Faculty of Biological Sciences

Dr Emanuele Paci

PhD - 1996
Associate Professor
School of Molecular and Cellular Biology

Contact:  Miall 6.01a, +44(0) 113 34 33806, email address for  

Research Interests

theoretical byophysics, computational chemistry and biological physics

Computational and theoretical studies of protein folding.

Mechanisms of forced unfolding and unbinding.

Protein and peptide aggregation.

Development of novel force fields.

Mechanism of pilus growth in bacteria.

 

Faculty Research and Innovation



Studentship information

See also:

Modules managed

BIOC3111 - Advanced Topics in Biochemistry I
BIOC3112 - Advanced Topics in Medical Biochemistry I
BIOC3221 - Advanced Topics in Biochemistry 2
BIOC3222 - Advanced Topics in Medical Biochemistry 2
BIOC3231 - Advanced Topics in Biochemistry 3
BIOC3232 - Advanced Topics in Medical Biochemistry 3
BIOL3112 - Advanced Topics for Biological Sciences 1
BIOL3210 - Advanced Topics for Biological Sciences 2
BIOL3211 - Advanced Topics for Biological Sciences 3
MICR3120 - Advanced Topics in Microbiology 1
MICR3211 - Advanced Topics in Microbiology 2
MICR3212 - Advanced Topics in Microbiology 3

Modules taught

BIOC1301 - Introductory Integrated Biochemistry: the Molecules and Processes of Life
BIOC1302 - Introductory Biochemistry: Practical Skills
BIOC1303 - Introductory Biochemistry: Problem Solving and Data Handling
BIOC2303 - Intermediate Biochemistry: Skills
BIOC3111/12 B - Protein Dynamics
BIOC3160 - Laboratory/Literature/Computing Research Project
BIOC3221/22/31/32/BIOL3210/11/MICR3211/12 - MCB ATU modules (all)
BIOL5294M - MSc Bioscience Research Project Proposal
BIOL5392M - Bioscience MSc Research Project
BIOW5901X - Foundation module
BIOW5905X - Membrane proteins

Centre membership: The Astbury Centre for Structural Molecular Biology

Group Leader Dr Emanuele Paci  (Associate Professor)

theoretical byophysics, computational chemistry and biological physics 

Postgraduates

Carla Gómez Santiago (Co-supervisor) 25% FTE

Gowdy J, Batchelor M, Neelov I, Paci E Non-Exponential Kinetics of Loop Formation in Proteins and Peptides: A Signature of Rugged Free Energy Landscapes? Journal of Physical Chemistry B 121 9518-9525, 2017
DOI:10.1021/acs.jpcb.7b07075
View abstract

Hickman SJ, Cooper REM, Bellucci L, Paci E, Brockwell DJ Gating of TonB-dependent transporters by substrate-specific forced remodelling NATURE COMMUNICATIONS 8 -, 2017
DOI:10.1038/ncomms14804

Wolny M, Batchelor M, Bartlett GJ, Baker EG, Kurzawa M, Knight PJ, Dougan L, Woolfson DN, Paci E, Peckham M Characterization of long and stable de novo single alpha-helix domains provides novel insight into their stability Scientific Reports 7 -, 2017
DOI:10.1038/srep44341
View abstract

Paci E Hydrogen-Deuterium Exchange Mass Spectroscopy to Determine Structure and Structural Dynamics of Protein Complexes, 2017

Batchelor M, Wolny M, Knight PJ, Paci E, Kalverda AP, Peckham M Structural Dynamics in the Myosin 7A Single alpha-Helix Domain, 2017

O'Connor M, Paci E, McIntosh-Smith S, Glowacki DR Adaptive free energy sampling in multidimensional collective variable space using boxed molecular dynamics Faraday Discussions 195 395-419, 2016
DOI:10.1039/c6fd00138f
View abstract

Gruszka DT, Mendonça CATF, Paci E, Whelan F, Hawkhead J, Potts JR, Clarke J Disorder drives cooperative folding in a multidomain protein Proceedings of the National Academy of Sciences of the United States of America 113 11841-11846, 2016
DOI:10.1073/pnas.1608762113
View abstract

Papachristos K, Muench SP, Paci E Characterization of the flexibility of the peripheral stalk of prokaryotic rotary A-ATPases by atomistic simulations. Proteins 84 1203-1212, 2016
DOI:10.1002/prot.25066
View abstract

