Curriculum vitae of Ciro Cecconi

Curriculum vitae of Ciro Cecconi
CONTACTS
• Department of Physics, Informatics and Mathematics,
University of Modena and Reggio Emilia,
Via Campi 213/A, 41125 Modena, Italy.
• CNR Institute of Nanoscience S3_Modena, Italy.
Via Campi 213/A, 41125 Modena, Italy.
Office: (+39) 0592055072
Lab: (+39) 0592055328
Email: [email protected]
EDUCATION
Ph.D. in Molecular and Cell Biology
University of California, Berkeley, USA - December 2003
Supervisor: Prof. Carlos J. Bustamante, Department of Physics and Molecular & Cell Biology
Thesis Title: Studies of the Mechanical Unfolding and Refolding of RNase H and T4 lysozyme.
SCIENTIFIC INTERESTS
- Protein folding pathways and energy landscapes
- Theoretical methods for the analysis of single molecule manipulation data
- Misfolding of amyloidogenic proteins
- Protein-protein and protein-lipid binding modes
- Sparsely populated states in intrinsically disordered proteins
- Molecular mechanism of chaperones in protein folding and misfolding
PROFESSIONAL EXPERIENCE
2014-present Associate Professor
Department of Physics, Informatics and Mathematics
University of Modena and Reggio Emilia
Modena, Italy.
2010-2014
Group Leader
CNR Institute of Nanoscience S3
c/o Department of Physics, Informatics and Mathematics
University of Modena and Reggio Emilia
Modena, Italy.
2006-2010
Researcher
within the program “Rientro dei Cervelli - Scientific field: Applied Physics”
Department of Physics
University of Modena and Reggio Emilia
Modena, Italy.
2004-2006
Postdoctoral fellow
Supervisor: Professor Carlos J. Bustamante
Lawrence Berkeley National Laboratory
Berkeley, CA – USA.
1996-2003
Graduate student
Supervisor: Professor Carlos J. Bustamante
Department of Physics and Molecular and Cell Biology
University of California, Berkeley – USA.
1995-1996
Visiting Scholar
NATO-CNR Advanced Fellowship - Scientific field: Physics
Supervisor: Professor Carlos J. Bustamante
Department of Molecular and Cell Biology
University of Oregon, Eugene – USA.
1992-1995
Researcher
Programma Nazionale di Ricerca e Formazione sulle Tecnologie per la
Bioelettronica (Technobiochip)
Supervisor: Professor Cesare Ascoli
Institute of Biophysics,
CNR Pisa - Italy.
1991-1992
Apprentice
Supervisor: Professor Cesare Ascoli
Institute of Biophysics,
CNR Pisa - Italy.
OTHER TITLES
- Eligible for the CNR fellowship as from Call no. 201.11.16 of 06/06/1990.
- Recipient of the INFM-CNR fellowship (call no. 999 of November 9 2005) to carry out at the
CNR-INFM S3 Research Center in Modena. The candidate did not accept this fellowship as he had
in the meanwhile been awarded the "Rientro dei Cervelli" competition.
FUNDED PROJECTS
•
Fondo di Ateneo per la Ricerca 2014 - Progetti di ricerca FAR2014. “Studio dei meccanismi di
interazione del sensore al calcio NCS-1 con partner biologici e chaperon molecolari a livello di
singola molecola”, 2015-2016.
•
Lundbeck Foundation (DK) - “Single-molecule investigations of folding and misfolding
pathways of NCS1: understanding ligand binding and chaperone interactions (R118-A11665)”,
15/04/2013 – 15/10/2014
•
Research Fellow Program for Training and Research in Italian laboratories (TRIL), ICTP,
Trieste, Italy, May 2011 – May 2012. Awarded to Mariela Otazo to spend one year as
postdoctoral fellow in my laboratory.
•
Marie Curie International Reintegration Grant (IRG) (Europe) – “SINgle protein folding
PATHways - SINPATH”- 2006-2008. This Grant has been used to reintegrate Dr. Cecconi in
Europe.
