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CurriculumVitae

October 2012

Name: Isabel Maria Travassos de Almeida de Jesus Bento

Place and date of birth: Guarda, 9th

October 1967

Nationality: Portuguese

Work address: Instituto de Tecnologia Química e Biológica

Universidade Nova de Lisboa

Av. Da República, ITQB II

Apartado 127

2781-901 Oeiras

Portugal

Tel: +351 21 4469662

Fax: +351 21 4433644

Email: bento@itqb.unl.pt

http://www.itqb.unl.pt/researchers/bento

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Academic degrees:

2003 - Ph.D. in Biochemistry defended in July of 2003 at Instituto de Tecnologia

Química e Biológica, Universidade Nova de Lisboa (ITQB-UNL), Portugal. Thesis title:

“Structural studies of the tetrahaem cytochrome c3 and nine haem cytochrome c from

Desulfovibrio desulfuricans ATCC 27774 in the oxidised and reduced state. Correlation

with cooperativiry effects”. This work was developed at the Crystallography laboratory

at ITQB, under the supervision of Professor Maria Arménia Carrondo and Doutor Pedro

Matias.

1994 - Licenciatura in Biochemistry at Faculdade de Ciências e Tecnologia da

Universidade de Coimbra, Portugal. Diploma thesis title: “Estrutura Terciária das

Proteínas: Estudo das Correlações entre a Sequência de Aminoácidos e a Organização

Espacial da Cadeia Peptidica”. This work was developed at the Instituto Gulbenkian the

Ciência, Oeiras, Portugal, under the supervision of Prof. Kelo Correia da Silva.

Present positions:

- From 2008 to the present day - Auxiliary Research at Macromolecular

Crystallography Unit, Structural Genomics Laboratory, at Instituto de Tecnologia

Química e Biológica, Unversidade Nova de Lisboa.

- September 2003 to present day - Head of the small molecule X-ray crystallography

service at Instituto de Tecnologia Química e Biológica.

Past positions:

2006 to 2008: Research Associate at the Protein Crystallography Laboratory at Instituto

de Tecnologia Química e Biológica.

2003-2006: Post-Doc Fellow at the Protein Crystallography group at ITQB, working in

collaboration with Prof. Peter Lindley.

1998-2003: PhD student in the Protein Crystallography group at ITQB, under the

supervision of Prof. Maria Arménia Carrondo and Doutor Pedro Matias

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1995 – 1997: graduate student in Protein Crystallography at ITQB, under the

supervision of Doutor Carlos Frazão.

1995 (October-December), “Short-term EC fellowship”, in EMBL, Hamburg.

1995 (June-August), “Short-term EC fellowship” at the Birkbeck College, London.

Scientific supervision

Diploma Students

- Ana Rita Ferreira. Diploma in Biochemistry - Graduation project entitled “Structural

Characterization of cotA laccase mutants”, from September 2006 to September 2007.

- João da Fonseca Francisco. Diploma in Microbiology - Graduation project entitled

"Crystallization and Biochemical Characterization of the cellulolytic complex from the

fungus Chrysonilia sitophila", from August 2009 to December 2009.

- Diana Araújo. Diploma in Biochemistry - Graduation project entitled “Biochemical

and structural characterization of proteins: PR10 and CotA laccase", from January to

July 2011

- Joana Rita Pinto de Magalhães, Diploma in Biochemistry, project entitled

“Biophysical characterization of cellulases from the fungus Chrysonilia sitophyla”,

from January to July 2011

- Catarina Faria de Almeida, Diploma in Biochemistry, project entitled “Crystallization

of cellulases from the fungus Chrysonilia sitophyla”, from January to July 2011

Master Students

- Tânia Isabel Paixão da Silva Madeira. Master student from November 2009 until

December 2010 - Master project entitled "Biochemical Characterization of cellulases

from Chrysonilia sitophyla- protein purification, crystallization and crystal

characterization".

Research Students

- Samarpita Lahiri, since January 2012 to the present day.

- Joana Vaz, from May 2010 to July 2010. Joint supervision with Prof. Cláudio Soares.

- Catarina Isabel Pires da Silva, from January 2007 to December 2007.