Tych KM, Batchelor M, Hoffmann T, Wilson MC, Hughes ML, Paci E, Brockwell DJ, Dougan L Differential Effects of Hydrophobic Core Packing Residues for Thermodynamic and Mechanical Stability of a Hyperthermophilic Protein Langmuir 32 7392-7402, 2016
DOI:10.1021/acs.langmuir.6b01550
View abstract

Tych KM, Batchelor M, Hoffmann T, Wilson MC, Paci E, Brockwell DJ, Dougan L Tuning protein mechanics through an ionic cluster graft from an extremophilic protein Soft Matter 12 2688-2699, 2016
DOI:10.1039/c5sm02938d
View abstract

Hickman SJ, Ross JF, Paci E Prediction of stability changes upon mutation in an icosahedral capsid Proteins: Structure, Function, and Bioinformatics 83 1733-1741, 2015
DOI:10.1002/prot.24859
View abstract

Gruszka DT, Whelan F, Farrance OE, Fung HKH, Paci E, Jeffries CM, Svergun DI, Baldock C, Baumann CG, Brockwell DJ, Potts JR, Clarke J Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein Nature Communications 6 -, 2015
DOI:10.1038/ncomms8271
View abstract

Batchelor M, Gowdy J, Paci E Effect of external pulling forces on the length distribution of peptides BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS 1850 903-910, 2015
DOI:10.1016/j.bbagen.2014.09.019

Batchelor M, Wolny M, Dougan L, Paci E, Knight PJ, Peckham M Myosin tails and singleα-helical domains, 2015
DOI:10.1042/BST20140302
View abstract

Farrance OE, Paci E, Radford SE, Brockwell DJ Extraction of accurate biomolecular parameters from single-molecule force spectroscopy experiments ACS Nano 9 1315-1324, 2015
DOI:10.1021/nn505135d
View abstract

Richardson RA, Papachristos K, Read DJ, Harlen OG, Harrison M, Paci E, Muench SP, Harris SA Understanding the apparent stator-rotor connections in the rotary ATPase family using coarse-grained computer modeling. Proteins 82 3298-3311, 2014
DOI:10.1002/prot.24680
View abstract

Wolny M, Batchelor M, Knight PJ, Paci E, Dougan L, Peckham M Stable singleα-helices are constant force springs in proteins. J Biol Chem 289 27825-27835, 2014
DOI:10.1074/jbc.M114.585679
View abstract

Radou G, Dreyer FN, Tuma R, Paci E Functional dynamics of hexameric helicase probed by hydrogen exchange and simulation. Biophys J 107 983-990, 2014
DOI:10.1016/j.bpj.2014.06.039
View abstract

Krivov SV, Fenton H, Goldsmith PJ, Prasad RK, Fisher J, Paci E Optimal reaction coordinate as a biomarker for the dynamics of recovery from kidney transplant. PLoS Comput Biol 10 e1003685-, 2014
DOI:10.1371/journal.pcbi.1003685
View abstract

Fu B, Sahakyan AB, Camilloni C, Tartaglia GG, Paci E, Caflisch A, Vendruscolo M, Cavalli A ALMOST: an all atom molecular simulation toolkit for protein structure determination. J Comput Chem 35 1101-1105, 2014
DOI:10.1002/jcc.23588
View abstract

Nogueira JJ, Wang Y, Martín F, Alcamí M, Glowacki DR, Shalashilin DV, Paci E, Fernández-Ramos A, Hase WL, Martínez-Núñez E, Vázquez SA Unraveling the factors that control soft landing of small silyl ions on fluorinated self-assembled monolayers Journal of Physical Chemistry C 118 10159-10169, 2014
DOI:10.1021/jp501841a
View abstract

Rimratchada S, McLeish TCB, Radford SE, Paci E The role of high-dimensional diffusive search, stabilization, and frustration in protein folding. Biophys J 106 1729-1740, 2014
DOI:10.1016/j.bpj.2014.01.051
View abstract

Song CF, Papachristos K, Rawson S, Huss M, Wieczorek H, Paci E, Trinick J, Harrison MA, Muench SP Flexibility within the Rotor and Stators of the Vacuolar H+-ATPase PLOS ONE 8 -, 2013
DOI:10.1371/journal.pone.0082207

