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João Paquete-Ferreira is a biochemist specialising in structural biology. He obtained a BSc in Biochemistry in 2017, an MSc in Biochemistry in 2019, and a PhD in Biochemistry in 2025, all awarded by the NOVA School of Science and Technology (NOVA FCT). His main scientific interests focus on protein production for structural determination using X-ray crystallography and cryo-electron microscopy (cryo-EM), the biophysical characterisation of protein–ligand interactions, and the application of structural biology approaches to rational drug development. Since the end of his BSc, Paquete-Ferreira has carried out his research activity at the Macromolecular Crystallography Laboratory of UCIBIO (NOVA FCT), where he acquired extensive experience in protein overexpression, purification, crystallisation, and biophysical characterisation using a wide range of experimental techniques. During his MSc thesis, he solved the first reported three-dimensional structure of a LytR–CpsA–Psr (LCP) protein from Streptococcus dysgalactiae subsp. dysgalactiae and performed an in-depth analysis of its interaction with multiple ligands. His PhD work built directly upon the knowledge and expertise developed during his master’s research. During this period, Paquete-Ferreira characterised an additional LCP protein from S. dysgalactiae subsp. dysgalactiae and investigated the molecular determinants governing ligand recognition within this protein family. This work led to the identification of ADP as a substrate for LCP proteins. He subsequently contributed to the development of a ^1H NMR-based method to monitor ADP hydrolysis. Using the crystal structure of the LytR protein, he also carried out virtual screening studies, identifying ten promising small molecules as putative inhibitors of the LCP protein family. Alongside his research activities, Paquete-Ferreira was involved in the tutoring and co-supervision of BSc and MSc students, reflecting increasing responsibility and academic maturity. Scientific communication was a central component of his training, resulting in five oral communications and five poster presentations at national and international conferences. In parallel, he participated in several internationally recognised training schools and scientific workshops, including CCP4 Study Weekends (2020–2024), Diamond Light Source SAXS workshops (2020), and the Macromolecular Crystallography and Cryo-EM School (2023). Beyond technical training, these events fostered interaction with researchers at different career stages and contributed to knowledge exchange and community building within the structural biology field. Paquete-Ferreira’s activities extend beyond the laboratory environment. He has been actively involved in academic organisations during both his undergraduate and doctoral studies, contributing to initiatives aimed at improving the academic experience of students. Taken together, his experience, technical expertise, and commitment to research and academic engagement make him a valuable asset to a research team in structural biology and related fields.
Identification

Personal identification

Full name
João Carlos Paquete Ferreira
Date of birth
1996/04/30
Gender
Male

Citation names

  • Paquete-Ferreira, João

Author identifiers

Ciência ID
9E13-6E78-66FF
ORCID iD
0000-0003-2846-6606

Email addresses

  • jc.paquete.f@gmail.com (Professional)

Websites

Knowledge fields

  • Natural sciences - Biological Sciences - Biochemistry
  • Natural sciences - Biological Sciences - Biophysics
  • Natural sciences - Biological Sciences - Biochemical Research Methods
  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Medical and Health Sciences - Health Sciences - Infectious Diseases

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Proficiency (C2) Advanced (C1) Intermediate (B1) Intermediate (B1)
French Beginner (A1) Elementary (A2) Beginner (A1) Beginner (A1) Beginner (A1)
Education
Degree Classification
2021/01/01 - 2025/07/16
Concluded
Doctoral Programme of Biochemistry (Doutoramento)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
"From Proteins to Bacteria: a multidisciplinary approach for the rational development of new anti-biofilm and antibacterial agents" (THESIS/DISSERTATION)
2020/03 - 2020/07
Concluded
Getting started in cryo-EM (Outros)
California Institute of Technology, United States
2019/12 - 2020/02
Concluded
Learn to Program: The Fundamentals (Outros)
University of Toronto Department of Computer Science, Canada
2017/09 - 2019/10
Concluded
Msc in Biochemistry (Mestrado)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
"LytR Inhibition, an Approach to Avoid Biofilm Formation in Streptococcus dysgalactiae subs. dysgalactiae" (THESIS/DISSERTATION)
2014/09 - 2017/06
Concluded
Bsc in Biochemistry (Licenciatura)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
"Análise Estrutural e Funcional de uma Proteína Envolvida na Formação de Biofilmes para Desenvolvimento de Fármacos" (THESIS/DISSERTATION)
Affiliation

Science

Category
Host institution
Employer
2021/01/01 - 2025/01/01 Research Trainee (Research) Unidade de Ciências Biomoleculares Aplicadas, Portugal
2018/07 - 2019/09 Research Trainee (Research) Unidade de Ciências Biomoleculares Aplicadas, Portugal
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
Outputs