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PhD Students

- Catarina Isabel Pires da Silva. PhD student since January 2008

- Ana Teresa Gonçalves, PhD student since May 2012

Post-Docs

-Drª Ana Maria Gonçalves, from May 2011 to the present day.

Teaching activities

PhD programs

- X-ray crystallography in the ITQB PhD program from 2005 to the present day.

- Protein Cloning, Purification and Crystallization in the PhD Program in Instituto

Gulbenkian de Ciência (IGC), 2011.

-X-ray Crystallography in the PhD program in Instituto Gulbenkian de Ciência - 2005,

2006, 2007.

Scientific Courses:

- “Management and dissemination of structural data” in BioCrys 2012 Course,

“Fundamentals of Modern Methods in Biocrystallography – What you always wanted to

know about crystallography but never dared to ask”, Oeiras October 2012.

- “Mechanisms underlying dioxygen reduction in laccases”, Training course in

Complementary Optical Spectroscopies in Macromolecular Crystallography, ESRF

Grenoble, September 2012.

- “Bio-Crystallography: State of the art and some applications”, Research Course on

“X-ray Scattering in Biology”, DESY Hamburg, March 2012

- “Management and Dissemination of Structural Data” in BioCrys 2010 Course,

“Fundamentals of Modern Methods in Biocrystallography – What you always wanted to

know about crystallography but never dared to ask”, Oeiras 2010.

-“The Crystallographic Web of Knowledge” and “Model Refinement and Completion”

in the BioCrys 2008 Course, “Fundamentals of Modern Methods in Biocrystallography.

What you always wanted to know about crystallography but never dared to ask”

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- “The Crystallographic Web of Knowledge” and “Model Refinement and Completion”

in the BioCrys 2006 Course, “Fundamentals of Modern Methods in Biocrystallography.

What you always wanted to know about crystallography but never dared to ask”.

Bachelor (or Licenciatura) programs

- Professor Auxiliar Convidado, in Biochemistry, na Faculdade de Engenharia da

Universidade Católica, no ano lectivo 2002-2003.

Financed research projects:

Projects as PI

PTDC/BIA-PRO/113064/2009- "GRIM-19, a novel protein involved in cell apoptosis:

structure-function characterization".

Projects as partner

PTDC/AGR-AAM/102345/2008 - "Breaking Down the Wall- Microbial hemicellulases

for saccharification"- Responsible for the X-ray Crystallography research at ITQB-

UNL.

PTDC/AGR-AAM/65611/2006 – “Tannin polymerase, a novel and previously unknown

enzyme that is required by obligate pathogens to invade grapevine tissues”- "-

Responsible for the X-ray Crystallography research at ITQB-UNL.

EU FP6-2004-NMP-NI-4/02456 IP project. “White biotechnology for added value

products from renewable plant polymers: Design of tailor-made biocatalysts and new

industrial bioprocesses” (acronym BIORENEW). Responsible for the X-ray

Crystallography research at ITQB-UNL.

POCI/BIO/57083/2004 - “Nano-engineering of bacterial laccases.” Responsible for the

X-ray Crystallography research at the ITQB-UNL.

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Fellowships

- Bolsa de Pós-doutoramento (Post-Doc fellowship), from Fundação para a Ciência e

Tecniologia, 2004-2006.

- Bolsa de Pós-doutoramento (Post-Doc fellowship), from Instituto de Tecnologia

Química e Biológica, 2003-2004.

- Bolsa de Doutoramento (PhD fellowship) from Fundação para a Ciência e

Tecniologia, 1998-2002.

- Bolsa de Iniciação à Investigação – BIC -, from PRAXIS XXI, 1995 - 1997.

- Short-term EC fellowship in EMBL, Hamburg, 1995 (October-December).

- Short-term EC fellowship at Birkbeck College, London, 1995 (June-August).

Scientific publications in peer-reviewed journals

28 – "Endo-beta-D-1,4-mannanase from Chrysonilia sitophila displays a novel loop

arrangement for substrate selectivity", A.M. Gonçalves, C.S. Silva, T.I. Madeira, R.