•
National Institute of Health (NIH) (USA) - “Physical Chemistry of Nucleic Acids
(5R37GM032543) “, 01/07/1999-30/06/2008.
•
US Department of Energy (DOE) (USA) - “Microscopies of Molecular Machines (DE-AC0376DF00098)“, 01/10/2003-30/06/2009.
•
National Science Foundation (USA) - “Force-induced Unfolding and Refolding of Single and
Poly-T4 Lysozyme Molecules by SFM”, 1997-1999.
FELLOWSHIPS
•
Rientro dei Cervelli - Scientific field: Applied Physics, 2006-2010.
•
NATO-CNR Advanced Fellowship - Scientific field: Physics, 1995-1996.
AWARDS
•
First poster award of the 5th International Symposium on Optical Tweezers in Life Sciences,
Berlin, Germany, June 18, 2013.
•
Best communication of section IVb: Biophysics and Medical Physics, SIF-XCII National
Congress - Turin, September 18–23, 2006.
TEACHING
- Undergraduate course: Nanobiotechnology (BI-40) - (12 credits) - Academic Year 2014/2015.
Master Degree in Industrial Biotechnology - University of Modena and Reggio Emilia. Teaching
shared with Prof. Fabio Biscarini. Hours of lecture: 48.
- Graduate course: “Molecular biophysics of proteins and RNA: basic principles and single
molecule studies”, for the PhD School in Nano and Physical Sciences of the University of Modena
and Reggio Emilia (2 ECTS). Academic year 2013/2014.
- Graduate course: “Molecular biophysics of proteins and RNA: basic principles and single
molecule studies”, for the PhD School in Nano and Physical Sciences of the University of Modena
and Reggio Emilia (3 ECTS). Academic year 2010/2011.
- Graduate course: “Molecular biophysics of proteins and RNA: basic principles and single
molecule studies”, for the PhD School in Nano and Physical Sciences of the University of Modena
and Reggio Emilia (4 ECTS). Academic year 2009/2010.
- Undergraduate course: “Nanotecnologie per lo Studio di Singole Molecole e Singole Cellule –
FIS/07” (4 CFU). Academic year 2009/2010. Master degree in Biotechnology and Biological
Sciences - University of Modena and Reggio Emilia.
- Undergraduate course: “Analisi sperimentale delle conformazioni di macromolecole singole” (2
CFU), within the course Structural Biology for Biotechnologists and Biologists. University of
Modena and Reggio Emilia. Academic year 2009/2010.
- Undergraduate course: “Analisi sperimentale delle conformazioni di macromolecole singole” (12
hours total, 3 CFU), within the course Structural Biology for Biotechnologists and Biologists.
University of Modena and Reggio Emilia. Academic year 2008/2009.
- Undergraduate course: “Analisi sperimentale delle conformazioni di macromolecole singole” (12
hours total, 3 CFU), within the course Structural Biology for Biotechnologists and Biologists.
University of Modena and Reggio Emilia. Academic year 2007/2008.
- Teaching assistant for the course entitled “Biochemistry and Molecular Biology” - Department of
Molecular and Cell Biology of the University of California, Berkeley, USA, 01/1999-05/1999.
- Teaching assistant for the course entitled “Cellular Biochemistry” - Department of Molecular and
Cell Biology of the University of Oregon, Eugene, USA, winter 1997.
MAJOR ACHIEVEMENTS AND RESULTS
- Development of a new experimental method to study protein folding at the single molecule
level with optical tweezers. For many years the mechanical manipulation of single proteins relied
on the use of the atomic force microscope (AFM). The development of this new experimental
approach, which is based on the use of molecular DNA handles to manipulate individual proteins
between two polystyrene beads, has extended the study of the mechanical behavior of single
proteins to the low force regime of optical tweezers, setting the stage for a whole array of new
experiments. The development of this method has been a breakthrough in the field of molecular
biophysics and various laboratories around the world have implemented it to study protein folding
at the single molecule level. This new experimental approach is described in a publication in the
European Biophysics Journal and in a book chapter.