Publications

Book chapter
  1. Paquete-Ferreira, João; Romão, Maria João; Santos-Silva, Teresa. Corresponding author: Santos-Silva, Teresa. "Exploring the three-dimensional structures of LytR-CpsA-Psr proteins: implications for the maturation of the peptidoglycan". In Carbohydrate Chemistry, 154-174. Royal Society of Chemistry, 2025.
    Published • 10.1039/9781837676101-00154
  2. Paquete-Ferreira, João; Leisico, Francisco; Correia, Márcia A. S.; Engrola, Filipa S. S.; Santos-Silva, Teresa; Santos, Marino F. A.. Corresponding author: Santos, Marino F. A.. "Using Small-angle X-ray Scattering to Characterize Biological Systems: A General Overview and Practical Tips". In Advanced Methods in Structural Biology, 381-403. Springer US, 2023.
    Published • 10.1007/978-1-0716-3147-8_22
  3. Engrola, Filipa S. S.; Paquete-Ferreira, João; Santos-Silva, Teresa; Correia, Márcia A. S.; Leisico, Francisco; Santos, Marino F. A.. Corresponding author: Santos, Marino F. A.. "Screening of Buffers and Additives for Protein Stabilization by Thermal Shift Assay: A Practical Approach". In Advanced Methods in Structural Biology, 199-213. Springer US, 2023.
    Published • 10.1007/978-1-0716-3147-8_11
Journal article
  1. João Paquete-Ferreira; Filipe Freire; Henrique S. Fernandes; Jayaraman Muthukumaran; João Ramos; Joana Bryton; Alejandro Panjkovich; et al. "Structural insights of an LCP protein–LytR–from Streptococcus dysgalactiae subs. dysgalactiae through biophysical and in silico methods". Frontiers in Chemistry (2024): http://dx.doi.org/10.3389/fchem.2024.1379914.
    10.3389/fchem.2024.1379914
  2. Alves-Barroco, Cinthia; Paquete-Ferreira, João; Santos-Silva, Teresa; Fernandes, Alexandra R.. "Singularities of Pyogenic Streptococcal Biofilms – From Formation to Health Implication". Frontiers in Microbiology 11 (2020): http://dx.doi.org/10.3389/fmicb.2020.584947.
    Published • 10.3389/fmicb.2020.584947
  3. João Ramos; Jayaraman Muthukumaran; Freire, Filipe; Ferreira, João; Ana Rita Otrelo-Cardoso; Dmitri Svergun; Alejandro Panjkovich; Teresa, Santos-Silva. "Shedding Light on the Interaction of Human Anti-Apoptotic Bcl-2 Protein with Ligands through Biophysical and in Silico Studies". International Journal of Molecular Sciences (2019): http://dx.doi.org/10.3390/ijms20040860.
    Published • 10.3390/ijms20040860 • Assistant staff
Preprint
  1. Paquete-Ferreira, João; Torres, Leonor; Bryton, Joana; Santos, Marino F. A.; Correia, Márcia A. S.; Fernandes, Alexandra R.; Romão, Maria João; Viegas, Aldino; Santos-Silva, Teresa. Corresponding author: Viegas, Aldino. "Structural and Functional Insights into a Previously Uncharacterized Psr LCP Protein from Streptococcus dysgalactiae subsp. dysgalactiae". 2025. https://doi.org/10.21203/rs.3.rs-8368946/v1.
    10.21203/rs.3.rs-8368946/v1
Thesis / Dissertation
  1. Ferreira, João Paquete. "From proteins to Bacteria: a multidisciplinary approach for the rational development of new anti-biofilm and antibacterial agents". PhD, Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, 2025.
  2. Paquete-Ferreira, João. "LytR Inhibition, as a New Approach to Avoid Biofilm Formation in Streptococcus dysgalactiae subs. dysgalactiae". Master, Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, 2019. https://drive.google.com/open?id=1KxvUWIP9IQh13Al6ruYvM0-s1e3TaaTI (~15 minutes video).
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2025/05/09 Targeting LytR-CpsA-Psr Proteins For Disruption of Biofilm Formation In Streptococcus dysgalactiae subsp. dysgalactiae Through Virtual Screening nnd Structural Insights 5th Meeting of Young Biophysicists
(Caparica, Portugal)
2024/05/10 From in silico to the Wet Lab: Paving the Way in LCP Family Inhibition 4th Meeting of Young Biophysicists
(Covilhã, Portugal)
2023/06/02 X-RAY CRYSTALLOGRAPHY AND NMR IN THE STUDY OF THE LYTR-CPSA-PSR FAMILY OF PROTEINS 3rd Meeting of Young Biophysicists
i3S - Instituto de Investigação e Inovação em Saúde (Porto, Portugal)
2023/01/17 Wall teichoic acids: a future target for antibiotics? GluPor 14
Sociedade Portuguesa de Química (Caparica, Portugal)
2023/01/17 Wall teichoic acids: a future target for antibiotics? GluPor14
(Caparica, Portugal)
2019/06/28 LytR from Streptococcus dysgalactiae subs. dysgalactiae: A Target for Biofilm Inhibition Presentation video (~10 minutes): https://drive.google.com/open?id=1lqgZa1RGyi4UOnaKXovbA7u_6PwJqbf3 VIII Encontro Nacional de Utilizadores de Radiação de Sincrotrão
Universidade do Porto, Faculdade de Ciências (Porto, Portugal)
2019/02/15 Structure-Based Desing of Promising Antibiofilm Formation Molecules Jornadas Intercalares das Dissertações Anuais dos Mestrados do DQ e do DCV
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia (Caparica, Portugal)

