Matteo Dal Peraro
Professeur associé
matteo.dalperaro@epfl.ch +41 21 69 31861 http://lbm.epfl.ch
Nationalité : Italian
Biography
Matteo Dal Peraro graduated in Physics at the University of Padua in 2000. He obtained his Ph.D. in Biophysics at the International School for Advanced Studies (SISSA, Trieste) in 2004. He then received postdoctoral training at the University of Pennsylvania (Philadelphia) under the guidance of Prof. M. L. Klein. He was nominated Tenure Track Assistant Professor at the EPFL School of Life Sciences in late 2007.
His research at the Laboratory for Biomolecular Modeling (LBM), within the Interfaculty Institute of Bioengineering (IBI), focuses on the multiscale modeling of large macromolecular systems.
Education
| B.S. and M.S. | Physics | University of Padua | 2000 |
| Ph.D. | Biophysics | International School for Advanced Studies (SISSA) | 2004 |
Compétences
Computational biophysics
Modeling of biological systems
Modeling of biological systems
Publications
Infoscience
Journal Articles
2018
M. Audagnotto; A. Lorkowski; M. Dal Peraro : Recruitment of the amyloid precursor protein by gamma-secretase at the synaptic plasma membrane; BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS. 2018. DOI : 10.1016/j.bbrc.2017.10.164.
N. Bologna; R. Iselin; L. Abriata; A. Sarazin; N. Pumplin et al. : Nucleo-cytosolic Shuttling of ARGONAUTE1 Prompts a Revised Model of the Plant MicroRNA Pathway; MOLECULAR CELL. 2018. DOI : 10.1016/j.molcel.2018.01.007.
A. Timon-Gomez; E. Nyvltova; L. Abriata; A. Vila; J. Hosler et al. : Mitochondrial cytochrome c oxidase biogenesis: Recent developments; SEMINARS IN CELL AND DEVELOPMENTAL BIOLOGY. 2018. DOI : 10.1016/j.semcdb.2017.08.055.
C. Cao; M. Li; N. Cirauqui; Y. Wang; M. Dal Peraro et al. : Mapping the sensing spots of aerolysin for single oligonucleotides analysis; Nature Communications. 2018. DOI : 10.1038/s41467-018-05108-5.
X. Wang; M. Roger; R. Clement; S. Lecomte; F. Biaso et al. : Electron transfer in an acidophilic bacterium: interaction between a diheme cytochrome and a cupredoxin; CHEMICAL SCIENCE. 2018. DOI : 10.1039/c8sc01615a.
L. Abriata; L. Kinch; G. Tamo; B. Monastyrskyy; A. Kryshtafovych et al. : Definition and classification of evaluation units for tertiary structure prediction in CASP12 facilitated through semi-automated metrics; PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. 2018. DOI : 10.1002/prot.25403.
A. Reidenbach; Z. Kemmerer; D. Aydin; A. Jochem; M. McDevitt et al. : Conserved Lipid and Small-Molecule Modulation of COQ8 Reveals Regulation of the Ancient Kinase-like UbiB Family; CELL CHEMICAL BIOLOGY. 2018. DOI : 10.1016/j.chembiol.2017.11.001.
L. Abriata; G. Tamo; B. Monastyrskyy; A. Kryshtafovych; M. Dal Peraro : Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods; PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. 2018. DOI : 10.1002/prot.25423.
G. Tamo; L. Abriata; G. Fonti; M. Dal Peraro : Assessment of data-assisted prediction by inclusion of crosslinking/mass-spectrometry and small angle X-ray scattering data in the 12(th) Critical Assessment of protein Structure Prediction experiment; PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. 2018. DOI : 10.1002/prot.25442.
D. Aydin; D. C. Lohman; D. J. Pagliarini; M. Dal Peraro : A Combined Computational and Experimental Study to Investigate the Role of COQ9 in Promoting COQ Biosynthesis; Biophysical Journal. 2018. DOI : 10.1016/j.bpj.2017.11.2541.
2017
L. L. Prieto-Godino; R. Rytz; S. Cruchet; B. Bargeton; L. Abuin et al. : Evolution of Acid-Sensing Olfactory Circuits in Drosophilids; Neuron. 2017. DOI : 10.1016/j.neuron.2016.12.024.
G. E. Tamo; A. Maesani; S. Träger; M. Degiacomi; D. Floreano et al. : Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies; Scientific Reports. 2017. DOI : 10.1038/s41598-017-00266-w.
2016
L. A. Abriata; C. Bovigny; M. Dal Peraro : Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server(vol 1, 242, 2016); Bmc Bioinformatics. 2016. DOI : 10.1186/s12859-016-1315-z.
L. L. Prieto-Godino; R. Rytz; B. Bargeton; L. Abuin; J. R. Arguello et al. : Olfactory receptor pseudo-pseudogenes; Nature. 2016. DOI : 10.1038/nature19824.
P. Murima; M. Zimmermann; T. Chopra; F. Pojer; G. Fonti et al. : A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria; Nature Communications. 2016. DOI : 10.1038/ncomms12527.
J. A. Stefely; F. Licitra; L. Laredj; A. G. Reidenbach; Z. A. Kemmerer et al. : Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity; Molecular Cell. 2016. DOI : 10.1016/j.molcel.2016.06.030.
L. A. Abriata; E. Spiga; M. Dal Peraro : Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics; Biophysical Journal. 2016. DOI : 10.1016/j.bpj.2016.07.011.
M. Audagnotto; T. Lemmin; A. Barducci; M. Dal Peraro : Effect of the Synaptic Plasma Membrane on the Stability of the Amyloid Precursor Protein Homodimer; Journal Of Physical Chemistry Letters. 2016. DOI : 10.1021/acs.jpclett.6b01721.
L. A. Abriata; C. Bovigny; M. Dal Peraro : Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server; Bmc Bioinformatics. 2016. DOI : 10.1186/s12859-016-1124-4.
I. Iacovache; S. De Carlo; N. Cirauqui; M. Dal Peraro; F. G. van der Goot et al. : Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process; Nature Communications. 2016. DOI : 10.1038/ncomms12062.
A. S. Song; T. A. Poor; L. A. Abriata; T. S. Jardetzky; M. Dal Peraro et al. : Immobilization of the N-terminal helix stabilizes prefusion paramyxovirus fusion proteins; Proceedings Of The National Academy Of Sciences Of The United States Of America. 2016. DOI : 10.1073/pnas.1608349113.