- Direct Observation of the Three-State Folding of a Single Protein Molecule. For the first time,
the folding process of a single globular protein (Ribonuclease H) was characterized at the single
molecule level using optical tweezers. Through mechanical manipulation, single Ribonuclease H
molecules were directly observed folding part way to an intermediate structure, and then go from
there to the folded protein. These studies provided information on the kinetic, thermodynamic and
mechanical properties of a folding intermediate state (molten globule) that had previously eluded
experimental characterization with more traditional ensemble techniques. The results of these
studies have been published in a highly cited paper in Science (more than 300 citations).
- Characterization of the cooperative communication between different structural regions of a
protein. The interaction energies between different structural domains of a protein (T4 lysozyme)
were characterized at the single molecule level using optical tweezers. By manipulating topological
variants (circular permutants) of T4 lysozyme, it was shown how the topological organization of a
protein affects the coupling and folding cooperativity between its domains. For the first time, the
Crooks fluctuation theorem was used to probe the status of a molecular region not subjected to the
denaturant (mechanical force). The results of these experiments were published in Nature.
- Characterization of the structure and energy of the transition state populated by a protein.
Through mechanical manipulation and molecular dynamics simulations it was shown that the
transition state populated by the Acyl-CoA-binding protein (ACBP) during its mechanical
denaturation has a surprisingly elongated conformation and it is quite similar, both for position
along the reaction coordinate and structure, to that populated by the protein during chemical
denaturation. These results showed that protein structures can be much more pliant to force than
previously anticipated and revealed unprecedented similarities between chemical and mechanical
denaturation of a protein. This work was published in Journal of the American Chemical Society.
- Elucidation of the folding mechanism of an EF-hand neuronal calcium sensor. Using a
combination of mechanical manipulation, molecular dynamics simulations and protein engineering
we characterized the folding mechanism of a neuronal calcium sensor (NCS-1) involved in neuronal
signaling and linked to several neurodegenerative disorders. A remarkable folding network was
revealed which was characterized by intermediate states modulated by complex calcium ion binding
processes. Using advanced statistical methods the molecular energy landscape of the molecule was
reconstructed. This work was published in Structure.
- Real-time observations of NCS-1 misfolding pathways. Through mechanical manipulations we
characterized the structural rearrangements leading to misfolded conformations of NCS1. We
identified two distinct and calcium-dependent misfolding trajectories originating from an onpathway folding intermediate and, remarkably for a calcium sensor, we showed that pathologically
high Ca2+ concentration impede correct folding of NCS1 by increasing the occupation probabilities
of its misfolded states. For the first time, these results show a putative link between Ca2+
dysregulation, neurodegeneration and protein misfolding paving the way for a new research avenue.
This work was published in PNAS.
- Development of a new method to synthesize polyproteins in the solid state and
characterization of the mechanical properties of the protein T4 lysozyme. This method involves
the formation of disulfide bonds between neighboring molecules inside a crystal and allows for the
synthesis of polyproteins made of 25 or more monomers, which can be used in AFM force
spectroscopy experiments. Using this method and a custom-built AFM, the mechanical properties of
an enzyme (T4 lysozyme) were characterized for the first time. This work was published in a highly
cited paper in Proceedings of the National Academy of Sciences of the United States of America.
- Structural characterization of protein-DNA complexes using atomic force microscopy. Of
particular importance were the studies on: i) P element transposition in Drosophila melanogaster,
which elucidated the structure of synaptic complexes formed during the early stages of this process,
and ii) replication mechanism of mitochondrial DNA (mtDNA), which provided evidence that
mtDNA replication occurs by strand displacement with alternative light-strand origins. These
studies resulted in two publications in the prestigious journal Genes & Development.
SELECTED PUBLICATIONS
[1] Naqvi M, Heidarsson PO, Otazo MR, Mossa A, Kragelund BB, Cecconi C, “Single-Molecule
Folding Mechanisms of the apo- and Mg2D-Bound States of Human Neuronal Calcium Sensor1”, Biophysical Journal 109, 113-123, (2015).