Heidarsson PO, Otazo MR, Bellucci L, Mossa A, Imparato A, Paci E, Corni S, Di Felice R, Kragelund BB, Cecconi C Single-Molecule Folding Mechanism of an EF-Hand Neuronal Calcium Sensor STRUCTURE 21 1812-1821, 2013
DOI:10.1016/j.str.2013.07.022

Radou G, Enciso M, Krivov SV, Paci E Modulation of a protein free-energy landscape by circular permutation Journal of Physical Chemistry B 117 13743-13747, 2013
DOI:10.1021/jp406818t
View abstract

Bellucci L, Corni S, Di Felice R, Paci E The Structure of Neuronal Calcium Sensor-1 in Solution Revealed by Molecular Dynamics Simulations PLOS ONE 8 -, 2013
DOI:10.1371/journal.pone.0074383

Settanni G, Serquera D, Marszalek PE, Paci E, Itzhaki LS Effects of Ligand Binding on the Mechanical Properties of Ankyrin Repeat Protein Gankyrin PLOS COMPUTATIONAL BIOLOGY 9 -, 2013
DOI:10.1371/journal.pcbi.1002864

Monteiro DCF, Kamdoum WVP, Paci E Growth kinetics of bacterial pili from pairwise pilin association rates. PLoS One 8 e63065-, 2013
DOI:10.1371/journal.pone.0063065
View abstract

Neelov I, Falkovich S, Markelov D, Paci E, Darinskii A, Tenhu H MOLECULAR DYNAMICS OF LYSINE DENDRIMERS. COMPUTER SIMULATION AND NMR DENDRIMERS IN BIOMEDICAL APPLICATIONS 99-114, 2013
DOI:10.1039/9781849737296-00099

Yew ZT, Paci E Simulation Studies of Force-Induced Unfolding, 2012
DOI:10.1016/B978-0-12-374920-8.00308-8
View abstract

Paci E Using models to design new bioinspired materials Biophysical Journal 103 1814-1815, 2012
DOI:10.1016/j.bpj.2012.09.029

Shalashilin DV, Beddard GS, Paci E, Glowacki DR Peptide kinetics from picoseconds to microseconds using boxed molecular dynamics: power law rate coefficients in cyclisation reactions. J Chem Phys 137 165102-, 2012
DOI:10.1063/1.4759088
View abstract

Ikeda-Kobayashi A, Taniguchi Y, Brockwell DJ, Paci E, Sakane I, Kawata Y, Kawakami M Erratum: Prying open single GroES ring complexes by force reveals cooperativity across domains (Biophysical Journal (2012) 102 (1961-1968)) Biophysical Journal 102 2412-, 2012
DOI:10.1016/j.bpj.2012.04.032

Ikeda-Kobayashi A, Taniguchi Y, Brockwell DJ, Paci E, Kawakami M Prying open single GroES Ring complexes by force reveals cooperativity across domains Biophysical Journal 102 1961-1968, 2012
DOI:10.1016/j.bpj.2012.03.046
View abstract

Yew ZT, Olmsted PD, Paci E FREE ENERGY LANDSCAPES OF PROTEINS: INSIGHTS FROM MECHANICAL PROBES SINGLE-MOLECULE BIOPHYSICS: EXPERIMENT AND THEORY, VOL 146 146 395-417, 2012

Yew ZT, Olmsted PD, Paci E Free Energy Landscapes of Proteins: Insights from Mechanical Probes In Single Molecule Biophysics: Experiment and Theory , 2011
DOI:10.1002/9781118131374.ch14

Ricchiuto P, Brukhno AV, Paci E, Auer S Communication: Conformation state diagram of polypeptides: A chain length induced alpha-beta transition JOURNAL OF CHEMICAL PHYSICS 135 -, 2011
DOI:10.1063/1.3624928

Glowacki DR, Paci E, Shalashilin DV Boxed Molecular Dynamics: Decorrelation Time Scales and the Kinetic Master Equation J CHEM THEORY COMPUT 7 1244-1252, 2011
DOI:10.1021/ct200011e

Schlierf M, Yew ZT, Rief M, Paci E Complex Unfolding Kinetics of Single-Domain Proteins in the Presence of Force BIOPHYS J 99 1620-1627, 2010

