Isabella Daidone Curriculum Vitae

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Isabella Daidone Curriculum Vitae

Address: University of L'Aquila Nationality: Italian, Finnish

Via Vetoio (Coppito 1) Email: isabella.daidone@univaq.it

67010 Coppito (AQ) - Italy

Current position

Current position* Associate professor (CHIM03 – Inorganic Chmistry) at the department of Physical and Chemical Sciences of the University of L’Aquila (Italy).

*23 Nov. 2012 – 22 Apr. 2013 and 15 Feb. 2015 – 14 Lug. 2015 maternity leave.

Research Interests

Keywords Brief Description

Theoretical chemistry The research activities of I. Daidone are focused on the field of molecular dynamics simulations, quantum mechanics and statistical mechanics of biomolecular systems (e.g. biopolymers, lipids) and more in general of complex molecular systems (e.g. liquids, polyatomic molecules). The main aim is the understanding and prediction of the macroscopic properties of these systems on the basis of their behavior as obtained from computer simulations and theoretical models. Her current research interests can be summarized as follows:

- Simulations of molecular and macromolecular systems with classical and combined quantum/classical methods

- Thermodynamics and statistical mechanics of molecular systems in general and more specifically of protein folding

- Kinetic models of protein folding and conformational diffusion - Algorithms for enhanced molecular dynamics sampling of proteins

(Essential Dynamics Sampling)

- Theoretical studies of chemical reactions in proteins

- Neutron scattering, fluorescence and infrared spectroscopies applied to biomolecules

Computational biophysics Statistical mechanics of macromolecules

Electron transfer processes Molecular dynamics simulation

Quantum mechanics Hybrid quantum mechanics/classical mechanics methods

Scientific Education

October 2004 Ph.D. in Chemistry

University of Rome "La Sapienza" (Italy)

Research project: Study of folding and misfolding processes by the use of computational methods

Supervisor: Prof. Alfredo Di Nola

May 2001 Degree (Laurea) in Chemistry - Summa cum laude University of Rome "La Sapienza" (Italy)

Thesis: Simulazioni di dinamica molecolare del citocromo c Supervisor: Prof. Alfredo Di Nola

July 1993 High School Diploma (Maturità Scientifica) – 60/60

Liceo "G.B. Morgagni", Rome (Italy)

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Positions and scientific experience

Jan. 2009 - May 2015 Research associate (Inorganic Chemistry) at the department of Physical and Chemical Sciences of the University of L’Aquila (Italy).

June 2007 – Feb. 2009 Marie Curie fellow (individual fellowship) at the "Computational Molecular Biophysics Group" of Prof. Jeremy C. Smith, IWR, Uni Heidelberg (Germany).

June 2005 – May 2007 Post Doctoral position at the "Computational Molecular Biophysics Group" of Prof.

Jeremy C. Smith, IWR, University of Heidelberg (Germany).

Nov. 2004 – May 2005 Post Doctoral position at the "Theoretical and Computational Physical Chemistry Group" of Prof. Alfredo Di Nola, University of Rome "La Sapienza" (Italy).

June 2007 Visiting researcher at the "Spallation Neutron Source" and the "Center for Molecular Biophysics", Oak Ridge National Laboratory - ORNL, Tennesse (USA).

Since July 2006 Collaboration with the "Applied Laserphysics & Laserspectroscopy" group of Prof.

Markus Sauer, department of physics, University of Bielefeld (Germany).

Jan. 2001 – May 2005 Collaboration with Dr. Giorgio Colombo, "Istituto di Chimica del Riconoscimento Molecolare" - CNR, Milano (Italy), and with Prof. Ehud Gazit, department of

"Molecular Microbiology and Biotechnology", University of Tel Aviv (Israel).

July 2003 Visiting researcher at the "School of Computing Sciences", group of Dr. Steven Hayward, University of East Anglia, Norwich (UK).

July 2002 Attendance to the "11

^a

Summer school on parallel computing", CINECA, Casalecchio di Reno - BO (Italy).

