The University of Queensland

Determining the Pore Size of Multimeric Peptide Ion Channels Using Cation Conductance Measures of Tethered Bilayer Lipid Membranes

Hartmann, Lissy M., Garcia, Alvaro, Deplazes, Evelyne and Cranfield, Charles G. (2022). Determining the Pore Size of Multimeric Peptide Ion Channels Using Cation Conductance Measures of Tethered Bilayer Lipid Membranes. Methods in Molecular Biology. (pp. 81-92) New York, NY: Humana Press Inc.. doi: 10.1007/978-1-0716-1843-1_7

Drug meets monolayer: understanding the interactions of sterol drugs with models of the lung surfactant monolayer using molecular dynamics simulations

Hossain, Sheikh I., Islam, Mohammad Z., Saha, Suvash C. and Deplazes, Evelyne (2022). Drug meets monolayer: understanding the interactions of sterol drugs with models of the lung surfactant monolayer using molecular dynamics simulations. Methods in molecular biology. (pp. 103-121) edited by Charles G. Cranfield. New York, NY United States: Humana Press. doi: 10.1007/978-1-0716-1843-1_9

Polypeptide and protein modeling for drug design

O’Mara, Megan L. and Deplazes, Evelyne (2014). Polypeptide and protein modeling for drug design. Encyclopedia of computational neuroscience. (pp. 1-9) New York, United States: Springer . doi: 10.1007/978-1-4614-7320-6_732-1

Polypeptide and protein modeling for drug design

O'Mara, Megan and Deplazes, Evelyne (2014). Polypeptide and protein modeling for drug design. Encyclopedia of computational neuroscience. (pp. 2439-2447) edited by Dieter Jaeger and Ranu Jung. Berlin, Germany: Springer. doi: 10.1007/978-1-4614-6675-8_732

A charge-neutral organic cage selectively binds strongly hydrated sulfate anions in water

Jing, Liuyang, Deplazes, Evelyne, Clegg, Jack K. and Wu, Xin (2024). A charge-neutral organic cage selectively binds strongly hydrated sulfate anions in water. Nature Chemistry. doi: 10.1038/s41557-024-01457-5

Hfe Permease and <i>Haemophilus influenzae</i> Manganese Homeostasis

Ganio, Katherine, Nasreen, Marufa, Yang, Zihao, Maunders, Eve A., Luo, Zhenyao, Hossain, Sheikh Imamul, Ngu, Dalton H. Y., Ellis, Daniel, Gu, Jin, Neville, Stephanie L., Wilksch, Jonathan, Gunn, Adam P., Whittall, Jonathan J., Kobe, Boštjan, Deplazes, Evelyne, Kappler, Ulrike and McDevitt, Christopher A. (2024). Hfe Permease and Haemophilus influenzae Manganese Homeostasis. ACS Infectious Diseases, 10 (2), 436-452. doi: 10.1021/acsinfecdis.3c00407

Biochemical interactions between the Atm1-like transporter from Novosphingobium aromaticivorans and heavy metals

Rottet, Sarah, Iqbal, Shagufta, Xifaras, Rachel, Singer, Michael T., Scott, Colin, Deplazes, Evelyne and Callaghan, Richard (2023). Biochemical interactions between the Atm1-like transporter from Novosphingobium aromaticivorans and heavy metals. Archives of Biochemistry and Biophysics, 744 109696, 109696. doi: 10.1016/j.abb.2023.109696

Influence of force field choice on the conformational landscape of rat and human islet amyloid polypeptide

Moore, Sandra J., Deplazes, Evelyne and Mancera, Ricardo L. (2023). Influence of force field choice on the conformational landscape of rat and human islet amyloid polypeptide. Proteins: Structure, Function, and Bioinformatics, 91 (3), 338-353. doi: 10.1002/prot.26432

The concentration-dependent effect of hydrocortisone on the structure of model lung surfactant monolayer by using an in silico approach

Islam, Mohammad Zohurul, Hossain, Sheikh I., Deplazes, E., Luo, Zhen and Saha, Suvash C. (2022). The concentration-dependent effect of hydrocortisone on the structure of model lung surfactant monolayer by using an in silico approach. RSC Advances, 12 (51), 33313-33328. doi: 10.1039/d2ra05268g

