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Nuno Filipe Baltazar Maia Costa de Oliveira. Completed the Mestrado in Bioquímica in 2021/01/18 by Universidade de Lisboa Faculdade de Ciências and Licenciatura in Bioquímica in 2018/06/14 by Universidade de Lisboa Faculdade de Ciências. Published 3 articles in journals. Has 1 section(s) of books. Participated in 5 event(s). Participates and/or participated as Research Fellow in 1 project(s). Works in the area(s) of Natural sciences with emphasis on Biological Sciences with emphasis on Biochemistry. In his curriculum Ciência Vitae the most frequent terms in the context of scientific, technological and artistic-cultural output are: Biofísica Computacional; Bioquímica; Dinâmica M; Computational Biochemistry; CpHMD; ForceField Development; Molecular Dynamics; Biophysics; Umbrella-Sampling, ; Membrane transporters; Bioquimica computational; Dinâmica Molecular; Física; Física de Particulas; enhanced sampling mechanics; Cristais; Quimica; agregação; amyloidose,; .
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Identification

Personal identification

Full name
Nuno Filipe Baltazar Maia Costa de Oliveira

Citation names

  • Oliveira, Nuno
  • Oliveira, N. F. B.

Author identifiers

Ciência ID
D91B-7E7D-89D2
ORCID iD
0000-0003-4368-2745

Knowledge fields

  • Natural sciences - Biological Sciences - Biochemistry

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Education
Degree Classification
2021/09/01 - 2025/09/01
Ongoing
 Biochemistry (Doutoramento)
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
2018/09/06 - 2021/01/18
Concluded
 Biochemistry (Mestrado)
Major in Biochemistry
Universidade de Lisboa Faculdade de Ciências, Portugal
"The role of electrostatics in the mechanism of ATP/ADP Carrier function: an in silico study" (THESIS/DISSERTATION)
 18
2018/06/14
Concluded
 Biochemistry (Licenciatura)
Universidade de Lisboa Faculdade de Ciências, Portugal
 14
2012 - 2014
Concluded
 Ciências e Tecnologias (Ensino secundário)
Escola Secundária José Saramago, Portugal
Affiliation

Others

Category
Host institution 		Employer
2021/09/01 - Current Bolseiro de Doutoramento Fundação para a Ciência e a Tecnologia, Portugal
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
2019/07/09 - 2021/04/09 Bolseiro de Investigação FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
2018 - 2019 Estágio Voluntário Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
2017 - 2018 Estágio Voluntário Universidade de Lisboa Centro de Química e Bioquímica, Portugal
Projects

Grant

Designation Funders
2019/07/09 - 2021/04/09 As bases física da doença: O caso da Amiloidose Relacionada com a Diálise Physical Basis of Disease: The case of Dialysis Related Amyloidosis
PTDC/FIS-OUT/28210/2017
Research Fellow
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
Outputs