Jan. 2001 – April 2001 Attendance to the course: "A hierarchy of models for simulating the real world" held by Prof. H.J.C. Berendsen of the University of Gröningen (NL).

Teaching

2015-2018 Lecturer: , “Esercitazioni di Preparazioni Chimiche”, Department of Chemistry, University of L'Aquila, Italy.

2008-2018 Lecturer: , “Metodi Computazionali”, Department of Chemistry, University of L'Aquila, Italy.

2015-2017 Lecturer: , “Chimica Teorica”, Department of Chemistry, University of L'Aquila, Italy.

2008-2012 Lecturer: “Chimica Inorganica Superiore”, Department of Chemistry, University of L'Aquila, Italy.

12 Oct. 2007 Lecturer: "Protein folding in silico" (within the program "BioNoCo – Biocatalysis using non-conventional media"), Forschungszentrum Jülich GmbH, Jülich (Germany).

Summer 2007 Lecturer: "Structural Biology Weekend Seminar", IWR, University of Heidelberg

(Germany).

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2006-2008 Lecturer: "Introduction to (bio)-molecular modeling and simulation", University of Heidelberg (Germany).

2001 - 2004 Teaching Assistant: Chemistry Department, University of Rome "La Sapienza"

(Italy). Courses: "Computational Chemistry", "Elements of Chemical Informatics",

"Mathematics".

2002 - 2004 Teaching Assistant: MASTER in "Bioinformatica: applicazioni biomediche e

farmaceutiche", Biochemistry Department “A. Ross Fanelli”, University of Rome "La Sapienza" (Italy)

Supervision of students

Nov. 2017 – present PhD thesis, Akash Deep Biswas.

Scuola Normale Superiore, Pisa, Italy.

Status: Ongoing

June 2017 – Dec. 2017 Diploma thesis, Noemi Labbate.

Department of Chemistry, University of L'Aquila, Italy.

Status: Completed

June 2016 – Dec. 2016 Diploma thesis, Mattia Colalongo.

Department of Chemistry, University of L'Aquila, Italy.

Status: Completed

June 2016 – Dec. 2016 Diploma thesis, Valerio Mazzilli.

Department of Chemistry, University of L'Aquila, Italy.

Status: Completed

Sep. 2011– July 2012 Diploma thesis, Giuseppe Guarracino.

Department of Chemistry, University of L'Aquila, Italy.

Status: Completed

Mar. 2011– Mar. 2012 Diploma thesis, Andrea Le Donne.

Department of Chemistry, University of L'Aquila, Italy.

Status: Completed

Oct. 2009 – Oct. 2010 Diploma thesis, Claudio Iacobucci.

Department of Chemistry, University of L'Aquila, Italy.

Status: Completed Jan. 2007 – July 2011 PhD thesis, Lipi Thukral

"Computational Molecular Biophysics Group", IWR, Uni Heidelberg, Germany.

Status: Completed

May 2006 – April 2007 Diploma thesis, Roland Schulz (with Prof. Jeremy C. Smith)

"Computational Molecular Biophysics Group", IWR, Uni Heidelberg, Germany.

Status: Completed

March 2004 – July 2005 Diploma thesis, Giulia Rossetti (with Prof. Alfredo Di Nola)

Department of Chemistry, University of Rome "La Sapienza", Italy.

Status: Completed

Gen. 2004 – May 2005 Diploma thesis, Daniele Narzi (with Prof. Alfredo Di Nola)

Department of Chemistry, University of Rome "La Sapienza", Italy.

Status: Completed

Selected publications

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1 Zanetti-Polzi L., Aschi M., Amadei A. and Daidone I.*

Alternative Electron-Transfer Channels Ensure Ultrafast Deactivation of Light-Induced Excited States in Riboflavin Binding Protein. J. Phys. Chem. Lett. 2017, 9: 3321-3327.

2 Daidone I.*, Thukral L., Smith J.C. and Amadei A.

Monitoring the folding kinetics of a β-hairpin by time-resolved IR spectroscopy in silico. J. Phys.

