Paraskevi Gkeka, PhD
Research Associate
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27, Athens
Greece
+302106597568
pgkeka bioacademy.gr
Curriculum vitae
Research Interests
Publications
Z Cournia, TW Allen, I Andricioaei, et al. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. J. Mem. Biol. 248 (4), 611-640. DOI: 10.1007/s00232-015-9802-0
P. Gkeka, P. Angelikopoulos, L. Sarkisov, Z. Cournia. Partitioning of anionic, ligand-functionalized nanoparticles in cholesterol containing membranes induces ligand rearrangement and local cholesterol depletion. PLOS Comput. Biol., 2014 (corresponding author). DOI: 10.1371/journal.pcbi.1003917
P. Gkeka, A. Papafotika, S. Christoforidis, Z. Cournia. Exploring a Non-ATP Pocket for Potential Allosteric Modulation of PI3Kα. J. Phys. Chem. B, 2014. DOI: 10.1021/jp506423e
P. Gkeka, T. Evangelidis, M. Pavlaki, V. Lazani, S. Christoforidis, B. Agianian, Z. Cournia. Investigating the structure and dynamics of the PIK3CA Wild-Type and H1047R oncogenic mutant. PLOS Comput. Biol., 2014. DOI: 10.1371/journal.pcbi.1003895.
P. Gkeka, L. Sarkisov, P. Angelikopoulos. Homogeneous Hydrophobic–Hydrophilic Surface Patterns Enhance Permeation of Nanoparticles through Lipid Membranes. J. Phys. Chem. Lett., 4(11), pp. 1907–1912 (Physical Processes in Nanomaterials and Nanostructures), 2013. DOI: 10.1021/jz400679z
P. Gkeka, S. Eleftheratos, A. Kolocouris, Z. Cournia. Free energy calculations reveal the origin of binding preference for aminoadamantane blockers of influenza A/M2TM pore. J. Chem. Theory Comput., 9 (2), pp 1272–1281, 2013. DOI: 10.1021/ct300899n
P. Gkeka and P. Angelikopoulos. The role of hydrophobic domains in nanoparticle translocation through a lipid bilayer. Current Nanoscience, 7 (6), pp. 690-698, 2011.
DOI: 10.2174/157341311797483754
J. P. Prates Ramalho, P. Gkeka and L. Sarkisov. Structure and phase transformations of DPPC lipid bilayers in the presence of nanoparticles: insights from coarse-grained molecular dynamics simulations. Langmuir, 27, pp. 3723–3730, 2011. DOI: 10.1021/la200236d
P. Gkeka and L. Sarkisov. Interactions of phospholipid bilayers with several classes of amphiphilic α-helical peptides: insights from coarse-grained molecular dynamics simulations. J. Phys. Chem. B., 114 (2), pp. 826-839, 2010. DOI: 10.1021/jp908320b
P. Gkeka and L. Sarkisov. Spontaneous formation of a barrel-stave pore in a coarse-grained model of the synthetic LS3 peptide and a DPPC lipid bilayer. J. Phys. Chem. B., 113 (1), pp. 6-8, 2009. DOI: 10.1021/jp808417a
Theses
'Molecular dynamics simulations of peptide-membrane interactions' (Ph.D. Thesis)
'Global modeling of the gas phase in a plasma reactor' (Master Thesis, in greek)
'Mathematical modeling in biology and contagious diseases' (Diploma Thesis)
Conference proceedings
P. Gkeka, E. Athanasiadis, G. Spyrou, and Z. Cournia, 12th IEEE International Conference on BioInformatics and BioEngineering, November 2012.
Enhancing the effectiveness of virtual screening by using the ChemBioServer: Application to the discovery of PI3Kα inhibitors.
________________________________________
Grants - Awards - Scholarships
________________________________________
"The significant problems we face cannot be solved at the same level of thinking we were at when we created them."
A. Einstein
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27, Athens
Greece
+302106597568
pgkeka bioacademy.gr
Curriculum vitae
- Research Associate, Biomedical Research Foundation, Academy of Athens, Greece.