Coelho, D. de Sanctis, M.V. San Romão and I. Bento, (2012), Acta Cryst. D68, in

press

27 – "Missing pieces in protein deposition and mobilization inside legume seed storage

vacuoles: calcium and magnesium ions", C.N. Santos, M.M. Alves, I. Bento and

Ricardo B. Ferreira, Seed Science Research (2012), in press

26 –“Generation of Carbon Monoxide Releasing Molecules (CO-RMs) as Drug

Candidates for the Treatment of Acute Liver Injury: Targeting of CO-RMs to the

Liver”, A.R. Marques, L. Kromer, D.J. Gallo, N. Penacho, S.S. Rodrigues, J.D. Seixas,

G.J.L. Bernardes, P.M. Reis, S.L. Otterbein, R.A. Ruggieri, A.S.G. Gonçalves, A.M.L.

Gonçalves, M.N. De Matos, I. Bento, L.E. Otterbein, W.A. Blättler, and C.C. Romão, ,

Organometallics (2012), 31 (16): 5810–5822.

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25 – The role of Asp116 in the reductive cleavage of dioxygen to water in CotA laccase:

assistance during the proton transfer mechanism. Silva CS, Damas JM, Chen Z,

Brissos V, Martins LO, Soares CM, Lindley PF, Bento I, Acta Crystallogr D Biol

Crystallogr, 2012, Feb;68(Pt 2):186-93.

24 - Crystal structure of the multicopper oxidase from the pathogenic bacterium

Campylobacter jejuni CGUG11284: characterization of a metallo-oxidase. Silva CS,

Durão P, Fillat A, Lindley PF, Martins LO, Bento I, Metallomics. 2012, Jan 3;4(1):37-

47.

23- The removal of a disulfide bridge in CotA-laccase changes the slower motion

dynamics involved in copper binding but has no effect on the thermodynamic stability.

Fernandes AT, Pereira MM, Silva CS, Lindley PF, Bento I, Melo EP, Martins LO. J

Biol Inorg Chem. 2011 Apr;16(4):641-51.

22- Crystallization and preliminary X-ray diffraction analysis of the azoreductase

PpAzoR from Pseudomonas putida MET94. Correia B, Chen Z, Mendes S, Martins

LO, Bento I. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Jan 1;67(Pt

1):121-3.

21- New evidence for the role of calcium in the glycosidase reaction of GH43

arabinanases., de Sanctis D, Inácio JM, Lindley PF, De Sá-Nogueira I, Bento I, FEBS

J. 2010 Sep 10. doi: 10.1111/j.1742-4658.2010.07870.x

20- Mechanisms underlying dioxygen reduction in laccases. Structural and modelling

studies focusing on proton transfer. Bento I, Silva CS, Chen Z, Martins LO, Lindley

PF, Soares CM, BMC Struct Biol. 2010 Sep 7;10:28.PMID: 20822511.

19- The role of Glu498 in the dioxygen reactivity of CotA-laccase from Bacillus

subtilis. Chen Z, Durão P, Silva CS, Pereira MM, Todorovic S, Hildebrandt P, Bento I,

Lindley PF, Martins LO. Dalton Trans. 2010 Mar 21;39(11):2875-82.

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18- Overproduction, crystallization and preliminary X-ray characterization of Abn2, an

endo-1,5-alpha-arabinanase from Bacillus subtilis. de Sanctis D, Bento I, Inácio JM,

Custódio S, de Sá-Nogueira I, Carrondo MA. Acta Crystallogr Sect F Struct Biol Cryst

Commun. 2008 Jul 1;64(Pt 7):636-8.

17- Proximal mutations at the type 1 copper site of CotA laccase: spectroscopic, redox,

kinetic and structural characterization of I494A and L386A mutants. Durão P, Chen Z,

Silva CS, Soares CM, Pereira MM, Todorovic S, Hildebrandt P, Bento I, Lindley PF,

Martins LO. Biochem J. 2008 Jun 1;412(2):339-46.

16- Synthesis and structural characterization of 1- and 2-substituted indazoles: ester and

carboxylic acid derivatives. Teixeira FC, Ramos H, Antunes IF, Curto MJ, Duarte MT,

Bento I, Molecules. 2006 Nov 14;11(11):867-89.

