Publications

Laboratory for Biomolecular Modeling, newest publications

See also most updated publication record in Google Scholar

Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η.
V Genna, R Gaspari, M Dal Peraro, M De Vivo
Nucleic acids research, 2016

Pore-forming toxins: ancient, but never really out of fashion
M Dal Peraro, FG van der Goot
Nature Reviews Microbiology 14 (2), 77-92, 2016

LipidBuilder: A Framework To Build Realistic Models for Biological Membranes
C Bovigny, G Tamò, T Lemmin, N Maïno, M Dal Peraro
Journal of chemical information and modeling 55 (12), 2491-2499, 2015

GtrA protein Rv3789 is required for arabinosylation of arabinogalactan in Mycobacterium tuberculosis
GS Kolly, R Mukherjee, E Kilacsková, LA Abriata, M Raccaud, J Blaško, …
Journal of Bacteriology 197 (23), 3686-3697, 2015

A coiled coil switch mediates cold sensing by the thermosensory protein DesK
E Saita, LA Abriata, YT Tsai, F Trajtenberg, T Lemmin, A Buschiazzo, …
Molecular microbiology 98 (2), 258-271, 2015

Outcome of the first wwPDB hybrid/integrative methods task force workshop
A Sali, HM Berman, T Schwede, J Trewhella, G Kleywegt, SK Burley, …
Structure 23 (7), 1156-1167, 2015

Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding
LA Abriata, M Dal Peraro
Scientific reports 5, 2015

Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp. 1519
H Pezeshgi Modarres, BD Dorokhov, VO Popov, NV Ravin, KG Skryabin, …
Biochemistry 54 (19), 3076-3085, 2015

The importance of dynamics in integrative modeling of supramolecular assemblies
GE Tamò, LA Abriata, M Dal Peraro
Current opinion in structural biology 31, 28-34, 2015

Crystal structure of Hop2–Mnd1 and mechanistic insights into its role in meiotic recombination
HA Kang, HC Shin, AS Kalantzi, CP Toseland, HM Kim, S Gruber, …
Nucleic acids research, gkv172, 2015

How structural and physicochemical determinants shape sequence constraints in a functional enzyme
LA Abriata, T Palzkill, M Dal Peraro
PloS one 10 (2), e0118684, 2015

Catalytic metal ions and enzymatic processing of DNA and RNA
G Palermo, A Cavalli, ML Klein, M Alfonso-Prieto, M Dal Peraro, …
Accounts of chemical research 48 (2), 220-228, 2015

Experimental and computational studies of the effects of highly concentrated solutes on proteins: Insights into the causes and consequences of quinary protein structure and cytoplasmic organization
L Abriata, M Dal Peraro
Protein Science 24 (EPFL-CONF-214087), 102-102, 2015

Computational Chemistry Strategies Tackling Function and Inhibition of Pharmaceutically Relevant Targets
M Cascella, M Dal Peraro, M De Vivo, 2015

Chapter Three-New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly
E Spiga, MT Degiacomi, M Dal Peraro
Advances in protein chemistry and structural biology 96, 77-111, 2014

HCV E2 core structures and mAbs: something is still missing
M Castelli, N Clementi, GA Sautto, J Pfaff, KM Kahle, T Barnes, BJ Doranz, …
Drug discovery today 19 (12), 1964-1970, 2014

A dimerization interface mediated by functionally critical residues creates interfacial disulfide bonds and copper sites in CueP
LA Abriata, LB Pontel, AJ Vila, M Dal Peraro, FC Soncini
Journal of inorganic biochemistry 140, 199-201, 2014
 

Laboratory for Biomolecular Modeling, erlier publications

Kudryashev M§, Stenta M§, Schmelz S§, Amstutz M, Wised U, Castaño-Díez D, Degiacomi MT, Mannish S, Beck CKE, Kowal J, Diepold A, Heinz DW, Dal Peraro M*, Cornelis GR*, Sahlberg H*, In situ structural analysis of the Yersinia enterocolitica injectisome, eLife, 2:e00792. doi: 10.7554/eLife.00792 , 2013.

