Dr. Daniele Dell'Orco
Date of Birth: May 21st 1978
Unravelling dynamic processes in vertebrate rods phototransduction: integrating biochemical/biophysical experiments with computational modelling at a systems-level
Education / Occupation
- August 2009 - present: Alexander von Humboldt Research fellow at the Department of Biology and Environmental Sciences, University of Oldenburg, Germany. Member of the Biochemistry of Neurosensory Processes Group (head Prof. Karl-Wilhelm Koch). Main Project: Unravelling dynamic processes in vertebrate rods phototransduction: integrating biochemical/biophysical experiments with computational modelling at a systems-level
- March 2009- June-2009: FEBS Research Fellow (short visit grant) at the Department of Biophysical Chemistry, Lund University (Sweden). Project on: 1) Calcium binding proteins in vision and their dynamics; 2) Modeling the time evolution of protein corona-nanoparticle interaction in biological fluids (still running)
- February 2007 - February 2009: Post-Doc position at the Department of Chemistry and Dulbecco Telethon Institute, University of Modena and Reggio Emilia, Computational Biochemistry and Biophysics Group. Project on: multiscale modeling of protein networks involved in signal transduction
- March-May 2008: Visiting Scientist at the Systems Biology and Bioinformatics group, Dept. of Computer Science, University of Rostock (prof. O. Wolkenhauer)
- April - May 2007: Visiting Scientist at the Fraunhofer Chalmers Research Centre - Department of Systems Biology, Gothenburg, Sweden. Host: Dr. Henning Schmidt
- January 2004- January 2007: PhD in Biotechnology and Molecular Medicine at the University of Modena and Reggio Emilia, Department of Chemistry and Dulbecco Telethon Institute. Work on computational modeling of point mutation effects on protein-protein binding and on structural features of key-proteins involved in the visual cascade signaling. Thesis title "Computational simulations of protein-protein recognition: predicting mutational effects on the binding thermodynamics".
- July 2003:"Laurea in Fisica" corresponding to B.Sc. degree in Physics and M.Sc. degree in Biophysics, obtained at University of Parme, Italy, with final grade 110/110 summa cum laude. Thesis Project about "Electrostatic contributions to the reconstitution and the stability of Calbindin D9k: Surface Plasmon Resonance studies".
- August 2002- June 2003: Research activity at the Department of Biophysical Chemistry of Lund University (Sweden) concerning new approaches to protein stability and kinetics as measured by Surface Plasmon Resonance spectroscopy and computational methods (Monte Carlo simulations of the affinity for reconstitutions of fragment-complementation proteins).
- 2010: Theoretical and practical tutorial on "Concepts in Computational Systems Biology" for Master students, Practical course of Biochemistry, University of Oldenburg
- 2008: Lecturer in biophysical chemistry for the specialization school in clinical biochemistry, medical school of University of Modena and Reggio Emilia
- 2008: cycle of seminars on introductory systems biology for Bs and Ms students in Medical, Pharmaceutical and Industrial Biotechnology
- 2004-2007: assistant in undergraduate courses of biophysical chemistry and structural biology
Invited Lectures and Seminars
- 2008: University of Ferrara, Department of Biology and Evolution
- 2008: Italian Society of Pure and Applied Biophysics Conference (Rome)
- 2008: European Conference on Computational Biology (Cagliari; BITS prize award and talk)
- 2008: University of Rostock, Department of Computer Science
- 2007: University of Parma, Department of Physics
- 2007: Fraunhofer Chalmers Research Centre, Gothenburg
- 2005: Lund University, Department of Biophysical Chemistry
- Member of the Biochemical Society (UK)
- Member of the Italian Society of Biochemistry and Molecular biology (SIB)
- Member of the Bioinformatics Italian Society (BITS)
- 2009: Alexander von Humboldt Research Fellowship for 24 month-project in Germany. Project Title: Unravelling dynamic processes in vertebrate rods phototransduction: integrating biochemical/biophysical experiments with computational modelling at a systems-level
- 2009: European Science Foundation - Short Visit Grant (Lund, Sweden). Project title: Mathematical model of nanoparticle-protein interaction dynamics in biological fluids and environments
- 2009: FEBS-Short Term Fellowship (Lund, Sweden): Project Title: Ca2+ signalling in vision: biophysical characterization of Ca2+-dependent conformational changes in the neuronal calcium sensors guanylate cyclase-activating proteins (GCAPs) and determination of the protein-ion binding constants
- 2009: Blancefor Boncompagni Ludovisi Grant (Stockholm, Sweden) for support of research expenses (170,000 SEK)
- 2008: Italian Bioinformatics Society (BITS) award for the best italian PhD thesis in Bioinformatics; international reviewing committee (Peter Rice, Rebecca Wade, Alvis Brazma and Des Higgins)
- Dell'Orco, D.*, Lundqvist, M., Cedervall, T. And Linse, S. Modeling the time evolution of the nanoparticle- protein corona in a body fluid. 2010, submitted for publication
- Dell'Orco, D. , Müller, M., and Koch, K-W, Quantitative detection of conformational transitions in calcium sensor proteins, 2010, submitted for publication
- Dell'Orco, D.* and Koch, K-W, Systems biochemistry approaches to vertebrate phototransduction: toward a molecular understanding of disease. Bioch. Soc. Trans. 2010, in press
- Behnen, P., Dell'Orco, D. and Koch, K-W. The involvement of the calcium sensor GCAP1 in hereditary cone dystrophies. Biol. Chem. 2010; in press
- Dell'Orco, D., Behnen, P., Linse, S. And Koch, K-W. Mutation-induced effects on calcium binding, structural stability and guanylate cyclase activation in GCAP1 variants associated with human cone dystrophy. Cell Mol Life Sci 2010; 67(6):973-984
- Dell'Orco, D.*, Schmidt, H., Mariani, S. And Fanelli, F. Network-level analysis of light adaptation in rod cell under normal and altered conditions. Mol. BioSyst. 2009; 5(10):1232-46.
