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My core research is focused on clarifying the events underlying the interaction between different proteins involved in electron transfer chains - particularly transient complexes, where the dissociation constant is in the micromolar range - using a suite of biophysics techniques where Nuclear Magnetic Resonance was the main choice. I was also involved in aiding the development of molecular docking software such as BiGGER/Chemera which, along with expertise and training in other docking programs (e.g. HADDOCK) lent me a deeper understanding of the underlying mechanisms guiding biomolecular interactions. I was awarded two FCT scholarships in my scientific career: PhD at NOVA School of Science and Technology, and post-doctoral at NOVA School of Science and Technology + University of Coimbra. I have authored/co-authored approximately 20 peer-reviewed publications and book chapters. I have also mentored an MSc student and a handful of undergraduate student projects.
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Identification

Personal identification

Full name
Rui Miguel Lourenço Rocha de Almeida

Citation names

  • Almeida, Rui
  • Rui M. Almeida

Author identifiers

Ciência ID
7914-74C1-E1C0
ORCID iD
0000-0003-3517-349X
Researcher Id
C-6384-2013

Email addresses

  • ralmeida@egasmoniz.edu.pt (Professional)

Telephones

Mobile phone
  • 918430593 (Personal)

Knowledge fields

  • Natural sciences - Biological Sciences - Biochemistry
  • Natural sciences - Biological Sciences - Biophysics
  • Natural sciences - Biological Sciences - Molecular Biology

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
French Upper intermediate (B2) Upper intermediate (B2) Upper intermediate (B2) Upper intermediate (B2) Upper intermediate (B2)
Education
Degree Classification
2006/01/01 - 2010/11/29
Concluded
 Bioquímica (Doutoramento)
Major in Especialidade: Bioquímica Física
Universidade NOVA de Lisboa Faculdade de Ciências e Tecnologia, Portugal
"NMR Studies of Transient Protein Complexes" (THESIS/DISSERTATION)
1998/10/01 - 2004/10/07
Concluded
 Bioquímica (Licenciatura)
Universidade de Lisboa Faculdade de Ciências, Portugal
 17
Affiliation

Science

Category
Host institution 		Employer
2011/06/01 - 2017/05/01 Postdoc (Research) Universidade NOVA de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2003/09/15 - 2004/10/06 Research Trainee (Research) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2022/02/07 - Current Assistant Professor (University Teacher) Egas Moniz Cooperativa de Ensino Superior CRL, Portugal
2018/09/01 - 2021/08/31 Invited Adjunct Teacher (Polytechnic Teacher) Instituto Politécnico de Lisboa Escola Superior de Tecnologia da Saúde de Lisboa, Portugal
Projects

Grant

Designation Funders
2016/01/01 - 2017/12/31 Denitrification - How to deal with NO and N2O
PTDC/BBB-BQB/0129/2014
Post-doc
Fundação para a Ciência e a Tecnologia
Concluded
2013/01/01 - 2017/03/31 NMR Net - National Facility for Nuclear Magnetic Resonance: from Molecular Structure and Dynamics to Protein Function, Cell Physiology, and Metabolomics
RECI/BBB-BQB/0230/2012
Post-doc
Fundação para a Ciência e a Tecnologia
Concluded
2012/01/01 - 2015/12/31 The Last Steps of the Denitrification Pathway
PTDC/QUI-BIQ/116481/2010
Post-doc
Fundação para a Ciência e a Tecnologia
Concluded

Contract

Designation Funders
2012/01/01 - 2014/12/31 As duas últimas etapas da desnitrificação
PTDC/QUI-BIQ/116481/2010
Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal

Associação para a Inovação e Desenvolvimento da FCT, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2010/01/01 - 2014/12/31 Redox-BioMaterials: Design of new redox biomaterials and their application in Biofuel cells for the production of electrical energy, feedstock chemicals and building blocks
PTDC/EBB-EBI/099237/2008
Post-doc Fellow
Concluded
Outputs