[2] Heidarsson PO, Naqvi MM, Otazo MR, Mossa A, Kragelund BB, and Cecconi C, “Direct
single-molecule observation of calcium-dependent misfolding in human neuronal calcium
sensor-1”, PNAS, 111 (36):13069-13074, (2014).
[3] Caldarini M, Sonar P, Valpapuram I, Tavella D, Volonté C, Pandini V, Vanoni MA, Aliverti A,
Broglia RA, Tiana G, Cecconi C, “The complex folding behavior of HIV-1-protease monomer
revealed by optical-tweezer single-molecule experiments and molecular dynamics simulations”,
Biophysical Chemistry 195, 32–42, (2014).
[4] Heidarsson PO, Otazo MR, Bellucci L, Mossa A, Imparato A, Paci E, Corni S, Di Felice
R, Kragelund BB, Cecconi C. “Single-Molecule Folding Mechanism of an EF-Hand Neuronal
Calcium Sensor.” Structure, 21 (10), 1812-1821, (2013).
[5] Heidarsson PO, Valpapuram I, Camilloni C, Imparato M, Tiana G, Poulsen FM, Kragelund BB,
Cecconi C, “A highly compliant protein native state with a spontaneous-like mechanical
unfolding pathway”, J. Am. Chem. Soc. 134(41), 17068-17065, (2012).
[6] Shank, E., Cecconi, C., Dill, J., Marqusee, S., Bustamante, C., “The folding cooperativity of a
protein is controlled by the topology of its polypeptide chain”, Nature 465 (7298), 637-641,
(2010).
[7] Cecconi, C., Shank, E., Marqusee, S., Bustamante, C., “Protein-DNA chimeras for single
molecule mechanical folding studies with the optical tweezers.” European Biophysics Journal,
37 (6), 729-738 (2008).
[8] Cecconi, C., Shank, E., Bustamante, C., Marqusee, S., “Direct Observation of the Three-State
Folding of a Single Protein Molecule.” Science, 309, 2057-2060, (2005).
[9] Tang, M., Cecconi, C., Kim, H., Bustamante, C., Rio, D.C., “Guanosine Triphosphate Acts as a
Cofactor to Promote Assembly of Initial P Element Transposase-DNA Synaptic Complexes.”
Genes & Development, 19, 1422-1425, (2005).
[10] Brown, T.A., Cecconi, C, Tkachuk, A.N., Bustamante, C, Clayton, D.A., “Replication of
Mitochondrial DNA Occurs by Strand Displacement with Alternative Light-Strand Origins, Not
via a Strand-Coupled Mechanism.” Genes & Development, 19, 2466-2476 (2005).
[11] Yang, G., Cecconi, C., Baase, W., Vetter, I., Bryer, W., Dahlquist, F.W., Matthews, B.,
Bustamante, C., “Solid state synthesis and mechanical unfolding of polymers of T4 lysozyme.”
Proceedings of the National Academy of Sciences of the United States of America, 97 (1), 139144, (2000).
BOOK CHAPTERS
[1] Heidarsson PO, Naqvi M, Sonar P, Valpapuram I, Cecconi C, “Conformational dynamics of
single protein molecules studied with direct mechanical manipulation”, in “Dynamics of Proteins
and nucleic acids”, series Advances in Protein Chemistry and Structural Biology, APCSB, UK:
Academic Press, 92, 93-133, (2013).
[2] Cecconi, C., Shank, E., Marqusee, S. and Bustamante, C. “DNA handles for single molecule
protein folding studies by optical tweezers.” pg 255-271, in "DNA Nanotechnology: Methods
and Protocols" , series Methods in Molecular Biology, vol. 749, The Humana Press Inc (New
York, NY, U.S.A.) ISBN 978-1-61779-141-3, (2011).
SELECTED TALKS AT CONFERENCES, WORKSHOPS AND SCHOOLS
1) “Direct Observation of Calcium-dependent Misfolding in Single Neuronal Calcium Sensor-1
Molecules”, Workshop "Single Molecule in Biology" SISSA, Trieste, Italy, June 23-24, 2015
(invited talk).
