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Institute for Research in Biomedicine
Istituto di Ricerca in Biomedicina

Via Vincenzo Vela 6 - CH-6500 Bellinzona
Tel. +41 91 820 0300 - Fax +41 91 820 0302 - info [at] irb [dot] usi [dot] ch

Andrea Cavalli, PhD

Biologia Strutturale Computazionale

Direttore di laboratorio

Via Vela, 6
6500 Bellinzona, Switzerland

Bio

Andrea Cavalli si è laureato in fisica teorica presso l'ETH di Zurigo nel 1995 e ha conseguito il dottorato di ricerca in matematica nel 2001. Dopo un periodo nel gruppo di Amedeo Caflisch presso l'Università di Zurigo, nel 2004 entra a far parte dei gruppi di Christopher Dobson e Michele Vendruscolo presso l'Università di Cambridge (UK), con un Advanced Research Fellowship dal Fondo Nazionale Svizzero. Durante questo periodo, il suo lavoro si è focalizzato sullo sviluppo di metodi teorici e computazionali per la determinazione della struttura delle proteine ​​da dati sperimentali. Questa linea di ricerca ha portato allo sviluppo del metodo CHESHIRE che ha reso possibile la prima determinazione accurata dello stato nativo di proteine ​​usando chemical shift NMR (Cavalli et al., Proc Natl Acad Sci USA (2007), vol. 104 (23) pp 9615-9620) e, successivamente, la caratterizzazione strutturale dello stato intermedio di una proteina (Neudecker et al., Science (2012), vol. 336 (6079), pp 362-36). Nel dicembre 2012 è entrato a far parte dell’IRB come ricercatore aggiunto ed è stato nominato group leader nel giugno del 2016. La sua ricerca è focalizzata sullo sviluppo di metodi computazionali per la determinazione della struttura dei vari stati di ripiegamento delle proteine ​​a partire da un numero esiguo di dati sperimentali.