Vinca alkaloid binding to P-glycoprotein occurs in a processive manner

Iqbal, Shagufta, Flux, Caitlin, Briggs, Deborah A., Deplazes, Evelyne, Long, Jiansi, Skrzypek, Ruth, Rothnie, Alice, Kerr, Ian D. and Callaghan, Richard (2022). Vinca alkaloid binding to P-glycoprotein occurs in a processive manner. Biochimica et Biophysica Acta - Biomembranes, 1864 (10) 184005, 1-10. doi: 10.1016/j.bbamem.2022.184005

The role of ion-lipid interactions and lipid packing in ion-induced pores and transient defects caused by phenolic compounds

Hossain, Sheikh I., Seppelt, Mathilda, Nguyen, Natalie, Stokes, Chelsea and Deplazes, Evelyne (2022). The role of ion-lipid interactions and lipid packing in ion-induced pores and transient defects caused by phenolic compounds. Biophysical Journal, 121 (18), 3520-3532. doi: 10.1016/j.bpj.2022.08.001

Concentration-dependent cortisone adsorption and interaction with model lung surfactant monolayer

Islam, Mohammad Zohurul, Hossain, Sheikh I., Deplazes, Evelyne and Saha, Suvash C. (2022). Concentration-dependent cortisone adsorption and interaction with model lung surfactant monolayer. Molecular Simulation, 48 (18), 1627-1638. doi: 10.1080/08927022.2022.2113397

Structural and biochemical characterization of Acinetobacter baumannii ZnuA

Alquethamy, Saleh, Ganio, Katherine, Luo, Zhenyao, Hossain, Sheikh I., Hayes, Andrew J., Ve, Thomas, Davies, Mark R., Deplazes, Evelyne, Kobe, Boštjan and McDevitt, Christopher A. (2022). Structural and biochemical characterization of Acinetobacter baumannii ZnuA. Journal of Inorganic Biochemistry, 231 111787, 1-11. doi: 10.1016/j.jinorgbio.2022.111787

The impact of chromate on Pseudomonas aeruginosa molybdenum homeostasis

Maunders, Eve A., Ngu, Dalton H. Y., Ganio, Katherine, Hossain, Sheikh I., Lim, Bryan Y. J., Leeming, Michael G., Luo, Zhenyao, Tan, Aimee, Deplazes, Evelyne, Kobe, Boštjan and McDevitt, Christopher A. (2022). The impact of chromate on Pseudomonas aeruginosa molybdenum homeostasis. Frontiers in Microbiology, 13 903146, 1-19. doi: 10.3389/fmicb.2022.903146

Concentration-dependent effect of the steroid drug prednisolone on a lung surfactant monolayer

Islam, Mohammad Zohurul, Krajewska, Martyna, Hossain, Sheikh I., Prochaska, Krystyna, Anwar, Azraf, Deplazes, Evelyne and Saha, Suvash C. (2022). Concentration-dependent effect of the steroid drug prednisolone on a lung surfactant monolayer. Langmuir, 38 (14), 4188-4199. doi: 10.1021/acs.langmuir.1c02817

The steroid mometasone alters protein containing lung surfactant monolayers in a concentration-dependent manner

Islam, Mohammad Zohurul, Hossain, Sheikh I., Deplazes, Evelyne and Saha, Suvash C. (2022). The steroid mometasone alters protein containing lung surfactant monolayers in a concentration-dependent manner. Journal of Molecular Graphics and Modelling, 111 108084, 1-11. doi: 10.1016/j.jmgm.2021.108084

Structural basis of dimerization and nucleic acid binding of human DBHS proteins NONO and PSPC1

Knott, Gavin J, Chong, Yee Seng, Passon, Daniel M, Liang, Xue-hai, Deplazes, Evelyne, Conte, Maria R, Marshall, Andrew C, Lee, Mihwa, Fox, Archa H and Bond, Charles S (2022). Structural basis of dimerization and nucleic acid binding of human DBHS proteins NONO and PSPC1. Nucleic Acids Research, 50 (1), 522-535. doi: 10.1093/nar/gkab1216

