Marta Andreia Da Silva Perez
I was born in 1984 in Santa Maria da Feira (Portugal). I finished my degree in Chemistry at the Faculty of Sciences, University of Porto, Portugal, in 2006. During my first degree theoretical and computational chemistry fascinated me and from then on I am working on this field. In 2006 I was awarded with a scientific initiation grant entitled Complex energies studies resorting to theoretical calculations. In 2008 I completed my master and in January 2013 my PhD both degrees in Chemistry and working on the Theoretical and Computational Chemistry and Biochemistry Lab in the Faculty of Sciences, University of Porto and under the supervision of Professor Maria João Ramos and Dr. Pedro Alexandrino Fernandes. My graduate work was focused on the enzymatic catalysis and inhibition and on computational mutagenesis. During my PhD, I developed my teaching skills being co-adjuvant in some practical courses and my organizational skills being one of the local organizers of the 5th Theoretical Biophysics International Symposium in Madeira Island. Since January 2013 I am post-doctoral research assistant in the group of Prof. Ursula Roethslisberger at École Polytechnique Féderale de Lausanne. At EPFL I am working on conformational search of biomolecules using ab-initio molecular dynamics and on the development and validation of a new Genetic Algorithm software for protein engineering.
Exploration of thermostable mutants via genetic algorithm.
Theoretical studies on gas-phase biomolecules.
Webmaster of the LCBC EPFL webpage.
Computational methods applied to systems of biological interest.
Soon to be publishedKamrath, M., Glover, M., Perez, M.A.S., Roetlhlisberger, U., Clemmer, D. and Rizzo, T., “Moving beyond collision cross sections: Using cryogenic infrared spectroscopy to determine the structures of the mobility-selected cabTRPs (APSGFLGMR-NH2) ”, in preparation. Perez, M.A.S., Bozkurt, E., Browning, N.J., and Roethlisberger, U., “Engineering Protein Thermostability via Genetic Algorithm Optimization”, in preparation. Perez, M.A.S., Aseev, O., Rizzo, T.R. and Roethlisberger, U., “Cryogenic spectroscopy and quantum molecular dynamics probe 3D structures and reactions of a cyclic b6 - [FAGFAGPG + H]+”, under review. Perez, M.A.S., Browning, N.J., Brunk, E. and Roethlisberger, U., “A Genetic Algorithm for the Design of Peptides and Proteins”, under review.
V. Scutelnic; M. A. S. Perez; M. Marianski; S. Warnke; A. Gregor et al. : The Structure of the Protonated Serine Octamer; Journal of the American Chemical Society. 2018-04-11. DOI : 10.1021/jacs.8b02118.
E. Bozkurt; M. A. S. Perez; R. Hovius; N. J. Browning; U. Rothlisberger : A genetic algorithm based design and experimental characterization of a highly thermostable metalloprotein; Journal of the American Chemical Society. 2018. DOI : 10.1021/jacs.7b10660.
E. Brunk; M. A. S. Perez; P. Athri; U. Rothlisberger : Genetic-Algorithm-Based Optimization of a Peptidic Scaffold for Sequestration and Hydration of CO; ChemPhysChem. 2016. DOI : 10.1002/cphc.201601034.
O. Aseev; M. A. S. Perez; U. Röthlisberger; T. R. Rizzo : Cryogenic Spectroscopy and Quantum Molecular Dynamics Determine the Structure of Cyclic Intermediates Involved in Peptide Sequence Scrambling; Journal of Physical Chemistry Letters. 2015. DOI : 10.1021/acs.jpclett.5b01088.
G. P. Pinto; N. F. Brás; M. A. S. Perez; P. A. Fernandes; N. Russo et al. : Establishing the Catalytic Mechanism of Human Pancreatic α-Amylase with QM/MM Methods; Journal of Chemical Theory and Computation. 2015. DOI : 10.1021/acs.jctc.5b00222.
A. Masson; M. K. Kamrath; M. A. S. Perez; M. S. Glover; U. Röthlisberger et al. : Infrared Spectroscopy of Mobility-Selected H+-Gly-Pro-Gly-Gly (GPGG); Journal of the American Society for Mass Spectrometry. 2015. DOI : 10.1007/s13361-015-1172-4.
E. Bozkurt; N. Ashari; N. Browning; E. Brunk; P. Campomanes et al. : Lessons from Nature: Computational Design of Biomimetic Compounds and Processes; Chimia. 2014. DOI : 10.2533/chimia.2014.642.
S. A. Martins; M. A. S. Perez; I. S. Moreira; S. F. Sousa; M. J. Ramos et al. : Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI; Journal of Chemical Theory and Computation. 2013. DOI : 10.1021/ct4000372.
F. De Rienzo; A. J. Moura Barbosa; M. A. Perez; P. A. Fernandes; M. J. Ramos et al. : The extracellular subunit interface of the 5-HT; Journal of Biomolecular Structure and Dynamics. 2012. DOI : 10.1080/07391102.2012.680029.
P. J. Silva; M. A. S. Perez; N. F. Brás; P. A. Fernandes; M. J. Ramos : Improving the study of proton transfers between amino acid side chains in solution: choosing appropriate DFT functionals and avoiding hidden pitfalls; Theoretical Chemistry Accounts. 2012. DOI : 10.1007/s00214-012-1179-x.
M. A. S. Perez; S. F. Sousa; E. F. T. Oliveira; P. A. Fernandes; M. J. Ramos : Detection of Farnesyltransferase Interface Hot Spots through Computational Alanine Scanning Mutagenesis; The Journal of Physical Chemistry B. 2011. DOI : 10.1021/jp205481y.
N. F. Brás; M. A. S. Perez; P. A. Fernandes; P. J. Silva; M. J. Ramos : Accuracy of Density Functionals in the Prediction of Electronic Proton Affinities of Amino Acid Side Chains; Journal of Chemical Theory and Computation. 2011. DOI : 10.1021/ct200309v.
M. A. S. Perez; P. A. Fernandes; M. J. Ramos : Understanding the Mechanism for Ribonucleotide Reductase Inactivation by 2′- Deoxy-2′-methylenecytidine-5′-diphosphate; Journal of Chemical Theory and Computation. 2010. DOI : 10.1021/ct1002175.
M. A. S. Perez; P. A. Fernandes; M. J. Ramos : Substrate Recognition in HIV-1 Protease: A Computational Study; The Journal of Physical Chemistry B. 2010. DOI : 10.1021/jp910958u.
M. A. S. Perez; N. M. F. S. A. Cerqueira; P. A. Fernandes; M. J. Ramos : Ribonucleotide Reductase: A Mechanistic Portrait of Substrate Analogues Inhibitors; Current Medicinal Chemistry. 2010. DOI : 10.2174/092986710792065054.
M. Perez; P. Fernandes; M. Ramos : Drug design: New inhibitors for HIV-1 protease based on Nelfinavir as lead; Journal of Molecular Graphics and Modelling. 2007. DOI : 10.1016/j.jmgm.2007.03.009.