Pubblicazioni
Compartmentalized activities of the pyruvate dehydrogenase complex sustain lipogenesis in prostate cancer
J. Chen, I. Guccini, D. D. Mitri, D. Brina, A. Revandkar, M. Sarti, E. Pasquini, A. Alajati, S. Pinton, M. Losa, G. Civenni, C. V. Catapano, J. Sgrignani, A. Cavalli, R. D'Antuono, J. M. Asara, A. Morandi, P. Chiarugi, S. Crotti, M. Agostini, M. Montopoli, I. Masgras, A. Rasola, R. Garcia-Escudero, N. Delaleu, A. Rinaldi, F. Bertoni, J. Bono, A. Carracedo, A. Alimonti
in Nat Genet (2018)
A Human Bi-specific Antibody against Zika Virus with High Therapeutic Potential
J. Wang, M. Bardelli, D. A. Espinosa, M. Pedotti, T. S. Ng, S. Bianchi, L. Simonelli, E. X. Y. Lim, M. Foglierini, F. Zatta, S. Jaconi, M. Beltramello, E. Cameroni, G. Fibriansah, J. Shi, T. Barca, I. Pagani, A. Rubio, V. Broccoli, E. Vicenzi, V. Graham, S. Pullan, S. Dowall, R. Hewson, S. Jurt, O. Zerbe, K. Stettler, A. Lanzavecchia, F. Sallusto, A. Cavalli, E. Harris, S. M. Lok, L. Varani, D. Corti
in Cell (2017) vol. 171 pp229-241 e15
* J. Wang and M. Bardelli contributed equally ; S-M Lok, L.Varani and D. Corti contributed equally.
Single or Multiple Access Channels to the CYP450s Active Site? an Answer from Free Energy Simulations of the Human Aromatase Enzyme
A. Magistrato, J. Sgrignani, R. Krause, A. Cavalli
in J Phys Chem Lett (2017) vol. 8 pp2036-2042
The Dynamic Basis for Signal Propagation in Human Pin1-WW
S. Olsson, D. Strotz, B. Vogeli, R. Riek, A. Cavalli
in Structure (2016) vol. 24 pp1464-75
S. Olsson and A. Cavalli are co-corresponding authors.
Enzymatic and Inhibition Mechanism of Human Aromatase (CYP19A1) Enzyme. A Computational Perspective from QM/MM and Classical Molecular Dynamics Simulations
J. Sgrignani, A. Cavalli, G. Colombo, A. Magistrato
in Mini Rev Med Chem (2016) vol. 16 pp1112-24
Metainference: A Bayesian inference method for heterogeneous systems
M. Bonomi, C. Camilloni, A. Cavalli, M. Vendruscolo
in Science Advances (2016) vol. 2 pp e1501177
Molecular Determinants for Unphosphorylated STAT3 Dimerization Determined by Integrative Modeling
J. Sgrignani, S. Olsson, D. Ekonomiuk, D. Genini, R. Krause, C. V. Catapano, A. Cavalli
in Biochemistry (2015) vol. 54 pp5489-501
Quantification of Entropy-Loss in Replica-Averaged Modeling
S. Olsson, A. Cavalli
in J Chem Theory Comput (2015) vol. 11 pp3973-7
Dynamic binding mode of a Synaptotagmin-1-SNARE complex in solution
K. D. Brewer, T. Bacaj, A. Cavalli, C. Camilloni, J. D. Swarbrick, J. Liu, A. Zhou, P. Zhou, N. Barlow, J. Xu, A. B. Seven, E. A. Prinslow, R. Voleti, D. Haussinger, A. M. Bonvin, D. R. Tomchick, M. Vendruscolo, B. Graham, T. C. Sudhof, J. Rizo
in Nat Struct Mol Biol (2015) vol. 22 pp555-64
Analysis of the performance of the CHESHIRE and YAPP methods at CASD-NMR round 3
A. * Cavalli, M. Vendruscolo
in J Biomol NMR (2015) vol. 62 pp503-9
* Co-corresponding author
Molecular Dynamics of Biomolecules through Direct Analysis of Dipolar Couplings
S. Olsson, D. Ekonomiuk, J. Sgrignani, A. Cavalli
in J Am Chem Soc (2015) vol. 137 pp6270-8
Insights into the coiled-coil organization of the Hendra virus phosphoprotein from combined biochemical and SAXS studies
M. Beltrandi, D. Blocquel, J. Erales, P. Barbier, A. * Cavalli, S. Longhi
in Virology (2015) vol. 477 pp42-55
* Co-corresponding author
Characterization of the Conformational Fluctuations in the Josephin Domain of Ataxin-3
D. Sanfelice, A. De Simone, A. Cavalli, S. Faggiano, M. Vendruscolo, A. Pastore
in Biophys J (2014) vol. 107 pp2923-2931
A probabilistic approach to the determination of native state ensembles of proteins
S. Olsson, B.R. Vögeli, A. Cavalli, W. Boomsma, J. Ferkinghoff-Borg, K. Lindorff-Larsen, T. Hamelryck
