Dr Conrado Pedebos

Postdoctoral Research Fellow

IMG_2563-edit

Research

Simulations of crowding effects within the E.coli cell envelope.

Publication list

  • Weerakoon D, Petrov K, Pedebos C, Khalid S (2021). “Polymyxin B1 within the E. coli cell envelope: insights from molecular dynamics simulations”. Biophysical Reviews. https://doi.org/10.1007/s12551-021-00869-8

  • van den Berg B, Pedebos C, Bolla JR, Robinson CV, Baslé A, Khalid S. (2021) “Structural basis for silicic acid uptake by higher plants”. J. Mol. Biol. https://doi.org/10.1016/j.jmb.2021.167226

  • Pedebos C, Smith IPS, Boags A, Khalid S. (2021) “The hitchhiker’s guide to the periplasm: unexpected molecular interactions of polymyxin B1 in E. coli”. Structure, doi:10.1016/j.str.2021.01.009.

  • Roman-Trufero M, Ito CM, Pedebos C, Magdalou I, Wang YF, Karimi MM, Moyon B, Webster Z, di Gregorio A, Azuara V, Khalid S, Speck C, Rodriguez T, Dillon N. (2020) “Evolution of an Amniote-Specific Mechanism for Modulating Ubiquitin Signaling via Phosphoregulation of the E2 Enzyme UBE2D3”. Molecular Biology and Evolution, 37 (7), 1986–2001.

  • Arantes PR*, Pedebos C*, Poleto MD, Pol-Fachin L, Verli H. (2020) “The Lazy Life of Lipid-Linked Oligosaccharides in All Life Domains”. Journal of Chemical Information and Modeling, 60 (2), 631-643.

  • Arantes PR, Poleto MD, John EBO, Pedebos C, Grisci BI, Dorn M, Verli H. (2019) “Development of GROMOS-Compatible Parameter Set for Simulations of Chalcones and Flavonoids.” Journal of Physical Chemistry B, 123 (5), 994–1008.

  • Shkurti A, Styliari ID, Balasubramanian V, Bethune I, Pedebos C, Jha S, Laughton CA. (2019) “CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space”. Journal of Chemical Theory and Computation, 15 (4), 2587–259.

  • Feltes BC*, Pedebos C*, Verli H, Bonatto D. (2018) “Dynamics of DDB2-DDB1 complex under different naturally-occurring mutants in Xeroderma Pigmentosum disease”. BBA – General Subjects, 1862, 2579-2589.

  • Da Costa CT, Pedebos C, Verli H, Fett-Neto A. (2017) “The role of Zn+2, dimerization and N-glycosylation in the interaction of Auxin Binding Protein 1 (ABP1) with different auxins.” Glycobiology, 27 (12), 1109-1119.

  • Pedebos C, Arantes PR, Giesel GM, Verli H. (2015) “In silico Investigation of the PglB Active Site Reveals Transient Catalytic States and Octahedral Metal Ion Coordination.” Glycobiology, 25 (11), 1183- 1195.

  • Pedebos C, Pol-Fachin L, Pons R, Teixeira C, Verli H. (2014) “Atomic Model and Micelle Dynamics of QS-21 Saponin.” Molecules, 19, 3744-3760.

  • De Paula FT, Frauches PQ, Pedebos C, Berger M, Gnoatto SCB, Gosmann G, Verli H, Guimaraes JA, Graebin CS. (2013) “Improving the Thrombin Inhibitory Activity of Glycyrrhizin, a Triterpenic Saponin, through a Molecular Simplification of the Carbohydrate Moiety”. Chemical Biology and Drug Design, 82, 756-760.

  • Pedebos C, Pol-Fachin L, Verli H. (2012) “Unrestrained Conformational Characterization of Stenocereus eruca Saponins in Aqueous and Nonaqueous Solvent.” Journal of Natural Products, 75, 1196-1200.

Contact details
Department of Biochemistry,
University of Oxford,
South Parks Road
Oxford
OX1 3QU
U.K.

Email: conrado.pedebos@bioch.ox.ac.uk