Publications

Book chapter
  1. Rui M. Almeida; Dell’ Acqua, Simone; Moura, Isabel; Pauleta, Sofia R.; Moura, José J. G.. "CHAPTER 11. Electron Transfer and Molecular Recognition in Denitrification and Nitrate Dissimilatory Pathways". In Metalloenzymes in Denitrification, 252-286. Royal Society of Chemistry, 2016.
    Published • 10.1039/9781782623762-00252
Journal article
  1. Samhan-Arias, Alejandro K.; Almeida, Rui M.; Ramos, Susana; Cordas, Cristina M.; Moura, Isabel; Gutierrez-Merino, Carlos; Moura, José J.G.. "Topography of human cytochrome b5/cytochrome b5 reductase interacting domain and redox alterations upon complex formation". Biochimica et Biophysica Acta (BBA) - Bioenergetics 1859 2 (2018): 78-87. http://dx.doi.org/10.1016/j.bbabio.2017.10.005.
    Published • 10.1016/j.bbabio.2017.10.005
  2. Ramos, Susana; Rui M. Almeida; Cordas, Cristina M.; Moura, José J.G.; Pauleta, Sofia R.; Moura, Isabel. Corresponding author: Moura, Isabel. "Insights into the recognition and electron transfer steps in nitric oxide reductase from Marinobacter hydrocarbonoclasticus". Journal of Inorganic Biochemistry 177 (2017): 402-411. http://dx.doi.org/10.1016/j.jinorgbio.2017.09.001.
    Published • 10.1016/j.jinorgbio.2017.09.001
  3. Maiti, Biplab K.; Rui M. Almeida; Moura, Isabel; Moura, José J.G.. "Rubredoxins derivatives: Simple sulphur-rich coordination metal sites and its relevance for biology and chemistry". Coordination Chemistry Reviews 352 (2017): 379-397. http://dx.doi.org/10.1016/j.ccr.2017.10.001.
    10.1016/j.ccr.2017.10.001
  4. Biplab K. Maiti; Rui M. Almeida; Luisa B. Maia; Isabel Moura; José J. G. Moura. "Insights into the Molybdenum/Copper Heterometallic Cluster Assembly in the Orange Protein: Probing Intermolecular Interactions with an Artificial Metal-Binding ATCUN Tag". Inorganic Chemistry 56 15 (2017): 8900-8911. https://doi.org/10.1021/acs.inorgchem.7b00840.
    10.1021/acs.inorgchem.7b00840
  5. Humberto A. Pedroso; Célia M. Silveira; Rui M. Almeida; Ana Almeida; Stéphane Besson; Isabel Moura; José J.G. Moura; M. Gabriela Almeida. "Electron transfer and docking between cytochrome cd 1 nitrite reductase and different redox partners — A comparative study". Biochimica et Biophysica Acta (BBA) - Bioenergetics 1857 9 (2016): 1412-1421. https://doi.org/10.1016/j.bbabio.2016.04.279.
    10.1016/j.bbabio.2016.04.279
  6. Almeida, M. Rui; Dell’Acqua, Simone; Krippahl, Ludwig; Moura, J. José; Pauleta, R. Sofia. "Predicting Protein-Protein Interactions Using BiGGER: Case Studies". Molecules 21 8 (2016):
    10.3390/molecules21081037
  7. Rui N. L. Carvalho; Rui M. Almeida; José J. G. Moura; Nuno T. Lourenço; Luís J. P. Fonseca; Cristina M. Cordas. "Sandwich-Type Enzymatic Fuel Cell Based on a New Electro-Conductive Material - Ion Jelly". ChemistrySelect 1 20 (2016): 6546-6552. http://dx.doi.org/10.1002/slct.201601640.
    10.1002/slct.201601640
  8. Pedroso, Humberto A.; Silveira, Célia M.; Almeida, Rui M.; Almeida, Ana; Besson, Stéphane; Moura, Isabel; Moura, José J G; Almeida, Maria Gabriela Machado de. "Electron transfer and docking between cytochrome cd1 nitrite reductase and different redox partners - A comparative study". (2016): https://doi.org/10.1016/j.bbabio.2016.04.279.
