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João’s research experience

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Postdoctoral Researcher

Postdoctoral Researcher
July 2021 – present
Dr. Alexandre Bonvin’s Lab
Utrecht University, The Netherlands.

Developing new protein-protein docking methodologies within the HADDOCK 3 framework.

Postdoctoral Research Fellow

Postdoctoral Research Fellow
Apr 2019 – May 2021
Dr. Julie Forman-Kay’s Lab,
The Hospital for Sick Children (SickKids), Toronto, Canada.

Developed novel integrative computational methods to generate and calculate structural ensembles of intrinsically disordered proteins. Active collaboration.

Independent Researcher in Structural Biology

Independent and ad honorem researcher
Jul 2018 – Mar 2019
Salamanca, Spain.

Active, independent and ad honorem scientific researcher in the field of Structural Biology focusing on software development in the following active and Open Source projects:

• Farseer-NMR, (founder and lead developer)

• taurenmd, (founder and lead developer)

• Tree-of-Life: (founder and lead developer)

• pdb-tools, (contributor)

Visiting Collaborator

Sept 2018 (2 week)
Group of Structural Biology, School of Medicinem Stanford University.
Collaborators: Dr. João P.G.L.M. Rodrigues, Susana Barrera-Vilarmau
Group leader: Dr. Michael Levitt
Theme: Simulation of a multicomponent system using OpenMM

Postdoctoral Researcher

Feb 2014 to June 2018 (4 years and 6 months)
BioNMR Group, University of Barcelona, Spain.
Group leader: Prof. Dr. Miquel Pons
Research line: «Dynamics of fuzzy complexes in Src Family Kinases; development of Farseer-NMR software suite»

Structural Biochemist investigating protein dynamics, partner binding and response to external stimuli mainly using Nuclear Magnetic Resonance spectroscopy.

Biological Systems in focus:
– Interaction between the disordered Unique and folder SH3 domain of Src Family Kinases (SFK) members: Lyn, Src, Yes
– Calcineurin’s structural dynamism
– Ubiquitination via RNF125
– Toxin-Antitoxin systems in biofilms

Technology development:
– Lead developer of Farseer-NMR software suite

Technical specializations:
– Protein cloning, expression and purification for NMR samples via E.Coli systems: folded domains and intrinsically disordered regions.
– Nuclear Magnetic Resonance (NMR): CSP, PRE, 3D protein assignment, large-scale and multivariable peaklist data bases.

– Mentored nine students (bachelor, master and PhD) in their introduction to science and structural biology, in their projects and all the protocols and good practices related to research in our field.

Scientific Meetings and Workshops:
– Organized and lectured four workshops on Farseer-NMR within the Iberian NMR community.
– Lecturer in the PhD Programme, NMR in health and disease: From Protein-Ligand Interactions to Small Molecules in Tissue, Coimbra, Portugal.
– three oral communications and four posters in national and international research meetings.

Developed Collaborations:
– Dr. Simon P. Skinner and Prof. Dr. Alexander L. Breeze (University of Leeds)
– Dr. Wiktor Koźmiński (University of Warsaw)
– Dr. Ignacio Fita and Dra. Alicia Guasch Mitjans (IBMB-CSIC)
– Dra. Mercè Perez Ribas (IDIBELL).
– Dra. Marie-José Bijlmakers (ALBA Synchrotron)

Visiting Collaborator

Sept 2017 (1 week)
Astbury Centre for Structural Molecular Biology, University of Leeds.
Group leader: Dr. Alexander L. Breeze
Collaborators: Dr. Simon P. Skinner
Theme: Development of Farseer-NMR Software.

Shoulder to shoulder and hands-on-keyboard development of Farseer-NMR software with Dr. Simon Skinner – pre-release candidate.

Transnational Knowledge Transfer

Nov 2013 (1 month)
BioNMR Group, University of Barcelona, Spain.
Supervisor: Prof. Dr. Miquel Pons Vallès
Theme: protocols for paramagnetic tagged proteins preparation and paramagnetic NMR data analysis.

Implementation and improvement of protocols for functionalization of proteins with paramagnetic tags for paramagnetic NMR investigations. Measurement and analysis of paramagnetic NMR observables. The invitation for this knowledge transfer mission came thanks to the skills I obtained during my PhD stay in CERM, University of Florence.

Visiting PhD. Student

April 2013 (15 days)
Bijvoet Center for Biomolecular Research, Utrecht, The Netherlands.
Supervisor: Dr. Alexander Bonvin
Collaborator: Dr. João P.G.L.M. Rodrigues
Theme: Protein-protein docking calculations and analysis using HADDOCK Web Server and Python scripting.

Calculatio and analysis restraints driven protein docking calculations on the HADDOCK Web Server. Modelled the MMP-1·Collagen interaction using the porfolio of NMR observables acquired during my stay at CERM, University of Florence. Data representation using Python scripting. The results were presented in my PhD thesis and in other oral communications, eg. on the EJIBCE Oporto, Portugal (2013).

