Deplazes, Evelyne - Curtin University - School of Biomedical Sciences

研究领域

My main research focus is the development and use of computational methods to understand the structure and dynamic properties of biomolecular systems. In particular, I use MD simulations in combination with data from experimental techniques such as surface plasmon resonance, vibrational spectroscopy, fluorescence correlation spectroscopy and NMR to study the binding of peptides to membranes. I am also interested in using molecular dynamics (MD) simulations and docking approaches to study the structure of membrane proteins and their interactions with peptides for aiding peptide-based drug design, including the evaluation of docking methods for predicting peptide-protein complexes. In addition, I am interested in developing computational methods that enable researchers to make better use of the data from spectroscopy experiment with a particular focus on vibrational spectroscopy and fluorescence resonance energy transfer (FRET). In my research I aim to combine computational approaches with experimental validation to develop methods that allow us to accurately describe the molecular interactions that govern the function of peptides and proteins. Only through rigorously validated methods can we take advantage of the predictive power of computational methods. When applied properly, computational methods are a powerful tool to gain insight into biological processes at the atomistic level and contribute to our understanding of normal physical functions and the molecular origins of diseases. My research allows me to integrate my knowledge and skills in chemistry, structural biology and computer science. I am experienced in a range of molecular modelling techniques and theoretical approaches including quantum mechanical calculations, Monte Carlo simulations, molecular dynamics simulations, homology modelling and docking. I am also knowledgeable in many spectroscopy methods such as infrared (IR), Raman, and fluorescence spectroscopy.

近期论文

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Deplazes, E., S. Henriques, J. Smith, G. King, D. Craik, A. Mark, and C. Schroeder. 2016.“Membrane-binding properties of gating modifier and pore-blocking toxins: Membrane interaction is not a prerequisite for modification of channel gating.”Biochimica et Biophysica Acta. Biomembranes 1858 (4): 872-882. Deplazes, E., J. Davies, A. Bonvin, G. King, and A. Mark. 2016.“Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion Channel (ASIC) 1a.”Journal of Chemical Information and Modeling 56 (1): 127-138. Deplazes, E., S. Begg, J. Van Wonderen, R. Campbell, B. Kobe, J. Paton, F. MacMillan, C. McDevitt, and M. O'Mara. 2015.“Characterizing the conformational dynamics of metal-free PsaA using molecular dynamics simulations and electron paramagnetic resonance spectroscopy.”Biophysical Chemistry 207: 51-60. Saez, N., E. Deplazes, B. Cristofori-Armstrong, I. Chassagnon, X. Lin, M. Mobli, A. Mark, L. Rash, and G. King. 2015.“Molecular dynamics and functional studies define a hot spot of crystal contacts essential for PcTx1 inhibition of acid-sensing ion channel 1a.”British Journal of Pharmacology 172 (20): 4985-4995. Walczewska-Szewc, K., E. Deplazes, and B. Corry. 2015.“Comparing the Ability of Enhanced Sampling Molecular Dynamics Methods to Reproduce the Behavior of Fluorescent Labels on Proteins.”Journal of Chemical Theory and Computation 11 (7): 3455-3465. Ujvari, B., N. Casewell, K. Sunagar, K. Arbuckle, W. Wüster, N. Lo, D. O'Meally, C. Beckmann, G. King, E. Deplazes et al. 2015.“Widespread convergence in toxin resistance by predictable molecular evolution.”Proceedings of the National Academy of Sciences of USA 112 (38): 11911-11916. O'Mara, M., and E. Deplazes. 2014. “Polypeptide and Protein Modeling for Drug Design..” In Encyclopedia of Computational Neuroscience. : . Deplazes, E., D. Jayatilaka, and B. Corry. 2012.“ExiFRET: Flexible tool for understanding FRET in complex geometries.”Journal of Biomedical Optics 17 (1). Deplazes, E., M. Louhivuori, D. Jayatilaka, S. Marrink, and B. Corry. 2012.“Structural Investigation of MscL Gating Using Experimental Data and Coarse Grained MD Simulations.”PLoS Computational Biology 8 (9). Nomura, T., C. Cranfield, E. Deplazes, D. Owen, A. Macmillan, A. Battle, M. Constantine, M. Sokabe, and B. Martinac. 2012.“Differential effects of lipids and lyso-lipids on the mechanosensitivity of the mechanosensitive channels MscL and MscS.”Proceedings of the National Academy of Sciences of USA 109 (22): 8770-8775. Deplazes, E., D. Jayatilaka, and B. Corry. 2011.“Testing the use of molecular dynamics to simulate fluorophore motions and FRET.”. Varganov, S., A. Gilbert, E. Deplazes, and P. Gill. 2008.“Resolutions of the Coulomb operator.”The Journal of Chemical Physics 128 (20). Deplazes, E., W. Van Bronswijk, F. Zhu, L. D. Barron, S. Ma, L. A. Nafie, and K. J. Jalkanen. 2008.“A combined theoretical and experimental study of the structure and vibrational adsorption, vibrational circular dichroism, Raman and raman optical activity spectra of the L-histidine zwitterion.”Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) 119: 155-176.