P. Roethlisberger; A. Istrate; M. J. M. Lopez; R. Visini; A. Stocker et al. : X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair; Chemical Communications. 2016. DOI : 10.1039/c6cc00374e.
V. Genna; R. Gaspari; M. Dal Peraro; M. De Vivo : Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-eta; Nucleic Acids Research. 2016. DOI : 10.1093/nar/gkw128.
2015
C. Bovigny; G. Tamo; T. Lemmin; N. Maino; M. Dal Peraro : Lipid Builder: A Framework To Build Realistic Models for Biological Membranes; Journal Of Chemical Information And Modeling. 2015. DOI : 10.1021/acs.jcim.5b00501.
M. Bartoloni; X. Jin; M. J. Marcaida; J. Banha; I. Dibonaventura et al. : Bridged bicyclic peptides as potential drug scaffolds: synthesis, structure, protein binding and stability; Chemical Science. 2015. DOI : 10.1039/c5sc01699a.
E. Saita; L. A. Abriata; Y. T. Tsai; F. Trajtenberg; T. Lemmin et al. : A coiled coil switch mediates cold sensing by the thermosensory protein DesK; Molecular Microbiology. 2015. DOI : 10.1111/mmi.13118.
G. S. Kolly; R. Mukherjee; E. Kilacskova; L. A. Abriata; M. Raccaud et al. : GtrA Protein Rv3789 Is Required for Arabinosylation of Arabinogalactan in Mycobacterium tuberculosis; Journal Of Bacteriology. 2015. DOI : 10.1128/Jb.00628-15.
H. P. Modarres; B. D. Dorokhov; V. O. Popov; N. V. Ravin; K. G. Skryabin et al. : Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp 1519; Biochemistry. 2015. DOI : 10.1021/bi501227b.
L. A. Abriata; M. Dal Peraro : Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding; Scientific Reports. 2015. DOI : 10.1038/srep10549.
M. Christen; M. J. Marcaida; C. Lamprakis; W. Aeschimann; J. Vaithilingam et al. : Structural insights on cholesterol endosynthesis: Binding of squalene and 2,3-oxidosqualene to supernatant protein factor; Journal Of Structural Biology. 2015. DOI : 10.1016/j.jsb.2015.05.001.
G. E. Tamo; L. A. Abriata; M. Dal Peraro : The importance of dynamics in integrative modeling of supramolecular assemblies; Current Opinion In Structural Biology. 2015. DOI : 10.1016/j.sbi.2015.02.018.
H.-A. Kang; H.-C. Shin; A.-S. Kalantzi; C. P. Toseland; H.-M. Kim et al. : NAR Breakthrough Article Crystal structure of Hop2-Mnd1 and mechanistic insights into its role in meiotic recombination; Nucleic Acids Research. 2015. DOI : 10.1093/nar/gkv172.
L. A. Abriata; T. Palzkill; M. Dal Peraro : How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme; Plos One. 2015. DOI : 10.1371/journal.pone.0118684.
2014
L. A. Abriata; L. B. Pontel; A. J. Vila; M. Dal Peraro; F. C. Soncini : A dimerization interface mediated by functionally critical residues creates interfacial disulfide bonds and copper sites in CueP; Journal Of Inorganic Biochemistry. 2014. DOI : 10.1016/j.jinorgbio.2014.07.022.
C. Bovigny; M. T. Degiacomi; T. Lemmin; M. Dal Peraro; M. Stenta : Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase; Journal Of Physical Chemistry B. 2014. DOI : 10.1021/jp411786z.
E. Spiga; L. A. Abriata; F. Piazza; M. Dal Peraro : Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics; Journal Of Physical Chemistry B. 2014. DOI : 10.1021/jp4126705.
L. A. Abriata; A. J. Vila; M. Dal Peraro : Molecular dynamics simulations of apocupredoxins: insights into the formation and stabilization of copper sites under entatic control; Journal Of Biological Inorganic Chemistry. 2014. DOI : 10.1007/s00775-014-1108-7.
T. Lemmin; M. Dimitrov; P. C. Fraering; M. Dal Peraro : Perturbations of the Straight Transmembrane alpha-Helical Structure of the Amyloid Precursor Protein Affect Its Processing by gamma-Secretase; Journal Of Biological Chemistry. 2014. DOI : 10.1074/jbc.M113.470781.
A. L. Vestergaard; J. A. Coleman; T. Lemmin; S. A. Mikkelsen; L. L. Molday et al. : Critical roles of isoleucine-364 and adjacent residues in a hydrophobic gate control of phospholipid transport by the mammalian P4-ATPase ATP8A2; Proceedings Of The National Academy Of Sciences Of The United States Of America. 2014. DOI : 10.1073/pnas.1321165111.
P. Seitz; H. Pezeshgi Modarres; S. Borgeaud; R. D. Bulushev; L. J. Steinbock et al. : ComEA Is Essential for the Transfer of External DNA into the Periplasm in Naturally Transformable Vibrio cholerae Cells; PLoS Genetics. 2014. DOI : 10.1371/journal.pgen.1004066.
2013
M. Kudryashev; M. Stenta; S. Schmelz; M. Amstutz; U. Wiesand et al. : In situ structural analysis of the Yersinia enterocolitica injectisome; Elife. 2013. DOI : 10.7554/eLife.00792.
B. I. M. Wicky; M. Stenta; M. Dal Peraro : TAL Effectors Specificity Stems from Negative Discrimination; Plos One. 2013. DOI : 10.1371/journal.pone.0080261.
M. T. Degiacomi; I. Lacovache; L. Pernot; M. Chami; M. Kudryashev et al. : Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism; Nature Chemical Biology. 2013. DOI : 10.1038/Nchembio.1312.
M. T. Degiacomi; M. Dal Peraro : Macromolecular Symmetric Assembly Prediction Using Swarm Intelligence Dynamic Modeling; Structure. 2013. DOI : 10.1016/j.str.2013.05.014.
L. A. Abriata; E. Spiga; M. Dal Peraro : All-atom simulations of crowding effects on ubiquitin dynamics; Physical Biology. 2013. DOI : 10.1088/1478-3975/10/4/045006.
E. Spiga; D. Alemani; M. T. Degiacomi; M. Cascella; M. Dal Peraro : Electrostatic-Consistent Coarse-Grained Potentials for Molecular Simulations of Proteins; Journal Of Chemical Theory And Computation. 2013. DOI : 10.1021/ct400137q.