15- Crystallographic evidence for dioxygen interactions with iron proteins. Carrondo

MA, Bento I, Matias PM, Lindley PF, J Biol Inorg Chem. 2007 May;12(4):429-42.

14- Ceruloplasmin revisited: structural and functional roles of various metal cation-

binding sites. Bento I, Peixoto C, Zaitsev VN, Lindley PF, Acta Crystallogr D Biol

Crystallogr. 2007 Feb;63(Pt 2):240-8.

13- Purification, crystallization and preliminary X-ray study of the fungal laccase from

Cerrena maxima. Lyashenko AV, Zhukhlistova NE, Gabdoulkhakov AG, Zhukova YN,

Voelter W, Zaitsev VN, Bento I, Stepanova EV, Kachalova GS, Koroleva OV,

Cherkashyn EA, Tishkov VI, Lamzin VS, Schirwitz K, Morgunova EY, Betzel C,

Lindley PF, Mikhailov AM, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006

Oct 1;62(Pt 10):954-7.

12- X-ray structural studies of the fungal laccase from Cerrena maxima. Lyashenko AV,

Bento I, Zaitsev VN, Zhukhlistova NE, Zhukova YN, Gabdoulkhakov AG, Morgunova

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EY, Voelter W, Kachalova GS, Stepanova EV, Koroleva OV, Lamzin VS, Tishkov VI,

Betzel C, Lindley PF, Mikhailov AM. J Biol Inorg Chem. 2006 Nov;11(8):963-73.

11- Reduction of dioxygen by enzymes containing copper. Bento I, Carrondo MA,

Lindley PF. J Biol Inorg Chem. 2006 Jul;11(5):539-47.

10- Condensed phase behaviour of ionic liquid-benzene mixtures: congruent melting of

a [emim][NTf2].C6H6 inclusion crystal. Lachwa J, Bento I, Duarte MT, Lopes JN,

Rebelo LP. Chem Commun (Camb). 2006 Jun 21;(23):2445-7.

9- Perturbations of the T1 copper site in the CotA laccase from Bacillus subtilis:

structural, biochemical, enzymatic and stability studies. Durão P, Bento I, Fernandes

AT, Melo EP, Lindley PF, Martins LO. J Biol Inorg Chem. 2006 Jun;11(4):514-26.

8- Dioxygen reduction by multi-copper oxidases; a structural perspective. Bento I,

Martins LO, Gato Lopes G, Arménia Carrondo M, Lindley PF. Dalton Trans. 2005

Nov 7;(21):3507-13.

7- Molecular basis for redox-Bohr and cooperative effects in cytochrome c3 from

Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies of

oxidized and reduced high-resolution structures at pH 7.6. Bento I, Matias PM,

Baptista AM, da Costa PN, van Dongen WM, Saraiva LM, Schneider TR, Soares CM,

Carrondo MA. Proteins. 2004 Jan 1;54(1):135-52.

6- Redox-Bohr and other cooperativity effects in the nine-heme cytochrome C from

Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies.

Bento I, Teixeira VH, Baptista AM, Soares CM, Matias PM, Carrondo MA. J Biol

Chem. 2003 Sep 19;278(38):36455-69.

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5- Conformational component in the coupled transfer of multiple electrons and protons

in a monomeric tetraheme cytochrome. Louro RO, Bento I, Matias PM, Catarino T,

Baptista AM, Soares CM, Carrondo MA, Turner DL, Xavier AV. J Biol Chem. 2001

Nov 23;276(47):44044-51.

4- Crystal structure of cardosin A, a glycosylated and Arg-Gly-Asp-containing aspartic

proteinase from the flowers of Cynara cardunculus L. Frazão C, Bento I, Costa J,

Soares CM, Veríssimo P, Faro C, Pires E, Cooper J, Carrondo MA. J Biol Chem. 1999

Sep 24;274(39):27694-701.

3- Crystallization and preliminary X-ray crystallographic studies of the plant aspartic

proteinase cardosin A. Bento I, Frazão C, Coelho R, Wilson K, Dauter Z, Carrondo

MA. Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):991-3.