Peptide-membrane interactions and biotechnology; enabling next-generation synthetic biology: general discussion

Aguilar, Mibel, Bassereau, Patricia, Bastos, Margarida, Beales, Paul, Bechinger, Burkhard, Bonev, Boyan, Brand, Izabella, Chalouhi, Edward, Clarke, Ronald J., Deplazes, Evelyne, Fraternali, Franca, Fuchs, Patrick, Hoogenboom, Bart, Lund, Reidar, Mahmoudi, Najet, Milán Rodríguez, Paula, O'Shea, Paul, Pabst, Georg, Pal, Sreetama, Rice, Amy, Sanderson, John, Seddon, John, Sengupta, Durba, Siegel, David P., Srivastava, Anand, Utterström, Johanna, Vácha, Robert, Van 'T Hag, Leonie, Vijayakumar, Aishwarya and Zoranić, Larisa (2021). Peptide-membrane interactions and biotechnology; enabling next-generation synthetic biology: general discussion. Faraday Discussions, 232, 463-481. doi: 10.1039/d1fd90068d

Theoretical and experimental comparisons of simple peptide-membrane systems; towards defining the reaction space: general discussion

Aguilar, Marie-Isabel, Al Nahas, Kareem, Barrera, Francisco N., Bassereau, Patricia, Bechinger, Burkhard, Brand, Izabella, Chattopadhyay, Amitabha, Clarke, Ronald J., Degrado, William F., Deplazes, Evelyne, Fletcher, Marcus, Fraternali, Franca, Fuchs, Patrick, Garcia-Saez, Ana J., Gilbert, Robert, Hoogenboom, Bart W., Jarin, Zack, O'Shea, Paul, Pabst, Georg, Pal, Sreetama, Sanderson, John M., Seddon, John M., Sengupta, Durba, Siegel, David P., Srivastava, Anand, Tieleman, D. Peter, Tripathy, Madhusmita, Utterström, Johanna, Vácha, Robert ... Voth, Gregory A. (2021). Theoretical and experimental comparisons of simple peptide-membrane systems; towards defining the reaction space: general discussion. Faraday Discussions, 232, 149-171. doi: 10.1039/d1fd90065j

The interaction of steroids with phospholipid bilayers and membranes

Crowley, Jackson, Withana, Minduli and Deplazes, Evelyne (2021). The interaction of steroids with phospholipid bilayers and membranes. Biophysical Reviews, 14 (1), 163-179. doi: 10.1007/s12551-021-00918-2

Theoretical and experimental studies of complex peptide-membrane systems: General discussion

Aguilar, Mibel, Al Nahas, Kareem, Barrera, Francisco, Bassereau, Patricia, Bastos, Margarida, Beales, Paul, Bechinger, Burkhard, Bonev, Boyan, Brand, Izabella, Chattopadhyay, Amitabha, Clarke, Ronald J., Degrado, William, Deplazes, Evelyne, Garcia Saez, Ana J., Hoogenboom, Bart, Lund, Reidar, Milán Rodríguez, Paula, O'Shea, Paul, Pabst, Georg, Pal, Sreetama, Roux, Aurélien, Sanderson, John, Semeraro, Enrico Federico, Sengupta, Durba, Siegel, David P., Van 'T Hag, Leonie, Vijayakumar, Aishwarya and Zoranić, Larisa (2021). Theoretical and experimental studies of complex peptide-membrane systems: General discussion. Faraday Discussions, 232, 256-281. doi: 10.1039/d1fd90066h

Calcium ion binding at the lipid–water interface alters the ion permeability of phospholipid bilayers

Deplazes, Evelyne, Tafalla, Beatriu Domingo, Murphy, Christopher, White, Jacqueline, Cranfield, Charles G. and Garcia, Alvaro (2021). Calcium ion binding at the lipid–water interface alters the ion permeability of phospholipid bilayers. Langmuir, 37 (48) acs.langmuir.1c02016, 14026-14033. doi: 10.1021/acs.langmuir.1c02016

Shape matters: the interaction of gold nanoparticles with model lung surfactant monolayers

