Curriculum Vitae et studiorum

For GIORGIO COLOMBO

 

Giorgio Colombo, born in Monza (Italy) on June, 24th 1971

 

Academic Year 94/95 Laurea in Chemistry at the University of Milano (Final Grade 110/110)

 

1996-99                      Works towards his Ph.D. dissertation on Structure, Reactivity and activity of proteases: computational studies under the direction of Prof.s Scolastico and Carrea

 

Jan 1998-Jan 99          visiting scientist in Ken Merz laboratory at Penn State University as part of his doctoral training. Works on the use of mixed Quantum/Molecular mechanics methods to describe the reactivity of enzymes in solution and on the application of molecular dynamics to the study of stability-activity relationships of proteins.

 

Feb 2000                     PhD at the University of Milano

 

Dec 1999-Apr 2001    Post-doctoral research associate in Prof.s Alan Mark and Herman Berendsen laboratories at the University of Groningen, working on protein folding simulations, and membrane protein simulations. Teaching experience in the course of Biophysics for graduate and undergraduate students.

 

May 2001                    Research scientist at the CNR Istituto di Chimica del Riconoscimento Molecolare in Milano, where he started up and currently runs the computational biochemistry group.

 

 

FELLOWSHIPS AND AWARDS

 

December 1999                       Recipient of a Training and Mobility Research Programme (TMR) fellowship by the European  Community (EC)

 

December 2000                       Recipient of a Marie Curie Fellowship from the European Community commission.

 

November 2004                       Recipient of the Young Investigator Award from the Division of Biological Systems of the Italian Chemical Society          

 

ABROAD EXPERIENCE

 

January 1998-January 1999     At the Pennsylvania State University (State College, PA, USA) in the Group of Prof. Ken Merz.

 

December 1999-April 2001     At the Biophysical Chemistry Department, University of Groningen (Groningen, The Netherlands) in the Group of Prof. Alan E. Mark and Herman Berendsen.

 

 

 

REFEREE ASSISTANCE FOR JOURNALS

 

 

PUBLICATIONS

 

38) de la Paz, M.L.; De Mori, G.M.S.; Serrano, L.; Colombo, G. Sequence Dependence of Amyloid Fibril Formation. Insights from Molecular Dynamics Simulations. J. Mol. Biol., Accepted for publication 2005

 

37) Plescia, J.; Salz, W.; Pennati, M.; Zaffaroni, N.; Daidone, M.G.; Meli, M.; Dohi, T.; Fortugno, P.; Nefedova, Y.; Gabrilovich, D.I.; Colombo, G.; Altieri, D.C. Rational Design of Shepherdin, a novel anti-cancer. Cancer Cell, Accepted for publication 2005

 

36) De Mori, G. M. S.; Meli, M.; Monticelli, L.; Colombo, G.; Folding and mis-folding of peptides and proteins: Insights from molecular simulations. Mini-Rev. Med. Chem., 2005, 5(4): 353-359

 

35) Colombo, G.; Meli, M.; Canada, J.; Asensio, J.L.; Jimenez-Barbero, J. A dynamic perspective on the molecular recognition of chitooligosaccharide ligands by hevein domains. Carbohydrate Research, 2005, 340(5): 1039-1049

 

34) Ragona, L.; Colombo, G.; Catalano, M.; Molinari, H.  Determinants of protein stability and folding: comparative analysis of beta-lactoglobulins and Liver basic fatty acid binding protein. Proteins: Structure, Function and Bioinformatics, Accepted for publication 2005

 

33) Colombo, G.; Daidone, I.; Gazit, E.; Amadei, A.; Di Nola, A. Molecular dynamics simulation of the aggregation of the core recognition motif of the islet amyloid polypeptide in explicit water. Proteins: Structure, Function and Bioinformatics, Accepted for publication 2005

 

32) De Mori, G.M.S.; Colombo, G.; Micheletti, C. Investigating protein folding by combining coarse-grained Monte Carlo sampling and all-atom Molecular Dynamics: characterization of the Villin Headpiece folding mechanism. Proteins: Structure, Function and Bioinformatics, 2005, 58(2): 459-471

 

31) Colombo, G.; Folding and mis-folding of peptides and proteins: Insights from molecular simulations. Mem. S.A. It., Suppl. Nr. 4, 2004, 24-36

 

30) Simona, F.; Tiana, G.; Broglia, R.A.; Colombo, G. Modeling the a-helix to b-hairpin transition mechanism and the formation of oligomeric aggregates of the fibrillogenic peptide Ab(12-28): Insights from all-atom molecular dynamics simulations. Journal of Molecular Graphics and Modelling, 2004, 23(3): 263-273

 

29) De Mori, G.M.S.; Micheletti, C.; Colombo, G. All-atom folding simulations of the Villin headpiece from stochastically-selected coarse-grained structures. Journal of Physical Chemistry B 2004, 33: 12267-12270

 

28) Soto, P.; Colombo, G. Characterization of the conformational space of a triple stranded b-sheet forming peptide with Molecular Dynamics simulations. Proteins: Structure, Function and Bioinformatics 2004, 57(4): 734-746

 

27) Colombo, G.; Meli, M.; Carrea, G.; Enzyme reactivity studied by Computer simulations. Handbook of theoretical and computational Nanotechnologies. Accepted for publication 2004

 

26) Daidone, I.; Simona, F.; Roccatano, D.; Broglia, R.A.; Tiana, G.; Colombo, G.; Di Nola, A.;

b-Hairpin conformation of fibrillogenic peptides: Structure and a-b transition mechanism revealed by molecular dynamics simulations.

Proteins: Structure, Function and Bioinformatics. 2004, 57(1): 198-204

 

25) Tiana, G.; Simona, F.; Broglia, R.A.; Colombo, G.; Thermodynamics of b-amyloid fibril formation. J. Chem. Phys., 2004, 120: 8307

 

24) L. Monticelli and G. Colombo. The influence of simulation conditions in Molecular Dynamics investigations of model b-sheet peptides. Theoretical Chemistry Accounts. 2004, 112: 145-157

 

23) Colombo, G.; Meli, M.; Canada, J.; Asensio, J.L.; Jimenez-Barbero, J. Towards the understanding of the structure and dynamics of Protein-Carbohydrate interactions: Molecular Dynamics studies of the complexes between hevein and oligosaccharidic ligands. Carbohydrate Research. 2004, 339: 985-994

22) Tiana, G.; Simona, F.; Broglia, R.A.; De Mori, G.M.S.; Colombo, G. Understanding the determinants of folding and stability of small proteins from their energetics. Protein Science 2004, 13(1): 113-124

21) Colombo, G.; Danieli, B.; Riva, S.  Remote control of enzyme selectivity: the case of stevioside and steviolbioside. Tetrahedron, 2004, 60(3): 741-746

20) Consonni, R.; Arosio, I.; Recca, T.; Longhi, R.; Colombo, G.; Vanoni, M.; Structure determination and dynamics of peptides overlapping the catalytic hairpin of the Ras-specific GEF CDC25Mm. Biochemistry. 2003, 42(42): 12154-12162

 

19) Volonterio, A.; Bellosta, S.; Bravin, F.; Bellucci, C.; Bravo, P.; Colombo, G.; Malpezzi, L.; Mazzini, S.; Meille, S.; Meli, M.; Ramírez de Arellano, C.; Zanda, M. Synthesis, Structure and Conformation of Partially-Modified Retro and Retro-inverso Y[NHCH(CF3)]Gly-Peptides. Chemistry - An European Journal. 2003, 84(18): 4510-4522

 

18) Colombo, G.; Marrink, S.J., Mark, A.E. Simulation of MscL gating in a membrane bilayer under stress. Biophysical J. 2003, 84: 2331-2337

 

17) Colombo, G.; de Mori, G.M.S., Roccatano, D. Interplay between hydrophobic cluster and loop propensity in b-hairpin formation: a Molecular Dynamics view. Protein Science. 2003, 12 (3): 538-550

