Curriculum Vitae 15/4/2008
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1 Curriculum Vitae 15/4/28 PERSONAL DATA Name Miguel Ângelo dos Santos Machuqueiro Place and Date of Birth Palmela, Civil Status Married Nationality Portuguese Address I Address II Phone Rua Manuel Simões R/c B (Frente Pap. Almeida), Brejos do Assa, Palmela, Portugal ITQB-Instituto de Tecnologia Química e Biológica, UNL Molecular Simulation Group - 6º Floor (Room 61) Av. da República, EAN, Apartado Oeiras, Portugal (+351) (+351) Mobile (+351) machuque@itqb.unl.pt Web MILITARY Reserve since 1996 LANGUAGES Portuguese all levels; English all levels; French reading and conversation; Spanish reading and conversation; Italian reading and conversation; German reading; INFORMATICS Advanced user in Windows and Linux (in their wide variety of versions); Advanced user in many scientific tools like GROMACS, AutoDock, PyMOL, Spartan, etc. Good programming skills in a wide variety of languages and scripting languages (bash, awk, Perl, C, Basic, Mathematica, etc.) ACADEMIC 26- Pos-doctoral fellow at the Instituto de Tecnologia Química e Biológica, Molecular Simulation Group and Protein Modelling Group, Oeiras, Portugal Pos-doctoral fellow at the Instituto de Tecnologia Química e Biológica, Molecular Simulation Group, Oeiras, Portugal. 1
2 PhD from the University of Bern, Switzerland (Doctor of Philosophy; PhD; Dr. phil.-nat.) with the final grade of 5 out of Diploma in Biochemistry, Faculdade de Ciências da Universidade de Lisboa, with the final grade of 15 out of 2. SPECIALIZATION DOMAINS Biochemistry Theoretical Biochemistry: - Systems Biology - Kinetic Models Bioorganic & Bioinorganic Synthesis: - Chemical Models of Enzymes - Metal Catalysts - Sugar Chemistry Biotechnology: - Peptidic Dendrimers - DNA Chips - Genetic Algorithms Protein Modelling & Molecular Simulation: - Molecular Dynamics - Continuum Electrostatics - Molecular Docking - Biological Membrane Biophysics SCIENTIFIC INTERESTS (Bio)chemistry Theoretical (Bio)chemistry Computational methods for biomolecular simulations ph and Redox induced conformational changes in proteins Protein/peptide structure, folding and stabilization Protein/peptide-membrane interactions Protein/peptide-receptor interactions TUTORING EXPERIENCE Tutor in the practical course of Continuum Electrostatics, which is a part of the PhD program in computational biology of Instituto Gulbenkian da Ciência, Oeiras, Portugal Tutor in the practical course on molecular visualization, which is a part of the PhD program at Instituto de Tecnologia Química e Biológica, Oeiras, Portugal Tutor in the practical course Chemie im alltag (transl: everyday chemistry), for students in Educational Chemistry, University of Bern, Switzerland Tutor in the practical course of Organic Chemistry for students in Pharmacy, University of Bern, Switzerland. This tutoring was a part of the PhD program of this University. 2
3 Scientific Activity 26- Instituto de Tecnologia Química e Biológica Molecular Simulation Group/Protein Modelling Group. Pos-Doc researcher in the field of protein/peptide and biological membranes simulations. The project is entitled: Membrane-induced structural changes in proteins: a computer simulation study under the coordination of Prof. António Baptista and Prof. Claudio Soares. Grant: FCT - SFRH/BPD/29358/ Instituto de Tecnologia Química e Biológica Molecular Simulation Group. Pos-Doc researcher in the field of biomolecular simulation and with the project: ph and redox effects in structure and dynamics of biomolecules: Studies in molecular modelling under the coordination of Prof. António