Mann RJ, Nasr NE, Sinfield JK, Paci E, Donnelly D The major determinant of exendin-4/glucagon-like peptide 1 differential affinity at the rat glucagon-like peptide 1 receptor N-terminal domain is a hydrogen bond from SER-32 of exendin-4 BRIT J PHARMACOL 160 1973-1984, 2010
DOI:10.1111/j.1476-5381.2010.00834.x

Taniguchi Y, Khatri BS, Brockwell DJ, Paci E, Kawakami M Dynamics of the Coiled-Coil Unfolding Transition of Myosin Rod Probed by Dissipation Force Spectrum BIOPHYS J 99 257-262, 2010
DOI:10.1016/j.bpj.2010.04.007

Khatri BS, Yew ZT, Krivov S, McLeish T, Paci E Fluctuation power spectra reveal dynamical heterogeneity of peptides JOURNAL OF CHEMICAL PHYSICS 133 -, 2010
DOI:10.1063/1.3456552

Allen LR, Paci E Simulation of fluorescence resonance energy transfer experiments: effect of the dyes on protein folding J PHYS-CONDENS MAT 22 -, 2010
DOI:10.1088/0953-8984/22/23/235103

Serquera D, Lee W, Settanni G, Marszalek PE, Paci E, Itzhaki LS Mechanical Unfolding of an Ankyrin Repeat Protein BIOPHYS J 98 1294-1301, 2010
DOI:10.1016/j.bpj.2009.12.4287

Yew ZT, Schlierf M, Rief M, Paci E Direct evidence of the multidimensionality of the free-energy landscapes of proteins revealed by mechanical probes. Phys Rev E Stat Nonlin Soft Matter Phys 81 031923-, 2010
DOI:10.1103/PhysRevE.81.031923
View abstract

Glowacki DR, Paci E, Shalashilin DV Boxed Molecular Dynamics: A Simple and General Technique for Accelerating Rare Event Kinetics and Mapping Free Energy in Large Molecular Systems J PHYS CHEM B 113 16603-16611, 2009
DOI:10.1021/jp9074898

Forman JR, Yew ZT, Qamar S, Sandford RN, Paci E, Clarke J Non-Native Interactions Are Critical for Mechanical Strength in PKD Domains STRUCTURE 17 1582-1590, 2009
DOI:10.1016/j.str.2009.09.013

Allen LR, Paci E Orientational averaging of dye molecules attached to proteins in Foumlrster resonance energy transfer measurements: Insights from a simulation study J CHEM PHYS 131 -, 2009
DOI:10.1063/1.3193724

Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M CHARMM: The Biomolecular Simulation Program J COMPUT CHEM 30 1545-1614, 2009
DOI:10.1002/jcc.21287

Allen LR, Krivov SV, Paci E Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations PLOS COMPUT BIOL 5 -, 2009
DOI:10.1371/journal.pcbi.1000428

Periole X, Allen LR, Tamiola K, Mark AE, Paci E Probing the Free Energy Landscape of the FBP28 WW Domain Using Multiple Techniques J COMPUT CHEM 30 1059-1068, 2009
DOI:10.1002/jcc.21128

Noronha M, Santos R, Paci E, Santos H, Macanita AL Fluorescence Lifetimes of Tyrosine Residues in Cytochrome c '' as Local Probes to Study Protein Unfolding J PHYS CHEM B 113 4466-4474, 2009
DOI:10.1021/jp805781r

Yew ZT, Krivov S, Paci E Free-Energy Landscapes of Proteins in the Presence and Absence of Force J PHYS CHEM B 112 16902-16907, 2008
DOI:10.1021/jp807316e

Yew ZT, McLeish T, Paci E New Dynamical Window onto the Landscape for Forced Protein Unfolding PHYS REV LETT 101 -, 2008
DOI:10.1103/PhysRevLett.101.248104

Verger D, Rose RJ, Paci E, Costakes G, Daviter T, Hultgren S, Remaut H, Ashcroft AE, Radford SE, Waksman G Structural Determinants of Polymerization Reactivity of the P pilus Adaptor Subunit PapF STRUCTURE 16 1724-1731, 2008
DOI:10.1016/j.str.2008.08.012

Feige MJ, Paci E Rate of loop formation in peptides: A simulation study J MOL BIOL 382 556-565, 2008
DOI:10.1016/j.jmb.2008.07.011

Rose RJ, Verger D, Daviter T, Remaut H, Paci E, Waksman G, Ashcroft AE, Radford SE Unraveling the molecular basis of subunit specificity in P pilus assembly by mass spectrometry P NATL ACAD SCI USA 105 12873-12878, 2008
DOI:10.1073/pnas.0802177105