T. Hofmeyer; S. Schmelz; M. T. Degiacomi; M. Dal Peraro; M. Daneschdar et al. : Arranged Sevenfold: Structural Insights into the C-Terminal Oligomerization Domain of Human C4b-Binding Protein; Journal Of Molecular Biology. 2013. DOI : 10.1016/j.jmb.2012.12.017.
S. E. Yan; T. Lemmin; S. Salvi; E. Lausch; A. Superti-Furga et al. : In-depth analysis of hyaline fibromatosis syndrome frameshift mutations at the same site reveal the necessity of personalized therapy; Human mutation. 2013. DOI : 10.1002/humu.22324.
T. Lemmin; C. Bovigny; D. Lancon; M. Dal Peraro : Cardiolipin Models for Molecular Simulations of Bacterial and Mitochondrial Membranes; Journal Of Chemical Theory And Computation. 2013. DOI : 10.1021/ct300590v.
T. Lemmin; C. S. Soto; G. Clinthorne; W. F. Degrado; M. Dal Peraro : Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations; Plos Computational Biology. 2013. DOI : 10.1371/journal.pcbi.1002878.
G. Paermo; M. Stenta; A. Cavalli; M. Dal Peraro; M. De Vivo : Molecular Simulations Highlight the Role of Metals in Catalysis and Inhibition of Type II Topoisomerase; Journal Of Chemical Theory And Computation. 2013. DOI : 10.1021/ct300691u.
2012
J. Sgrignani; A. Magistrato; M. Dal Peraro; A. J. Vila; P. Carloni et al. : On the active site of mononuclear B1 metallo beta-lactamases: a computational study; Journal Of Computer-Aided Molecular Design. 2012. DOI : 10.1007/s10822-012-9571-0.
A. K. K. Lakkaraju; L. Abrami; T. Lemmin; S. Blaskovic; B. Kunz et al. : Palmitoylated calnexin is a key component of the ribosome-translocon complex; Embo Journal. 2012. DOI : 10.1038/emboj.2012.15.
S. Ittig; B. Lindner; M. Stenta; P. Manfredi; E. Zdorovenko et al. : The Lipopolysaccharide from Capnocytophaga canimorsus Reveals an Unexpected Role of the Core-Oligosaccharide in MD-2 Binding; PLoS Pathogens. 2012. DOI : 10.1371/journal.ppat.1002667.
2011
B. Blasco; M. Stenta; L. Alonso-Sarduy; G. Dietler; M. Dal Peraro et al. : Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis; Molecular Microbiology. 2011. DOI : 10.1111/j.1365-2958.2011.07813.x.
I. Iacovache; M. T. Degiacomi; L. Pernot; S. Ho; M. Schiltz et al. : Dual Chaperone Role of the C-Terminal Propeptide in Folding and Oligomerization of the Pore-Forming Toxin Aerolysin; PLoS Pathogens. 2011. DOI : 10.1371/journal.ppat.1002135.
M. Stenta; M. Dal Peraro : An introduction to quantum chemical methods applied to drug design; Frontiers in Bioscience. 2011. DOI : 10.2741/311.
E. Khurana; R. H. Devane; M. D. Peraro; M. L. Klein : Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus; Biochimica et Biophysica Acta (BBA) - Biomembranes. 2011. DOI : 10.1016/j.bbamem.2010.03.025.
2010
M.-H. Ho; M. De Vivo; M. Dal Peraro; M. L. Klein : Understanding the Effect of Magnesium Ion Concentration on the Catalytic Activity of Ribonuclease H through Computation: Does a Third Metal Binding Site Modulate Endonuclease Catalysis?; Journal Of The American Chemical Society. 2010. DOI : 10.1021/ja102933y.
S. Wagner; M. Stenta; L. C. Metzger; M. Dal Peraro; G. R. Cornelis : Length control of the injectisome needle requires only one molecule of Yop secretion protein P (YscP); PNAS. 2010. DOI : 10.1073/pnas.1006985107.
D. Alemani; F. Collu; M. Cascella; M. Dal Peraro : A nonradial coarse-grained potential for proteins produces naturally stable secondary structure elements; Journal of Chemical Theory and Computation. 2010. DOI : 10.1021/ct900457z.
2009
E. Khurana; M. Dal Peraro; R. Devane; S. Vemparala; W. F. Degrado et al. : Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus; Proceedings of the National Academy of Sciences. 2009. DOI : 10.1073/pnas.0811720106.
M. Cascella; M. Dal Peraro : Challenges and perspectives in biomolecular simulations: from atomistic picture to multiscale modeling; CHIMIA International Journal for Chemistry. 2009. DOI : 10.2533/chimia.2009.14.
M.-H. Ho; M. De Vivo; M. Dal Peraro; M. L. Klein : Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation; Journal of Chemical Theory and Computation. 2009. DOI : 10.1021/ct8004722.
F. Simona; A. Magistrato; M. Dal Peraro; A. Cavalli; A. J. Vila et al. : Common mechanistic features among metallo-β-lactamases: a computational study of Aeromonas hydrophila CphA enzyme; The Journal of biological chemistry. 2009. DOI : 10.1074/jbc.M109.049502.
S. Wagner; I. Sorg; M. Degiacomi; L. Journet; M. Dal Peraro et al. : The helical content of the YscP molecular ruler determines the length of the Yersinia injectisome; Molecular Microbiology. 2009. DOI : 10.1111/j.1365-2958.2008.06556.x.
2008
M. De Vivo; M. Dal Peraro; M. L. Klein : Phosphodiester Cleavage in Ribonuclease H Occurs via an Associative Two-Metal-Aided Catalytic Mechanism; Journal of the American Chemical Society. 2008. DOI : 10.1021/ja8005786.
M. Cascella; M. A. Neri; P. Carloni; M. Dal Peraro : Topologically based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins; Journal of Chemical Theory Computation. 2008. DOI : 10.1021/ct800122x.
J. R. Calhoun; W. Liu; K. Spiegel; M. Dal Peraro; M. L. Klein et al. : Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement; Structure. 2008. DOI : 10.1016/j.str.2007.11.011.
2007
J. Moran-Barrio; J. M. Gonzalez; M. N. Lisa; A. L. Costello; M. Dal Peraro et al. : The metallo-beta-lactamase GOB is a mono-Zn(II) enzyme with a novel active site; Journal of Biological Chemistry. 2007. DOI : 10.1074/jbc.M700467200.
M. De Vivo; B. Ensing; M. Dal Peraro; G. A. Gomez; D. W. Christianson et al. : Proton shuttles and phosphatase activity in soluble epoxide hydrolase; J Am Chem Soc. 2007. DOI : 10.1021/ja066150c.
