol..

Allostery in Its Many Disguises: From Theory to Applications.

Ruth Nussinov, Ivet Bahar, Dima Kozakov, 2019, Structure.

Probing the free energy landscape of the FBP28WW domain using multiple techniques

Alan E. Mark, Emanuele Paci, Xavier Periole, 2009, J. Comput. Chem..

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

Lorna J. Smith, L. Greene, E. Paci, 2005, The FEBS journal.

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

C. Dobson, K. Lindorff-Larsen, E. Paci, 2004, Nature Structural &Molecular Biology.

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

S. Radford, E. Paci, D. Brockwell, 2015, ACS nano.

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

E. Paci, D. Brockwell, M. Kawakami, 2012, Biophysical journal.

Periscope Proteins are variable-length regulators of bacterial cell surface interactions

A. Bateman, E. Paci, F. Whelan, 2020, Proceedings of the National Academy of Sciences.

Mechanical resistance of proteins explained using simple molecular models.

S. Radford, E. Paci, P. Olmsted, 2006, Biophysical journal.

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

Emanuele Paci, Sheena E Radford, David J Brockwell, 2003, Nature Structural Biology.

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

Amedeo Caflisch, Emanuele Paci, A. Caflisch, 2005, Protein science : a publication of the Protein Society.

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

A Caflisch, M Karplus, E Paci, 2001, Journal of molecular biology.

Flexibility within the Rotor and Stators of the Vacuolar H+-ATPase

E. Paci, J. Trinick, S. Rawson, 2013, PloS one.

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

Matthias J. Feige, E. Paci, J. Buchner, 2008, Proceedings of the National Academy of Sciences.

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

M. R. Otazo, E. Paci, B. Kragelund, 2013, Structure.

The Structure of Neuronal Calcium Sensor-1 in Solution Revealed by Molecular Dynamics Simulations

E. Paci, S. Corni, R. Di Felice, 2013, PloS one.

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

Emanuele Paci, Sheena E Radford, S. Radford, 2007, Journal of molecular biology.

Protein folding: bringing theory and experiment closer together.

Michele Vendruscolo, Emanuele Paci, E. Paci, 2003, Current opinion in structural biology.

Molecular Dynamics of Lysine Dendrimers. Computer Simulation and NMR

E. Paci, H. Tenhu, D. Markelov, 2013 .

Effect of external pulling forces on the length distribution of peptides.

E. Paci, J. Gowdy, M. Batchelor, 2015, Biochimica et biophysica acta.

Rate of loop formation in peptides: a simulation study.

Matthias J. Feige, Emanuele Paci, E. Paci, 2008, Journal of molecular biology.

Powerful Avidity with a Limited Valency for Virus-Attachment Blockers on DC-SIGN: Combining Chelation and Statistical Rebinding with Structural Plasticity of the Receptor

E. Paci, A. Bernardi, F. Fieschi, 2023, ACS Central Science.

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

S. Radford, E. Paci, G. Waksman, 2008, Journal of molecular biology.

Activation of PKA via asymmetric allosteric coupling of structurally conserved cyclic nucleotide binding domains

Susan S. Taylor, Rodrigo A. Maillard, E. Paci, 2019, Nature Communications.

Activation of a Protein Kinase Via Asymmetric Allosteric Coupling of Structurally Conserved Signaling Modules

Susan S. Taylor, Rodrigo A. Maillard, E. Paci, 2019, bioRxiv.

Comparative proximity biotinylation implicates RAB18 in sterol mobilization and biosynthesis

Mark T. Handley, A. von Kriegsheim, E. Paci, 2019, bioRxiv.

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

E. Paci, F. Sobott, M. Stofella, 2022, Journal of the American Society for Mass Spectrometry.

Estimating Constraints for Protection Factors from HDX-MS Data

Emanuele Paci, Simon P Skinner, Gael Radou, 2019, Biophysical journal.