Supervision

Thesis Title
Role
Degree Subject (Type)
Institution / Organization
2023/02 - 2023/06 Análise da estrutura e da função de uma proteína envolvida na formação de biofilme bacteriano
Co-supervisor
Biochemistry (Degree)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2022/04 - 2022/06 DA ESTRUTURA 3D À FUNÇÃO DE UMA PROTEÍNA RESPONSÁVEL PELA FORMAÇÃO DE BIOFILME BACTERIANO
Co-supervisor
Biotecnologia (Degree)
Instituto Politécnico de Setúbal Escola Superior de Tecnologia do Barreiro, Portugal
2022/02 - 2022/04 From 3D structure to function of a protein responsible for the formation of bacterial biofilms
Co-supervisor
Bioquímica (Degree)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal

Event organisation

Event name
Type of event (Role)
Institution / Organization
2019/04/24 - 2019/04/24 Volunteer in the annual presentation event of Faculdade de Ciências e Tecnologia educational offer (EXPO-FCT), which aims to provide orientation to pre-university students, when choosing a higher education course, through scientific demonstrations and workshop activities. As well, as demonstrate to the community, it's innovative research in the different fields. (2019/04/24 - 2019/04/24)
Exhibition (Other)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2016/11 - 2017/02 JorTec - Jornadas Tecnológicas da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa – it is an event open to all people (inside and outsider FCT/NOVA), either students, professors, investigators and/or companies. It takes place at the FCT campus in Monte de Caparica and is organized exclusively by students from FCT-NOVA. The biggest objective of JorTec is to let know to all the participants the different realities existing in the several different areas of the faculty. (2017/02/03 - 2017/02/10)
Conference (President of the Organising Committee)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2016/04/06 - 2016/04/06 Volunteer in the annual presentation event of Faculdade de Ciências e Tecnologia educational offer (EXPO-FCT), which aims to provide orientation to pre-university students, when choosing a higher education course, through scientific demonstrations and workshop activities. As well, as demonstrate to the community, it's innovative research in the different fields. (2016/04/06 - 2016/04/06)
Exhibition (Other)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2015/11 - 2016/02 JorTec - Jornadas Tecnológicas da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa – it is an event open to all people (inside and outsider FCT/NOVA), either students, professors, investigators and/or companies. It takes place at the FCT campus in Monte de Caparica and is organized exclusively by students from FCT-NOVA. The biggest objective of JorTec is to let know to all the participants the different realities existing in the several different areas of the faculty. (2016/01/29 - 2016/02/05)
Conference (Member of the Organising Committee)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal

Event participation

Activity description
Type of event
Event name
Institution / Organization
2015/02/13 - 2015/02/13 JorTec - Jornadas Tecnológicas da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa – it is an event open to all people (inside and outsider FCT/NOVA), either students, professors, investigators and/or companies. It takes place at the FCT campus in Monte de Caparica and is organized exclusively by students from FCT-NOVA. The biggest objective of JorTec is to let know to all the participants the different realities existing in the several different areas of the faculty.
Conference
JORTEC Química e Bioquímica - Química à Portuguesa
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal

Committee member

Activity description
Role
Institution / Organization
2016/11 - 2017/06 Treasurer at Núcleo de Estudantes de Bioquímica FCT-NOVA (NuBioq). NuBioq was funded in 2016 by a group of students that aim to organize dynamic activities associated with the bachelor degree of Biochemistry. The activities organized by NuBioq enrich the academic experience of the students through workshops and lectures among other activities.
Member
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2015/04 - 2016/03 The pedagogical commission main objective is to facilitate the communication between the students and professors of the Biochemistry graduation of FCT-NOVA. It is also the linkage unit between the Biochemistry degree e the exterior providing important information, like scholarships, lectures and workshops; and revealing the degree in several institutions for the students to develop projects or ideas.
Member
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal