Matteo Dal Peraro
Associate Professor
matteo.dalperaro@epfl.ch +41 21 693 18 61 http://lbm.epfl.ch
Citizenship: Italian
EPFL SV IBI-SV UPDALPE
AAB 0 48 (Bâtiment AAB)
Station 19
1015 Lausanne
+41 21 693 18 61
+41 21 693 21 52
Office:
AAB 0 48
EPFL
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SV
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IBI-SV
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UPDALPE
Web site: Web site: https://lbm.epfl.ch/
+41 21 693 18 61
EPFL
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SV-SSV
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SSV-ENS
Web site: Web site: https://sv.epfl.ch/education
EPFL SV IBI-GE
AAB
Station 15
1015 Lausanne
+41 21 693 18 61
EPFL
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SV
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IBI-SV
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IBI-SV-GE
Web site: Web site: https://bioengineering.epfl.ch/
Web site: Web site: https://go.epfl.ch/phd-edcb
EPFL STI IBI-GE
AAB
Station 15
1015 Lausanne
+41 21 693 18 61
EPFL
>
STI
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IBI-STI
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IBI-STI-GE
Web site: Web site: https://bioengineering.epfl.ch/
+41 21 693 18 61
EPFL
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STI
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STI-DEC
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STI-DIR
+41 21 693 18 61
EPFL
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SV
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SV-DEC
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SV-DIR
Fields of expertise
Computational biophysics
Modeling of biological systems
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
Publications
Infoscience publications
Journal Articles
2023
Updates on moleculARweb, the Swiss Portal for Chemistry and Structural Biology Education Using Augmented and now also Virtual Reality
Chimia. 2023-04-01. DOI : 10.2533/chimia.2023.264.2022
Article Structure and functionality of a multimeric human COQ7:COQ9 complex
Molecular Cell. 2022-11-17. DOI : 10.1016/j.molcel.2022.10.003.Online tools to easily build virtual molecular models for display in augmented and virtual reality on the web
Journal Of Molecular Graphics & Modelling. 2022-07-01. DOI : 10.1016/j.jmgm.2022.108164.Ultrasensitive Label-Free Detection of Protein–Membrane Interaction Exemplified by Toxin-Liposome Insertion
The Journal of Physical Chemistry Letters. 2022-04-04. DOI : 10.1021/acs.jpclett.1c04011.Visualization, Interactive Handling and Simulation of Molecules in Commodity Augmented Reality in Web Browsers Using moleculARweb's Virtual Modeling Kits
Chimia. 2022-02-01. DOI : 10.2533/chimia.2022.145.2021
Prolyl endopeptidase-like is a (thio)esterase involved in mitochondrial respiratory chain function
Iscience. 2021-12-17. DOI : 10.1016/j.isci.2021.103460.BET1 variants establish impaired vesicular transport as a cause for muscular dystrophy with epilepsy
Embo Molecular Medicine. 2021-11-15. DOI : 10.15252/emmm.202013787.S-acylation controls SARS-CoV-2 membrane lipid organization and enhances infectivity
Developmental Cell. 2021-10-25. DOI : 10.1016/j.devcel.2021.09.016.Democratizing interactive, immersive experiences for science education with WebXR
Nature Computational Science. 2021-10-01. DOI : 10.1038/s43588-021-00142-8.Specific Protein-Membrane Interactions Promote Packaging of Metallo-beta-Lactamases into Outer Membrane Vesicles
Antimicrobial Agents And Chemotherapy. 2021-09-01. DOI : 10.1128/AAC.00507-21.MoleculARweb: A Web Site for Chemistry and Structural Biology Education through Interactive Augmented Reality out of the Box in Commodity Devices
Journal Of Chemical Education. 2021-07-13. DOI : 10.1021/acs.jchemed.1c00179.Reviewing Challenges of Predicting Protein Melting Temperature Change Upon Mutation Through the Full Analysis of a Highly Detailed Dataset with High-Resolution Structures