16) Colombo, G.; De Mori, G.M.S.; Curnis, F.; Gasparri, A.; Longoni, C.; Sacchi, A.; Longhi, R.; Corti, A. Structure activity relationships of linear and cyclic peptides containing the NGR tumor homing motif. Journal of Biological Chemistry 2002, 49, 47891-47897

 

15) De Filippis, V.; Colombo, G.; Russo, I.; Spadari, B.; Fontana, A.; Probing hirudin-thrombin interaction by incorporation of noncoded aminoacids and molecular dynamics simulations. Biochemistry 2002, 41, 13556-13569

 

14) Roccatano, D.; Colombo, G.; Fioroni, M.; Mark, A.E. Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: a molecular dynamics study. Proceedings of the National Academy of Sciences, USA 2002, 99, 12179-12184

 

13) Colombo, G.; Carrea, G. Modelling Enzyme Reactivity in Organic Solvents and Water through Computer Simulations. Journal of Biotechnology 2002, 96, 23-33

 

12) Colombo, G.; Roccatano, D.; Mark, A.E. Folding and Stability of the Three-Stranded-b peptide Betanova: Insights from Molecular Dynamics Simulations. Proteins: Structure, Function and Genetics, 2002, 46, 380-392

 

11) Bernardi, A.; Belvisi, L.; Galgano, M.; Colombo, G. Simulation of Carbohydrate-Protein Interactions: Computer Aided Design of a Second Generation Mimics. Journal of Computer Aided Molecular Design, 2001, 117-128

 

10) Kassi, L.; DeAmici, M.; DeMicheli, C.; Carrea, G.; Ottolina, G.; Colombo, G. b3-Adrenergic Receptor Ligands: Insights into Structure-Activity Relationships Using MC Conformational Analysis in Water. Tetrahedron, 2001, 57, 1849-1855

 

9) Colombo, G.; Carrea G. Coupling High Enzyme Activity and Stability: a Challenging Target. Trends in Biotechnology, 2000, 18, 401-402

 

8) Colombo, G.; Ottolina, G.; Carrea, G. Modeling of Enzyme Properties in Organic Solvents, Review. Chemistry Monthly-Monatschefte fur Chemie, 2000, 131, 527-547

 

7) Colombo, G.; Ottolina, G.; Carrea, Merz, K.M. Jr. Modeling the Enantioselectivity of Subtilisin in Water and Organic Solvents: Insights from MD and QM/MM studies. Chemical Communication, 2000, 559-560

 

6) Colombo, G.; Toba, S.; Merz, K.M. Jr. Rationalization of the Enantioselectivity of Subtilisin in DMF. Journal of the American Chemical Society, 1999, 121, 3486-3493

 

5) Toba, S.; Colombo, G.; Merz, K.M. Jr. Solvent Dynamics and Mechanism of Proton Transfer in Human Carbonic Anhydrase II. Journal of the American Chemical Society, 1999, 121, 2290-2302

 

4) Colombo, G.; Merz, K.M. Jr. Stability and Activity of a Mesophilic Protein and its Thermophilic Homolog: Insights from Molecular Dynamics Simulations. Journal of the American Chemical Society, 1999, 121, 6895-6903

 

3) Colombo, G.; Ottolina, G.; Carrea, G.; Bernardi, A.; Scolastico, C. Application of Structure-based Thermodynamic Calculations to the Rationalization of the Enantioselectivity of Subtilisin in Organic Solvents. Tetrahedron: Asimmetry, 1998, 3, 1205-1214

 

2) Bernardi, A.; Colombo, G.; Scolastico, C. Enantioselective Mukaiyama-Michael Reactions of 2-Carbomethoxycyclopentenone Catalyzed by Chiral Bis(Oxazoline)-Cu(II) Complexes. Tetrahedron Lett. 1996, 49, 8921-8924

 

1) Ottolina, G.; Secundo, F.; Colombo, G.; Carrea, G. Optimization of Enantiomeric Resolutions Through Solvent Selection. Book section in Enzymes in non-aqueous media”, Ed. John Walker, Humana Press, Inc.