Conference Papers
2014
B. Bargeton; M. Dal Peraro; R. Benton : A Computational Study of Ligand Binding in Chemosensory Ionotropic Glutamate Receptors. 2014. 58th Annual Meeting of the Biophysical-Society, San Francisco, CA, FEB 15-19, 2014. p. 152A-152A.
T. Lemmin; M. Dimitrov; P. Fraering; M. Dal Peraro : The Amyloid Precursor Protein Maintains an Ideal&Alpha-Helical Conformation in the Lipid Bilayer. 2014. 58th Annual Meeting of the Biophysical-Society, San Francisco, CA, FEB 15-19, 2014. p. 53A-53A.
2013
G. Palermo; M. Stenta; A. Cavalli; M. Dal Peraro; M. De Vivo : Dynamics of catalytic metals during DNA cleavage in type II topoisomerase. 2013. 245th National Meeting of the American-Chemical-Society (ACS), New Orleans, LA, APR 07-11, 2013.
M. Degiacomi; I. Iacovache; G. Van Der Goot; M. Dal Peraro : The Molecular Assembly of the Aerolysin Pore Reveals a Unique Swirling Membrane-Insertion Mechanism. 2013. 57th Annual Meeting of the Biophysical-Society. p. 395A-395A.
T. Lemmin; M. Dimitrov; P. Fraering; M. Dal Peraro : Intrinsic Transmembrane Flexibility of the Amyloid Precursor Protein Explored by Molecular Simulations. 2013. 57th Annual Meeting of the Biophysical-Society, Philadelphia, PA, FEB 02-06, 2013. p. 226A-226A.
2011
M. Dal Peraro; M. Cascella; D. Alemani; E. Spiga : Development of a chemical-detailed coarse-grained force field for proteins. 2011. 242nd National Meeting of the American-Chemical-Society (ACS), Denver, CO, Aug 28-Sep 01, 2011. p. 28-COMP.
2010
M. Ho; M. De Vivo; M. Dal Peraro; M. L. Klein : Effect of magnesium ion concentration on the catalytic activity of ribonuclease H: Does a third metal bound at the active site modulate endonuclease catalysis?. 2010. p. 394-PHYS.
M. Stenta; M. Dal Peraro; M. Garavelli; P. Altoe; M. Di Domenico et al. : Shedding a new light on photolyases: Accurate molecular modeling as a tool for undestanding DNA repairing enzymes. 2010. p. 20-PHYS.
M. Stenta; P. Altoe; M. Dal Peraro; M. Garavelli; A. Bottoni : Common catalytic features among cofactor independent racemases and epimerases: A computational perspective. 2010. p. 88-COMP.
M. Stenta; M. Dal Peraro : Conformational coupling between LOV and kinase domains in phototropins: A computational perspective. 2010. p. 436-COMP.
M. Dal Peraro : Assembly and function of large Gram-negative bacterial machines studied by molecular simulation integrated with experimental data. 2010. p. 425-COMP.
D. Alemani; F. Collu; E. Spiga; M. Cascella; M. Dal Peraro : Coarse-graining electrostatics in multiscale molecular simulations. 2010. p. 391-COMP.
M. Degiacomi; I. Iacovache; G. van der Goot; M. Dal Peraro : A model for the assembly and activation process of the pore-forming toxin Aerolysin. 2010. 35th Congress of the Federation-of-European-Biochemical-Societies, Gothenburg, SWEDEN, Jun 26-Jul 01, 2010. p. 194-194.
T. Lemmin; M. Dal Peraro : A four-helix bundle model for E-coli PhoO transmembrane domain. 2010. 35th Congress of the Federation-of-European-Biochemical-Societies, Gothenburg, SWEDEN, Jun 26-Jul 01, 2010. p. 193-194.
2008
M. Dal Peraro; M. Neri; M. Cascella : Topologically-based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins. 2008. 236th National Meeting of the American-Chemical-Society, Philadelphia, PA, Aug 17-21, 2008. p. 57-COMP.
M.-H. Ho; M. De Vivo; M. Dal Peraro; M. L. Klein : Unraveling the enzymatic mechanism of the protein farnesyltransferase: A QM/MM study. 2008. 236th National Meeting of the American-Chemical-Society, Philadelphia, PA, Aug 17-21, 2008. p. 258-COMP.
Reviews
2016
M. Dal Peraro; F. G. Van Der Goot : Pore-forming toxins: ancient, but never really out of fashion; Nature Reviews Microbiology. 2016. DOI : 10.1038/nrmicro.2015.3.
2015
A. Sali; H. M. Berman; T. Schwede; J. Trewhella; G. Kleywegt et al. : Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop; Structure. 2015. DOI : 10.1016/j.str.2015.05.013.
G. Palermo; A. Cavalli; M. L. Klein; M. Alfonso-Prieto; M. Dal Peraro et al. : Catalytic Metal Ions and Enzymatic Processing of DNA and RNA; Accounts Of Chemical Research. 2015. DOI : 10.1021/ar500314j.
2014
M. Castelli; N. Clementi; G. A. Sautto; J. Pfaff; K. M. Kahle et al. : HCV E2 core structures and mAbs: something is still missing; Drug Discovery Today. 2014. DOI : 10.1016/j.drudis.2014.08.011.
2013
M. Castelli; F. Cappelletti; R. A. Diotti; G. Sautto; E. Criscuolo et al. : Peptide-Based Vaccinology: Experimental and Computational Approaches to Target Hypervariable Viruses through the Fine Characterization of Protective Epitopes Recognized by Monoclonal Antibodies and the Identification of T-Cell-Activating Peptides; Clinical & Developmental Immunology. 2013. DOI : 10.1155/2013/521231.
Theses
2018
G. E. Tamo / M. Dal Peraro (Dir.) : Constrained optimization applied to multiscale integrative modeling. EPFL, 2018. DOI : 10.5075/epfl-thesis-8630.
2017
M. Audagnotto / M. Dal Peraro (Dir.) : Studying membrane-protein interplay by modeling realistic conditions. Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-7934.
2015
H. Pezeshgi Modarres / M. Dal Peraro (Dir.) : Modeling and Engineering Proteins Thermostability. Lausanne, EPFL, 2015. DOI : 10.5075/epfl-thesis-6637.
2014
C. Bovigny / M. Dal Peraro; S. Gerber (Dir.) : New models and techniques to simulate realistic biological membranes. Lausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6310.