Hossain, Sheikh I., Luo, Zhen, Deplazes, Evelyne and Saha, Suvash C. (2021). Shape matters: the interaction of gold nanoparticles with model lung surfactant monolayers. Journal of The Royal Society Interface, 18 (183) 20210402, 1-10. doi: 10.1098/rsif.2021.0402

Conformation of the solute-binding protein AdcAII influences zinc uptake in Streptococcus pneumoniae

Župan, Marina L., Luo, Zhenyao, Ganio, Katherine, Pederick, Victoria G., Neville, Stephanie L., Deplazes, Evelyne, Kobe, Boštjan and McDevitt, Christopher A. (2021). Conformation of the solute-binding protein AdcAII influences zinc uptake in Streptococcus pneumoniae. Frontiers in Cellular and Infection Microbiology, 11 729981, 1-15. doi: 10.3389/fcimb.2021.729981

A trap-door mechanism for zinc acquisition by Streptococcus pneumoniae AdcA

Luo, Zhenyao, Morey, Jacqueline R., Deplazes, Evelyne, Motygullina, Alina, Tan, Aimee, Ganio, Katherine, Neville, Stephanie L., Eleftheriadis, Nikolaos, Isselstein, Michael, Pederick, Victoria G., Paton, James C., Cordes, Thorben, Harmer, Jeffrey R., Kobe, Bostjan and McDevitt, Christopher A. (2021). A trap-door mechanism for zinc acquisition by Streptococcus pneumoniae AdcA. mBio, 12 (1) e01958-20, 1-14. doi: 10.1128/mBio.01958-20

Identification and characterisation of putative drug binding sites in human ATP-binding cassette B5 (ABCB5) transporter

Tangella, Lokeswari P., Arooj, Mahreen, Deplazes, Evelyne, Gray, Elin S. and Mancera, Ricardo L. (2021). Identification and characterisation of putative drug binding sites in human ATP-binding cassette B5 (ABCB5) transporter. Computational and Structural Biotechnology Journal, 19, 691-704. doi: 10.1016/j.csbj.2020.12.042

Phenolic compounds alter the ion permeability of phospholipid bilayers via specific lipid interactions

Hossain, Sheikh I., Saha, Suvash C. and Deplazes, Evelyne (2021). Phenolic compounds alter the ion permeability of phospholipid bilayers via specific lipid interactions. Physical Chemistry Chemical Physics, 23 (39), 22352-22366. doi: 10.1039/d1cp03250j

The role of structure and biophysical properties in the pleiotropic effects of statins

Murphy, Christopher, Deplazes, Evelyne, Cranfield, Charles G. and Garcia, Alvaro (2020). The role of structure and biophysical properties in the pleiotropic effects of statins. International Journal of Molecular Sciences, 21 (22) 8745, 1-29. doi: 10.3390/ijms21228745

Structural characterization of a cation-selective, self-assembled peptide pore in planar phospholipid bilayers

Deplazes, Evelyne, Hartmann, Lissy M., Cranfield, Charles G. and Garcia, Alvaro (2020). Structural characterization of a cation-selective, self-assembled peptide pore in planar phospholipid bilayers. The Journal of Physical Chemistry Letters, 11 (19), 8152-8156. doi: 10.1021/acs.jpclett.0c02335

Design, synthesis and biological evaluation of biphenylglyoxamide-based small molecular antimicrobial peptide mimics as antibacterial agents

Yu, Tsz Tin, Kuppusamy, Rajesh, Yasir, Muhammad, Hassan, Md. Musfizur, Alghalayini, Amani, Gadde, Satyanarayana, Deplazes, Evelyne, Cranfield, Charles, Willcox, Mark D. P., Black, David StC and Kumar, Naresh (2020). Design, synthesis and biological evaluation of biphenylglyoxamide-based small molecular antimicrobial peptide mimics as antibacterial agents. International Journal of Molecular Sciences, 21 (18) 6789, 1-38. doi: 10.3390/ijms21186789

Role of ion-phospholipid interactions in zwitterionic phospholipid bilayer ion permeation

Deplazes, Evelyne, Tafalla, Beatriu Domingo, Cranfield, Charles G. and Garcia, Alvaro (2020). Role of ion-phospholipid interactions in zwitterionic phospholipid bilayer ion permeation. The Journal of Physical Chemistry Letters, 11 (15), 6353-6358. doi: 10.1021/acs.jpclett.0c01479