  • Highlighted in BBC “Dara O’Briain’s Science Club” episode: “Size Matters” and Science Daily.

Degiacomi MT§, Iacovache I§, Pernot L, Chami M, Kudryashev M, Stahlberg H, van der Goot FG*, Dal Peraro M*, Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism. Nature Chemical Biology 9, 623–629 (2013).

  • A News and Views comment appeared on the issue of October of Nature Chemical Biology. This article was also highlighted in EPFL News, BBC Mundo, RTS Info, Science Daily, and local newspapers like 24 Heures and Le Matin.

Dimitrov M, Althea JR, Lemmin L, Lehal R, Fligier A, Houacine J, Hussain I, Radtke F, Dal Peraro M, Beher D, Fraering PC*, Alzheimer’s disease mutations in APP but not γ-secretase modulators affect epsilon-cleavage-dependent AICD production, Nature Communications, 4:2246, doi:10.1038/ncomms3246, 2013.

  • Highlighted in EPFL News, RTS Radio and TV and local newspapers.

Abriata LA, Spiga E, Dal Peraro M*,  All-atom simulations of crowding effects on ubiquitin dynamics, Physical Biology, 10(4):045006, 2013.

Yan SE, Lemmin T, Salvi S, Lausch E, Superti-Furga A, Rokicki D, Dal Peraro M, van der Goot FG*, In-Depth Analysis of Hyaline Fibromatosis Syndrome Frameshift Mutations at the Same Site Reveal the Necessity of Personalized Therapy. Human Mutation, 34:1005, 2013.

Degiacomi M, Dal Peraro M*, Macromolecular Symmetric Assembly Prediction Using Swarm Intelligence Dynamic Modeling, Structure, 21(7):1097, 2013.

  • This article was selected as Featured Article for the issue of July of Structure, and was on the “Top 20 Papers” list of most downloaded papers during the months of July and August.

Spiga E, Alemani D, Degiacomi M, Cascella M, Dal Peraro M*, Electrostatic-Consistent Coarse-Grained Potentials for Molecular Simulations of Proteins, Journal of Chemical Theory and Computation, 9(8):3515, 2013.

Lemmin T, Soto C, Clinthorne G, DeGrado WF, Dal Peraro M*, Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations. PLoS Computational Biology, 9(1): e1002878, 2013.

Lemmin T, Bovigny C, Lancon D, Dal Peraro M*, Cardiolipin Models for Molecular Simulations of Bacterial and Mitochondrial Membranes, Journal of Chemical Theory Computation, 9(1):670, 2013.

Hofmeyer T, Schmelz S, Degiacomi MT, Dal Peraro M, Daneschdar M, Scrima A, van den Heuvel J, Heinz DW, Kolmar H*, Arranged Sevenfold: Structural Insights into the C-Terminal Oligomerization Domain of Human C4b-Binding Protein, Journal of Molecular Biology, 425, 1302, 2013.

Palermo G§, Stenta M§, Cavalli A, Dal Peraro M*, De Vivo M*, Molecular Simulations Highlight the Role of Metals in Catalysis and Inhibition of Type II Topoisomerase, Journal of Chemical Theory Computation, 9(2): 857, 2013.

  • Cover article in the issue of February 2013.

Ittig S, Lindner B, Stenta M, Manfredi P, Zdorovenko E, Knirel YA, Dal Peraro M, Cornelis GA and Zähringer U*, The Lipopolysaccharide from Capnocytophaga canimorsus Reveals an Unexpected Role of the Core-Oligosaccharide in MD-2 Binding, PLoS Pathogens, 8(5):e1002667, 2012.