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

J. Houwing-Duistermaat, E. Paci, R. Tuma, 2018, bioRxiv.

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

E. Paci, S. Muench, K. Papachristos, 2016, Proteins.

Detection of non-native hydrophobic interactions in the denatured state of lysozyme by molecular dynamics simulations

E. Paci, M. Vendruscolo, 2005 .

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

E. Paci, Michael C Wilson, D. Brockwell, 2016, Soft matter.

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

M. Karplus, E. Paci, M. Vendruscolo, 2003, Proceedings of the National Academy of Sciences of the United States of America.

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

Jane Clarke, Robert B Best, Emanuele Paci, 2002, Journal of molecular biology.

Assessment of ab initio models of protein complexes by molecular dynamics

Andreas Plückthun, Emanuele Paci, Filip Radom, 2018, PLoS Comput. Biol..

Mechanical unfolding of an ankyrin repeat protein.

Laura S. Itzhaki, Emanuele Paci, Piotr E. Marszalek, 2010, Biophysical journal.

Mechanically unfolding the small, topologically simple protein L.

Emanuele Paci, Sheena E Radford, David J Brockwell, 2005, Biophysical journal.

Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange.

Michele Vendruscolo, Emanuele Paci, Martin Karplus, 2003, Journal of the American Chemical Society.

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

Emanuele Paci, David R Glowacki, Dmitrii V Shalashilin, 2012, The Journal of chemical physics.

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

H. Santos, E. Paci, M. Noronha, 2009, The journal of physical chemistry. B.

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

A. Imberty, E. Paci, M. Lelimousin, 2019, European journal of medicinal chemistry.

Induction of Rare Conformation of Oligosaccharide by Binding to Calcium-dependent Bacterial Lectin: X-ray Crystallography and Modelling Study

A. Imberty, E. Paci, A. Varrot, 2019, bioRxiv.

Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations

Sergei V. Krivov, Emanuele Paci, Lucy R. Allen, 2009, PLoS Comput. Biol..

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

E. Paci, J. Clarke, R. Sandford, 2005, Journal of molecular biology.

ORAC: A Molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions

Piero Procacci, Emanuele Paci, Massimo Marchi, 1997 .

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

E. Paci, L. R. Allen, 2009, The Journal of chemical physics.

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

E. Paci, I. Neelov, J. Gowdy, 2017, The journal of physical chemistry. B.

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

M Karplus, E Paci, M. Karplus, 2000, Proceedings of the National Academy of Sciences of the United States of America.

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

Simon McIntosh-Smith, Emanuele Paci, David R Glowacki, 2016, Faraday discussions.

High pressure simulations of biomolecules.

E. Paci, 2002, Biochimica et biophysica acta.

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

E. Paci, D. Brockwell, L. Bellucci, 2017, Nature Communications.

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

E. Paci, M. Vendruscolo, J. Clarke, 2006, Biophysical journal.

On the volume of macromolecules

E. Paci, B. Velikson, 1997 .

Activation energies by molecular dynamics with constraints

G. Ciccotti, E. Paci, R. Kapral, 1991 .

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

Emanuele Paci, David R Glowacki, Dmitrii V Shalashilin, 2011, Journal of chemical theory and computation.

Stable Single α-Helices Are Constant Force Springs in Proteins

Michelle Peckham, Emanuele Paci, Peter J. Knight, 2014, The Journal of Biological Chemistry.

Mechanical unfolding of a titin Ig domain: structure of transition state revealed by combining atomic force microscopy, protein engineering and molecular dynamics simulations.

E. Paci, J. Clarke, R. Best, 2003, Journal of molecular biology.

Free Energy Landscapes of Proteins: Insights from Mechanical Probes

E. Paci, P. Olmsted, Z. T. Yew, 2011 .

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

E. Paci, Rebecca F. Thompson, M. Webb, 2019, Journal of the American Chemical Society.

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

Herman K. H. Fung, E. Paci, J. Clarke, 2015, Nature Communications.

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

Michele Vendruscolo, Emanuele Paci, Andrea Cavalli, 2005, Biophysical journal.

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

Kresten Lindorff-Larsen, Michele Vendruscolo, Emanuele Paci, 2003, Biophysical journal.

Protein folding and the organization of the protein topology universe.

Kresten Lindorff-Larsen, Michele Vendruscolo, Peter Røgen, 2005, Trends in biochemical sciences.