Molecular Biotechnology. 2021-06-08. DOI : 10.1007/s12033-021-00349-0.CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles
Bioinformatics. 2021-04-01. DOI : 10.1093/bioinformatics/btaa742.Palmitoylated acyl protein thioesterase APT2 deforms membranes to extract substrate acyl chains
Nature Chemical Biology. 2021-04-01. DOI : 10.1038/s41589-021-00753-2.Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase
Chemical Science. 2021-01-14. DOI : 10.1039/d0sc04394j.Assessment of transferable forcefields for protein simulations attests improved description of disordered states and secondary structure propensities, and hints at multi-protein systems as the next challenge for optimization
Computational and Structural Biotechnology Journal. 2021-04-25. DOI : 10.1016/j.csbj.2021.04.050.Extensive tissue-specific expression variation and novel regulators underlying circadian behavior
Science Advances. 2021-01-01. DOI : 10.1126/sciadv.abc3781.2020
Aerolysin nanopores decode digital information stored in tailored macromolecular analytes
Science Advances. 2020-12-09. DOI : 10.1126/sciadv.abc2661.The Human RNA Helicase DDX21 Presents a Dimerization Interface Necessary for Helicase Activity
iScience. 2020-11-18. DOI : 10.1016/j.isci.2020.101811.Molecular Bases of the Membrane Association Mechanism Potentiating Antibiotic Resistance by New Delhi Metallo-beta-lactamase 1
Acs Infectious Diseases. 2020-10-09. DOI : 10.1021/acsinfecdis.0c00341.The Polyglutamine Expansion at the N-Terminal of Huntingtin Protein Modulates the Dynamic Configuration and Phosphorylation of the C-Terminal HEAT Domain
Structure. 2020-09-01. DOI : 10.1016/j.str.2020.06.008.Editorial: Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations
Frontiers In Molecular Biosciences. 2020-08-28. DOI : 10.3389/fmolb.2020.00194.Will Cryo-Electron Microscopy Shift the Current Paradigm in Protein Structure Prediction?
Journal Of Chemical Information And Modeling. 2020-05-26. DOI : 10.1021/acs.jcim.0c00177.Ligand Binding to the Collagen VI Receptor Triggers a Talin-to-RhoA Switch that Regulates Receptor Endocytosis
Developmental Cell. 2020-05-18. DOI : 10.1016/j.devcel.2020.04.015.De novo protein design enables the precise induction of RSV-neutralizing antibodies
Science. 2020-05-15. DOI : 10.1126/science.aay5051.Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms
Nature Communications. 2020-05-08. DOI : 10.1038/s41467-020-16128-5.About the need to make computational models of biological macromolecules available and discoverable
Bioinformatics. 2020-05-01. DOI : 10.1093/bioinformatics/btaa086.Salt enhances the thermostability of enteroviruses by stabilizing capsid protein interfaces
Journal of Virology. 2020-03-25. DOI : 10.1128/JVI.02176-19.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.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.Directional Local Field Potentials in the Subthalamic Nucleus During Deep Brain Implantation of Parkinson's Disease Patients
Frontiers In Human Neuroscience. 2020-09-30. DOI : 10.3389/fnhum.2020.521282.2019
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.Transmembrane Prolines Mediate Signal Sensing and Decoding in Bacillus subtilis DesK Histidine Kinase
mBio. 2019-11-01. DOI : 10.1128/mBio.02564-19.Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores
Nature Communications. 2019-10-29. DOI : 10.1038/s41467-019-12690-9.Modelling structures in cryo-EM maps
Current Opinion In Structural Biology. 2019-10-01. DOI : 10.1016/j.sbi.2019.05.024.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.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.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.KAP1 is an antiparallel dimer with a functional asymmetry