2) “Single-molecule folding mechanism of an EF-hand neuronal calcium sensor”. II Workshop of
Nanoscience Institute, Modena, Italy, June 10-11 2013.
3) “Single-Molecule Folding Pathways of an EF-Hand Calcium Sensor and a Four-Helix Bundle
Protein” - International Congress "Theory and Applications in Computational Chemistry", TACC2012, Pavia, Italy, September 2-7 2012 (invited talk).
4) “Folding and misfolding pathways of an EF-hand calcium sensor and a four-helix bundle
protein” - Workshop on Nanomedicine and Nanobiosystems (WoMen), Lecce, Italy, September 6-8
2012.
5) “Manipolazione meccanica di singole molecole di lisozima T4 con pinzette ottiche: l’importanza
della topologia nel ripiegamento cooperativo di una proteina”, XV Convegno Nazionale di Fisica
Statistica e dei Sistemi Complessi, Parma, Italy, June 21-23 2010.
6) “Studying protein folding using laser tweezers”, Workshop “Physics of Protein Folding and
Aggregation”, Bressanone (BZ), Italy, February 11-12, 2010.
7) “Single molecule mechanical unfolding of T4 lysozyme: The importance of topology in the
cooperative unfolding of a protein”, Exploratory workshop “Unraveling the structure of
biomolecules: from nonequilibrium statistical mechanics to mechanical manipulation”
(BioStruct09), Florence, Italy, February 16-18, 2009, (invited talk).
8) “Mechanical Denaturation of Single T4 Lysozyme Molecules: Effect of Topology on Folding
Pathways”, 22nd General Conference of the Condensed Matter Division of the European Physical
Society, Rome, Italy, August 25-29, 2008.
9) “Mechanical unfolding/refolding of single T4 Lysozyme molecules”, Exploratory workshop
"Physics Of The Cell: From Single Molecules To Collective Behavior''(CELLMOLL), Barcelona,
Spain, November 29th/December 1st 2006, (invited talk).
10) “Force-induced unfolding of single T4 lysozyme molecules by laser tweezers”, SIF-XCII
National Congress, Turin, Italy, September 18–23, 2006 – Awarded as best communication of
Section IVb: Biophysics and Medical Physics.
11) “Studying protein folding using laser tweezers”, International School of Physics Enrico Fermi,
Varenna (Como Lake), Italy, July 4-14, 2006.
12) “Direct Observation of the Three-State Folding of a Single Protein Molecule Using Optical
Tweezers”, Corso di perfezionamento in Microscopie Innovative per le Biotecnologie, University of
Florence, Florence, Italy, June 6-10, 2005.
INVITED SEMINARS AND LECTURES
1) “Studying protein folding through mechanical manipulation with optical tweezers”, Departament
de Fisica Fonamental, Facultat de Fisica, Universitat de Barcelona, Spain, December 13 2012,
(seminar).
2) “Single-Molecule Multi-State Folding Mechanism of an EF-Hand Calcium Sensor”, Physics
Department, University of Munich, Munich, Germany, December 16 2011, (seminar).
3) “Studying Protein Folding at Single Molecule Level Using Optical Tweezers.” Department of
Biomolecular Sciences and Biotechnology, University of Milan, Milan, Italy, November 24 2011,
(lecture for the PhD School in Biotechnology).
4) “Studying protein folding on single molecules: an application of optical tweezers”, Department
of Physics, University of Trento, Trento, Italy, March 23 2011, (seminar).
5) “Studying protein folding with laser tweezers”, Structural Biology and NMR Laboratory,
University of Copenhagen, Copenhagen N, Denmark, November 29 2010, (seminar).
6) “Studying protein folding on single molecules: an application of optical tweezers”, Department
of Molecular Medicine – Biochemistry Institute - University of Pavia, Pavia, Italy, September 24
2010, (seminar).