Best RB, Paci E, Hummer G, Dudko OK Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules J PHYS CHEM B 112 5968-5976, 2008
DOI:10.1021/jp075955j

Rose RJ, Welsh TS, Waksman G, Ashcroft AE, Radford SE, Paci E Donor-strand exchange in chaperone-assisted pilus assembly revealed in atomic detail by molecular dynamics J MOL BIOL 375 908-919, 2008
DOI:10.1016/j.jmb.2007.10.077

Morton VL, Friel CT, Allen LR, Paci E, Radford SE The effect of increasing the stability of non-native interactions on the folding landscape of the bacterial immunity protein Im9 J MOL BIOL 371 554-568, 2007
DOI:10.1016/j.jmb.2007.05.010

Allen LR, Paci E Transition states for protein folding using molecular dynamics and experimental restraints JOURNAL OF PHYSICS-CONDENSED MATTER 19 -, 2007
DOI:10.1088/0953-8984/19/28/285211

Noronha M, Lima JC, Paci E, Santos H, Macanita AL Tracking local conformational changes of ribonuclease A using picosecond time-resolved fluorescence of the six tyrosine residues BIOPHYS J 92 4401-4414, 2007
DOI:10.1529/biophysj.106.093625

West DK, Paci E, Olmsted PD Internal protein dynamics shifts the distance to the mechanical transition state PHYS REV E 74 -, 2006
DOI:10.1103/PhysRevE.74.061912

Seeber M, Fanelli F, Paci E, Caflisch A Sequential unfolding of individual helices of bacterioopsin observed in molecular dynamics simulations of extraction from the purple membrane BIOPHYS J 91 3276-3284, 2006
DOI:10.1529/biophysj.106.088591

West DK, Olmsted PD, Paci E Free energy for protein folding from nonequilibrium simulations using the Jarzynski equality. Journal of Chemical Physics 125 pp.204910-, 2006

Neelov IM, Adolf DB, McLeish TCB, Paci E Molecular dynamics simulation of dextran extension by constant force in single molecule AFM BIOPHYS J 91 3579-3588, 2006
DOI:10.1529/biophysj.105.079236

West DK, Brockwell DJ, Paci E Prediction of the translocation kinetics of a protein from its mechanical properties BIOPHYS J 91 L51-L53, 2006
DOI:10.1529/biophysj.106.089490

Geierhaas CD, Best RB, Paci E, Vendruscolo M, Clarke J Structural comparison of the two alternative transition states for folding of TI I27 BIOPHYS J 91 263-275, 2006
DOI:10.1529/biophysj.105.077057

West DK, Olmsted PD, Paci E Mechanical unfolding revisited through a simple but realistic model J CHEM PHYS 124 -, 2006
DOI:10.1063/1.2185100

Gsponer J, Hopearuoho H, Whittaker SBM, Spence GR, Moore GR, Paci E, Radford SE, Vendruscolo M Determination of an ensemble of structures representing the intermediate state of the bacterial immunity protein Im7 P NATL ACAD SCI USA 103 99-104, 2006

West DK, Brockwell DJ, Olmsted PD, Radford SE, Paci E Mechanical resistance of proteins explained using simple molecular models BIOPHYS J 90 287-297, 2006
DOI:10.1529/biophysj.105.071035

Curcio R, Caflisch A, Paci E Change of the unbinding mechanism upon a mutation: a molecular dynamics study of an antibody-hapten complex. Protein Sci 14 2499-2514, 2005
DOI:10.1110/ps.041280705
View abstract

Paci E, Lindorff-Larsen K, Dobson CM, Karplus M, Vendruscolo M Transition state contact orders correlate with protein folding rates J MOL BIOL 352 495-500, 2005
DOI:10.1016/j.jmb.2005.06.081

Paci E, Greene LH, Jones RM, Smith LJ Characterization of the molten globule state of retinol-binding protein using a molecular dynamics simulation approach FEBS Journal 272 4826-4838, 2005
View abstract

Ng SP, Rounsevell RWS, Steward A, Geierhaas CD, Williams P, Paci E, Clarke J Mechanical unfolding of TNfn3: The unfolding pathway of a fnIII domain probed by protein engineering, AFM and MD simulation Methods in Molecular Biology 350 776-789, 2005
View abstract