Life Science Alliance. 2019-08-01. DOI : 10.26508/lsa.201900349.Molecular Profiling and Functional Analysis of Macrophage-Derived Tumor Extracellular Vesicles
Cell Reports. 2019-06-04. DOI : 10.1016/j.celrep.2019.05.008.An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis
Molecular Cell. 2019-02-21. DOI : 10.1016/j.molcel.2018.11.033.2018
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.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.Mitochondrial cytochrome c oxidase biogenesis: Recent developments
SEMINARS IN CELL AND DEVELOPMENTAL BIOLOGY. 2018. DOI : 10.1016/j.semcdb.2017.08.055.Mapping the sensing spots of aerolysin for single oligonucleotides analysis
Nature Communications. 2018. DOI : 10.1038/s41467-018-05108-5.Electron transfer in an acidophilic bacterium: interaction between a diheme cytochrome and a cupredoxin
CHEMICAL SCIENCE. 2018. DOI : 10.1039/c8sc01615a.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.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.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.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.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
Evolution of Acid-Sensing Olfactory Circuits in Drosophilids
Neuron. 2017. DOI : 10.1016/j.neuron.2016.12.024.Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies
Scientific Reports. 2017. DOI : 10.1038/s41598-017-00266-w.2016
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.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.Olfactory receptor pseudo-pseudogenes
Nature. 2016. DOI : 10.1038/nature19824.A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria
Nature Communications. 2016. DOI : 10.1038/ncomms12527.Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity
Molecular Cell. 2016. DOI : 10.1016/j.molcel.2016.06.030.Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics
Biophysical Journal. 2016. DOI : 10.1016/j.bpj.2016.07.011.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.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.Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process
Nature Communications. 2016. DOI : 10.1038/ncomms12062.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.X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair
Chemical Communications. 2016. DOI : 10.1039/c6cc00374e.2015
Lipid Builder: A Framework To Build Realistic Models for Biological Membranes
Journal Of Chemical Information And Modeling. 2015. DOI : 10.1021/acs.jcim.5b00501.Bridged bicyclic peptides as potential drug scaffolds: synthesis, structure, protein binding and stability
Chemical Science. 2015. DOI : 10.1039/c5sc01699a.A coiled coil switch mediates cold sensing by the thermosensory protein DesK
Molecular Microbiology. 2015. DOI : 10.1111/mmi.13118.GtrA Protein Rv3789 Is Required for Arabinosylation of Arabinogalactan in Mycobacterium tuberculosis
Journal Of Bacteriology. 2015. DOI : 10.1128/Jb.00628-15.Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp 1519
Biochemistry. 2015. DOI : 10.1021/bi501227b.Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding
Scientific Reports. 2015. DOI : 10.1038/srep10549.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.The importance of dynamics in integrative modeling of supramolecular assemblies
Current Opinion In Structural Biology. 2015. DOI : 10.1016/j.sbi.2015.02.018.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.How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme
Plos One. 2015. DOI : 10.1371/journal.pone.0118684.2014
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.Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase
Journal Of Physical Chemistry B. 2014. DOI : 10.1021/jp411786z.Conference Papers
2023
Structural characterization of Prolyl endopeptidase-like, a mitochondrial protein involved in congenital myasthenic syndrome-22
2023-07-01. p. S109-S109.Using integrative structural biology for the identification of novel aerolysin-like pore forming toxins for nanopore sensing
