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I am a PhD student of Theoretical Biochemistry, currently studying the biophysical impact of the accurate description of the mitochondrial electrochemical gradient in the proton pumping function of Cytochrome C Oxidase. I have a BSc. degree in Biochemistry and a MSc. in Biochemistry and Biomedicine from the Faculty of Sciences of the University of Lisbon, finished with the grades of 13/20 and 18/20, respectively. Midway into my Bachelor¿s degree (in 2017), I joined the Molecular Modelling and Simulation group, now the Machuqueiro Lab ( Biosystems & Integrative Sciences Institute/BioISI), where I was involved in two projects that yielded my first scientific poster presentation entitled ¿pH-dependent permeability of outer membrane protein G: an in silico study¿ (in 2018) and a publication entitled ¿Improved GROMOS 54A7 Charge Sets for Phosphorylated Tyr, Ser, and Thr to Deal with pH-Dependent Binding Phenomena¿ in J. Chem. Theory Comput. (in 2020; 10.1021/acs.jctc.0c0052). During my Master¿s degree I was the student representative, being involved in the organization of the annual event that showcases the preliminary results of student¿s research. I received a grant to work on my dissertation project, on evaluating the biophysical profile of metallodrug delivery systems. With this work, I learned a great deal about Molecular Dynamics and other computational techniques like Umbrella Sampling scheme implementation, Quantum Mechanics, and membrane permeability calculations, receiving a 20/20 grade on my thesis discussion. The results of my thesis work were presented at multiple conferences, namely at Encontro de Jovens Investigadores de Biologia Computacional Estrutural (2021), 2nd Chem & Biochem Students Meeting (2022) and 3D-BIOINFO-PT Annual Meeting (2022) as posters; at Virtual Winter School on Computational Chemistry (2023) as a Single Figure Presentation (SPF); and at BioData.pt Talks - 3D BioTalks (2023) and Bioinformatics Open Days as oral presentations. Additionally, due to the integration of my thesis work in a larger research project, there were frequent report meetings where I also presented preliminary results for the other contributing researchers. More recently, I was heavily involved in a project showcasing the potential of the in-house analysis tool MembIT, which led to a poster presentation at 3D-BIOINFO-PT Annual Meeting (2022) and a SPF at Virtual Winter School on Computational Chemistry (2023). This culminated in the publication of a scientific paper entitled ¿MembIT - a tool to calculate solute membrane insertions and deformations in molecular dynamics simulations¿ in J. Comput. Biophys. Chem. (10.1142/S2737416523500254) for which I am co-first author. Member of the Portuguese Society of Biophysics (SPB) since 2024.
Identification

Personal identification

Full name
INÊS DOMINGOS DA SILVA PIRES

Citation names

  • Pires, I.D.S.

Author identifiers

Ciência ID
AF1A-F82A-8B24
ORCID iD
0000-0002-4129-6923
Researcher Id
V-5853-2017

Websites

Knowledge fields

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

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Advanced (C1)
Japanese Intermediate (B1) Intermediate (B1) Intermediate (B1) Upper intermediate (B2)
Education
Degree Classification
2023/09/01 - 2027/09/01
Ongoing
Bioquímica (Doutoramento)
Major in Bioquímica Teórica
Universidade de Lisboa Faculdade de Ciências, Portugal
2020/09/01 - 2022/03/14
Concluded
Biochemistry and Biomedicine (Mestrado)
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
"Computational biophysics evaluation of promising smart metallodrug delivery systems" (THESIS/DISSERTATION)
18
2014/09/01 - 2020/02/29
Concluded
Biochemistry (Licenciatura)
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
13
Affiliation

Science

Category
Host institution
Employer
2021/09/01 - Current Researcher (Research) Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
Projects

Grant

Designation Funders
2023/09/01 - Current In silico study of the electrochemical gradient role in Cytochrome c Oxidase proton gating mechanism
2023.01155.BD
PhD Student Fellow
Fundação para a Ciência e a Tecnologia, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2021/09/01 - 2022/08/31 New antitumor Ru-based compound derivatives optimized using in silico methods
PTDC/QUI-QIN/0146/2020
Master Student Fellow
Fundação para a Ciência e a Tecnologia, Portugal
FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências
Ongoing

Other

Designation Funders
2021/09/01 - 2023/03/14 Strategic Project of BioISI (UIDB/04046/2020 and UIDP/04046/2020)
UIDB/04046/2020
UIDP/04046/2020
Researcher
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
Outputs