2013
E. Spiga / M. Dal Peraro (Dir.) : Multiscale simulations of protein dynamics. Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5841.
T. Lemmin / M. Dal Peraro (Dir.) : Molecular Modeling of Membrane Embedded Proteins. Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5695.
2012
M. T. Degiacomi / M. Dal Peraro (Dir.) : Molecular Modeling of Bacterial Nanomachineries. Lausanne, EPFL, 2012. DOI : 10.5075/epfl-thesis-5404.
Book Chapters
2014
E. Spiga; M. T. Degiacomi; M. Dal Peraro : New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly; Biomolecular Modelling And Simulations; San Diego: Elsevier Academic Press Inc, 2014. p. 77-111.
Infoscience
M. Audagnotto; A. Lorkowski; M. Dal Peraro : Recruitment of the amyloid precursor protein by gamma-secretase at the synaptic plasma membrane; BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS. 2018. DOI : 10.1016/j.bbrc.2017.10.164.
N. Bologna; R. Iselin; L. Abriata; A. Sarazin; N. Pumplin et al. : Nucleo-cytosolic Shuttling of ARGONAUTE1 Prompts a Revised Model of the Plant MicroRNA Pathway; MOLECULAR CELL. 2018. DOI : 10.1016/j.molcel.2018.01.007.
A. Timon-Gomez; E. Nyvltova; L. Abriata; A. Vila; J. Hosler et al. : Mitochondrial cytochrome c oxidase biogenesis: Recent developments; SEMINARS IN CELL AND DEVELOPMENTAL BIOLOGY. 2018. DOI : 10.1016/j.semcdb.2017.08.055.
C. Cao; M. Li; N. Cirauqui; Y. Wang; M. Dal Peraro et al. : Mapping the sensing spots of aerolysin for single oligonucleotides analysis; Nature Communications. 2018. DOI : 10.1038/s41467-018-05108-5.
X. Wang; M. Roger; R. Clement; S. Lecomte; F. Biaso et al. : Electron transfer in an acidophilic bacterium: interaction between a diheme cytochrome and a cupredoxin; CHEMICAL SCIENCE. 2018. DOI : 10.1039/c8sc01615a.
L. Abriata; L. Kinch; G. Tamo; B. Monastyrskyy; A. Kryshtafovych et al. : Definition and classification of evaluation units for tertiary structure prediction in CASP12 facilitated through semi-automated metrics; PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. 2018. DOI : 10.1002/prot.25403.
A. Reidenbach; Z. Kemmerer; D. Aydin; A. Jochem; M. McDevitt et al. : Conserved Lipid and Small-Molecule Modulation of COQ8 Reveals Regulation of the Ancient Kinase-like UbiB Family; CELL CHEMICAL BIOLOGY. 2018. DOI : 10.1016/j.chembiol.2017.11.001.
L. Abriata; G. Tamo; B. Monastyrskyy; A. Kryshtafovych; M. Dal Peraro : Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods; PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. 2018. DOI : 10.1002/prot.25423.
G. Tamo; L. Abriata; G. Fonti; M. Dal Peraro : Assessment of data-assisted prediction by inclusion of crosslinking/mass-spectrometry and small angle X-ray scattering data in the 12(th) Critical Assessment of protein Structure Prediction experiment; PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. 2018. DOI : 10.1002/prot.25442.
D. Aydin; D. C. Lohman; D. J. Pagliarini; M. Dal Peraro : A Combined Computational and Experimental Study to Investigate the Role of COQ9 in Promoting COQ Biosynthesis; Biophysical Journal. 2018. DOI : 10.1016/j.bpj.2017.11.2541.
G. E. Tamo / M. Dal Peraro (Dir.) : Constrained optimization applied to multiscale integrative modeling. EPFL, 2018. DOI : 10.5075/epfl-thesis-8630.
M. Audagnotto / M. Dal Peraro (Dir.) : Studying membrane-protein interplay by modeling realistic conditions. Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-7934.
L. L. Prieto-Godino; R. Rytz; S. Cruchet; B. Bargeton; L. Abuin et al. : Evolution of Acid-Sensing Olfactory Circuits in Drosophilids; Neuron. 2017. DOI : 10.1016/j.neuron.2016.12.024.
G. E. Tamo; A. Maesani; S. Träger; M. Degiacomi; D. Floreano et al. : Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies; Scientific Reports. 2017. DOI : 10.1038/s41598-017-00266-w.
L. A. Abriata; C. Bovigny; M. Dal Peraro : Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server(vol 1, 242, 2016); Bmc Bioinformatics. 2016. DOI : 10.1186/s12859-016-1315-z.
L. L. Prieto-Godino; R. Rytz; B. Bargeton; L. Abuin; J. R. Arguello et al. : Olfactory receptor pseudo-pseudogenes; Nature. 2016. DOI : 10.1038/nature19824.
P. Murima; M. Zimmermann; T. Chopra; F. Pojer; G. Fonti et al. : A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria; Nature Communications. 2016. DOI : 10.1038/ncomms12527.
J. A. Stefely; F. Licitra; L. Laredj; A. G. Reidenbach; Z. A. Kemmerer et al. : Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity; Molecular Cell. 2016. DOI : 10.1016/j.molcel.2016.06.030.
L. A. Abriata; E. Spiga; M. Dal Peraro : Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics; Biophysical Journal. 2016. DOI : 10.1016/j.bpj.2016.07.011.
M. Audagnotto; T. Lemmin; A. Barducci; M. Dal Peraro : Effect of the Synaptic Plasma Membrane on the Stability of the Amyloid Precursor Protein Homodimer; Journal Of Physical Chemistry Letters. 2016. DOI : 10.1021/acs.jpclett.6b01721.
L. A. Abriata; C. Bovigny; M. Dal Peraro : Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server; Bmc Bioinformatics. 2016. DOI : 10.1186/s12859-016-1124-4.
I. Iacovache; S. De Carlo; N. Cirauqui; M. Dal Peraro; F. G. van der Goot et al. : Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process; Nature Communications. 2016. DOI : 10.1038/ncomms12062.
A. S. Song; T. A. Poor; L. A. Abriata; T. S. Jardetzky; M. Dal Peraro et al. : Immobilization of the N-terminal helix stabilizes prefusion paramyxovirus fusion proteins; Proceedings Of The National Academy Of Sciences Of The United States Of America. 2016. DOI : 10.1073/pnas.1608349113.
P. Roethlisberger; A. Istrate; M. J. M. Lopez; R. Visini; A. Stocker et al. : X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair; Chemical Communications. 2016. DOI : 10.1039/c6cc00374e.