PhD. Candidate

May 2009 to Jan 2014
Inorganic Biochemistry and Molecular Imaging Group, CNC – Center for Neuroscience and Cell Biology, University of Coimbra, Portugal. (present link)
Supervisors: Prof. Dr. Carlos F.G.C. Geraldes and Dr. Claudio Luchinat (CERM)
Thesis title: «Paramagnetic NMR of Proteins to study the Collagenolytic Mechanism of MMP-1»

Project funded by PhD Scholarship from Fundação para a Ciência e a Tecnologia (FCT). My PhD thesis is available here:

PhD in joint collaboration with CERM, University of Florence, where I spent 9 months every  year.

Abroad stays:
– CERM, University of Florence: sample preparation, NMR data acquisition and most of the NMR analysis (see card bellow)
– Bijvoet Center for Biomolecular Research, Utrecht: calculation and analysis of MMP-1·Collagen models
– Charles University, Prague: synthesis of CLaNP–5.2 metal-bearing tag (see card bellow)

Biological relevance:
– Understanding unwinding mechanism of triple helical collagen peptide driven by the inter-domain dynamics of the MMP-1 collagenase. MMP-1 is a key player in metastatic invasion.
– Described the MMP-1-Collagen complex.
– Described the inter-domain dynamics of ligand-free MMP-1 in solution.

Technical Expertise:
– Paramagnetic Nuclear Magnetic Resonance: protein functionalization with Lanthanide(III) tags, pseudo contact shifts (PCS) and residual dipolar couplings (RDCs).
– Domain-domain dynamics via paramagnetic NMR restraints.
– Cloning, mutation, expression and purification of recombinant proteins for NMR samples.
– Protein refolding of tandem multiple domains.

National and international scientific meetings:
– four oral communications
– nine poster participations

Obtained the PhD in Biochemistry with specialization in Biophysics approved Unanimously with Distinction and Honours in January, 9th 2014 by the University of Coimbra, Portugal.

PhD. Student in International Training

Jun 2009 to Jan 2013 (9 months per year)
CERM University of Florence, Italy.
Supervisor: Prof. Dr. Claudio Luchinat

During my PhD studies in the University of Coimbra, I worked for 9 months each year in CERM, University of Florence, Italy, where I mostly developed my project. Please read above for details.

Short Term Scientific Mission

Sep 2009 (3 months)
Charles University, Prague, Czech Republic.
Supervisor: Dr. Petr Hermann
Theme: Chemical Synthesis of Metal-based systems for Molecular Imaging Applications and Paramagnetic Solution NMR Probes.

Work co-financed by COST D38 Actions.
Chemical synthesis of CLaNP-5.2 tag and its precursors which are metal-based probes for Molecular Imaging Applications and Paramagnetic Solution NMR Probes

Short Term Scientific Mission

Jan 2009 (3 weeks)
NMR and molecular recognition Group, Cenro de Investigaciones Biológicas (CIB), CSIC, Spain.
Supervisor: Dr. Jesús Jiménez-Barbero
Theme: Protein-ligand interaction studies using Autodock 4.

Autodock 4 calculations on the interaction between glucoconjugates, DOTA- and DTPA-based contrast-agent models and their protein receptors. Studies supporting the experimental results obtained by Saturation Transfer Difference NMR (in Coimbra).

Research Technician

Oct 2008 to Apr 2009 (6 months)
Inorganic Biochemistry and Molecular Imaging Group, Center for Neuroscience and Cell Biology (CNC), Coimbra, Portugal.
Supervisor: Prof. Dr. Carlos F.G.C. Geraldes

As a Biochemist Licentiate and NMR spectroscopist with experience in Saturation Transfer Difference NMR methodology.

Medical Relevance:
– Interaction studies between MRI contrast-agents and respective protein receptors

Technical skills:
– Experience as Varian NMR Spectroscopist (VnmrJ Software) – data acquisition and analysis.
– Saturation Transfer Difference (STD) NMR
– MestreNova Software

International Scientific Meetings:
– one poster communication

Achieved Collaborations:
– Prof. Dr. Jesús Jiménez-Barbero (CIB-CSIC, Spain)
– Prof. Dr. David Parker (Durham University, UK)

Researcher under licentiate thesis training

Sep 2007 to Sep 2008 (1 year)
Inorganic Biochemistry and Molecular Imaging Group, Center for Neuroscience and Cell Biology (CNC), Coimbra, Portugal.
Supervisor: Prof. Dr. Carlos F.G.C. Geraldes
Theme: «Interaction of imaging probes with their respective protein receptors by Saturation Transfer Difference (STD) NMR».

Thesis title: «Study of the interaction of Ln(III) complexes of targeted contrast agents to HSA and RCA120 binding models using High Resolution Saturation Transfer Difference (STD) NMR techniques».

Medical Relevance:
– Interaction studies between MRI contrast-agents and respective protein receptors.

Technical skills:
– Experience as Varian NMR Spectroscopist (VnmrJ Software) – data acquisition and analysis.
– Saturation Transfer Difference (STD) NMR
– MestreNova Software

International Scientific Meetings:
– one poster communication

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