 


Submitted

 

39) Curnis, F.; Longhi, R.; Colombo, G.; Corti, A. Immunogenic and structural properties of the NGR tumor homing motif. Submitted 2004

 

40) Castiglione, F.; Marazzi, A.; Meli, M.; Colombo, G. Structure elucidation and 3D solution conformation of the antibiotica Enduracidin determined by NMR and Molecular Dynamics. Submitted 2005

 

41) Floek, D.; Colombo, G.; Colacino, S.; Di Nola, A. Misfolding of the beta-Amyloid peptide: A molecular dynamics study. Submitted 2005

 

42) Roccatano, D.; Fioroni, M.; Zacharias, M.; Colombo, G. Effect of hexafluoroisopropanol alcohol on the structure of Melittin: a molecular dynamics simulation study. Submitted 2005

 

43) Colacino, S.; Tiana, G.; Broglia, R.A..; Colombo, G. The determinants of stability in the Human Prion Protein: Insights into folding and misfolding from the analysis of the change in the stabilization energy distribution in different conditions. Submitted 2005

 

44) Colombo, G.; Micheletti C. Protein folding simulations: increasing sampling by the combination of coarse-grained and all-atom simulations.  Submitted  2005

 

MOST RELEVANT PRESENTATIONS

 

Invited Lecture at the School of Medicine, University of Massachusetts, Worcester, USA, April 15th 2005.

Title of the Lecture: Exploring Folding and Aggregation with Molecular Simulations.

 

Invited Lecture at the Department of Physiology and Biophysics, The Mount Sinai School of Medicine, New York, USA, April 8th 2005.

Title of the Lecture: Exploring Folding and Recognition with Molecular Dynamics.

 

Award Lecture at the National Congress of the Division of Biological Systems-Italian Chemical Society. November 11th-13th 2004, Caserta, Italy.

 

Invited Speaker at the Workshop Theoretical Physics Methods in Quantitative Biology,

Sept. 23rd-25th 2004, Università di Milano Bicocca, Milano, Italy.

Title of the Presentation: All-atom folding simulations of small protein from stochastically selected coarse grained structures.

 

Invited Speaker at the International Summer School: Advanced Modeling of Biological Function, August 7th-13th 2004, International University of Bremen, Germany.

Title of the Lecture: The investigation of Biomolecular Systems: What an Simulations Tell Us? 

 

Invited speaker at the 2004 ISQBP President's Meeting, the biannual meeting of the International Society for Quantum Biology and Pharmacology, June 5-8th 2004, Como, Italy.

Title of the presentation: Study of the Villin Headpiece folding by computing
coarse-grained Monte Carlo evolution and all-atom Molecular dynamics

 

Invited Lecture at the Department of Organic Chemistry, CSIC Madrid, Spain, April 15-18th 2004.

Title of the Lecture: Molecular Simulations of Biological Systems.

 

Invited Seminar presso l’Istituto Nazionale per lo Studio e la Cura dei Tumori, Milano January 21st  2004.

Titol of the presentation: Mechanism, folding and design of biological systems: what can molecular simulations tell us?

 

Invited Plenary lecture at the V meeting of the Italian Computational Chemistry Group, December 18-19th 2003, Siena, Italy.

Title of the presentation: QM/MM studies of enzyme selectivity.

 

Invited lecture at the Faculty of Pharmacy of the University of Coimbra, Portugal, December 4th 2003.

Title of the lecture: Folding, Stability and Mechanisms of Biomolecules. Lessons from Biomolecular simulations.

 

Invited Speaker at the XXI National Congress of the Italian Chemical Society, June 22-27th 2003, Turin Italy.

Title of the presentation: Folding and Stability of small proteins and peptides: what can MD simulations tell us? 

 

Invited Lecture at the SCMBB-Bruxelles, Universite Libre Bruxelles (Belgium), May 19th  2003.

Title of the presentation: New Methods to investigate protein folding.

 

Invited for an Oral Communication at the 2nd Workshop on Molecular theories and simulations. Gaeta, Italy, May 13-15th, 2003.

Title of the presentation: Combining Simplified and all-atom methods to investigate protein folding.

