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Computational Design of Membrane Proteins pp 3–28Cite as

Guardians of the Cell: State-of-the-Art of Membrane Proteins from a Computational Point-of-View

Part of the Methods in Molecular Biology book series (MIMB,volume 2315)

Abstract

Membrane proteins (MPs) encompass a large family of proteins with distinct cellular functions, and although representing over 50% of existing pharmaceutical drug targets, their structural and functional information is still very scarce. Over the last years, in silico analysis and algorithm development were essential to characterize MPs and overcome some limitations of experimental approaches. The optimization and improvement of these methods remain an ongoing process, with key advances in MPs’ structure, folding, and interface prediction being continuously tackled. Herein, we discuss the latest trends in computational methods toward a deeper understanding of the atomistic and mechanistic details of MPs.

Key words

  • Membrane proteins
  • Computational methods
  • Interfaces
  • Molecular dynamics
  • Machine learning
  • Sequence–structure–function Prediction

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Acknowledgments

This work was funded by COMPETE 2020—Operational Programme for Competitiveness and Internationalisation and Portuguese national funds via FCT—Fundação para a Ciência e a Tecnologia, under projects DSAIPA/DS/0118/2020, POCI-01-0145-FEDER-031356, PTDC/QUI-OUT/32243/2017, UIDB/04539/2020 and LA/P/0058/2020. The authors would also like to acknowledge ERNEST—European Research Network on Signal Transduction, CA18133, and STRATAGEM—New diagnostic and therapeutic tools against multidrug-resistant tumors, CA17104. Nícia Rosário-Ferreira and Catarina Marques-Pereira were also supported by FCT, through Ph.D. scholarships PD/BD/135179/2017 and 2020.07766.BD (DOCTORATES 4 COVID-19), respectively. Raquel Pina Gouveia was also supported by FCT and DGES—Direção Geral do Ensino Superior, through fellowship for Curso de Verão in “Metodologias de Investigação Científica”—Módulo de I&D “Metodologias Avançadas para o Estudo do Cérebro”, under the program “Verão com Ciência.”

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Authors and Affiliations

  1. Coimbra Chemistry Center, Department of Chemistry, University of Coimbra, Coimbra, Portugal

    Nícia Rosário-Ferreira

  2. Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal

    Nícia Rosário-Ferreira, Catarina Marques-Pereira & Raquel P. Gouveia

  3. PhD Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal

    Catarina Marques-Pereira

  4. Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal

    Joana Mourão

  5. Department of Life Sciences, University of Coimbra, Coimbra, Portugal

    Irina S. Moreira

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  1. Nícia Rosário-Ferreira
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  3. Raquel P. Gouveia
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  5. Irina S. Moreira
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Correspondence to Irina S. Moreira .

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  1. Department of Life Sciences, University of Coimbra, Coimbra, Portugal

    Dr. Irina S. Moreira

  2. BioISI, University of Lisboa, Lisboa, Portugal

    Miguel Machuqueiro

  3. Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal

    Joana Mourão

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Rosário-Ferreira, N., Marques-Pereira, C., Gouveia, R.P., Mourão, J., Moreira, I.S. (2021). Guardians of the Cell: State-of-the-Art of Membrane Proteins from a Computational Point-of-View. In: Moreira, I.S., Machuqueiro, M., Mourão, J. (eds) Computational Design of Membrane Proteins. Methods in Molecular Biology, vol 2315. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1468-6_1

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