Label-free, real-time phospholipase-A isoform assay

Garcia, Alvaro, Deplazes, Evelyne, Aili, Samira, Padula, Matthew P., Touchard, Axel, Murphy, Christopher, Lankage, Upeksha Mirissa, Nicholson, Graham M., Cornell, Bruce and Cranfield, Charles G. (2020). Label-free, real-time phospholipase-A isoform assay. ACS Biomaterials Science & Engineering, 6 (8), 4714-4721. doi: 10.1021/acsbiomaterials.0c00632

Molecular dynamics simulation of small molecules interacting with biological membranes

Martinotti, Carlo, Ruiz-Perez, Lanie, Deplazes, Evelyne and Mancera, Ricardo L. (2020). Molecular dynamics simulation of small molecules interacting with biological membranes. ChemPhysChem: a European journal of chemical physics and physical chemistry, 21 (14), 1486-1514. doi: 10.1002/cphc.202000219

Revisiting the interaction of melittin with phospholipid bilayers: the effects of concentration and ionic strength

Sabapathy, Thiru, Deplazes, Evelyne and Mancera, Ricardo L. (2020). Revisiting the interaction of melittin with phospholipid bilayers: the effects of concentration and ionic strength. International Journal of Molecular Sciences, 21 (3) 746, 746. doi: 10.3390/ijms21030746

Effect of H3O+ on the structure and dynamics of water at the interface with phospholipid bilayers

Deplazes, Evelyne, Sarrami, Farzaneh and Poger, David (2020). Effect of H3O+ on the structure and dynamics of water at the interface with phospholipid bilayers. The Journal of Physical Chemistry B, 124 (8) acs.jpcb.9b10169, 1361-1373. doi: 10.1021/acs.jpcb.9b10169

The unusual conformation of cross‐strand disulfide bonds is critical to the stability of β‐hairpin peptides

Deplazes, Evelyne, Chin, Yanni K.‐Y., King, Glenn F. and Mancera, Ricardo L. (2019). The unusual conformation of cross‐strand disulfide bonds is critical to the stability of β‐hairpin peptides. Proteins, 88 (3) prot.25828, 485-502. doi: 10.1002/prot.25828

Competing for the same space: protons and alkali ions at the interface of phospholipid bilayers

Deplazes, Evelyne, White, Jacqueline, Murphy, Christopher, Cranfield, Charles G. and Garcia, Alvaro (2019). Competing for the same space: protons and alkali ions at the interface of phospholipid bilayers. Biophysical Reviews, 11 (3), 483-490. doi: 10.1007/s12551-019-00541-2

The effect of H3O+ on the membrane morphology and hydrogen bonding of a phospholipid bilayer

Deplazes, Evelyne, Poger, David, Cornell, Bruce and Cranfield, Charles G. (2018). The effect of H3O+ on the membrane morphology and hydrogen bonding of a phospholipid bilayer. Biophysical Reviews, 10 (5), 1371-1376. doi: 10.1007/s12551-018-0454-z

Characterisation of the structure and oligomerisation of Islet Amyloid Polypeptides (IAPP): a review of molecular dynamics simulation studies

Moore, Sandra J., Sonar, Krushna, Bharadwaj, Prashant, Deplazes, Evelyne and Mancera, Ricardo L. (2018). Characterisation of the structure and oligomerisation of Islet Amyloid Polypeptides (IAPP): a review of molecular dynamics simulation studies. Molecules, 23 (9) 2142, 1-37. doi: 10.3390/molecules23092142

The Biological and Biophysical Properties of the Spider Peptide Gomesin

Tanner, John D., Deplazes, Evelyne and Mancera, Ricardo L. (2018). The Biological and Biophysical Properties of the Spider Peptide Gomesin. Molecules, 23 (7) 1733, 1-19. doi: 10.3390/molecules23071733

Molecular simulations of venom peptide-membrane interactions: progress and challenges

Deplazes, Evelyne (2018). Molecular simulations of venom peptide-membrane interactions: progress and challenges. Peptide Science, 110 (3) e24060, e24060. doi: 10.1002/pep2.24060