Chem. B 2015, 119: 4849-4856.

3 Zanetti-Polzi L., Daidone I., Bortolotti, C.A and Corni S.

Surface packing determines the redox potential shift of cytochrome c adsorbed on gold. J. Am. Chem.

3Soc. 2014, 136: 12929-12937.

4 Daidone I., Amadei A., Zaccanti F., Borsari M. and Bortolotti C.A.

How the reorganization free energy affects the reduction potential of structurally homologous cytochromes. J. Phys. Chem. Lett., 2014, 5:1534-1540.

5 Bortolotti C.A., Amadei A., Aschi M., Borsari M., Corni S., Sola M. and Daidone I. The reversible* opening of two water channels in cytochrome c modulates the redox potential. J. Am. Chem. Soc.

2012, 134:13670-13678.

6 Zanetti-Polzi L., Amadei A., Aschi M. and Daidone I. Insight into the IR-spectra/structure relationship in* amyloid fibrils: a theoretical study on a prion peptide. J. Am. Chem. Soc. 2011, 133:11414-11417.

7 Daidone I., Di Nola A.* and Smith J.C. Molecular origin of Gerstmann-Strässler-Scheinker syndrome:*

insight from computer simulation of an amyloidogenic prion peptide. Biophys. J. 2011, 100:3000- 3007.

Press/media release: UT Scientist Uncovers Trigger to Fatal Neurodegenerative Disease (http://www.utk.edu/tntoday/2011/06/22/jeremy-smith-gss-protein/)

8 Noé F., Doose S., Daidone I., Löllmann M., Sauer M., Chodera J. and Smith J.C. Dynamical Fingerprints: Understanding biomolecular processes by combination of simulation and kinetic experiments. Proc. Natl. Acad. Sci. USA 2011, 108:4822-4827.

9 Amadei A., Daidone I., Di Nola A. and Aschi M. Theoretical-computational modelling of infrared spectra in peptides and proteins: a new frontier for combined theoretical-experimental investigations. Curr.

Opin. Struct. Biol. 2010, 20:155-161.

10 Daidone I., Neuweiler H., Doose S., Sauer M. and Smith J.C. Hydrogen-bond driven loop-closure* kinetics in unfolded polypeptide chains. PloS Comput. Biol. 2010, 6(1): e1000645.

11 Thukral L., Smith J.C. and Daidone I.* Common folding mechanism of a β-hairpin peptide via non-* native turn formation revealed by unbiased molecular dynamics simulations. J. Am. Chem. Soc. 2009, 131: 18147-18152.

12 McLain S.E., Soper A.K., Daidone I., Smith J.C. and Watts A. Charge based interactions between peptides observed as the dominant force for association in aqueous solution. Angew. Chem. Int. Ed.

2008, 47: 9059-9062.

13 Neusius T., Daidone I., Sokolov I.M. and Smith J.C. Subdiffusion in peptides originates from fractal-like structure of configuration space. Phys. Rev. Lett. 2008, 100: 188103.

14 Daidone I., Ulmschneider M., Di Nola A., Amadei A. and Smith J.C. Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding. Proc. Natl. Acad. Sci. USA 2007, 104:15230-15235.

Press/media release: UT-ORNL Governor’s Chair Unlocks Secrets of Protein Folding

( http://www.utk.edu/tntoday/2007/09/17/ut-ornl-governors-chair-unlocks-secrets-of-protein-folding/ )

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15 Daidone I., Amadei A. and Di Nola A. Theoretical characterization of α-helix and β-hairpin folding kinetics. J. Am. Chem. Soc. 2005, 127:14825-14832.

16 Daidone I., Amadei A., Roccatano D. and Di Nola A. Molecular dynamics simulation of protein folding by essential dynamics sampling: folding landscape of horse heart cytochrome c. Biophys. J., 2003, 85:2865-2871.

* corresponding author

Selected conferences & talks

May 2018 Invited Speaker: “Conference on the Complex Interactions of Light and Biological Matter:

Experiments meet Theory”, ICTP, Trieste (Italy).

