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João’s Biography

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I was born in a (neither little nor big) border village in the south of Portugal, called Vila Real de Santo António. Actually, the village borders everything: Spain, the Guadiana river, the Atlantic Ocean, the rest of the Algarve and Portugal also (6 hours were necessary to drive 300km and reach Lisbon at that time). I guess that always had a very interesting influence on me.

camaleãoI was lucky to grow in a village so surrounded by Nature, land but mostly sea; summer time goes from May to October :-) This contact with Nature made me develop great respect for our environment, which perdures until today and, from when I have memory, I remember being involved in cleaning activities in the beach and nearby forest.

tkdvrsa_logopkI always had a close relationship with sports, I have been practitioner of many but definitively the one I dedicated most and had greatest impact on my life at that time was TaeKwonDo. We had a local TKD club, that was actually founded by a very close familiar: my father; he was the teacher and manager of the club which is still running nowadays with very nice achievements! We were few, but strong-willed and, thanks to everyone around me, I became National Champion in Combat sub 17 (back in 2003) and achieved Black belt.

2286707My interests in natural sciences grew up with me and when the moment arrived to choose a University career, I definitively wanted to become a Biochemist. However, getting an accurate advice on career progression was not easy back then, specially in a small town in the south, which almost made me blunder the most important move in my career (yet to be started). Fortunately, a very close person showed me how important it is for one to pursue and travel along the road of his/her dreams (Obrigado Primo!). He offered me this book here in the picture and alea iacta est. I decided to course Biochemistry and in one of the most important universities in Portugal, definitively the ancientest, the University of Coimbra.

coimbraCoimbra filled me with intense personal experiences. Student activism was zealous, student life was definitively very active, they were the last years before YouTube, smartphones and the Bologna Process. Life’s was just too intense to explain in few words here. Continuing pursuing my goals, I eventually came to know about Nuclear Magnetic Resonance (NMR) and the study of protein’s structure and dynamics; I got it from the hand of Prof. Dr. Carlos Geraldes. The kind of experimental setup and analysis of NMR completely fit my brain and I knew at that moment what I was looking for.

spectrometer_600I chose to perform my Licentiate thesis with Prof. Geraldes studying contrast-agents·protein interactions through Saturation Transfer Difference NMR, aiming to describe the interaction binding epitope and  provide clues to organic chemists for compound improvement. We had a Varian 600MHz, it was my video game console at the time ;-) it is actually the one in the photo, currently in a new facility lab (click on the photo to visit). The STD technique was not implemented in the NMR Lab in Coimbra, and I had the opportunity to implement and set it up during my Licentiate thesis, the operation was a success. After receiving the title in Biochemistry (2008), I continued and expanded the project in the Prof. Geraldes’ lab for another 6 months.

gelateria-firenze-0009_8RtThe year after, I was granted with the National PhD Scholarship – I had decided to continue my studies in Structural Biochemistry. The fellowship allowed me to develop my PhD project between Coimbra and Centre for Magnetic Resonance (CERM), in the University of Florence, Italy, co-supervised by Dr. Claudio Luchinat. I spent 9 months per year there (4 years in total). CERM had a great infrastructure, several magnets (there was always a bigger one in the room next door) and highly equipped molecular biology laboratories, there’s no need to deny that this and the amassed know-how there was the reason for my choice. If Italy=Pizza; then Florence=Gelato (ice cream), I could put a random picture of the city here, but would you miss a home made gelato in Gelateria de Medici? Best in town, luckily for me I lived nearby :-P