V. Genna; R. Gaspari; M. Dal Peraro; M. De Vivo : Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-eta; Nucleic Acids Research. 2016. DOI : 10.1093/nar/gkw128.
M. Dal Peraro; F. G. Van Der Goot : Pore-forming toxins: ancient, but never really out of fashion; Nature Reviews Microbiology. 2016. DOI : 10.1038/nrmicro.2015.3.
C. Bovigny; G. Tamo; T. Lemmin; N. Maino; M. Dal Peraro : Lipid Builder: A Framework To Build Realistic Models for Biological Membranes; Journal Of Chemical Information And Modeling. 2015. DOI : 10.1021/acs.jcim.5b00501.
M. Bartoloni; X. Jin; M. J. Marcaida; J. Banha; I. Dibonaventura et al. : Bridged bicyclic peptides as potential drug scaffolds: synthesis, structure, protein binding and stability; Chemical Science. 2015. DOI : 10.1039/c5sc01699a.
E. Saita; L. A. Abriata; Y. T. Tsai; F. Trajtenberg; T. Lemmin et al. : A coiled coil switch mediates cold sensing by the thermosensory protein DesK; Molecular Microbiology. 2015. DOI : 10.1111/mmi.13118.
G. S. Kolly; R. Mukherjee; E. Kilacskova; L. A. Abriata; M. Raccaud et al. : GtrA Protein Rv3789 Is Required for Arabinosylation of Arabinogalactan in Mycobacterium tuberculosis; Journal Of Bacteriology. 2015. DOI : 10.1128/Jb.00628-15.
H. P. Modarres; B. D. Dorokhov; V. O. Popov; N. V. Ravin; K. G. Skryabin et al. : Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp 1519; Biochemistry. 2015. DOI : 10.1021/bi501227b.
L. A. Abriata; M. Dal Peraro : Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding; Scientific Reports. 2015. DOI : 10.1038/srep10549.
M. Christen; M. J. Marcaida; C. Lamprakis; W. Aeschimann; J. Vaithilingam et al. : Structural insights on cholesterol endosynthesis: Binding of squalene and 2,3-oxidosqualene to supernatant protein factor; Journal Of Structural Biology. 2015. DOI : 10.1016/j.jsb.2015.05.001.
G. E. Tamo; L. A. Abriata; M. Dal Peraro : The importance of dynamics in integrative modeling of supramolecular assemblies; Current Opinion In Structural Biology. 2015. DOI : 10.1016/j.sbi.2015.02.018.
H.-A. Kang; H.-C. Shin; A.-S. Kalantzi; C. P. Toseland; H.-M. Kim et al. : NAR Breakthrough Article Crystal structure of Hop2-Mnd1 and mechanistic insights into its role in meiotic recombination; Nucleic Acids Research. 2015. DOI : 10.1093/nar/gkv172.
A. Sali; H. M. Berman; T. Schwede; J. Trewhella; G. Kleywegt et al. : Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop; Structure. 2015. DOI : 10.1016/j.str.2015.05.013.
H. Pezeshgi Modarres / M. Dal Peraro (Dir.) : Modeling and Engineering Proteins Thermostability. Lausanne, EPFL, 2015. DOI : 10.5075/epfl-thesis-6637.
L. A. Abriata; T. Palzkill; M. Dal Peraro : How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme; Plos One. 2015. DOI : 10.1371/journal.pone.0118684.
G. Palermo; A. Cavalli; M. L. Klein; M. Alfonso-Prieto; M. Dal Peraro et al. : Catalytic Metal Ions and Enzymatic Processing of DNA and RNA; Accounts Of Chemical Research. 2015. DOI : 10.1021/ar500314j.
M. Castelli; N. Clementi; G. A. Sautto; J. Pfaff; K. M. Kahle et al. : HCV E2 core structures and mAbs: something is still missing; Drug Discovery Today. 2014. DOI : 10.1016/j.drudis.2014.08.011.
E. Spiga; M. T. Degiacomi; M. Dal Peraro : New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly; Biomolecular Modelling And Simulations; San Diego: Elsevier Academic Press Inc, 2014. p. 77-111.
L. A. Abriata; L. B. Pontel; A. J. Vila; M. Dal Peraro; F. C. Soncini : A dimerization interface mediated by functionally critical residues creates interfacial disulfide bonds and copper sites in CueP; Journal Of Inorganic Biochemistry. 2014. DOI : 10.1016/j.jinorgbio.2014.07.022.
C. Bovigny / M. Dal Peraro; S. Gerber (Dir.) : New models and techniques to simulate realistic biological membranes. Lausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6310.
C. Bovigny; M. T. Degiacomi; T. Lemmin; M. Dal Peraro; M. Stenta : Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase; Journal Of Physical Chemistry B. 2014. DOI : 10.1021/jp411786z.
B. Bargeton; M. Dal Peraro; R. Benton : A Computational Study of Ligand Binding in Chemosensory Ionotropic Glutamate Receptors. 2014. 58th Annual Meeting of the Biophysical-Society, San Francisco, CA, FEB 15-19, 2014. p. 152A-152A.
T. Lemmin; M. Dimitrov; P. Fraering; M. Dal Peraro : The Amyloid Precursor Protein Maintains an Ideal&Alpha-Helical Conformation in the Lipid Bilayer. 2014. 58th Annual Meeting of the Biophysical-Society, San Francisco, CA, FEB 15-19, 2014. p. 53A-53A.
E. Spiga; L. A. Abriata; F. Piazza; M. Dal Peraro : Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics; Journal Of Physical Chemistry B. 2014. DOI : 10.1021/jp4126705.
L. A. Abriata; A. J. Vila; M. Dal Peraro : Molecular dynamics simulations of apocupredoxins: insights into the formation and stabilization of copper sites under entatic control; Journal Of Biological Inorganic Chemistry. 2014. DOI : 10.1007/s00775-014-1108-7.
T. Lemmin; M. Dimitrov; P. C. Fraering; M. Dal Peraro : Perturbations of the Straight Transmembrane alpha-Helical Structure of the Amyloid Precursor Protein Affect Its Processing by gamma-Secretase; Journal Of Biological Chemistry. 2014. DOI : 10.1074/jbc.M113.470781.
A. L. Vestergaard; J. A. Coleman; T. Lemmin; S. A. Mikkelsen; L. L. Molday et al. : Critical roles of isoleucine-364 and adjacent residues in a hydrophobic gate control of phospholipid transport by the mammalian P4-ATPase ATP8A2; Proceedings Of The National Academy Of Sciences Of The United States Of America. 2014. DOI : 10.1073/pnas.1321165111.