7) “Pinzette ottiche: principi ed applicazioni in biologia”, Chemistry Department, University of
Bologna, Bologna, Italy, December 10 2008, (lecture for undergraduate course entitled
Nanobiotechnology).
8) “Following folding trajectories of single T4 lysozyme molecules using laser tweezers: effect of
topology on folding pathways”, Polo Scientifico di Sesto Fiorentino, University of Florence,
Florence, Italy, October 16 2008, (seminar).
9) “Studio del protein folding mediante l’uso delle pinzette ottiche”, Polytechnic University of
Turin, Turin, Italy, March 12 2007, (lecture for the PhD School in Physics).
10) “Direct Observation of the Three-State Folding of a Single Protein Molecule Using Optical
Tweezers”, University of Rome La Sapienza, Rome, Italy, June 8 2005, (seminar).
11) “Guanosine Triphosphate Acts as a Cofactor to Promote Assembly of Initial P Element
Transposase-DNA Synaptic Complexes”, Institute for Chemical-Physical Processes IPCF-CNR,
Pisa, Italy, June 2 2005, (seminar).
12) “Replication of Mitochondrial DNA Occurs by Strand Displacement with Alternative LightStrand Origins, Not via a Strand-Coupled Mechanism”, Institute for Chemical-Physical Processes
IPCF-CNR, Pisa, Italy, June 1 2005, (seminar).
13) “Direct Observation of the Three-State Folding of a Single Protein Molecule Using Optical
Tweezers”, S3 Research Center, c/o University of Modena and Reggio Emilia, Modena, Italy, May
31 2005, (seminar).
14) “Direct Observation of the Three-State Folding of a Single Protein Molecule Using Optical
Tweezers”, University of Bologna, Bologna, Italy, May 30 2005, (seminar).
15) “Direct Observation of the Three-State Folding of a Single Protein Molecule Using Optical
Tweezers”, Scuola Normale Superiore di Pisa, Pisa, Italy, May 25 2005, (seminar).
16) “Study of the force-induced unfolding/refolding of RNase H by laser tweezers”, Institute of
Biophysics, CNR, Pisa, Italy, January 12 2004, (seminar).
SUPERVISOR OF GRADUATE STUDENTS AND POSTDOCTORAL FELLOWS
Supervisor of three postdoctoral fellows at the Physics Department of the University of Modena and
Reggio Emilia.
Supervisor of three graduate students of the PhD School in Nano and Physical Sciences at the
University of Modena and Reggio Emilia.
Co-Supervisor of a graduate student of the PhD School of Science at the University of Copenhagen,
Ole Maaløes vej 5, 2200 Copenhagen N, Denmark.
REFEREE FOR INTERNATIONAL JOURNALS AND PROPOSALS
International journals: Nature Chemical Biology, Journal of the American Chemical Society, ACS
Nano, The Journal of Physical Chemistry, Biophysical Journal, Journal of Molecular Recognition,
International Journal of Molecular Sciences, Beilstein Journal of Nanotechnology, International
Journal of Advanced Innovations, Thoughts & Ideas.
International proposal: Proposal for a Lise Meitner-Postdoctoral position, for the Austrian Science
Fund (FWF), 2013.
INTERNATIONAL COLLABORATIONS
- Professor Carlos J. Bustamante – University of California at Berkeley / Howard Hughes Medical
Institute, Berkeley CA 94720 - USA.
- Professor Birthe B. Kragelund - Structural Biology and NMR Laboratory, Department of Biology,
University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark.
- Professor Vittorio Bellotti - National Amyloidosis Centre, Centre for Amyloidosis and Acute
Phase Proteins, University College London, NW3 2PF London, United Kingdom & Department of
Molecular Medicine, Institute of Biochemistry, University of Pavia, 27100 Pavia, Italy.
- Dr. Emanuele Paci - Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds,
United Kingdom.
- Professor Alberto Imparato - Department of Physics and Astronomy, University of Aarhus, Ny
Munkegade, Building 1520, 8000 Aarhus C, Denmark.