- Dell'Orco, D*. Fast predictions of thermodynamics and kinetics of protein-protein recognition from structures: from molecular design to systems biology. Mol. BioSyst., 2009; 5(4):323-34
- Dell'Orco, D*. and Schmidt, H. Mesoscopic Monte Carlo simulations of stochastic encounters between photoactivated rhodopsin and transducin in the ROS-disc membrane. J. Phys. Chem. 2008; 112(14):4419-26
- Casciari, D., Dell'Orco, D., and Fanelli. F. Homo-dimerization of neurotensin 1 receptor involves helices 1, 2 and 4: insights from quaternary structure predictions and dimerization free energy estimations. J. Chem. Inf. Mod., 2008; 48(8):1669-78
- Dell'Orco, D., Casciari, D., and Fanelli. F. Quaternary structure predictions and estimation of mutational effects on the free energy of dimerization of a β-barrel transmembrane protein. J Struct Biol. 2008; 163(2):155-62
- Dell'Orco, D. and De Benedetti, P.G. Quantitative Structure-Activity Relationship analysis of canonical inhibitors of serine proteases. J Comput Aided Mol Des. 2008 ;22(6-7):469-78
- Fanelli, F. and Dell'Orco, D. Dark and photoactivated rhodopsin share common binding modes to transducin. FEBS Lett. 2008; 582(6):991-6
- Dell'Orco D., De Benedetti PG, Fanelli F. In Silico Screening of Mutational Effects on Enzyme-Proteic Inhibitor Affinity: a Docking-based approach. BMC Struct Biol. 2007; 7:37
- Dell'Orco D., De Benedetti PG, Fanelli F. In silico screening of mutational effects on transmembrane helix dimerization: insights from rigid-body docking and molecular dynamics simulations. J Phys Chem B. 2007 Aug 2; 111(30):9114-24
- Dell'Orco, D., Seeber, M., and Fanelli, F. Monomeric dark rhodopsin holds the molecular determinants for transducin recognition: insights from computational analysis. FEBS Lett. 2007 Mar 6;581(5):944-8.
- Dell'Orco, D., Xue, W-F., Thulin, E., and Linse, S., Electrostatic contributions to the kinetics and thermodynamics of protein assembly, Biophys. J. 2005; 88(3): 1-12
- Dell'Orco, D., Seeber, M., De Benedetti PG., and Fanelli, F., Probing fragment complementation by rigid body docking: In silico reconstitution of calbindin D9k, J. Chem. Inf. Mod., 2005 Sep-Oct;45(5):1429-38.
- Fanelli, F., and Dell'Orco, D., Rhodopsin activation follows precoupling with transducin: inferences from computational analysis. Biochemistry. 2005 Nov 15;44(45):14695-700.
- Dell'Orco, D.*, De Benedetti, P.G., and Fanelli F. Single Amino Acid Contributions to Binding Affinity in Enzyme-Inhibitor Interactions: a Docking-Based Screening of BPTI-Beta Trypsin interaction, NIC Workshop 2006, From Computational Biophysics to Systems Biology, 2006 34: 67-72
* corresponding author
Current address (office):
Carl von Ossietzky Universität Oldenburg
Institut für Biologie und Umweltwissenschaften
Carl-von-Ossietzky-Str. 9 - 11
Phone: +49 (0) 441 - 798 3674