Gomesin peptides prevent proliferation and lead to the cell death of devil facial tumour disease cells

Fernandez-Rojo, Manuel A., Deplazes, Evelyne, Pineda, Sandy S., Brust, Andreas, Marth, Tano, Wilhelm, Patrick, Martel, Nick, Ramm, Grant A., Mancera, Ricardo L., Alewood, Paul F., Woods, Gregory M., Belov, Katherine, Miles, John J., King, Glenn F. and Ikonomopoulou, Maria P. (2018). Gomesin peptides prevent proliferation and lead to the cell death of devil facial tumour disease cells. Cell Death Discovery, 4 (1) 19, 19. doi: 10.1038/s41420-018-0030-0

The effect of hydronium ions on the structure of phospholipid membranes

Deplazes, Evelyne, Poger, David, Cornell, Bruce and Cranfield, Charles G. (2017). The effect of hydronium ions on the structure of phospholipid membranes. Physical Chemistry Chemical Physics, 20 (1), 357-366. doi: 10.1039/c7cp06776c

Spider peptide toxin HwTx-IV engineered to bind to lipid membranes has an increased inhibitory potency at human voltage-gated sodium channel hNa(V)1.7 (vol 1859, pg 835, 2017)

Agwa, Akello J., Lawrence, Nicole, Deplazes, Evelyne, Cheneval, Olivier, Chen, Rachel M., Craik, David J., Schroeder, Christina I. and Henriques, Sonia T. (2017). Spider peptide toxin HwTx-IV engineered to bind to lipid membranes has an increased inhibitory potency at human voltage-gated sodium channel hNa(V)1.7 (vol 1859, pg 835, 2017). Biochimica Et Biophysica Acta-Biomembranes, 1859 (11), 2277-2277. doi: 10.1016/j.bbamem.2017.08.008

A potential new, stable state of the E-cadherin strand-swapped dimer in solution

Schumann-Gillett, Alexandra, Mark, Alan E., Deplazes, Evelyne and O'Mara, Megan L. (2017). A potential new, stable state of the E-cadherin strand-swapped dimer in solution. European Biophysics Journal, 47 (1), 59-67. doi: 10.1007/s00249-017-1229-3

Spider peptide toxin HwTx-IV engineered to bind to lipid membranes has an increased inhibitory potency at human voltage-gated sodium channel hNaV1.7

Agwa, Akello J., Lawrence, Nicole, Deplazes, Evelyne, Cheneval, Olivier, Chen, Rachel M., Craik, David J., Schroeder, Christina I. and Henriques, Sónia T. (2017). Spider peptide toxin HwTx-IV engineered to bind to lipid membranes has an increased inhibitory potency at human voltage-gated sodium channel hNaV1.7. Biochimica et Biophysica Acta. Biomembranes, 1859 (5), 835-844. doi: 10.1016/j.bbamem.2017.01.020

Molecular simulations of disulfide-rich venom peptides with ion channels and membranes

Deplazes, Evelyne (2017). Molecular simulations of disulfide-rich venom peptides with ion channels and membranes. Molecules, 22 (3) 362, 362. doi: 10.3390/molecules22030362

Interaction of tarantula venom peptide ProTx-II with lipid membranes is a prerequisite for its inhibition of human voltage-gated sodium channel NaV1.7

Troeira Henriques, Sonia, Deplazes, Evelyne, Lawrence, Nicole, Cheneval, Olivier, Chaousis, Stephanie, Inserra, Marco, Thongyoo, Panumart, King, Glenn F., Mark, Alan E., Vetter, Irina, Craik, David J. and Schroeder, Christina Ingrid (2016). Interaction of tarantula venom peptide ProTx-II with lipid membranes is a prerequisite for its inhibition of human voltage-gated sodium channel NaV1.7. The Journal of Biological Chemistry, 291 (33), 17049-17065. doi: 10.1074/jbc.M116.729095

Membrane-binding properties of gating modifier and pore-blocking toxins: membrane interaction is not a prerequisite for modification of channel gating

Deplazes, Evelyne, Troeira Henriques, Sonia, Smith, Jennifer J., King, Glenn F., Craik, David J., Mark, Alan E. and Schroeder, Christina I. (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. doi: 10.1016/j.bbamem.2016.02.002