Lakkaraju A, Abrami L, Lemmin T, Kunz, B Blaskovic S, Kihara A, Dal Peraro M, van der Goot FG*, Palmitoylated calnexin is a key component of the ribosome-translocon complex, EMBO Journal, 7;31(7):1823-35, 2012.

Sgrignani J, Magistrato A, Dal Peraro M, Vila AJ, Carloni P, Pierattelli R*, On the active site of mononuclear B1 metallo beta-lactamases: a computational study, Journal of Computer-Aided Molecular  Design, 26(4): 425-435, 2012.

Blasco B, Stenta M, Alonso-Sarduy L, Dietler G, Dal Peraro M, Cole S, Pojer F*, Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis, Molecular Microbiology, 82:251–264, 2011.

Iacovache I§, Degiacomi MT§, Pernot L, Schiltz M, Dal Peraro M*, van der Goot FG*, Folding of the pore-forming toxin aerolysin is catalyzed by the C-terminal propeptide, PLoS Pathogens, 7(7):e1002135, 2011.

Ho M, De Vivo M, Dal Peraro M*, Klein ML*, 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, 132(39):13702, 2010.

Wagner S§, Stenta M§, Metzger L, Dal Peraro M*, Cornelis GR*, Length control of the injectisome needle requires only one molecule of YscP, Proceeding of the National Academy of Sciences USA, 107(31):13860, 2010.

Alemani D, Collu F, Cascella M*, Dal Peraro M*, A nonradial coarse-grained potential for proteins produces naturally stable secondary structure elements, Journal of Chemical Theory and Computation, 6(1):315. 2010.

Ho M, De Vivo M, Dal Peraro M, Klein ML*, Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation, Journal of Chemical Theory and Computation, 5(6): 1657, 2009.

Cascella M*, Dal Peraro M, Challenges and perspectives in biomolecular simulations: from atomistic picture to multiscale modeling, Chimia, 63(3), 2009.

Wagner S, Sorg I, Degiacomi M, Journet L, Dal Peraro M, Cornelis GR*,The helical content of the YscP molecular ruler determines the length of the Yersinia injectisome, Molecular Microbiology, 71(2): 692, 2009.

Cascella M*, Neri M, Carloni P, Dal Peraro M, Topologically-based multipolar reconstruction of electrostatic interactions in multiscale simulation of proteins, Journal of Chemical Theory and Computation, 4(8): 1378, 2008.

  • Cover article in the issue of August 2008.

De Vivo M§*, Dal Peraro M§*, Klein ML, Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism, Journal of the American Chemical Society, 130(33):10955, 2008.

  • Highlighted in JACS Select #3 on “Molecular Modeling of Complex Chemical Systems”.

Khurana E, Devane R, Dal Peraro M, Klein ML*, Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus, Biochimica et Biophysica Acta (BBA) – Biomembranes, 1808:530, 2011.

Khurana E§, Dal Peraro M§*, Vemparala S, Devane R, DeGrado WF*, Klein ML, Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus, Proceeding of the National Academy of Sciences USA, 106(4): 1069, 2009.

Calhoun JR, Liu W, Spiegel K, Dal Peraro M, Klein ML, Wand AJ, DeGrado WF*, Solution NMR structure and molecular dynamics modeling of a designed diiron protein, Structure, 16: 210, 2008.

De Vivo M, Ensing B, Dal Peraro M, Gomez GA, Christianson DW, Klein ML*, Proton shuttles in enzymatic catalysis: phosphatase activity in soluble epoxide hydrolase, Journal of the American Chemical Society, 129: 387, 2007.

Dal Peraro M*, Spiegel K, Lamoureux G, De Vivo M, DeGrado WF, Klein ML, Modeling the charge distribution at metal sites in proteins for molecular dynamic simulations, Journal of Structural Biology, 157: 444, 2007.
Selected for the Faculty of 1000, Biology: www.f1000biology.com.

Simona F, Magistrato A, Dal Peraro M, Cavalli A, Vila AJ, Carloni P*, Common mechanistic features among metallo-β-lactamases: a computational study of Aeromonas hydrophila CphA enzyme, Journal of Biological Chemistry, 284: 28164, 2009.

Moran Barrio J, Gonzalez JM. Lisa MN, Costello AL, Dal Peraro M, Carloni P, Bennett B, Tierney DL, Limansky AS, Viale AM, Vila AJ*, The metallo-β-lactamase GOB is a mono-Zn(II) enzyme with a novel active site, Journal of Biological Chemistry, 282: 18286, 2007.

Dal Peraro M*, Vila AJ, Carloni P, Klein ML, Role of zinc content and the catalytic efficiency of B1 metallo β-lactamases. Journal of the American Chemical Society, 129: 2808, 2007. 
Selected for the Highlighted in Projects in scientific computing, Pittsburgh Supercomputing Center 2006: www.psc.edu/science/2006/enzyme.

Bucher D, Raugei S, Guidoni L, Dal Peraro M, Rothlisberger U, Carloni P*, Klein ML, Polarization effects and charge transfer in the KcsA potassium channel, Biophysical Chemistry, 124(3): 292, 2006.

Dal Peraro M*, Raugei S, Carloni P, Klein ML*, Solute-solvent charge transfer in aqueous solution. ChemPhysChem, 6: 1715, 2005. Michele Parrinello‘s Festschrift.

Dal Peraro M, Llarrull LI, Rothlisberger U, Vila AJ, Carloni P*, Water-assisted reaction mechanism of monozinc β-lactamases. Journal of the American Chemical Society, 126: 12661, 2004.

Dal Peraro M, Vila AJ, Carloni P*, Substrate binding to mononuclear metallo β-lactamase from Bacillus cereus, Proteins: Structure, Function, and Bioinformatics, 54: 412, 2004.

Dal Peraro M, Vila AJ, Carloni P*, Protonation state of Asp120 in binuclear CcrA metallo β-lactamase from Bacteroides fragilis, Inorganic Chemistry, 42: 4245, 2003. [IF: 4.6, citation: 22]

Dal Peraro M, Vila AJ, Carloni P*, Structural determinants and H-bond network of the mononuclear zinc β-lactamase active site, Journal of Biological Inorganic Chemistry, 7: 704, 2002.

Dal Peraro M, Alber F, Carloni P*, Ser133 phosphate-KIX interactions in the CREB-CBP complex: an ab initio molecular dynamics study, European Biophysical Journal, 3: 75, 2001.
 

  • Reviews

Castelli M, Cappelletti F, Diotti FA, Sauté G, Criscuolo E, Dal Peraro M, Clementi N, 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 and Developmental Immunology, doi:10.1155/2013/521231, 2013.

Stenta M, Dal Peraro, M*, An introduction to quantum chemical methods applied to drug design, Frontiers in Bioscience, E3(1):1061-1078, 2011.

Cascella M*, Dal Peraro M, Challenges and perspectives in biomolecular simulations: from atomistic picture to multiscale modeling, Chimia, 63(3), 2009.

Dal Peraro M, Ruggerone P, Raugei S, Gervasio FL, Carloni P*, Investigating biological systems with first principles Car-Parrinello molecular dynamics simulations, Current Opinion in Structural Biology, 17(2): 149, 2007.

 

  • Books and book chapters

Robertazzi A, Magistrato A, Dal Peraro M, Carloni P, First Principles DFT Studies of Metal-Based Biological and Biomimetic Systems in Metallic systems: a quantum chemists perspective, Taylor & Francis, London, 2011.

Dal Peraro M, Vila AJ, Carloni P, Catalytic Mechanism of Metallo β-Lactamases: Insights from Calculations and Experiments in Quantum Biochemistry: Electronic Structure and Biological Activity, Wiley-VCH, Weinheim, 2010.
 

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