- Ph.D. in ‘Molecular dynamics simulations of peptide-membrane interactions’, University of Edinburgh, Institute for Materials and Processes, Edinburgh, UK.
- Research collaborator, Institute of Microelectronics (IMEL), NCSR ‘Demokritos’ Institute, Athens, Greece.
- M.Sc. in ‘Mathematical modelling in modern technologies’, National Technical University of Athens, Greece.
- 5 year Diploma in ‘Applied mathematics and physical sciences’, National Technical University of Athens, Greece.
Research Interests
- Computer-aided drug design
- Targeted drug delivery
- Molecular simulations methods
- Study of nanoparticle-membrane interactions
- Predictive modeling
- Systems biology
Publications
Z Cournia, TW Allen, I Andricioaei, et al. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. J. Mem. Biol. 248 (4), 611-640. DOI: 10.1007/s00232-015-9802-0
P. Gkeka, P. Angelikopoulos, L. Sarkisov, Z. Cournia. Partitioning of anionic, ligand-functionalized nanoparticles in cholesterol containing membranes induces ligand rearrangement and local cholesterol depletion. PLOS Comput. Biol., 2014 (corresponding author). DOI: 10.1371/journal.pcbi.1003917
P. Gkeka, A. Papafotika, S. Christoforidis, Z. Cournia. Exploring a Non-ATP Pocket for Potential Allosteric Modulation of PI3Kα. J. Phys. Chem. B, 2014. DOI: 10.1021/jp506423e
P. Gkeka, T. Evangelidis, M. Pavlaki, V. Lazani, S. Christoforidis, B. Agianian, Z. Cournia. Investigating the structure and dynamics of the PIK3CA Wild-Type and H1047R oncogenic mutant. PLOS Comput. Biol., 2014. DOI: 10.1371/journal.pcbi.1003895.
P. Gkeka, L. Sarkisov, P. Angelikopoulos. Homogeneous Hydrophobic–Hydrophilic Surface Patterns Enhance Permeation of Nanoparticles through Lipid Membranes. J. Phys. Chem. Lett., 4(11), pp. 1907–1912 (Physical Processes in Nanomaterials and Nanostructures), 2013. DOI: 10.1021/jz400679z
P. Gkeka, S. Eleftheratos, A. Kolocouris, Z. Cournia. Free energy calculations reveal the origin of binding preference for aminoadamantane blockers of influenza A/M2TM pore. J. Chem. Theory Comput., 9 (2), pp 1272–1281, 2013. DOI: 10.1021/ct300899n
P. Gkeka and P. Angelikopoulos. The role of hydrophobic domains in nanoparticle translocation through a lipid bilayer. Current Nanoscience, 7 (6), pp. 690-698, 2011.
DOI: 10.2174/157341311797483754
J. P. Prates Ramalho, P. Gkeka and L. Sarkisov. Structure and phase transformations of DPPC lipid bilayers in the presence of nanoparticles: insights from coarse-grained molecular dynamics simulations. Langmuir, 27, pp. 3723–3730, 2011. DOI: 10.1021/la200236d
P. Gkeka and L. Sarkisov. Interactions of phospholipid bilayers with several classes of amphiphilic α-helical peptides: insights from coarse-grained molecular dynamics simulations. J. Phys. Chem. B., 114 (2), pp. 826-839, 2010. DOI: 10.1021/jp908320b
P. Gkeka and L. Sarkisov. Spontaneous formation of a barrel-stave pore in a coarse-grained model of the synthetic LS3 peptide and a DPPC lipid bilayer. J. Phys. Chem. B., 113 (1), pp. 6-8, 2009. DOI: 10.1021/jp808417a
Theses
'Molecular dynamics simulations of peptide-membrane interactions' (Ph.D. Thesis)
'Global modeling of the gas phase in a plasma reactor' (Master Thesis, in greek)
'Mathematical modeling in biology and contagious diseases' (Diploma Thesis)
Conference proceedings
P. Gkeka, E. Athanasiadis, G. Spyrou, and Z. Cournia, 12th IEEE International Conference on BioInformatics and BioEngineering, November 2012.