2023-07-01. p. S116-S116.2021
Decoding Digital Information Stored in Polymer by Nanopore
2021-02-12. p. 98A-98A. DOI : 10.1016/j.bpj.2020.11.802.2020
Structural and functional divergence of duplicated mosquito Toll and Spz compared to Drosophila
2020-05-01. Annual Meeting of the American-Association-of-Immunologists - Immunology 2020, Honolulu, HI, May 08-12, 2020.2019
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.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
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.Reviews
2022
Biological nanopores for single-molecule sensing
iScience. 2022-04-07. DOI : 10.1016/j.isci.2022.104145.2021
Computational Approaches to Explore Bacterial Toxin Entry into the Host Cell
Toxins. 2021-06-28. DOI : 10.3390/toxins13070449.State-of-the-art web services for de novo protein structure prediction
Briefings In Bioinformatics. 2021-05-01. DOI : 10.1093/bib/bbaa139.2020
Single-molecule studies of amyloid proteins: from biophysical properties to diagnostic perspectives
Quarterly Reviews Of Biophysics. 2020-01-01. DOI : 10.1017/S0033583520000086.2016
Pore-forming toxins: ancient, but never really out of fashion
Nature Reviews Microbiology. 2016. DOI : 10.1038/nrmicro.2015.3.2015
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop
Structure. 2015. DOI : 10.1016/j.str.2015.05.013.Catalytic Metal Ions and Enzymatic Processing of DNA and RNA
Accounts Of Chemical Research. 2015. DOI : 10.1021/ar500314j.2014
HCV E2 core structures and mAbs: something is still missing
Drug Discovery Today. 2014. DOI : 10.1016/j.drudis.2014.08.011.Theses
2020
Characterization of Protein-Membrane Interfaces through a Synergistic Computational-Experimental Approach
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-7278.2019
Structural and functional characterisation of the KRAB-domain associated protein 1
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-7154.Characterization of Coenzyme Q Biosynthesis Proteins through Integrative Modeling at the Protein-Membrane Interface
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9641.Exploring on Protein-DNA interactions
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9426.2018
Constrained optimization applied to multiscale integrative modeling
EPFL, 2018. DOI : 10.5075/epfl-thesis-8630.2017
Studying membrane-protein interplay by modeling realistic conditions
Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-7934.2015
Modeling and Engineering Proteins Thermostability
Lausanne, EPFL, 2015. DOI : 10.5075/epfl-thesis-6637.2014
New models and techniques to simulate realistic biological membranes
Lausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6310.Book Chapters
2014
New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly
Biomolecular Modelling And Simulations; San Diego: Elsevier Academic Press Inc, 2014. p. 77-111.Infoscience
Structural characterization of Prolyl endopeptidase-like, a mitochondrial protein involved in congenital myasthenic syndrome-22
2023-07-01. p. S109-S109.Using integrative structural biology for the identification of novel aerolysin-like pore forming toxins for nanopore sensing
2023-07-01. p. S116-S116.Updates on moleculARweb, the Swiss Portal for Chemistry and Structural Biology Education Using Augmented and now also Virtual Reality
Chimia. 2023-04-01. DOI : 10.2533/chimia.2023.264.Article Structure and functionality of a multimeric human COQ7:COQ9 complex
Molecular Cell. 2022-11-17. DOI : 10.1016/j.molcel.2022.10.003.Online tools to easily build virtual molecular models for display in augmented and virtual reality on the web
Journal Of Molecular Graphics & Modelling. 2022-07-01. DOI : 10.1016/j.jmgm.2022.108164.Biological nanopores for single-molecule sensing