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

Deplazes, Evelyne, Davies, Josephine, Bonvin, Alexandre M. J. J., King, Glenn F. and Mark, Alan E. (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. doi: 10.1021/acs.jcim.5b00529

Characterizing the conformational dynamics of metal-free PsaA usingmolecular dynamics simulations and electron paramagnetic resonance spectroscopy

Deplazes, Evelyne, Begg, Stephanie L., van Wonderen, Jessica H., Campbell, Rebecca, Kobe, Bostjan, Paton, James C., MacMillan, Fraser, McDevitt, Christopher A. and O'Mara, Megan L. (2015). Characterizing the conformational dynamics of metal-free PsaA usingmolecular dynamics simulations and electron paramagnetic resonance spectroscopy. Biophysical Chemistry, 207, 51-60. doi: 10.1016/j.bpc.2015.08.004

Molecular dynamics and functional studies define a hot spot of crystal contacts essential for PcTx1 inhibition of acid-sensing ion channel 1a

Saez, Natalie J., Deplazes, Evelyne, Cristofori-Armstrong, Ben, Chassagnon, Irene R., Lin, Xiaozhen, Mobli, Mehdi, Mark, Alan E., Rash, Lachlan D. and King, Glenn F. (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. doi: 10.1111/bph.13267

Widespread convergence in toxin resistance by predictable molecular evolution

Ujvari, Beata, Casewell, Nicholas R., Sunagar, Kartik, Arbuckle, Kevin, Wuester, Wolfgang, Lo, Nathan, O'Meally, Denis, Beckmann, Christa, King, Glenn F., Deplazes, Evelyne and Madsen, Thomas (2015). Widespread convergence in toxin resistance by predictable molecular evolution. Proceedings of the National Academy of Sciences of the United States of America, 112 (38), 11911-11916. doi: 10.1073/pnas.1511706112

Comparing the Ability of Enhanced Sampling Molecular Dynamics Methods To Reproduce the Behavior of Fluorescent Labels on Proteins

Walczewska-Szewc, Katarzyna, Deplazes, Evelyne and Corry, Ben (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. doi: 10.1021/acs.jctc.5b00205

Bacterial mechanosensitive channels: models for studying mechanosensory transduction

Martinac, Boris, Nomura, Takeshi, Chi, Gamma, Petrov, Evgeny, Rohde, Paul R., Battle, Andrew R., Foo, Alexander, Constantine, Maryrose, Rothnagel, Rosalba, Carne, Sonia, Deplazes, Evelyne, Cornell, Bruce, Cranfield, Charles G., Hankamer, Ben and Landsberg, Michael J. (2014). Bacterial mechanosensitive channels: models for studying mechanosensory transduction. Antioxidants and Redox Signaling, 20 (6), 952-969. doi: 10.1089/ars.2013.5471

Structural investigation of MscL gating using experimental data and coarse grained MD simulations

Deplazes, Evelyne, Louhivuori, Martti, Jayatilaka, Dylan, Marrink, Siewert J. and Corry, Ben (2012). Structural investigation of MscL gating using experimental data and coarse grained MD simulations. PLoS Computational Biology, 8 (9) e1002683, e1002683. doi: 10.1371/journal.pcbi.1002683

Differential effects of lipids and lyso-lipids on the mechanosensitivity of the mechanosensitive channels MscL and MscS

Nomura, Takeshi, Cranfield, Charles G., Deplazes, Evelyne, Owen, Dylan M., Macmillan, Alex, Battle, Andrew R., Constantine, Maryrose, Sokabe, Masahiro and Martinac, Boris (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 the United States of America, 109 (22), 8770-8775. doi: 10.1073/pnas.1200051109

ExiFRET: Flexible tool for understanding FRET in complex geometries

Deplazes, Evelyne, Jayatilaka, Dylan and Corry, Ben (2012). ExiFRET: Flexible tool for understanding FRET in complex geometries. Journal of Biomedical Optics, 17 (1) 011005, 011005.1-011005.11. doi: 10.1117/1.JBO.17.1.011005