Enhancing the effectiveness of virtual screening by using the ChemBioServer: Application to the discovery of PI3Kα inhibitors.
________________________________________
Grants - Awards - Scholarships
- Financial support from the EU FP7 Framework Programme for research, technological development and demonstration under grant agreement number 289454 to attend the NANODRUG Meeting. (July 2014 and Feb. 2015)
- Computational award as PI in the project entitled `NanoTox - Camouflaging nanoparticles for reduced toxicity through limited aggregation and membrane disruption.' Partnership for Advanced Computing in Europe (Grant No. 2014112562 - 8.6 Million core hours). (Feb. 2015)
- Computational award as PI in the project `Nanoparticle-membrane interactions: insights through Molecular Dynamics simulations' High Performance Computing (Grant No. pro14a115s2 - 186,000 core hours). (Dec. 2014)
- Computational award as co-PI in the project `Targeted Molecular Dynamics Simulations of the Arp2/3 complex.' LinkSCEEMPreparatory Access (Grant No. lspre225s1 - 200,000 core hours). (Dec. 2014)
- Computational award as co-PI in the project `Inhibition of the Arp2/3 complex with small molecules studied with MD simulations.' LinkSCEEM Preparatory Access (Grant No. lspre190s1 - 200,000 core hours). (Oct. 2014)}
- Computational award as PI in the project entitled `Insights into the molecular basis of action of the AT1 antagonist losartan using Molecular Dynamics simulations.' LinkSCEEM/High Performance Computing (Grant No. pro14b117s2 - 200,000 core hours). (Sept. 2014)
- Bursary Financial support from EU FP7 ITN Network to attend the NANODRUG Meeting (July 2014).
- Best poster at the CECAM Workshop: Coupling between protein, water, and lipid dynamics in complex biological systems (Sept. 2013).
- GRC travel award to attend the Computer-aided Drug Design Gordon Research Conference (July 2013).
- CPOW travel award to attend the 57th Biophysical Society Meeting (Feb. 2013).
- co-PI in the SYNERGASIA II grant entitled: “Magnetic Nanoparticles for targeted MRI therapy” (Jan 2013).
- Travel grant to attend the LinkSCEEM/Cy-Tera GPU workshop (Dec. 2012).
- Financial support to attend the CECAM Coarse-Grained Biomolecular Modeling (Oct. 2011).
- Financial support from the Bettencourt Schueller Foundation to attend the Paris Interdisciplinary PhD Symposium (June 2011).
- 3-year scholarship and fee coverage by the Institute for Materials and Processes, University of Edinburgh, UK (Dec. 2006-Feb. 2010).
- 1-year fellowship for working on the project `Nanoplasma' (IST-NMP-3, Contract No 016424).
- Financial support to attend the Psi-k Summer School on ‘Simulation Approaches to Problems in Molecular and Cellular Biology’ provided by ESF and CECAM (Aug. 2009).
- Travel bursary to attend FD144 Discussion ‘Multiscale Modelling of Soft Matter’ from Royal Society of Chemistry (July 2009).
- Bursary to attend the workshop ‘Understanding Molecular Simulations’ provided by Marie Curie Actions-MolSimu and CECAM (Jan. 2007).
- Award by State Scholarships Foundation of Greece for fulfilling my M.Sc. studies with first distinction (June 2006).
- Travel award. Expenses covered by the European Commission grant to participate to the European Conference on Mathematical and Theoretical Biology (ECMTB) (July 2005).
- Bursary to attend ‘Euroschola’, Strasbourg, France, representing Greece after an essay competition on the ‘Effects of the Maastricht treaty in Greece’ (March 1998).
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"The significant problems we face cannot be solved at the same level of thinking we were at when we created them."
A. Einstein