Baptista. Grant: FCT - SFRH/BPD/1454/23 & Project: POCTI/BME/4581/ Department of Chemistry and Biochemistry, University of Bern, Switzerland. PhD student under the supervision of Dr. Tamis Darbre within the group of Prof. Jean-Louis Reymond. The work was entitled: Chemical Models of Zincdependent Enzymes: Methyltransferases and Class II Aldolases Grant: Swiss National Science Foundation (Project ) Grupo de Bioquímica e Biologia Teóricas, Instituto Bento da Rocha Cabral, Lisboa, Portugal. Diploma s final year work under the supervision of Dr. Armindo Salvador and Prof. Ruy Pinto. The work done was entitled: Simulation of the redox cycle of ubiquinones in an electron transport model Application to the peroxissome SPECIALIZATION COURSES 22 Course: Genetic Algorithms Prof. Christian Leumann, Universität Bern, Switzerland (PhD program) 22 Course: DNA Chips Prof. Christian Leumann & Prof. Robert Häner, Universität Bern, Switzerland (PhD program) 22 Course: Dendrimers Prof. Jean-Louis Reymond, Universität Bern, Switzerland (PhD program) 2 Course: Modern Methods in Chemical Information Retrieval, 3ème Cycle, Prof. E. Zass, ETH, Zürich, Switzerland THESIS 23 PhD: Chemical Models of Zinc-dependent Enzymes: Methyltransferases and Class II Aldolases, (23) Department für Chemie und Biochemie, Universität Bern, Switzerland Diploma: Simulação do Ciclo de Oxidação e Redução das Ubiquinonas num Modelo de Transporte Electrónico - Aplicação ao Peroxissoma, (1998) Faculdade de Ciências da Universidade de Lisboa, Portugal. 3
4 PUBLICATIONS Times Cited: 28 Machuqueiro, M., Baptista, A.M. (28) Constant-pH/redox Molecular Dynamics: The protonation reduction conformation coupling in Cyt. c 3, J. Phys. Chem. B, to be submitted. 28 Machuqueiro, M., Darbre, T. (28) Synthesis of 2,2-disubstituted 1,3 dithiolpropanes and 3,3 disubstituted thietanes bearing a pyridine ring at the 2-position, Eur. J. Org. Chem., to be submitted. 28 Machuqueiro, M., Baptista, A.M. (27) Acidic range titration of HEWL using a constant-ph molecular dynamics method, Proteins, in press Machuqueiro, M., Baptista, A.M. (27) The ph-dependent conformational states of kyotorphin: a constant-ph molecular dynamics study, Biophys. J., 92, Machuqueiro, M., Baptista, A.M. (26) Constant-pH Molecular Dynamics with ionic strength effects: The protonation conformation coupling in decalysine, J. Phys. Chem. B, 11, Fernandez-Lopez, R., Kofoed, J., Machuqueiro, M., Darbre, T. (25) A selective direct aldol reaction in aqueous media catalyzed by zincproline, Eur. J. Org. Chem., Teixeira, V.H., Cunha, C.A., Machuqueiro, M., Oliveira, A.S.F., Victor, B.L., Soares, C.M., Baptista, A.M. (25) "On the use of different dielectric constants for computing individual and pairwise terms in Poisson-Boltzmann studies of protein ionization equilibrium", J. Phys. Chem. B, 19, Kofoed J, Machuqueiro, M., Reymond, J.-Louis, Darbre, T. (24) Zinc proline catalyzed pathway for the formation of sugars, Chem. Comm., Darbre, T., Machuqueiro, M. (23) Zn-Proline catalyzed direct Aldol reaction in aqueous medium, Chem. Commun., Machuqueiro, M., Darbre, T. (23) Zinc mediated methyl transfer from trimethyl phosphate to chelating and non-chelating thiols. Model for Zn-dependent methyltransferases, J. Inorg. Biochem., 94, PAPERS IN CONFERENCE PROCEEDINGS 21 Machuqueiro, M., Darbre, T. (21) Models for Zn-dependent methyltransferases, J. Inorg. Biochem., 86, Machuqueiro, M., Darbre, T. (21) Models for Zn-dependent methyltransferases, Chimia, 55,