Publications

Book chapter
  1. Oliveira, N. F. B.; Reis, P. B. P. S. (BA1A-8F17-5F20); Silva, T. F. D. (A31B-EA41-A32E); Machuqueiro, M. (D416-CB5B-AC3D). "pKa Calculations in Membrane Proteins". In Methods in Molecular Biology: Computational Design of Membrane Proteins, edited by Irina Moreira; Joana Mourão; Miguel Machuqueiro. Springer US, 2021.
    In press • 10.1007/978-1-0716-1468-6
Conference abstract
  1. Oliveira, Nuno; Pires, Inês; Machuqueiro, Miguel. "New phosphorylated amino acid parametrization to correctly reproduce their acid/base equilibria, including in protein binding events". Paper presented in EJIBCE-02: Meeting of Young Researchers in Structural Computational Biology, Porto, 2018.
    10.3390/mol2net-04-06082
Conference poster
  1. Vitorino, João N. M.; Oliveira, Nuno; Filipe E. P. Rodrigues; Faísca, Patrícia FN; Machuqueiro, Miguel. "Predicting Aggregation-Triggering ¿2m Oligomers With The Help Of MMPBSA Calculations". Paper presented in 3D-BIOINFO-PT Annual Meeting, 2022.
  2. Silva, T. F. D; Suzano, P. M. S; Pires, I. D. S.; Oliveira, N. F. B.; Reis, P; Machuqueiro, M. (D416-CB5B-AC3D). "MembIT – a tool to calculate membrane-insertion properties of solutes". Paper presented in 3D-BIOINFO-PT Annual Meeting, 2022.
  3. Guerra, R.F.C.C; Oliveira, N. F. B.; Suzano, P.M.S; Victor, B.L; Machuqueiro, M. (D416-CB5B-AC3D). "A computational study on the impact of adding anionic groups to tyrosine kinase inhibitors". Paper presented in 3D-Bioinfo-PT Anual Meeting 2022, 2022.
  4. Oliveira, N. F. B.; Yousef, Mohannad; Machuqueiro, Miguel. "Computational estimation of protein/drug pH-dependent binding affinities". Paper presented in 3D-BIOINFO-PT Annual Meeting, 2022.
  5. Teixeira, G. R.; Belisaro, D.; Oliveira, Nuno; Sequeira, João G. N.; Romero, I.; Riganti, C.; Machuqueiro, M. (D416-CB5B-AC3D); et al. "Targeting P-gp with Ru-cyclopentadienyl compounds: an approach to overcome cancer multidrug resistance". Paper presented in CQE Days 2022, 2022.
  6. Oliveira, N. F. B.; Machuqueiro, Miguel. "The Role of Electrostatics in the Mechanism of ATP/ADP Carrier Function: An in silico Study". Paper presented in Hünfeld 2021: Workshop on Computer Simulation and Theory of Macromolecules, 2021.
  7. Vitorino, João N. M.; Oliveira, N. F. B.; Rodrigues, F. E. P.; Machuqueiro, Miguel. Corresponding author: Vitorino, João N. M.. "Develop a Simple and Fast MM-PBSA Method Based on DelPhi to Study Protein/Protein Binding Affinities". Paper presented in Hünfeld 2021: Workshop on Computer Simulation and Theory of Macromolecules, 2021.
  8. Rodrigues, F. E. P.; Oliveira, N. F. B.; Vila-Viçosa, D; Faìsca, P. F. N. (3F14-4793-6882); Machuqueiro, M. (D416-CB5B-AC3D). "An MD-based protocol to assess the stability of ß2M dimers obtained from MC-ED". Paper presented in 7º Encontro Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE2019), 2019.
Journal article
  1. Mohannad Jawad Mustafa Yousef; Nuno F. B. Oliveira; João Vitorino; Pedro B. P. S. Reis; Piotr Draczkowski; Maciej Maj; Krzysztof Jozwiak; Miguel Machuqueiro. "Toward Accurate pH-Dependent Binding Constant Predictions Using Molecular Docking and Constant-pH MD Calculations". Journal of Chemical Theory and Computation (2025): http://dx.doi.org/10.1021/acs.jctc.4c01291.
    10.1021/acs.jctc.4c01291
  2. Nuno F.B. Oliveira; Alexey S. Ladokhin; Miguel Machuqueiro. "Constant-pH MD simulations of the protonation-triggered conformational switching in diphtheria toxin translocation domain". Biophysical Journal (2024): http://dx.doi.org/10.1016/j.bpj.2024.08.023.
    10.1016/j.bpj.2024.08.023
  3. Iris C. Salaroglio; Denitsa Stefanova; Ricardo G. Teixeira; Nuno F.B. Oliveira; Amer Ahmed; Fabio Fusi; Virginia Tzankova; et al. "A novel combinatory treatment against a CDDP-resistant non-small cell lung cancer based on a Ruthenium(II)-cyclopentadienyl compound". Pharmacological Research (2024): http://dx.doi.org/10.1016/j.phrs.2024.107353.
    10.1016/j.phrs.2024.107353
  4. Ricardo G. Teixeira; Iris C. Salaroglio; Nuno F. B. Oliveira; João G. N. Sequeira; Xavier Fontrodona; I. Romero; Miguel Machuqueiro; et al. "Fighting Multidrug Resistance with Ruthenium–Cyclopentadienyl Compounds: Unveiling the Mechanism of P-gp Inhibition". Journal of Medicinal Chemistry (2023): http://dx.doi.org/10.1021/acs.jmedchem.3c01120.
    10.1021/acs.jmedchem.3c01120
  5. Nuno F. B. Oliveira; Filipe E. P. Rodrigues; João Vitorino; PFN Faisca; Miguel Machuqueiro. "Interfacial Dynamics and Growth Modes of ß2-Microglobulin Dimers". Journal of Chemical Information and Modeling (2023): http://dx.doi.org/10.1021/acs.jcim.3c00399.
    10.1021/acs.jcim.3c00399
  6. Mykola V. Rodnin; Victor Vasques-Montes; Alexander Kyrychenko; Nuno F. B. Oliveira; Maithri M. Kashipathy; Kevin P. Battaile; Justin Douglas; et al. "Histidine Protonation and Conformational Switching in Diphtheria Toxin Translocation Domain". Toxins (2023): http://dx.doi.org/10.3390/toxins15070410.
    10.3390/toxins15070410
  7. Nuno F. B. Oliveira; Miguel Machuqueiro. "Novel US-CpHMD Protocol to Study the Protonation-Dependent Mechanism of the ATP/ADP Carrier". Journal of Chemical Information and Modeling 62 10 (2022): 2550-2560. http://dx.doi.org/10.1021/acs.jcim.2c00233.
    10.1021/acs.jcim.2c00233
  8. Oliveira, N. F. B.; Rodrigues, Filipe E.P.; Vitorino, João N.M.; Loureiro, Rui J.S.; Faísca, Patrícia F.N.; Machuqueiro, Miguel. "Predicting stable binding modes from simulated dimers of the D76N mutant of B2-microglobulin". Computational and Structural Biotechnology Journal 19 (2021): 5160-5169. http://dx.doi.org/10.1016/j.csbj.2021.09.003.
    Accepted • 10.1016/j.csbj.2021.09.003
  9. Oliveira, N. F. B.. "Improved GROMOS 54A7 Charge Sets for Phosphorylated Tyr, Ser, and Thr to Deal with pH-Dependent Binding Phenomena". Journal of Chemical Theory and Computation (2020): http://dx.doi.org/10.1021/acs.jctc.0c00529.
    10.1021/acs.jctc.0c00529
Thesis / Dissertation
  1. Oliveira, N. F. B.. "The role of electrostatics in the mechanism of ATP/ADP Carrier function: an in silico study". Master, Universidade de Lisboa Faculdade de Ciências, 2021.

