Matteo Dal Peraro
matteo.dalperaro@epfl.ch +41 21 693 18 61 http://lbm.epfl.ch
Nationalité : Italian
EPFL SV IBI-SV UPDALPE
AAB 0 48 (Bâtiment AAB)
Station 19
CH-1015 Lausanne
+41 21 693 18 61
+41 21 693 21 52
Local: AAB 0 48
EPFL > SV > IBI-SV > UPDALPE
Web site: Site web: https://lbm.epfl.ch/
+41 21 693 18 61
EPFL > E > E-DOC > CDOCT
EPFL E EDCB-GE
AAB 0 48 (Bâtiment AAB)
Station 19
CH-1015 Lausanne
+41 21 693 18 61
+41 21 693 78 82
Local: AAB 0 48
EPFL > E > E-DOC > EDCB-GE
Web site: Site web: https://go.epfl.ch/edcb
+41 21 693 18 61
EPFL > ENT-R > SCITAS > SCITAS-CD
Publications
Publications Infoscience
Journal Articles
2020
S. Meister; A. Prunotto; M. Dal Peraro; T. Kohn : Salt enhances the thermostability of enteroviruses by stabilizing capsid protein interfaces; Journal of Virology. 2020-03-25. DOI : 10.1128/JVI.02176-19.
N. T. Odermatt; M. Lelli; T. Herrmann; L. A. Abriata; A. Japaridze et al. : Structural and DNA binding properties of mycobacterial integration host factor mIHF; Journal Of Structural Biology. 2020-03-01. DOI : 10.1016/j.jsb.2019.107434.
L. A. Abriata : Building blocks for commodity augmented reality-based molecular visualization and modeling in web browsers; Peerj Computer Science. 2020-02-17. DOI : 10.7717/peerj-cs.260.
2019
B. S. Belluzo; L. A. Abriata; E. Giannini; D. Mihovilcevic; M. Dal Peraro et al. : An experiment-informed signal transduction model for the role of the Staphylococcus aureus MecR1 protein in beta-lactam resistance; Scientific Reports. 2019-12-20. DOI : 10.1038/s41598-019-55923-z.
P. Fernandez; L. Porrini; D. Albanesi; L. A. Abriata; M. Dal Peraro et al. : Transmembrane Prolines Mediate Signal Sensing and Decoding in Bacillus subtilis DesK Histidine Kinase; mBio. 2019-11-01. DOI : 10.1128/mBio.02564-19.
C. Cao; N. Cirauqui; M. J. Marcaida; E. Buglakova; A. Duperrex et al. : Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores; Nature Communications. 2019-10-29. DOI : 10.1038/s41467-019-12690-9.
S. Malhotra; S. Trager; M. Dal Peraro; M. Topf : Modelling structures in cryo-EM maps; Current Opinion In Structural Biology. 2019-10-01. DOI : 10.1016/j.sbi.2019.05.024.
M. Dal Peraro; J.-J. Song : Editorial overview: The future after the cryo-EM resolution revolution; Current Opinion In Structural Biology. 2019-10-01. DOI : 10.1016/j.sbi.2019.07.007.
L. A. Abriata; G. E. Tamo; M. Dal Peraro : A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments; Proteins-Structure Function And Bioinformatics. 2019-08-07. DOI : 10.1002/prot.25787.
A. Mayorov; M. Dal Peraro; L. A. Abriata : Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes; Molecular Biology And Evolution. 2019-08-01. DOI : 10.1093/molbev/msz096.
G. Fonti; M. J. Marcaida; L. C. Bryan; S. Traeger; A. S. Kalantzi et al. : KAP1 is an antiparallel dimer with a functional asymmetry; Life Science Alliance. 2019-08-01. DOI : 10.26508/lsa.201900349.
C. Cianciaruso; T. Beltraminelli; F. Duval; S. Nassiri; R. Hamelin et al. : Molecular Profiling and Functional Analysis of Macrophage-Derived Tumor Extracellular Vesicles; Cell Reports. 2019-06-04. DOI : 10.1016/j.celrep.2019.05.008.
D. C. Lohman; D. Aydin; H. C. Von Bank; R. W. Smith; V. Linke et al. : An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis; Molecular Cell. 2019-02-21. DOI : 10.1016/j.molcel.2018.11.033.
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
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. 2016-03-01. DOI : 10.1093/nar/gkw128.
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.
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.
Conference Papers
2019
D. Aydin; D. Lohman; D. Pagliarini; M. Dal Peraro : Overcoming the hydrophobic barrier of the membrane: The role of COQ9 in promoting coenzyme Q biosynthesis. 2019-03-31. National Meeting of the American-Chemical-Society (ACS), Orlando, FL, Mar 31-Apr 04, 2019.
A. Prunotto; G. Bahr; L. Gonzalez; A. Vila; M. Dal Peraro : Molecular Simulations Give Insights into the NDM-1/Membrane Interaction that Causes Rise of a Super-Bacterium. 2019-02-15. 63rd Annual Meeting of the Biophysical-Society, Baltimore, MD, Mar 02-06, 2019. p. 205A-205A. DOI : 10.1016/j.bpj.2018.11.1132.