5 ORAL COMMUNICATIONS AND POSTERS IN CONFERENCES 28 Machuqueiro, M., Soares, C.M., Baptista, A.M. (28) "The membrane induced conformational space of kyotorphin", 1 st Portuguese-Spanish-British Joint Biophysics Congress, Lisbon, Portugal. (Poster) 28 Machuqueiro, M., Soares, C.M., Baptista, A.M. (28) "Can the biological membrane help kyotorphin to find and bind to its receptor?", Computational Molecular Science 28, Bristol, England. (Poster) 27 Machuqueiro, M., Soares, C.M., Baptista, A.M. (27) "The mode of action of Neuropeptide Y: a computer simulation study", 2 nd European Conference on Chemistry for Life Sciences, Wroclaw, Poland. (Poster) 27 Machuqueiro, M., Baptista, A.M. (27) " Constant-pH Molecular Dynamics: methodology and application to kyotorphin", 2 nd workshop on biophysics of membrane-active peptides, FCUL, Lisbon, Portugal. (Poster) 26 Machuqueiro, M., Baptista, A.M. (26) " Constant-pH Molecular Dynamics: methodology and applications", Workshop on Protein Science, CFTC, Lisbon, Portugal. (Oral) 26 Machuqueiro, M., Baptista, A.M. (26) " The ph-dependent conformational states of kyotorphin: a constant-ph molecular dynamics study", MGMS-26, Oxford, England. (Poster) 25 Miguel Machuqueiro (25) "Constant ph Molecular Dynamics: the protonation-conformation coupling in decalysine", SCAN conferences cycle, ITQB-UNL, Lisbon, Portugal. (Oral) 25 Machuqueiro, M., Baptista, A.M. (25) "Constant ph Molecular Dynamics: Complete ph-dependent conformational study of the neuropeptide kyotorphin", MGMS-25, Dublin, Ireland. (Poster) 24 Machuqueiro, M., Baptista, A. M. (24) "Constant ph Molecular Dynamics: A study of protonation-conformation coupling in decalysine", 3rd Portuguese- Spanish Biophysics Congress, Lisbon, Portugal. (Poster) 24 Machuqueiro, M., Baptista, A. M. (24) "Constant ph Molecular Dynamics: A study of protonation-conformation coupling in decalysine", MGMS-24 Biomolecular Recognition and Reactivity, Manchester, England. (Poster) 21 Machuqueiro, M., Darbre, T. (21) "Models for Zn-dependent Methyltransferases", Spring Meeting SCS, Lausanne, Switzerland. (Poster) 21 Machuqueiro, M., Darbre, T. (21) "Methyl Transfer to Zinc Thiolates: A model for Zn - dependent methyltransferases, 1 th ICBIC, Florence, Italy. (Poster) 21 Machuqueiro, M., Darbre, T. (21) "Methyl Transfer to Zinc Thiolates: A Model for Zn-dependent Methyltransferases, Catalysis in Organic and Bioorganic Chemistry, Champéry, Switzerland. (Oral) 21 Machuqueiro, M., Darbre, T. (21) "Models for Zn-dependent Methyltransferases", Fall Meeting SCS, Zurich, Switzerland. (Oral) 1999 Machuqueiro, M., Darbre, T. (1999) Models for Zn-dependent Methyltransferases: The Ada Protein Model, Strain in Chemistry Meeting, Gregynog, Wales, UK. (Oral) 5
6 REFEREES CONTACTS António M. Baptista Cláudio M. Soares Tamis Darbre Jean-Louis Reymond Armindo Salvador Fernando Antunes Instituto de Tecnologia Química e Biológica Universidade Nova de Lisboa Av. da República, EAN, ITQB II, Apartado Oeiras, Portugal Phone : Fax : baptista@itqb.unl.pt Instituto de Tecnologia Química e Biológica Universidade Nova de Lisboa Av. da República, EAN, ITQB II, Apartado Oeiras, Portugal Phone : Fax : claudio@itqb.unl.pt University of Berne Department of Chemistry and Biochemistry Freiestrasse 3, CH-312 Bern, Switzerland Phone : Fax : tamis.darbre@ioc.unibe.ch University of Berne Department of Chemistry and Biochemistry Freiestrasse 3, CH-312 Bern, Switzerland Phone : Fax : jean-louis.reymond@ioc.unibe.ch Departamento de Química, 4º Andar Rua Larga Coimbra, Portugal Phone: Fax: salvador@cnc.uc.pt Departamento de Química e Bioquímica Faculdade de Ciências da Universidade de Lisboa P Lisboa, Portugal Phone : Fax : fantunes@fc.ul.pt 6
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