Publications

Conference poster
  1. Pires, ines; Baptista, António M.; Machuqueiro, Miguel. Corresponding author: Pires, ines. "Improving the accuracy of a computational model of Cytochrome c Oxidase to study the proton gating mechanism". Paper presented in 3D-BIOINFO-PT Annual Meeting, 2024.
  2. Pires, ines; Baptista, António M.; Machuqueiro, Miguel. Corresponding author: Pires, ines. "Insights into the Cytochrome c Oxidase proton pumping mechanism from Constant-pH simulations". Paper presented in 21st IUPAB Congress 2024 and 62nd Annual Meeting of the Biophysical Society of Japan, 2024.
  3. Pires, ines; BAPTISTA, ANTÓNIO; Machuqueiro, Miguel. "Insights into the Cytochrome c Oxidase proton pumping mechanism from Constant-pH simulations". Paper presented in IUPAB 2024 Eve Fest, 2024.
  4. Pires, I.D.S.; Baptista, António M.; Machuqueiro, Miguel. Corresponding author: Pires, I.D.S.. "Studying Cytochrome c Oxidase proton pumping mechanism with Constant-pH simulations". Paper presented in 4th Biophysics Festival, 2024.
  5. Pires, ines; Baptista, António M.; Machuqueiro, Miguel. Corresponding author: Pires, ines. "Constant-pH MD simulations of Cytochrome c Oxidase". Paper presented in Hünfeld 2024: Workshop on Computer Simulation and Theory of Macromolecules - Online Workshop, 2024.
  6. Pires, I.D.S.; Morais, Tânia S.; Machuqueiro, Miguel. "In silico study of promising ruthenium metalodrug delivery systems". Paper presented in 3rd Chem & Biochem Students Meeting, FCUL, Lisboa, Portugal, 2023.
  7. Pires, I.D.S.; Machuqueiro, Miguel. "How protein pKa predictions are affected by the choice of experimental structure?". Paper presented in Protein Electrostatics 2023, Genoa, IT., 2023.
  8. Suzano, Pedro M. S.; Silva, Tomás F.D.; Pires, I.D.S.; Oliveira, Nuno F. B.; Pedro Reis; Machuqueiro, Miguel. Corresponding author: Suzano, Pedro M. S.. "MembIT - a Powerful Tool for Analyzing Solute Membrane Insertions and Deformations in MD Simulations". Paper presented in Protein Electrostatics 2023, Genoa, IT., 2023.
  9. Pires, I.D.S.; Morais, Tânia S.; Machuqueiro, Miguel. "Evaluating the membrane biophysical profile of smart metallodrugs for cancer therapy". Paper presented in Virtual Winter School on Computational Chemistry, Online Workshop, 2023.
  10. Suzano, Pedro; Pires, I.D.S.; Oliveira, Nuno F. B.; Silva, Tomás F.D.; Reis, Pedro B P S; Machuqueiro, Miguel. "MembIT - a tool to calculate membrane-insertion properties of solutes". Paper presented in Virtual Winter School on Computational Chemistry, Online Workshop, 2023.
  11. Silva, Tomás F.D.; Suzano, Pedro; Pires, I.D.S.; Oliveira, Nuno F. B.; Reis, Pedro B P S; Machuqueiro, Miguel. Corresponding author: Suzano, Pedro. "MembIT - a tool to calculate membrane-insertion properties of solutes". Paper presented in 3D-BIOINFO-PT Annual Meeting, 2022.
  12. Pires, I.D.S.; Morais, Tânia S.; Machuqueiro, Miguel. "Computational biophysics evaluation of promising smart metallodrug delivery system". Paper presented in 3D-BIOINFO-PT Annual Meeting, 2022.
  13. Pires, ines; Morais, T. S.; Machuqueiro, M.. "In silico approaches to study membrane permeability of new antitumor Ru compounds". Paper presented in 2nd Chem & Biochem Students Meeting, 2022.
  14. Pires, Ines; Morais, T. S.; Machuqueiro, M.. "New antitumor Ru-based compound deriva- tives optimized using in silico methods". Paper presented in EJIBCE2, 2021.
  15. Oliveira, N.F.B.; Pires, ines; Machuqueiro, M.. "New phosphorylated amino acid parametrization to correctly reproduce their acid/base equilibria, including in protein binding events". Paper presented in EJIBCE, 2018.
  16. Pires, ines; Machuqueiro, M.. "pH-dependent permeability of outer membrane protein G: an in silico study". Paper presented in EJIBCE,, 2018.
Journal article
  1. Suzano, Pedro M. S.; Pires, I.D.S.; Silva, Tomas F. D.; Oliveira, Nuno F. B.; Reis, Pedro B. P. S.; Machuqueiro, Miguel. "MembIT - a tool to calculate solute membrane insertions and deformations in molecular dynamics simulations". Journal of Computational Biophysics and Chemistry (2023): http://dx.doi.org/10.1142/s2737416523500254.
    Accepted • 10.1142/s2737416523500254
  2. Oliveira, Nuno F. B.; Pires, ines; Machuqueiro, Miguel. "Improved GROMOS 54A7 Charge Sets for Phosphorylated Tyr, Ser, and Thr to Deal with pH-Dependent Binding Phenomena". Journal of Chemical Theory and Computation 16 10 (2020): 6368-6376. http://dx.doi.org/10.1021/acs.jctc.0c00529.
    10.1021/acs.jctc.0c00529
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2023/12/18 Are protein pKa predictions affected by the choice of experimental structure? 3D-BIOINFO-PT Annual Meeting
3D-BIOINFO-PT (Coimbra, Portugal)
2023/03/16 Computational study of promising smart metallodrug delivery systems Bioinformatics Open Days
Bioinformatics department of University of Minho (Braga, Portugal)
2023/02/08 Computational biophysics evaluation of promising smart metallodrug delivery systems BioData.pt Talks - 3D BioTalks (https://www.biodata.pt/node/446)
BioData.pt (Lisboa, Portugal)
2023/01/25 Computational biophysics evaluation of promising smart metallodrug delivery systems - Computational Report Arrows2cancer Consultory Meeting
Tânia S. Morais (Lisbon, Portugal)
2022/11/24 Computational biophysics evaluation of promising smart metallodrug delivery systems - Computational Report Arrows2cancer Consultory Meeting
Tânia S. Morais (Lisbon, Portugal)
2022/04/10 Arrows2cancer - Computational Report Arrows2cancer Internal Results Meeting
Tânia S. Morais (Lisbon, Portugal)
2022/02/18 New antitumor Ru-based compound derivatives optimized using in silico methods 4º Encontro do Mestrado em Bioquímica
Mestrado em Bioquímica (Lisbon, Portugal)