January 2015 Invited Seminar: “Protein folding in silico”, Scuola Normale Superiore, Pisa (Italy).

September 2011 Contributed Talk: "XXIV Congresso Nazionale della Società Chimica Italiana", Lecce (Italy) October 2010 Invited Speaker: "Protein folding dynamics: Bridging the gap between theory and

experiment", Lausanne (Switzerland)

July 2010 Invited Speaker: "2

^nd

Meeting of the Italian and Spanish Crystallographic Associations (MISCA II)", Oviedo (Spain)

February 2010 Invited Speaker: "Physics of Protein Folding and Aggregation", Bressanone, (Italy) May 2008 Invited Seminar: EMBIO meeting “Emergent organisation in complex biomolecular

systems”, ECLT - Venice (Italy)

October 2006 Invited Speaker: Workshop ”Neutron Scattering Highlights on Biological Systems”, Taormina (Italy)

June 2005 Invited Seminar: RTN meeting “Protein (mis)folding”, Institut Pasteur de Lille (France) March 2005 Invited Seminar.“Thermodynamic and kinetic characterization of peptide folding by

extended molecular dynamics simulations”, ETH Zurich – RGP, Zurich (Switzerland) January 2004 Poster: GRC “Protein folding dynamics”, Ventura, California (USA)

June 2003 Poster: PROTEINE 2002 “XVI Meeting of the protein group of the Italian Society of Biochemistry and Molecular Biology”, L’Aquila (Italy)

Years 2005-2009 Contributed Talk: Annual workshop on “Methods of Molecular Simulation”, Heidelberg (Germany)

Years 2002-2010 Invited Speaker: Annual "Workshop on Molecular theories and simulations”, Gaeta (Italy)

Honors and Awards

10/04/2017 –

10/04/2023 Habilitation to Ordinary Professor in Physical Chemistry (sector 03/A2) 12/04/2017 -

12/04/2023 Habilitation to Ordinary Professor in Inorgnic Chemistry (sector 03/B1) 29/01/2014-

29/01/2020 Habilitation to Associate Professor in Physical Chemistry (sector 03/A2) 23/12/2013 -

23/12/2019 Habilitation to Associate Professor in Inorganic Chemistry (sector 03/B1)

Year 2010 Prize: “Enrico Gavuzzo 2008-2009 per ricercatori nel campo del DRUG DESIGN” from the

Institute of Crystallography (IC) of the CNR of Bari (Italy)

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Granted Projects

Year Title Programme Value (euro)

2006 [PI]

A computational study of protein folding and fluorescence

EMBO long term fellowship 55000

2006 [PI]

A computational study of protein folding and

fluorescence (ProtFoldDyn)

Marie Curie Intra-European

Fellowship 120000

2006 [I]

Investigating the mechanism of beta-hairpin folding: a combined fluorescence- based experimental and computational approach

DFG Research Grant (Deutsche

Forschungsgemeinschaft - German Research

Foundation)

200000

2014 [I]

Prediction of optical properties of dyes and application for the rational design of time temperature integrators

Fortissimo:

Factories of the Future Resources, Technology, Infrastructure and Services for Simulation and

Modelling (7th Framework Programme)

250000

2014 [Participant]

Innovazione di prodotto e di processo per una

manutenzione,

conservazione e restauro sostenibile e programmato del patrimonio culturale

MIUR "SMART Cities and Comunities and Social Innovation” – Decreto Direttoriale 5 Luglio 2012 n.

391/RIC

13200000

Doctoral committees

01-10-2017- present Member of the committe of the PhD program in “Methods and Models for Molecuar Sciences”, Scuola Normale Superiore, Pisa (Italy).

01-10-2012 al 30-09-2017 Member of the committe of the PhD program in "Scienze Fisiche e Chimiche", University of L'Aquila (Italy).

01-10-2009 al 30-09-2012 Member of the committe of the PhD program in "Chimica per l'ambiente e per i beni culturali" University of L'Aquila (Italy).