P. Seitz; H. Pezeshgi Modarres; S. Borgeaud; R. D. Bulushev; L. J. Steinbock et al. : ComEA Is Essential for the Transfer of External DNA into the Periplasm in Naturally Transformable Vibrio cholerae Cells; PLoS Genetics. 2014. DOI : 10.1371/journal.pgen.1004066.
M. Kudryashev; M. Stenta; S. Schmelz; M. Amstutz; U. Wiesand et al. : In situ structural analysis of the Yersinia enterocolitica injectisome; Elife. 2013. DOI : 10.7554/eLife.00792.
B. I. M. Wicky; M. Stenta; M. Dal Peraro : TAL Effectors Specificity Stems from Negative Discrimination; Plos One. 2013. DOI : 10.1371/journal.pone.0080261.
G. Palermo; M. Stenta; A. Cavalli; M. Dal Peraro; M. De Vivo : Dynamics of catalytic metals during DNA cleavage in type II topoisomerase. 2013. 245th National Meeting of the American-Chemical-Society (ACS), New Orleans, LA, APR 07-11, 2013.
E. Spiga / M. Dal Peraro (Dir.) : Multiscale simulations of protein dynamics. Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5841.
M. T. Degiacomi; I. Lacovache; L. Pernot; M. Chami; M. Kudryashev et al. : Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism; Nature Chemical Biology. 2013. DOI : 10.1038/Nchembio.1312.
M. Castelli; F. Cappelletti; R. A. Diotti; G. Sautto; E. Criscuolo et al. : Peptide-Based Vaccinology: Experimental and Computational Approaches to Target Hypervariable Viruses through the Fine Characterization of Protective Epitopes Recognized by Monoclonal Antibodies and the Identification of T-Cell-Activating Peptides; Clinical & Developmental Immunology. 2013. DOI : 10.1155/2013/521231.
M. T. Degiacomi; M. Dal Peraro : Macromolecular Symmetric Assembly Prediction Using Swarm Intelligence Dynamic Modeling; Structure. 2013. DOI : 10.1016/j.str.2013.05.014.
L. A. Abriata; E. Spiga; M. Dal Peraro : All-atom simulations of crowding effects on ubiquitin dynamics; Physical Biology. 2013. DOI : 10.1088/1478-3975/10/4/045006.
E. Spiga; D. Alemani; M. T. Degiacomi; M. Cascella; M. Dal Peraro : Electrostatic-Consistent Coarse-Grained Potentials for Molecular Simulations of Proteins; Journal Of Chemical Theory And Computation. 2013. DOI : 10.1021/ct400137q.
T. Hofmeyer; S. Schmelz; M. T. Degiacomi; M. Dal Peraro; M. Daneschdar et al. : Arranged Sevenfold: Structural Insights into the C-Terminal Oligomerization Domain of Human C4b-Binding Protein; Journal Of Molecular Biology. 2013. DOI : 10.1016/j.jmb.2012.12.017.
S. E. Yan; T. Lemmin; S. Salvi; E. Lausch; A. Superti-Furga et al. : In-depth analysis of hyaline fibromatosis syndrome frameshift mutations at the same site reveal the necessity of personalized therapy; Human mutation. 2013. DOI : 10.1002/humu.22324.
T. Lemmin / M. Dal Peraro (Dir.) : Molecular Modeling of Membrane Embedded Proteins. Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5695.
M. Degiacomi; I. Iacovache; G. Van Der Goot; M. Dal Peraro : The Molecular Assembly of the Aerolysin Pore Reveals a Unique Swirling Membrane-Insertion Mechanism. 2013. 57th Annual Meeting of the Biophysical-Society. p. 395A-395A.
T. Lemmin; M. Dimitrov; P. Fraering; M. Dal Peraro : Intrinsic Transmembrane Flexibility of the Amyloid Precursor Protein Explored by Molecular Simulations. 2013. 57th Annual Meeting of the Biophysical-Society, Philadelphia, PA, FEB 02-06, 2013. p. 226A-226A.
T. Lemmin; C. Bovigny; D. Lancon; M. Dal Peraro : Cardiolipin Models for Molecular Simulations of Bacterial and Mitochondrial Membranes; Journal Of Chemical Theory And Computation. 2013. DOI : 10.1021/ct300590v.
T. Lemmin; C. S. Soto; G. Clinthorne; W. F. Degrado; M. Dal Peraro : Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations; Plos Computational Biology. 2013. DOI : 10.1371/journal.pcbi.1002878.
G. Paermo; M. Stenta; A. Cavalli; M. Dal Peraro; M. De Vivo : Molecular Simulations Highlight the Role of Metals in Catalysis and Inhibition of Type II Topoisomerase; Journal Of Chemical Theory And Computation. 2013. DOI : 10.1021/ct300691u.
M. T. Degiacomi / M. Dal Peraro (Dir.) : Molecular Modeling of Bacterial Nanomachineries. Lausanne, EPFL, 2012. DOI : 10.5075/epfl-thesis-5404.
J. Sgrignani; A. Magistrato; M. Dal Peraro; A. J. Vila; P. Carloni et al. : On the active site of mononuclear B1 metallo beta-lactamases: a computational study; Journal Of Computer-Aided Molecular Design. 2012. DOI : 10.1007/s10822-012-9571-0.
A. K. K. Lakkaraju; L. Abrami; T. Lemmin; S. Blaskovic; B. Kunz et al. : Palmitoylated calnexin is a key component of the ribosome-translocon complex; Embo Journal. 2012. DOI : 10.1038/emboj.2012.15.
S. Ittig; B. Lindner; M. Stenta; P. Manfredi; E. Zdorovenko et al. : The Lipopolysaccharide from Capnocytophaga canimorsus Reveals an Unexpected Role of the Core-Oligosaccharide in MD-2 Binding; PLoS Pathogens. 2012. DOI : 10.1371/journal.ppat.1002667.
M. Dal Peraro; M. Cascella; D. Alemani; E. Spiga : Development of a chemical-detailed coarse-grained force field for proteins. 2011. 242nd National Meeting of the American-Chemical-Society (ACS), Denver, CO, Aug 28-Sep 01, 2011. p. 28-COMP.
B. Blasco; M. Stenta; L. Alonso-Sarduy; G. Dietler; M. Dal Peraro et al. : Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis; Molecular Microbiology. 2011. DOI : 10.1111/j.1365-2958.2011.07813.x.