2018
A. Prunotto; G. Bahr; L. Gonzalez; A. Vila; M. Dal Peraro : Exploiting the role of membrane anchoring on the peculiar biological behaviour of multi-drug resistant enzyme New Delhi metallo-beta-lactamase 1. 2018-08-19. 256th National Meeting and Exposition of the American-Chemical-Society (ACS) - Nanoscience, Nanotechnology and Beyond, Boston, MA, Aug 19-23, 2018.
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.
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
S. Meister; A. Prunotto; M. Dal Peraro; T. Kohn : Salt enhances the thermostability of enteroviruses by stabilizing capsid protein interfaces; Journal of Virology. 2020-03-25. DOI : 10.1128/JVI.02176-19.
N. T. Odermatt; M. Lelli; T. Herrmann; L. A. Abriata; A. Japaridze et al. : Structural and DNA binding properties of mycobacterial integration host factor mIHF; Journal Of Structural Biology. 2020-03-01. DOI : 10.1016/j.jsb.2019.107434.
L. A. Abriata : Building blocks for commodity augmented reality-based molecular visualization and modeling in web browsers; Peerj Computer Science. 2020-02-17. DOI : 10.7717/peerj-cs.260.
B. S. Belluzo; L. A. Abriata; E. Giannini; D. Mihovilcevic; M. Dal Peraro et al. : An experiment-informed signal transduction model for the role of the Staphylococcus aureus MecR1 protein in beta-lactam resistance; Scientific Reports. 2019-12-20. DOI : 10.1038/s41598-019-55923-z.
P. Fernandez; L. Porrini; D. Albanesi; L. A. Abriata; M. Dal Peraro et al. : Transmembrane Prolines Mediate Signal Sensing and Decoding in Bacillus subtilis DesK Histidine Kinase; mBio. 2019-11-01. DOI : 10.1128/mBio.02564-19.
C. Cao; N. Cirauqui; M. J. Marcaida; E. Buglakova; A. Duperrex et al. : Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores; Nature Communications. 2019-10-29. DOI : 10.1038/s41467-019-12690-9.
S. Malhotra; S. Trager; M. Dal Peraro; M. Topf : Modelling structures in cryo-EM maps; Current Opinion In Structural Biology. 2019-10-01. DOI : 10.1016/j.sbi.2019.05.024.
M. Dal Peraro; J.-J. Song : Editorial overview: The future after the cryo-EM resolution revolution; Current Opinion In Structural Biology. 2019-10-01. DOI : 10.1016/j.sbi.2019.07.007.
L. A. Abriata; G. E. Tamo; M. Dal Peraro : A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments; Proteins-Structure Function And Bioinformatics. 2019-08-07. DOI : 10.1002/prot.25787.
A. Mayorov; M. Dal Peraro; L. A. Abriata : Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes; Molecular Biology And Evolution. 2019-08-01. DOI : 10.1093/molbev/msz096.
G. Fonti; M. J. Marcaida; L. C. Bryan; S. Traeger; A. S. Kalantzi et al. : KAP1 is an antiparallel dimer with a functional asymmetry; Life Science Alliance. 2019-08-01. DOI : 10.26508/lsa.201900349.
C. Cianciaruso; T. Beltraminelli; F. Duval; S. Nassiri; R. Hamelin et al. : Molecular Profiling and Functional Analysis of Macrophage-Derived Tumor Extracellular Vesicles; Cell Reports. 2019-06-04. DOI : 10.1016/j.celrep.2019.05.008.
D. Aydin; D. Lohman; D. Pagliarini; M. Dal Peraro : Overcoming the hydrophobic barrier of the membrane: The role of COQ9 in promoting coenzyme Q biosynthesis. 2019-03-31. National Meeting of the American-Chemical-Society (ACS), Orlando, FL, Mar 31-Apr 04, 2019.
D. C. Lohman; D. Aydin; H. C. Von Bank; R. W. Smith; V. Linke et al. : An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis; Molecular Cell. 2019-02-21. DOI : 10.1016/j.molcel.2018.11.033.
A. Prunotto; G. Bahr; L. Gonzalez; A. Vila; M. Dal Peraro : Molecular Simulations Give Insights into the NDM-1/Membrane Interaction that Causes Rise of a Super-Bacterium. 2019-02-15. 63rd Annual Meeting of the Biophysical-Society, Baltimore, MD, Mar 02-06, 2019. p. 205A-205A. DOI : 10.1016/j.bpj.2018.11.1132.
A. Prunotto; G. Bahr; L. Gonzalez; A. Vila; M. Dal Peraro : Exploiting the role of membrane anchoring on the peculiar biological behaviour of multi-drug resistant enzyme New Delhi metallo-beta-lactamase 1. 2018-08-19. 256th National Meeting and Exposition of the American-Chemical-Society (ACS) - Nanoscience, Nanotechnology and Beyond, Boston, MA, Aug 19-23, 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.
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.
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. 2016-03-01. DOI : 10.1093/nar/gkw128.
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.
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.
Enseignement & Phd
Enseignement
Life Sciences Engineering