 

Invited Speaker in the Monthly Seminars Series at The department of Chemistry of Penn State University. The Pennsylvania State University, October 11th 2002.

Title of the presentation: The factors influencing the folding and stability of secondary structure forming peptides: MD investigations

 

Invited for a seminar at the Abdus Salam international centre for theoretical physics, May 30th 2002, Trieste, Italy.

Title of the presentation: Molecular dynamics simulations of the folding and stability of peptides.

 

Invited for an Oral Communication at the 1st Workshop on Molecular theories and simulations. Gaeta, Italy, May 10-12th, 2002.

Title of the presentation: Simulation MscL gating under pressure.

 

Invited speaker at the 10th European Congress on Biotechnology July 8-11th 2001, Madrid, Spain.

Title of the presentation: Understanding Enzyme Mechanism, Stability and Activity via Molecular Simulations

 

Invited for an Oral Communication at the International Workshop: Structural characterization of Proteins by NMR, X-ray diffraction and computational methods. San Vito di Cadore, Italy, September 27-30th, 2001.

Title of the presentation: Folding and Stability of a three stranded b-sheet peptide: Molecular dynamics simulations.

 

Invited for an Oral Communication at the International Congress: Biostabilization. Lisbon, Portugal April 9-12th, 2000.

Title of the Presentation: . Stability and Activity of a Mesophilic Protein and its Thermophilic Homolog: Insights from Molecular Dynamics Simulations.

 

Invited for a seminar at the Instituto de Quimica Organica General (CSIC), July 11th 2001 Madrid, Spain.

Title of the presentation: Molecular dynamics simulations of three stranded b-peptides folding

 

Invited for an Oral Communication at the Giornata di studio della divisione dei sistemi biologici della Società Chimica Italiana – Modeling and computational methods: New perspectives in the study of folding and binding mechanisms of biomolecules, March 29th 2001, Milano, Italy

Title of the presentation: Molecular dynamics simulations of three stranded b-peptides folding

 

Invited for an Oral Communication at the 10th Annual Biomos Meeting September 6-8th 2000, Burg Arras, Alf-Mosel, Germany.

Title of the presentation: Folding and Stability of the Three-Stranded-b peptide Betanova: Insights from Molecular Dynamics Simulations

 

Invited for an Oral Communication at the International Symposium: Modulation of enzyme properties by protein and medium engineering. October 20th, 2000, Milano, Italy.

Title of the Presentation: . Stability and Activity of a Mesophilic Protein and its Thermophilic Homolog: Insights from Molecular Dynamics Simulations.

 

 

Communications to Congresses

 

2004 Gordon Research Conference on Biopolymers, June 13-18th 2004, Newport RI, USA.

Poster Titled: All-atom folding simulations of Small Proteins from stochastically-selected coarse-grained structures

 

2004 ISQBP President's Meeting, the biannual meeting of the International Society for Quantum Biology and Pharmacology, June 5-8th 2004, Como, Italy

Poster Titled: All-atom folding simulations of Small Proteins from stochastically-selected coarse-grained structures

 

SCI Workshop: From Genes to Molecules, February 8-10th, 2002. Certosa di Pontignano, Siena, Italy.

1          Poster Titled: Molecular dynamics simulations of secondary structure forming peptides in 2,2,2-trifluoroethanol/water mixtures. (Winner of the best poster award) M. Fioroni, D. Roccatano and G. Colombo.

2          Poster Titled: Reverse turn mimetic bicyclic lactams: Application to the design of beta-hairpin like peptides. L. Belvisi, G. Colombo, M. Colombo, L. Manzoni, D. Potenza, C. Scolastico.

 

ESS Workshop: Flexibility and Function of Proteins, January 25-27th, 2002. Heidelberg, Germany.

Poster Titled: A systematic molecular dynamics study of the conformational behavior of Betanova and its mutants. P. Soto, G. Colombo, A.E. Mark

 

Workshop on Carbohydrate Recognition, September 21th, 2001 Università di Milano, Milano Italy.

Poster Titled: Design and synthesis of ganglioside GM1 mimics. D. Arosio, A. Bernardi, G. Colombo, S. Sonnino, D. Potenza.