Testing the use of molecular dynamics to simulate fluorophore motions and FRET

Deplazes, Evelyne, Jayatilaka, Dylan and Corry, Ben (2011). Testing the use of molecular dynamics to simulate fluorophore motions and FRET. Physical Chemistry Chemical Physics, 13 (23), 11045-11054. doi: 10.1039/c1cp20447e

Resolutions of the Coulomb operator

Varganov, Sergey A., Gilbert, Andrew T. B., Deplazes, Evelyne and Gill, Peter M. W. (2008). Resolutions of the Coulomb operator. Journal of Chemical Physics, 128 (20) 201104, 201104.1-201104.4. doi: 10.1063/1.2939239

A combined theoretical and experimental study of the structure and vibrational absorption, vibrational circular dichroism, Raman and Raman optical activity spectra of the L-histidine zwitterion

Deplazes, E., van Bronswijk, W., Zhu, F., Barron, L.D., Ma, S., Nafie, L.A. and Jalkanen, K.J. (2008). A combined theoretical and experimental study of the structure and vibrational absorption, vibrational circular dichroism, Raman and Raman optical activity spectra of the L-histidine zwitterion. Theoretical Chemistry Accounts, 119 (1-3), 155-176. doi: 10.1007/s00214-007-0276-8

Molecular dynamics study of prednisolone concentration on cholesterol based lung surfactant monolayer

Islam, M. Z., Hossain, S. I., Deplazes, E., Bhowmick, S. and Saha, S. C. (2021). Molecular dynamics study of prednisolone concentration on cholesterol based lung surfactant monolayer. International Conference on Mechanical Engineering, Dhaka, Bangladesh, 18–20 December 2019. Melville, NY, United States: A I P Publishing. doi: 10.1063/5.0037471

The use of peptide-membrane interactions in the design of selective and potent sodium channel inhibitors

Schroeder, Christina, Agwa, Akello, Mueller, Alexander, Chow, Chun Yuen, Peigneur, Steve, Lawrence, Nicole, Deplazes, Evelyne, Mark, Alan, Craik, David, Tytgat, Jan, King, Glenn, Vetter, Irina and Henriques, Sonia Troeira (2018). The use of peptide-membrane interactions in the design of selective and potent sodium channel inhibitors. 35th European Peptide Symposium, Dublin City University, Ireland, 26-31 August 2018. Oxford, United Kingdom: John Wiley & Sons.

The importance of peptide-membrane interactions in toxin inhibitions of sodium channels

Schroeder, Christina I., Deplazes, Evelyn, Lawrence, Nicole, Agwa, Akello and Henriques, Sonia T. (2017). The importance of peptide-membrane interactions in toxin inhibitions of sodium channels. 58th Annual Meeting of the Biophysical Society, San Francisco, United States, 15-19 February 2014. St. Louis, MO, United States: Cell Press. doi: 10.1016/j.bpj.2016.11.1247

Membrane-binding properties of gating-modifier and pore blocking toxins: membrane interaction is not a prerequisite for modification of channel gating

Deplazes, Evelyne, Henriques, Sonia Troeira, King, Glenn F., Craik, David J., Mark, Alan E. and Schroeder, Christina I. (2016). Membrane-binding properties of gating-modifier and pore blocking toxins: membrane interaction is not a prerequisite for modification of channel gating. 60th Annual Meeting of the Biophysical-Society, Los Angeles, United States, February 27- March 2 2016. St Louis, United States: Cell Press. doi: 10.1016/j.bpj.2015.11.220

On the Combination of Restraint-Driven Docking of Flexible Peptides to Ion Channels - Lessons Learnt from the Complex Formed by the Spider Venom PcTx1 and the Acid Sensing Ion Channel1

Deplazes, Evelyne, Davies, Josephine, Bonvin, Alexandre M. J. J. and Mark, Alan E. (2016). On the Combination of Restraint-Driven Docking of Flexible Peptides to Ion Channels - Lessons Learnt from the Complex Formed by the Spider Venom PcTx1 and the Acid Sensing Ion Channel1. 60th Annual Meeting of the Biophysical-Society, Los Angeles, CA, United States, February 27- March 2 2016. St Louis, United States: Cell Press. doi: 10.1016/j.bpj.2015.11.2872