2- Crystallisation, structure solution, and initial refinement of plant cardosin-A. Bento I,

Coelho R, Frazão C, Costa J, Faro C, Veríssimo P, Pires E, Cooper J, Dauter Z, Wilson

K, Carrondo MA. Adv Exp Med Biol. 1998;436:445-52. Review.

1- The glycosylation of the aspartic proteinases from barley (Hordeum vulgare L.) and

cardoon (Cynara cardunculus L.). Costa J, Ashford DA, Nimtz M, Bento I, Frazäo C,

Esteves CL, Faro CJ, Kervinen J, Pires E, Veríssimo P, Wlodawer A, Carrondo MA.

Eur J Biochem. 1997 Feb 1;243(3):695-700.

Book Chapters

- I. Bento, R.O. Louro, C.M. Soares, M.A. Carrondo, “Tetraheme Cytochrome c3”,

in Handbook of Metalloproteins (2011), Vol 4 & 5, Ed. A. Messerschmidt,

Chichester, UK: John Wiley & Sons, Ltd., pp 5-15.

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- G. Leonard, D. Nurizzo, C. Dieckmann-Mueller, E. Mitchell, J. McCarthy, D. Flot, I.

Bento and P. Lindley, "Crystallographic Research Developments" in Astrophysics and

Condensed Matter – Horizons in World Physics, (2008) Ed. T.G. Hardwell, Nova

Science Publishers, Inc., Vol. 262, pp 11-69.

Communications in scientific meetings

Oral communications

- C.S. Silva, D. de Sanctis, M. I. Correia, M. Petoukhov, D. Svergun, P.F. Lindley, I. de

Sá Nogueira and I. Bento, “Mapping conformational changes of the transcription factor

AraR”, ECM27, Bergen, 2012.

- Bento I, Gago G, Martins LO, Carrondo MA, Lindley PF, “The Mechanism of

Dioxygen Reduction by the Multi-Copper Oxidases”, Lisboa, 2004.

- Bento I, Martins LO, Gago G, Carrondo MA, and Lindley PF, “A Putative Mechanism

for Dioxygen Reduction by the Multi-Copper Oxidases”, Nottinngham, 2005.

Poster communications

- Daniele de Sanctis, Jose M. Inacio, Peter F. Lindley, Isabel de Sá-Nogueira and Isabel

Bento, “New evidence for the role of calcium in the glycosidase reaction of GH43

arabinanases”, Carbohydrate Bioengineering Meeting (CBM9), Lisbon, May 2011.

- Sónia Mendes, Luciana Pereira, Zenghia Chen, Bruno Correia, Isabel Bento and Lígia

O. Martins, “Molecular Determinants of the Azo Reduction Activity by Pseudomonas

putida MET94 Strain”, INTERBIO Symposium: Frontiers in Protein Research, Oeiras,

May 2011.

- Catarina S. Silva, Zhenjia Chen, Paulo Durão, Peter F. Lindley, Lígia O. Martins,

Cláudio M. Soares and Isabel Bento, “Proton transfer mechanisms in multi-copper

oxidases: studies in CotA-laccase”, European Crystallographic Meetings 25 (ECM25),

Istanbul, August 2009.

- Catarina S. Silva, Zhenjia Chen, Paulo Durão, Lígia O.Martins, Isabel Bento and Peter

F. Lindley, “Structural Studies in CotA mutants from Bacillus Subtilis”, 4th European

Meeting on Oxizymes, Helsinki, June 2008.

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- I. Bento, P. Durão, A. T. Fernandes, L. O. Martins, and P. F. Lindley, “Structural

studies in CotA mutants: understanding of the protonation events that occur during

oxygen reduction to water”, Oeiras, 2006.

- I. Bento, P. Durão, A. T. Fernandes, L. O. Martins, and P. F. Lindley, “Structural

studies in CotA mutants from Bacillus stubtilis”, Aveiro, 2006.

- I. Bento, G. Gago, L. O. Martins, M. A. Carrondo, P. F. Lindley, “The Mechanism of

Dioxygen Reduction by the Multi-Copper Oxidases”, Lisboa, 2004.

- I. Bento, G. Gago, L. O. Martins, M. A. Carrondo, P. F. Lindley, “Structural studies on

CotA a bacterial laccase from Bacillus subtilis.”, Naples, 2004.