 

FEBS Forum of Young Scientists. Protein Structure-Function, Trafficking and Signaling. Instituto de Tecnologia Quimica e Biologica ITQB, June 28-30th, 2001. Oeiras, Portugal.

Poster Titled: A molecular dynamics study of a three stranded antiparallel beta-sheet forming peptide and some of its mutants. P.Soto, G. Colombo, A.E. Mark

 

27th meeting of the Federation of European biochemical societies FEBS. June 30th to July 5th 2001, Lisbon, Portugal

Poster Titled: A molecular dynamics study of a three stranded antiparallel beta-sheet orming peptide and some of its mutants. P.Soto, G. Colombo, A.E. Mark

 

Conference of the SIMU Programme "Bridging the Time-Scale Gap", Konstanz, Germany, September 10 -13, 2001.

Poster Titled: A molecular dynamics study of a three stranded antiparallel beta-sheet forming peptide and some of its mutants. P.Soto, G. Colombo, A.E. Mark

 

Biotrans 1999. 4th International conference on Biocatalysis and Biotransformations. Taormina, Italy. September 26-October 1 1999.

1          Poster Titled: Rationalization of the enantioselectivity of subtilisin in DMF and hexane. G Colombo, G. Ottolina, G. Carrea, K.M. Merz, Jr.

2          Poster Titled: Enzymatic modification of natural glycosides: the case of stevioside and steviolbioside. G. Colombo, B. Danieli, S. Riva.

 

TEACHING EXPERIENCE

 

Appointed as professor for the Bioinformatics course at the faculty of Biotechnology, University of Milano, year 2004.

 

Taught several graduate and undergraduate courses in biophysics, computational chemistry and computational biology at the graduate and undergraduate level (IRCCS Candiolo (Italy), Politecnico di Milano (Italy), University of Groningen (Holland))

 

Dr. Colombo has been and currently is the supervisor of several master and Ph.D. students.

 

                                                          

 

INDUSTRIAL COLLABORATIONS

 

Since March 2002                   Scientific Consultant for Vicuron S.P.A. in the field of drug design of new antibiotic molecules.

 

Since September 2002             Scientific Consultant for Nicox Research Institute S.r.l.

 

COMPUTER SKILLS:

 

Operating Systems:                                         Linux, Unix, Windows (95-98), MS-DOS

                                                                       Set up and run a Bouwolf PC cluster

Programming Languages:                                 C, Fortran

Known Programs:                                           Biochemical Systems Simulation:

AMBER, ROAR,DivCon, MACROMODEL, Biosym-Insight, GROmacs

                                                                       Gaussian94, Midas Plus

                                                                       Utility Programs

                                                                       Microsoft Word, Excel, Isis-Draw  Microsoft Office.

 

ACADEMIC REFERENCES:

 

                       Dr. Kenneth M. Merz, Jr.

                                                                       152 Davey Laboratory

                                                                                  Department of Chemistry

                                                                       The Pennsylvania State University

                                                                       University Park, PA 16802 (USA)

                                                                       E-mail: merz@roar.chem.psu.edu

 

                                                                       Prof. Anna Bernardi

                                                                       Dipartimento di Chimica Organica e Industriale

                                                                       Università degli Studi di Milano

                                                                       Via Venezian 21, 20133

                                                                       Milano(Italy)

                                                                       Tel: ++39-02-2367593

                                                                       E-mail: Anna.Bernardi @unimi.it

 

                                                                       Prof. Dr. Alan E. Mark

                                                                       Department of Biophysical Chemistry

                                                                       Nijenborgh 4, 9747 AG

                                                                       Groningen (The Netherlands)

                                                                       E-mail: A.E.Mark @chem.rug.nl

 

 

Working Address                                                      Giorgio Colombo

                                                                       Istituto di Chimica del Riconoscimento Molecolare

                                                                       Via Mario Bianco 9, 20131

                                                                       Milano, Italy

Tel:++39-02-28500031

E-Mail: giorgio.colombo@icrm.cnr.it