Brockwell DJ, Beddard GS, Paci E, West DK, Olmsted PD, Smith DA, Radford SE Mechanically unfolding the small, topologically simple protein L BIOPHYS J 89 506-519, 2005
DOI:10.1529/biophysj.105.061465

Cavalli A, Vendruscolo M, Paci E Comparison of sequence-based and structure-based energy functions for the reversible folding of a peptide. Biophys J 88 3158-3166, 2005
DOI:10.1529/biophysj.104.055335
View abstract

Forman JR, Qamar S, Paci E, Sandford RN, Clarke J The remarkable mechanical strength of polycystin-1 supports a direct role in mechanotransduction Journal of Molecular Biology 349 861-871, 2005

Lindorff-Larsen K, Røgen P, Paci E, Vendruscolo M, Dobson CM Protein folding and the organization of the protein topology universe. Trends Biochem Sci 30 13-19, 2005
DOI:10.1016/j.tibs.2004.11.008
View abstract

Geierhaas CD, Paci E, Vendruscolo M, Clarke J Comparison of the transition states for folding of two Ig-like proteins from different superfamilies Journal of Molecular Biology 343 1111-1123, 2004
View abstract

Paci E, Gsponer J, Salvatella X, Vendruscolo M Molecular dynamics studies of the process of amyloid aggregation of peptide fragments of transthyretin. J Mol Biol 340 555-569, 2004
DOI:10.1016/j.jmb.2004.05.009
View abstract

Lindorff-Larsen K, Vendruscolo M, Paci E, Dobson CM Transition states for protein folding have native topologies despite high structural variability Nature Structural&Molecular Biology 11 443-449, 2004
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Paci E, Friel CT, Lindorff-Larsen K, Radford SE, Karplus M, Vendruscolo M Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints. Proteins 54 513-525, 2004
DOI:10.1002/prot.10595
View abstract

Catflisch A, Paci E Molecular dynamics simulations to study protein folding and unfolding, 2004

Vendruscolo M, Paci E, Dobson CM, Karplus M Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange J AM CHEM SOC 125 15686-15687, 2003
DOI:10.1021/ja036523z

Vendruscolo M, Paci E, Karplus M, Dobson CM Structures and relative free energies of partially folded states of proteins. Proc Natl Acad Sci U S A 100 14817-14821, 2003
DOI:10.1073/pnas.2036516100
View abstract

Brockwell DJ, Paci E, Zinober RC, Beddard GS, Olmsted PD, Smith DA, Perham RN, Radford SE Pulling geometry defines the mechanical resistance of a beta-sheet protein (vol 10, pg 731, 2003) NAT STRUCT BIOL 10 872-872, 2003
DOI:10.1038/nsb1003-872b

Cavalli A, Haberthür U, Paci E, Caflisch A Fast protein folding on downhill energy landscape. Protein Sci 12 1801-1803, 2003
DOI:10.1110/ps.0366103
View abstract

Lindorff-Larsen K, Paci E, Serrano L, Dobson CM, Vendruscolo M Calculation of mutational free energy changes in transition states for protein folding. Biophys J 85 1207-1214, 2003
DOI:10.1016/S0006-3495(03)74556-1
View abstract

Paci E, Cavalli A, Vendruscolo M, Caflisch A Analysis of the distributed computing approach applied to the folding of a small beta peptide. Proc Natl Acad Sci U S A 100 8217-8222, 2003
DOI:10.1073/pnas.1331838100
View abstract

Best RB, Fowler SB, Toca-Herrera JL, Steward A, Paci E, Clarke J Mechanical unfolding of a titin Ig domain: Structure of transition state revealed by combining atomic force microscopy, protein engineering and molecular dynamics simulations Journal of Molecular Biology 330 867-877, 2003
View abstract

Vendruscolo M, Paci E Protein folding: bringing theory and experiment closer together Current Opinion in Structural Biology 13 82-87, 2003
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Paci E, Clarke J, Steward A, Vendruscolo M, Karplus M Self-consistent determination of the transition state for protein folding: application to a fibronectin type III domain. Proc Natl Acad Sci U S A 100 394-399, 2003
DOI:10.1073/pnas.232704999
View abstract

Paci E, Vendruscolo M, Karplus M Validity of Go models: Comparison with a solvent-shielded empirical energy decomposition BIOPHYS J 83 3032-3038, 2002