    https://doi.org/10.1016/j.bbabio.2016.04.279
  9. Fliedel, Christophe; Rosa, Vitor; Santos, Carla I. M.; Gonzalez, Pablo J.; Almeida, Rui M.; Gomes, Clara S. B.; Gomes, Pedro T.; et al. "Copper(ii) complexes of bis(aryl-imino)acenaphthene ligands: synthesis, structure, DFT studies and evaluation in reverse ATRP of styrene". Dalton Transactions 43 34 (2014): 13041-13054.
    10.1039/C4DT01069H
  10. Almeida, Rui M; Turano, Paola; Moura, Isabel; Moura, Jose J G; Pauleta, Sofia R. "Superoxide reductase: different interaction modes with its two redox partners.". Chembiochem : a European journal of chemical biology 14 14 (2013): 1858-66.
    10.1002/cbic.201300196
  11. Mathies, Guinevere; Almeida, Rui M.; Gast, Peter; Moura, Jose J. G.; Groenen, Edgar J. J.. "Multifrequency EPR Study of Fe3+ and Co2+ in the Active Site of Desulforedoxin". Journal of Physical Chemistry B 116 24 (2012): 7122-7128.
    10.1021/jp3025655
  12. Ramos, Susana; Almeida, Rui M.; Moura, Jose J. G.; Aureliano, Manuel. "Implications of oxidovanadium(IV) binding to actin". Journal of Inorganic Biochemistry 105 6 (2011): 777-783.
    10.1016/j.jinorgbio.2011.02.010
  13. Mathies, G.; Blok, H.; Disselhorst, J. A. J. M.; Gast, P.; van der Meer, H.; Miedema, D. M.; Almeida, R. M.; et al. "Continuous-wave EPR at 275 GHz: Application to high-spin Fe3+ systems". Journal of Magnetic Resonance 210 1 (2011): 126-132.
    10.1016/j.jmr.2011.03.009
  14. Almeida, Rui M.; Geraldes, Carlos F. G. C.; Pauleta, Sofia R.; Moura, Jose J. G.. "Gd(III) Chelates as NMR Probes of Protein-Protein Interactions. Case Study: Rubredoxin and Cytochrome c(3)". Inorganic Chemistry 50 21 (2011): 10600-10607.
    10.1021/ic200858c
  15. Ramos, Susana; Almeida, Rui M.; Moura, José J. G.; Aureliano, M.. "Implications of oxidovanadium(IV) binding to actin". (2011): http://hdl.handle.net/10400.1/1327.
  16. Almeida, Rui M.; Geraldes, Carlos F. G. C.; Pauleta, Sofia R.; Moura, José J. G.. "Gd(III) chelates as NMR probes of protein-protein interactions. Case study: rubredoxin and cytochrome c3". (2011): http://hdl.handle.net/10362/8610.
  17. Almeida, Rui M.; Pauleta, Sofia R.; Moura, Isabel; Moura, Jose J. G.. "Rubredoxin as a paramagnetic relaxation-inducing probe". Journal of Inorganic Biochemistry 103 9 (2009): 1245-1253.
    10.1016/j.jinorgbio.2009.07.006
  18. Gomes, Catarina; Palma, Angelina S.; Almeida, Rui; Regalla, Manuela; McCluskey, Leo F.; Trojanowski, John Q.; Costa, Julia. "Establishment of a cell model of ALS disease: Golgi apparatus disruption occurs independently from apoptosis". Biotechnology Letters 30 4 (2008): 603-610.
    10.1007/s10529-007-9595-z
  19. Pereira, Alice S.; Tavares, Pedro; Folgosa, Filipe; Almeida, Rui M.; Moura, Isabel; Moura, Jose J. G.. "Superoxide reductases". European Journal of Inorganic Chemistry 18 (2007): 2569-2581.
    10.1002/ejic.200700008
Activities

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2013/10/01 - 2014/11/02 Clonagem, sobre-expressão, purificação e caracterização bioquímica da proteína MreB de Marinobacter hydrocarbonoclasticus
Co-supervisor of Raquel Alexandra Rodrigues Amador
 Bioquímica (Master)
Universidade NOVA de Lisboa Faculdade de Ciências e Tecnologia, Portugal