Other

Other output
  1. A new ruthenium-cyclopentadienyl compound as a promising cancer MDR reversing agent. Oral communication given at CQE Days 2023.. 2023. Valente, Andreia; Ricardo G. Teixeira; Maximiano, Inês; Oliveira, N. F. B.; Sequeira, João G. N.; Antunes A; Machuqueiro, Miguel.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2023/06/26 Improving the sampling of CpHMD simulations by coupling with Replica-Exchange/Umbrella Sampling techniques Protein Electrostatics
IIT (Genova, Italy)
2021/12/20 A novel US-CpHMD protocol to study the protonation-dependent mechanism of the ATP/ADP carrier 8º Encontro Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE2021)
Universidade de Coimbra (Coimbra, Portugal)

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2021/12/20 - Current º Encontro Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE2021)
Conference
Universidade de Coimbra, Portugal
2021/04/23 - Current Computer Simulation and Theory of Macromolecules 2021
Conference
 Computer Simulation and Theory of Macromolecules 2021
Max-Planck-Institut für Multidisziplinäre Naturwissenschaften, Germany
2019/12/20 - 2019/12/20 Participation on Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE)
Meeting
 Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE)
Universidade de Lisboa Faculdade de Ciências, Portugal
2018/12/21 - 2018/12/21 Participation on Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE)
Meeting
 Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE)
Universidade do Porto Faculdade de Medicina, Portugal
2017/12/22 - 2017/12/22 Participation on Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE)
Meeting
 Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE)
Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
2014 - 2014 Participation on projecto "Saramago on the Rocks"
Other
 10th Edition of European Science Day for Youth “Crystals”
Escola Secundária José Saramago, Portugal
2012/03/12 - 2012/03/12 Participation on the conference "International Masterclasses hands on particle physics
Conference
 International Masterclasses hands on particle physics
Universidade de Lisboa Faculdade de Ciências, Portugal