iScience. 2022-04-07. DOI : 10.1016/j.isci.2022.104145.Ultrasensitive Label-Free Detection of Protein–Membrane Interaction Exemplified by Toxin-Liposome Insertion
The Journal of Physical Chemistry Letters. 2022-04-04. DOI : 10.1021/acs.jpclett.1c04011.Visualization, Interactive Handling and Simulation of Molecules in Commodity Augmented Reality in Web Browsers Using moleculARweb's Virtual Modeling Kits
Chimia. 2022-02-01. DOI : 10.2533/chimia.2022.145.Prolyl endopeptidase-like is a (thio)esterase involved in mitochondrial respiratory chain function
Iscience. 2021-12-17. DOI : 10.1016/j.isci.2021.103460.BET1 variants establish impaired vesicular transport as a cause for muscular dystrophy with epilepsy
Embo Molecular Medicine. 2021-11-15. DOI : 10.15252/emmm.202013787.S-acylation controls SARS-CoV-2 membrane lipid organization and enhances infectivity
Developmental Cell. 2021-10-25. DOI : 10.1016/j.devcel.2021.09.016.Democratizing interactive, immersive experiences for science education with WebXR
Nature Computational Science. 2021-10-01. DOI : 10.1038/s43588-021-00142-8.Specific Protein-Membrane Interactions Promote Packaging of Metallo-beta-Lactamases into Outer Membrane Vesicles
Antimicrobial Agents And Chemotherapy. 2021-09-01. DOI : 10.1128/AAC.00507-21.MoleculARweb: A Web Site for Chemistry and Structural Biology Education through Interactive Augmented Reality out of the Box in Commodity Devices
Journal Of Chemical Education. 2021-07-13. DOI : 10.1021/acs.jchemed.1c00179.Computational Approaches to Explore Bacterial Toxin Entry into the Host Cell
Toxins. 2021-06-28. DOI : 10.3390/toxins13070449.Reviewing Challenges of Predicting Protein Melting Temperature Change Upon Mutation Through the Full Analysis of a Highly Detailed Dataset with High-Resolution Structures
Molecular Biotechnology. 2021-06-08. DOI : 10.1007/s12033-021-00349-0.State-of-the-art web services for de novo protein structure prediction
Briefings In Bioinformatics. 2021-05-01. DOI : 10.1093/bib/bbaa139.CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles
Bioinformatics. 2021-04-01. DOI : 10.1093/bioinformatics/btaa742.Palmitoylated acyl protein thioesterase APT2 deforms membranes to extract substrate acyl chains
Nature Chemical Biology. 2021-04-01. DOI : 10.1038/s41589-021-00753-2.Decoding Digital Information Stored in Polymer by Nanopore
2021-02-12. p. 98A-98A. DOI : 10.1016/j.bpj.2020.11.802.Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase
Chemical Science. 2021-01-14. DOI : 10.1039/d0sc04394j.Assessment of transferable forcefields for protein simulations attests improved description of disordered states and secondary structure propensities, and hints at multi-protein systems as the next challenge for optimization
Computational and Structural Biotechnology Journal. 2021-04-25. DOI : 10.1016/j.csbj.2021.04.050.Extensive tissue-specific expression variation and novel regulators underlying circadian behavior
Science Advances. 2021-01-01. DOI : 10.1126/sciadv.abc3781.Aerolysin nanopores decode digital information stored in tailored macromolecular analytes
Science Advances. 2020-12-09. DOI : 10.1126/sciadv.abc2661.The Human RNA Helicase DDX21 Presents a Dimerization Interface Necessary for Helicase Activity
iScience. 2020-11-18. DOI : 10.1016/j.isci.2020.101811.Molecular Bases of the Membrane Association Mechanism Potentiating Antibiotic Resistance by New Delhi Metallo-beta-lactamase 1
Acs Infectious Diseases. 2020-10-09. DOI : 10.1021/acsinfecdis.0c00341.The Polyglutamine Expansion at the N-Terminal of Huntingtin Protein Modulates the Dynamic Configuration and Phosphorylation of the C-Terminal HEAT Domain
Structure. 2020-09-01. DOI : 10.1016/j.str.2020.06.008.Editorial: Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations
Frontiers In Molecular Biosciences. 2020-08-28. DOI : 10.3389/fmolb.2020.00194.Will Cryo-Electron Microscopy Shift the Current Paradigm in Protein Structure Prediction?
Journal Of Chemical Information And Modeling. 2020-05-26. DOI : 10.1021/acs.jcim.0c00177.Ligand Binding to the Collagen VI Receptor Triggers a Talin-to-RhoA Switch that Regulates Receptor Endocytosis
Developmental Cell. 2020-05-18. DOI : 10.1016/j.devcel.2020.04.015.De novo protein design enables the precise induction of RSV-neutralizing antibodies
Science. 2020-05-15. DOI : 10.1126/science.aay5051.Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms
Nature Communications. 2020-05-08. DOI : 10.1038/s41467-020-16128-5.About the need to make computational models of biological macromolecules available and discoverable
Bioinformatics. 2020-05-01. DOI : 10.1093/bioinformatics/btaa086.Salt enhances the thermostability of enteroviruses by stabilizing capsid protein interfaces
Journal of Virology. 2020-03-25. DOI : 10.1128/JVI.02176-19.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.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.Structural and functional divergence of duplicated mosquito Toll and Spz compared to Drosophila
2020-05-01. Annual Meeting of the American-Association-of-Immunologists - Immunology 2020, Honolulu, HI, May 08-12, 2020.Single-molecule studies of amyloid proteins: from biophysical properties to diagnostic perspectives
Quarterly Reviews Of Biophysics. 2020-01-01. DOI : 10.1017/S0033583520000086.Directional Local Field Potentials in the Subthalamic Nucleus During Deep Brain Implantation of Parkinson's Disease Patients
Frontiers In Human Neuroscience. 2020-09-30. DOI : 10.3389/fnhum.2020.521282.Characterization of Protein-Membrane Interfaces through a Synergistic Computational-Experimental Approach
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-7278.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.Transmembrane Prolines Mediate Signal Sensing and Decoding in Bacillus subtilis DesK Histidine Kinase
mBio. 2019-11-01. DOI : 10.1128/mBio.02564-19.Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores
Nature Communications. 2019-10-29. DOI : 10.1038/s41467-019-12690-9.Modelling structures in cryo-EM maps
Current Opinion In Structural Biology. 2019-10-01. DOI : 10.1016/j.sbi.2019.05.024.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.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.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.KAP1 is an antiparallel dimer with a functional asymmetry
Life Science Alliance. 2019-08-01. DOI : 10.26508/lsa.201900349.Molecular Profiling and Functional Analysis of Macrophage-Derived Tumor Extracellular Vesicles
Cell Reports. 2019-06-04. DOI : 10.1016/j.celrep.2019.05.008.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.An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis
Molecular Cell. 2019-02-21. DOI : 10.1016/j.molcel.2018.11.033.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.Structural and functional characterisation of the KRAB-domain associated protein 1
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-7154.Characterization of Coenzyme Q Biosynthesis Proteins through Integrative Modeling at the Protein-Membrane Interface
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9641.Exploring on Protein-DNA interactions
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9426.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.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.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.Mitochondrial cytochrome c oxidase biogenesis: Recent developments
SEMINARS IN CELL AND DEVELOPMENTAL BIOLOGY. 2018. DOI : 10.1016/j.semcdb.2017.08.055.Mapping the sensing spots of aerolysin for single oligonucleotides analysis
Nature Communications. 2018. DOI : 10.1038/s41467-018-05108-5.Electron transfer in an acidophilic bacterium: interaction between a diheme cytochrome and a cupredoxin
CHEMICAL SCIENCE. 2018. DOI : 10.1039/c8sc01615a.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.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.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.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.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.Constrained optimization applied to multiscale integrative modeling
EPFL, 2018. DOI : 10.5075/epfl-thesis-8630.Studying membrane-protein interplay by modeling realistic conditions
Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-7934.Evolution of Acid-Sensing Olfactory Circuits in Drosophilids
Neuron. 2017. DOI : 10.1016/j.neuron.2016.12.024.Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies
Scientific Reports. 2017. DOI : 10.1038/s41598-017-00266-w.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.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.Olfactory receptor pseudo-pseudogenes
Nature. 2016. DOI : 10.1038/nature19824.A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria
Nature Communications. 2016. DOI : 10.1038/ncomms12527.Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity
Molecular Cell. 2016. DOI : 10.1016/j.molcel.2016.06.030.Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics
Biophysical Journal. 2016. DOI : 10.1016/j.bpj.2016.07.011.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.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.Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process
Nature Communications. 2016. DOI : 10.1038/ncomms12062.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.X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair
Chemical Communications. 2016. DOI : 10.1039/c6cc00374e.Pore-forming toxins: ancient, but never really out of fashion
Nature Reviews Microbiology. 2016. DOI : 10.1038/nrmicro.2015.3.Lipid Builder: A Framework To Build Realistic Models for Biological Membranes
Journal Of Chemical Information And Modeling. 2015. DOI : 10.1021/acs.jcim.5b00501.Bridged bicyclic peptides as potential drug scaffolds: synthesis, structure, protein binding and stability
Chemical Science. 2015. DOI : 10.1039/c5sc01699a.A coiled coil switch mediates cold sensing by the thermosensory protein DesK
Molecular Microbiology. 2015. DOI : 10.1111/mmi.13118.GtrA Protein Rv3789 Is Required for Arabinosylation of Arabinogalactan in Mycobacterium tuberculosis
Journal Of Bacteriology. 2015. DOI : 10.1128/Jb.00628-15.Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp 1519
Biochemistry. 2015. DOI : 10.1021/bi501227b.Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding
Scientific Reports. 2015. DOI : 10.1038/srep10549.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.The importance of dynamics in integrative modeling of supramolecular assemblies
Current Opinion In Structural Biology. 2015. DOI : 10.1016/j.sbi.2015.02.018.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.Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop
Structure. 2015. DOI : 10.1016/j.str.2015.05.013.Modeling and Engineering Proteins Thermostability
Lausanne, EPFL, 2015. DOI : 10.5075/epfl-thesis-6637.How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme
Plos One. 2015. DOI : 10.1371/journal.pone.0118684.Catalytic Metal Ions and Enzymatic Processing of DNA and RNA
Accounts Of Chemical Research. 2015. DOI : 10.1021/ar500314j.HCV E2 core structures and mAbs: something is still missing
Drug Discovery Today. 2014. DOI : 10.1016/j.drudis.2014.08.011.New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly
Biomolecular Modelling And Simulations; San Diego: Elsevier Academic Press Inc, 2014. p. 77-111.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.New models and techniques to simulate realistic biological membranes
Lausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6310.Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase
Journal Of Physical Chemistry B. 2014. DOI : 10.1021/jp411786z.Teaching & PhD
Teaching
Life Sciences Engineering
PhD Students
Agerova Alissa, Anton Jana Susanne, Bibekar Parth, Burov Artemiy, Cavani Edoardo, Mitsioni Marianna Fanouria, Rukes Verena, Samurkas Arthur, Singer Benedikt, Teixeira Pinto Meireles Fernando Augusto,Past EPFL PhD Students
Audagnotto Martina , Aydin Deniz , Bovigny Christophe , Bragina Maiia , Degiacomi Matteo Thomas , Fonti Giulia , Gallusser Benjamin Tobias , Kalantzi Alexandra Styliani , Krapp Lucien Fabrice , Lemmin Thomas , Mayer Simon Finn , Pezeshgi Modarres Hasan , Plattner Michel , Prunotto Alessio , Spiga Enrico , Tamo Giorgio Elikem , Theodoropoulou Anastasia , Träger Sylvain , Zhang Zhidian ,Courses
Structural biology
The course will focus on the following topics:
1. Structure: intermolecular interactions, structure of biomolecules, experimental methods in structural biology (i.e., X-ray crystallography, NMR, cryo-electron microscopy), structural classification, protein structure prediction using genomic data and machine learning.
2. Dynamics: elements of stati
Scientific literature analysis in computational molecular biology
The goal of this course is to learn to analyze a scientific paper critically, asking whether the data presented support the conclusions that are drawn. The analysis is presented in the form of a summary presentation and critical, constructive assessments of the paper.