- I. Bento, P. M. Matias, V. H. Teixeira, A. M. Baptista, C. M. Soares, M. A. Carrondo,

“Structural analysis of the oxidised and reduced forms of the nine haem cytochrome c

from D. desulfuricans ATCC 27774 at pH 7.5”, Lisboa, 2002.

- I. Bento, P. M. Matias, V. H. Teixeira, A. M. Baptista, C. M. Soares, M- A. Carrondo,

“Structural analysis of the oxidised and reduced forms of the nine haem cytochrome c

from D. desulfuricans ATCC 27774 at pH 7.5”, Istanbul, 2002.

- I. Bento, P. M. Matias, and M. A. Carrondo, “Three-dimensional structures of the

reduced and oxidised forms of cytochrome c3 from Desulfovibrio desulfuricans ATCC

27774 at pH 7.6”, Lisboa, 2001

- I. Bento, P. M. Matias, and M. A. Carrondo, “Three-dimensional structures of the

reduced and oxidised forms of cytochrome c3 from Desulfovibrio desulfuricans ATCC

27774 at pH 7.6”, Nancy, 2000.

- I. Bento, P. M. Matias, R. Coelho and M. A. Carrondo, “Three-dimensional structure

of the reduced form of a nine haem cytochrome c at pH 7.5 and pH 9.5”, Glasgow,1999.

- I. Bento, P. M. Matias and M. A. Carrondo, “Three-Dimensional Structure of the

Reduced Form of Cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774 at 2Å

resolution”, Oeiras, 1998.

- I. Bento, C. Frazão, R. Coelho, J. Costa, C. Faro, P. Veríssimo, E. Pires, J. Cooper, Z.

Dauter, K. Wilson, and M. A. Carrondo, “ Structure of the Glycosylated Plant Aspartic

Proteinase Cardosin A to 1.72Å Resolution” HERCULES, Grenoble, 1998.

- C. Frazão, I. Bento, L. Sieker, F. Capozzi, C. Luchinat, Z. Dauter, K. R. Herbst-Irmer,

G. Sheldrick G., and M. A. Carrondo, “Ectothiorhodospira halophila HiPIP II from a

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Pseudo-Merohedric Twinned Crystal”, “Seventeenth European Crystallographic

Meeting”, Lisboa, 1997.

- I. Bento, C. Frazão, R. Coelho, J. Costa, C. Faro, P. Veríssimo, E. Pires, J. Cooper, Z.

Dauter, K. Wilson, and M. A. Carrondo, “ Structure of the Glycosylated Plant Aspartic

Proteinase Cardosin A to 2.9Å Resolution”, “Seventeenth European Crystallographic

Meeting”, Lisboa, 1997.

- I. Bento, C. Frazão, R. Coelho, J. Costa, C. Faro, P. Veríssimo, E. Pires, J. Cooper, Z.

Dauter, K. Wilson, and M. A. Carrondo, “ 3-D structure of Cardosin A”, “Methods and

Structure in Macromolecular Crystallography”, Hamburgo, 1996.

- C. Frazão, I. Bento, R. Coelho, J. Costa, C. Faro, P. Veríssimo, E. Pires, J. Cooper, Z.

Dauter, K. Wilson, and M. A. Carrondo," Crystallographic studies of cardosin A, Part

II: Refinement to 2.9Å resolution and structure analysis.", “VIIth International Aspartic

Proteinases Conference”, Alberta, 1996.

- C. Frazão, I. Bento, R. Coelho, J. Costa, C. Faro, P. Veríssimo, E. Pires, J. Cooper, Z.

Dauter, K. Wilson, and M. A.,"Three Dimensional Structure of a Plant Cardoon

Aspartic Proteinase", “IUCr XVII Congress and General Assembly”, Seattle, 1996.

- I.T. Bento & K.Correia da Silva, " Tertiary structure of protein: Correlation with the

aminoacid sequence.", IX Congresso National de Bioquimica, Algarve, 1993.

Language knowledge

i) Portuguese – native language

ii) Fluent in written and spoken English.

iii) Good working knowledge of French.