ph_thesis_portraitI was determined to develop myself as a structural biochemist, and for my PhD project I chose to study the interdomain mobility of Matrix MetalloProteinase-1 (MMP-1), a collagenase of two folded domains linked by a flexible 16-residue linker, and how such movements trigger the collagen triple helix unwinding – an unknown process under considerable debate within the scientific community. I should approach this issue using Paramagnetic NMR. I must say I really enjoyed the project. I worked through all its phases, from conception, to mutants and protein preparation, CLaNP-5.2 tag synthesis, NMR data acquisition and analysis, structural calculations and modelling. Using paramagnetic NMR, we were able to refine crystallographic structures of the individual domains and describe the interdomain dynamics of MMP-1 when free in solution by providing a 3D map of the relative position and orientation distribution of both domains. These results were successfully published [1, 2], it was the first time that such methodologies were used in non-model systems. But the project was not yet complete. By combining X-ray, NMR data (CSPs, relaxation, PCS and RDCs), SAXS data and computational calculations with MaxOcc and HADDOCK we could propose a model of MMP-1·Collagen binding event which was beautifully described by a rigidity of both domains directly positioned to unwind the collagen triple helix, which was presented in our model already partially unwound. Though this results were not published in peer reviewed journals, they are described in my PhD thesis and were presented orally in scientific meetings. I obtained my PhD degree January 9th, 2014, after two hours of fierceful questions from Prof. Eurico Cabrita and Prof. Marcelus Ubbink.☺

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The approach of Dr. Miquel Pons to science and his interests in intrinsically disordered proteins and complex systems made me look for him to continue my career as an early postdoctoral researcher. I started in the BioNMR group of Barcelona right after my PhD defence (early 2014). An amazingly valuable experience with Miquel was possibility to engage so many different projects and to know many different people. It was really a new and demanding situation for me, managing collaborations, lab work, analysis and student mentoring, simultaneously and on the daily basis. Organization and protocol optimization was more than a request, it was an absolute need to keep the pace and track of everything. Eventually I got known as the “hands of Shiva” ✋. However, my main project focused on studying the fuzzy interaction between the unique domain of Lyn (Src Family Kinase member) with its structural and regulatory SH3 domain and how such regulation is fine tuned by the two natural Lyn isoforms; a combination of order and disorder, conventional and paramagnetic NMR (manuscript in preparation).

Farseer-NMR_logo_inkscake_twitterIn parallel to my life as a spectroscopist and a molecular biologist, I always had great interest in computers and programming, specifically, programming for biological sciences. During my postdoc in Barcelona, as projects started to grow in complexity, I faced an amount of NMR data that would render inhuman the task to analyse them manually. I had just found a vehicle to express my programming interests. I started developing an automated process (Python coded) to allow the analysis of vast and multivariable NMR peaklists datasets. Developing such a project for myself was already satisfactory, but having something closed in one’s drawer makes no sense for me. As a researcher, I wanted to take this project to the whole NMR community. The project was running already in a command line interface; I was looking for a collaborator with whom to draw the Graphical User Interface (GUI). I met Simon at the perfect moment, he was than developing the CCPNMRv3, and we started coding together on what was then forged as the Farseer-NMR Project (openly published in J. Biomol. NMR). The project is unique within the community, there is no other software available that is so specialized in its task and user oriented, and that fills us with energy to continue to improving and expanding it.

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If you arrived this far reading, I am pretty sure you’ve noticed that for us is difficult to stay at home, we’d rather bivvy outside ⛺. From when we arrived in Barcelona, Susana introduced me to the world of mountaineering, and little by little we started hiking, hiking higher, rock climbing, getting more fascinated, we start attending courses and getting specialized in mountaineering and winter alpine skills. We have performed winter alpine climbs in Pyrenees, Morocco Atlas, Bulgaria, and looking forward for more ⛰. Maybe our most peculiar characteristic in our mountaineer style is that we love commitment, where knowledge of the situation and risk management is a must; yet far from senseless risky activities where adrenaline is the sole reward. Because we are researchers (or we are researchers because of this) we love cataloguing stuff, so we have a bunch of logbooks were we keep a record of all our outdoors activities with some story-telling also. ☺

peace_flowerRather than tourists, we are travellers. Travelling is the action of visiting other communities and places, let yourself be painted by their culture and share yours, always with maximum respect and leaving no negative trace behind – that we love to do. We are honoured to have met all those persons along the way: Portugal, Spain, Ireland, Scotland, Bulgaria, Morocco, India (Susana have been twice, I wanna go also!), Costa Rica, … we make all our efforts and commitment to this style, specially also when performing activities in the mountains.

I got introduced to Chess some time ago by a student of mine (Héctor), I am getting fascinated also by this mixture of game-sport-art-strategy. I am always up for a game, find me on Lichess

Currently, we are living in Salamanca, and navigating between Spain and Portugal, dedicating time to family and personal projects (which includes obviously research :-P).

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Summer 2018

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