I. Iacovache; M. T. Degiacomi; L. Pernot; S. Ho; M. Schiltz et al. : Dual Chaperone Role of the C-Terminal Propeptide in Folding and Oligomerization of the Pore-Forming Toxin Aerolysin; PLoS Pathogens. 2011. DOI : 10.1371/journal.ppat.1002135.
M. Stenta; M. Dal Peraro : An introduction to quantum chemical methods applied to drug design; Frontiers in Bioscience. 2011. DOI : 10.2741/311.
E. Khurana; R. H. Devane; M. D. Peraro; M. L. Klein : Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus; Biochimica et Biophysica Acta (BBA) - Biomembranes. 2011. DOI : 10.1016/j.bbamem.2010.03.025.
M. Ho; M. De Vivo; M. Dal Peraro; M. L. Klein : Effect of magnesium ion concentration on the catalytic activity of ribonuclease H: Does a third metal bound at the active site modulate endonuclease catalysis?. 2010. p. 394-PHYS.
M. Stenta; M. Dal Peraro; M. Garavelli; P. Altoe; M. Di Domenico et al. : Shedding a new light on photolyases: Accurate molecular modeling as a tool for undestanding DNA repairing enzymes. 2010. p. 20-PHYS.
M. Stenta; P. Altoe; M. Dal Peraro; M. Garavelli; A. Bottoni : Common catalytic features among cofactor independent racemases and epimerases: A computational perspective. 2010. p. 88-COMP.
M. Stenta; M. Dal Peraro : Conformational coupling between LOV and kinase domains in phototropins: A computational perspective. 2010. p. 436-COMP.
M. Dal Peraro : Assembly and function of large Gram-negative bacterial machines studied by molecular simulation integrated with experimental data. 2010. p. 425-COMP.
D. Alemani; F. Collu; E. Spiga; M. Cascella; M. Dal Peraro : Coarse-graining electrostatics in multiscale molecular simulations. 2010. p. 391-COMP.
M. Degiacomi; I. Iacovache; G. van der Goot; M. Dal Peraro : A model for the assembly and activation process of the pore-forming toxin Aerolysin. 2010. 35th Congress of the Federation-of-European-Biochemical-Societies, Gothenburg, SWEDEN, Jun 26-Jul 01, 2010. p. 194-194.
T. Lemmin; M. Dal Peraro : A four-helix bundle model for E-coli PhoO transmembrane domain. 2010. 35th Congress of the Federation-of-European-Biochemical-Societies, Gothenburg, SWEDEN, Jun 26-Jul 01, 2010. p. 193-194.
M.-H. Ho; M. De Vivo; M. Dal Peraro; M. L. Klein : Understanding the Effect of Magnesium Ion Concentration on the Catalytic Activity of Ribonuclease H through Computation: Does a Third Metal Binding Site Modulate Endonuclease Catalysis?; Journal Of The American Chemical Society. 2010. DOI : 10.1021/ja102933y.
S. Wagner; M. Stenta; L. C. Metzger; M. Dal Peraro; G. R. Cornelis : Length control of the injectisome needle requires only one molecule of Yop secretion protein P (YscP); PNAS. 2010. DOI : 10.1073/pnas.1006985107.
D. Alemani; F. Collu; M. Cascella; M. Dal Peraro : A nonradial coarse-grained potential for proteins produces naturally stable secondary structure elements; Journal of Chemical Theory and Computation. 2010. DOI : 10.1021/ct900457z.
E. Khurana; M. Dal Peraro; R. Devane; S. Vemparala; W. F. Degrado et al. : Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus; Proceedings of the National Academy of Sciences. 2009. DOI : 10.1073/pnas.0811720106.
M. Cascella; M. Dal Peraro : Challenges and perspectives in biomolecular simulations: from atomistic picture to multiscale modeling; CHIMIA International Journal for Chemistry. 2009. DOI : 10.2533/chimia.2009.14.
M.-H. Ho; M. De Vivo; M. Dal Peraro; M. L. Klein : Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation; Journal of Chemical Theory and Computation. 2009. DOI : 10.1021/ct8004722.
F. Simona; A. Magistrato; M. Dal Peraro; A. Cavalli; A. J. Vila et al. : Common mechanistic features among metallo-β-lactamases: a computational study of Aeromonas hydrophila CphA enzyme; The Journal of biological chemistry. 2009. DOI : 10.1074/jbc.M109.049502.
S. Wagner; I. Sorg; M. Degiacomi; L. Journet; M. Dal Peraro et al. : The helical content of the YscP molecular ruler determines the length of the Yersinia injectisome; Molecular Microbiology. 2009. DOI : 10.1111/j.1365-2958.2008.06556.x.
M. Dal Peraro; M. Neri; M. Cascella : Topologically-based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins. 2008. 236th National Meeting of the American-Chemical-Society, Philadelphia, PA, Aug 17-21, 2008. p. 57-COMP.
M.-H. Ho; M. De Vivo; M. Dal Peraro; M. L. Klein : Unraveling the enzymatic mechanism of the protein farnesyltransferase: A QM/MM study. 2008. 236th National Meeting of the American-Chemical-Society, Philadelphia, PA, Aug 17-21, 2008. p. 258-COMP.
M. De Vivo; M. Dal Peraro; M. L. Klein : Phosphodiester Cleavage in Ribonuclease H Occurs via an Associative Two-Metal-Aided Catalytic Mechanism; Journal of the American Chemical Society. 2008. DOI : 10.1021/ja8005786.
M. Cascella; M. A. Neri; P. Carloni; M. Dal Peraro : Topologically based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins; Journal of Chemical Theory Computation. 2008. DOI : 10.1021/ct800122x.
J. R. Calhoun; W. Liu; K. Spiegel; M. Dal Peraro; M. L. Klein et al. : Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement; Structure. 2008. DOI : 10.1016/j.str.2007.11.011.
J. Moran-Barrio; J. M. Gonzalez; M. N. Lisa; A. L. Costello; M. Dal Peraro et al. : The metallo-beta-lactamase GOB is a mono-Zn(II) enzyme with a novel active site; Journal of Biological Chemistry. 2007. DOI : 10.1074/jbc.M700467200.
M. De Vivo; B. Ensing; M. Dal Peraro; G. A. Gomez; D. W. Christianson et al. : Proton shuttles and phosphatase activity in soluble epoxide hydrolase; J Am Chem Soc. 2007. DOI : 10.1021/ja066150c.