Paci E, Vendruscolo M, Dobson CM, Karplus M Determination of a transition state at atomic resolution from protein engineering data. J Mol Biol 324 151-163, 2002
View abstract

Fowler SB, Best RB, Toca-Herrera JL, Rutherford TJ, Steward A, Paci E, Karplus M, Clarke J Mechanical unfolding of a titin Ig domain: Structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering Journal of Molecular Biology 322 841-849, 2002
View abstract

Vendruscolo M, Dokholyan NV, Paci E, Karplus M Small-world view of the amino acids that play a key role in protein folding PHYS REV E 65 -, 2002
DOI:10.1103/PhysRevE.65.061910

Vendruscolo M, Dokholyan NV, Paci E, Karplus M Small-world view of the amino acids that play a key role in protein folding Physical review. E, Statistical, nonlinear, and soft matter physics 65 61910-, 2002
DOI:10.1103/PhysRevE.65.061910
View abstract

Paci E, Vendruscolo M, Karplus M Native and non-native interactions along protein folding and unfolding pathways PROTEINS 47 379-392, 2002
DOI:10.1002/prot.10089

Paci E High pressure simulations of biomolecules BBA-PROTEIN STRUCT M 1595 185-200, 2002

Paci E, Caflisch A, Pluckthun A, Karplus M Forces and energetics of hapten-antibody dissociation: A biased molecular dynamics simulation study J MOL BIOL 314 589-605, 2001

Paci E, Smith LJ, Dobson CM, Karplus M Exploration of partially unfolded states of human alpha-lactalbumin by molecular dynamics simulation J MOL BIOL 306 329-347, 2001
DOI:10.1006/jmbi.2000.4337

Vendruscolo M, Paci E, Dobson CM, Karplus M Three key residues form a critical contact network in a protein folding transition state Nature 409 641-645, 2001
DOI:10.1038/35054591

Paci E, Karplus M Unfolding proteins by external forces and temperature: The importance of topology and energetics Proceedings of the National Academy of Sciences of the United States of America 97 6521-6526, 2000
View abstract

Paci E, Karplus M Forced unfolding of fibronectin type 3 modules: An analysis by biased molecular dynamics simulations Journal of Molecular Biology 288 441-459, 1999
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Procacci P, Darden TA, Paci E, Marchi M ORAC: A molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions J COMPUT CHEM 18 1848-1862, 1997

Paci E, Velikson B On the volume of macromolecules BIOPOLYMERS 41 785-797, 1997

Paci E, Marchi M Intrinsic compressibility and volume compression in solvated proteins by molecular dynamics simulation at high pressure Proceedings of the National Academy of Sciences of the United States of America 93 11609-11614, 1996
View abstract

Paci E, Marchi M Constant-pressure molecular dynamics techniques applied to complex molecular systems and solvated proteins Journal of Physical Chemistry B 100 4314-4322, 1996
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Falconi M, Gallimbeni R, Paci E Dimer asymmetry in superoxide dismutase studied by molecular dynamics simulation Journal of Computer - Aided Molecular Design 10 490-498, 1996

Paci E, Marchi M MEMBRANE CROSSING BY A POLAR MOLECULE - A MOLECULAR-DYNAMICS SIMULATION Molecular Simulation 14 1-10, 1994
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Depaepe JM, Ryckaert JPO, Paci E, Ciccotti G SAMPLING OF MOLECULAR-CONFORMATIONS BY MOLECULAR-DYNAMICS TECHNIQUES Molecular Physics 79 515-522, 1993
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Paci E, Ciccotti G VACANCY MIGRATION RATES BY MOLECULAR-DYNAMICS WITH CONSTRAINTS Journal of Physics: Condensed Matter 4 2173-2184, 1992
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PACI E, CICCOTTI G, FERRARIO M, KAPRAL R ACTIVATION-ENERGIES BY MOLECULAR-DYNAMICS WITH CONSTRAINTS CHEMICAL PHYSICS LETTERS 176 581-587, 1991
DOI:10.1016/0009-2614(91)90259-C

Wolny M, Batchelor M, Bartlett GJ, Baker EG, Kurzawa M, Knight PJ, Dougan L, Takagi Y, Woolfson DN, Paci E, Peckham M Design and Characterization of Long and Stable de novo Single alpha-Helix Domains,