in J. Chem. Theory Comput. (2014) vol. 10 pp3484-3491
Archaeal MBF1 binds to 30S and 70S ribosomes via its helix-turn-helix domain
F. Blombach, H. Launay, A. P. Snijders, V. Zorraquino, H. Wu, B. de Koning, S. J. Brouns, T. Ettema, C. Camilloni, A. Cavalli, M. Vendruscolo, M. J. Dickman, L. D. Cabrita, A. La Teana, D. Benelli, P. Londei, J. Christodoulou, J. van der Oost
in Biochem J (2014)
ALMOST: An all atom molecular simulation toolkit for protein structure determination
B. Fu, A. B. Sahakyan, C. Camilloni, G. G. Tartaglia, E. Paci, A. Caflisch, M. Vendruscolo, A. Cavalli
in J Comput Chem (2014) vol. 35 pp1101-5
Determination of the individual roles of the linker residues in the interdomain motions of calmodulin using NMR chemical shifts
P. Kukic, C. Camilloni, A. Cavalli, M. Vendruscolo
in J Mol Biol (2014) vol. 426 pp1826-38
A conformational ensemble derived using NMR methyl chemical shifts reveals a mechanical clamping transition that gates the binding of the HU protein to DNA
A. Kannan, C. Camilloni, A. B. Sahakyan, A. Cavalli, M. Vendruscolo
in J Am Chem Soc (2014) vol. 136 pp2204-7
Replica-Averaged Metadynamics
C. Camilloni, A. Cavalli, M. Vendruscolo
in J. Chem. Theory Comput. (2013) vol. 12 pp5610-17
Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle
A. Cavalli, C. Camilloni, M. Vendruscolo
in J Chem Phys (2013) vol. 138 pp094112
Assessment of the use of NMR chemical shifts as replica-averaged structural restraints in molecular dynamics simulations to characterize the dynamics of proteins
C. Camilloni, A. Cavalli, M. Vendruscolo
in J Phys Chem B (2013) vol. 117 pp1838-43
Blind testing of routine, fully automated determination of protein structures from NMR data
A. Rosato, J. M. Aramini, C. Arrowsmith, A. Bagaria, D. Baker, A. Cavalli, J. F. Doreleijers, A. Eletsky, A. Giachetti, P. Guerry, A. Gutmanas, P. Guntert, Y. He, T. Herrmann, Y. J. Huang, V. Jaravine, H. R. Jonker, M. A. Kennedy, O. F. Lange, G. Liu, T. E. Malliavin, R. Mani, B. Mao, G. T. Montelione, M. Nilges, P. Rossi, G. van der Schot, H. Schwalbe, T. A. Szyperski, M. Vendruscolo, R. Vernon, W. F. Vranken, Sd Vries, G. W. Vuister, B. Wu, Y. Yang, A. M. Bonvin
in Structure (2012) vol. 20 pp227-36
Characterization of the conformational equilibrium between the two major substates of RNase A using NMR chemical shifts
C. Camilloni, P. Robustelli, A. De Simone, A. Cavalli, M. Vendruscolo
in J Am Chem Soc (2012) vol. 134 pp3968-71
MYD88 somatic mutations in MALT lymphomas
Z. M. Li, A. Rinaldi, A. Cavalli, A. A. Mensah, M. Ponzoni, R. D. Gascoyne, G. Bhagat, E. Zucca, F. Bertoni
in Br J Haematol (2012) vol. 158 pp662-4
Protein Structure Validation Using Side-Chain Chemical Shifts
A. B. Sahakyan, A. Cavalli, W. F. Vranken, M. Vendruscolo
in J Phys Chem B (2012)
Structure of an intermediate state in protein folding and aggregation
P. Neudecker, P. Robustelli, A. Cavalli, P. Walsh, P. Lundstrom, A. Zarrine-Afsar, S. Sharpe, M. Vendruscolo, L. E. Kay
in Science (2012) vol. 336 pp362-6
Structure-based prediction of methyl chemical shifts in proteins
A. B. Sahakyan, W. F. Vranken, A. Cavalli, M. Vendruscolo
in J Biomol NMR (2011) vol. 50 pp331-46
Using chemical shifts to determine structural changes in proteins upon complex formation
A. Cavalli, R. W. Montalvao, M. Vendruscolo
in J Phys Chem B (2011) vol. 115 pp9491-4
Using side-chain aromatic proton chemical shifts for a quantitative analysis of protein structures
A. B. Sahakyan, W. F. Vranken, A. Cavalli, M. Vendruscolo
in Angew Chem Int Ed Engl (2011) vol. 50 pp9620-3
Insights into protein-protein and enzyme-substrate interactions in modular polyketide synthases
L. Tran, R. W. Broadhurst, M. Tosin, A. Cavalli, K. J. Weissman
in Chem Biol (2010) vol. 17 pp705-16
Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins
P. Robustelli, K. Kohlhoff, A. Cavalli, M. Vendruscolo
in Structure (2010) vol. 18 pp923-33
Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins
A. De Simone, A. Cavalli, S. T. Hsu, W. Vranken, M. Vendruscolo
in J Am Chem Soc (2009) vol. 131 pp16332-3
CASD-NMR: critical assessment of automated structure determination by NMR
A. Rosato, A. Bagaria, D. Baker, B. Bardiaux, A. Cavalli, J. F. Doreleijers, A. Giachetti, P. Guerry, P. Guntert, T. Herrmann, Y. J. Huang, H. R. Jonker, B. Mao, T. E. Malliavin, G. T. Montelione, M. Nilges, S. Raman, G. van der Schot, W. F. Vranken, G. W. Vuister, A. M. Bonvin
in Nat Methods (2009) vol. 6 pp625-6
Fast and accurate predictions of protein NMR chemical shifts from interatomic distances
K. J. Kohlhoff, P. Robustelli, A. Cavalli, X. Salvatella, M. Vendruscolo
in J Am Chem Soc (2009) vol. 131 pp13894-5
Folding of small proteins by Monte Carlo simulations with chemical shift restraints without the use of molecular fragment replacement or structural homology
P. Robustelli, A. Cavalli, C. M. Dobson, M. Vendruscolo, X. Salvatella
in J Phys Chem B (2009) vol. 113 pp7890-6
A coupled equilibrium shift mechanism in calmodulin-mediated signal transduction
J. Gsponer, J. Christodoulou, A. Cavalli, J. M. Bui, B. Richter, C. M. Dobson, M. Vendruscolo
in Structure (2008) vol. 16 pp736-46
Determination of protein structures in the solid state from NMR chemical shifts
P. Robustelli, A. Cavalli, M. Vendruscolo
in Structure (2008) vol. 16 pp1764-9
Identification of aggregation-prone elements by using interaction-energy matrices
J. M. Bui, A. Cavalli, J. Gsponer
in Angew Chem Int Ed Engl (2008) vol. 47 pp7267-9
Structure determination of protein-protein complexes using NMR chemical shifts: case of an endonuclease colicin-immunity protein complex
R. W. Montalvao, A. Cavalli, X. Salvatella, T. L. Blundell, M. Vendruscolo
in J Am Chem Soc (2008) vol. 130 pp15990-6
Prediction of local structural stabilities of proteins from their amino acid sequences
G. G. Tartaglia, A. Cavalli, M. Vendruscolo
in Structure (2007) vol. 15 pp139-43
Protein structure determination from NMR chemical shifts
A. Cavalli, X. Salvatella, C. M. Dobson, M. Vendruscolo
in Proc Natl Acad Sci U S A (2007) vol. 104 pp9615-20
Geometry, energetics, and dynamics of hydrogen bonds in proteins: structural information derived from NMR scalar couplings
J. Gsponer, H. Hopearuoho, A. Cavalli, C. M. Dobson, M. Vendruscolo
in J Am Chem Soc (2006) vol. 128 pp15127-35
Comparison of sequence-based and structure-based energy functions for the reversible folding of a peptide
A. Cavalli, M. Vendruscolo, E. Paci
in Biophys J (2005) vol. 88 pp3158-66
Organism complexity anti-correlates with proteomic beta-aggregation propensity
G. G. Tartaglia, R. Pellarin, A. Cavalli, A. Caflisch
in Protein Sci (2005) vol. 14 pp2735-40
Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences
G. G. Tartaglia, A. Cavalli, R. Pellarin, A. Caflisch
in Protein Sci (2005) vol. 14 pp2723-34
The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates
G. G. Tartaglia, A. Cavalli, R. Pellarin, A. Caflisch
in Protein Sci (2004) vol. 13 pp1939-41
Analysis of the distributed computing approach applied to the folding of a small beta peptide
E. Paci, A. Cavalli, M. Vendruscolo, A. Caflisch
in Proc Natl Acad Sci U S A (2003) vol. 100 pp8217-22
Fast protein folding on downhill energy landscape
A. Cavalli, U. Haberthur, E. Paci, A. Caflisch
in Protein Sci (2003) vol. 12 pp1801-3
Weak temperature dependence of the free energy surface and folding pathways of structured peptides
A. Cavalli, P. Ferrara, A. Caflisch
in Proteins (2002) vol. 47 pp305-14