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

Emanuele Paci, E. Paci, T. McLeish, 2006, Biophysical journal.

Mechanical unfolding revisited through a simple but realistic model.

Emanuele Paci, E. Paci, P. Olmsted, 2006, The Journal of chemical physics.

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

Emanuele Paci, Sheena E Radford, David J Brockwell, 2003, Nature structural biology.

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

Michele Vendruscolo, Emanuele Paci, Martin Karplus, 2002, Biophysical journal.

Partial Opening of Cytochrome P450cam (CYP101A1) Is Driven by Allostery and Putidaredoxin Binding.

J. Houwing-Duistermaat, T. Poulos, E. Paci, 2021, Biochemistry.

Single Stable single alpha helices are constant-force springs in proteins

E. Paci, P. Knight, M. Peckham, 2014 .

Helical Polyampholyte Sequences Have Unique Thermodynamic Properties.

E. Paci, M. Batchelor, 2018, The journal of physical chemistry. B.

ALMOST: An all atom molecular simulation toolkit for protein structure determination

Carlo Camilloni, Michele Vendruscolo, Andrea Cavalli, 2014, J. Comput. Chem..

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

Emanuele Paci, David J Brockwell, E. Paci, 2006, Biophysical journal.

3.7 Simulation Studies of Force-Induced Unfolding

E. Paci, Z. T. Yew, 2012 .

Effects of Ligand Binding on the Mechanical Properties of Ankyrin Repeat Protein Gankyrin

Laura S. Itzhaki, Emanuele Paci, Piotr E. Marszalek, 2013, PLoS Comput. Biol..

Constant-Pressure Molecular Dynamics Techniques Applied to Complex Molecular Systems and Solvated Proteins

Emanuele Paci, Massimo Marchi, E. Paci, 1996 .

Myosin tails and single α-helical domains.

Michelle Peckham, Emanuele Paci, E. Paci, 2015, Biochemical Society transactions.

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

E. Paci, M. Vendruscolo, J. Clarke, 2004, Journal of molecular biology.

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

Bhavin S. Khatri, E. Paci, D. Brockwell, 2010, Biophysical journal.

Non-Native Interactions Are Critical for Mechanical Strength in PKD Domains

E. Paci, J. Clarke, R. Sandford, 2009, Structure.

Using models to design new bioinspired materials.

Emanuele Paci, E. Paci, 2012, Biophysical journal.

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

M. L. Hughes, E. Paci, Michael C Wilson, 2016, Langmuir : the ACS journal of surfaces and colloids.

Sequential unfolding of individual helices of bacterioopsin observed in molecular dynamics simulations of extraction from the purple membrane.

A. Caflisch, E. Paci, M. Seeber, 2006, Biophysical journal.

Simulation of fluorescence resonance energy transfer experiments: effect of the dyes on protein folding

E. Paci, L. R. Allen, 2010, Journal of physics. Condensed matter : an Institute of Physics journal.

Comparative proximity biotinylation implicates RAB18 in sterol mobilization and biosynthesis

Mark T. Handley, A. von Kriegsheim, E. Paci, 2019, bioRxiv.

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

Christopher M. Dobson, Emanuele Paci, Martin Karplus, 2001 .

Modulation of a Protein Free-Energy Landscape by Circular Permutation

Emanuele Paci, Marta Enciso, Sergei Krivov, 2012, The journal of physical chemistry. B.

Transition states for protein folding using molecular dynamics and experimental restraints

E. Paci, L. R. Allen, 2007 .

Disorder drives cooperative folding in a multidomain protein

Jane Clarke, Emanuele Paci, E. Paci, 2016, Proceedings of the National Academy of Sciences.

1 Disorder drives cooperative folding in a multi-domain protein

E. Paci, J. Clarke, F. Whelan, 2016 .

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

Emanuele Paci, E. Paci, P. Olmsted, 2006, The Journal of chemical physics.

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

Emanuele Paci, Sergei Krivov, E. Paci, 2008, The journal of physical chemistry. B.

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

Gerhard Hummer, Robert B Best, Emanuele Paci, 2008, The journal of physical chemistry. B.