Publications

2024

Erin C. Yang, Robby Divine, Marcos C. Miranda, Andrew J. Borst, Will Sheffler, Jason Z. Zhang, Justin Decarreau, Amijai Saragovi, Mohamad Abedi, Nicolas Goldbach, Maggie Ahlrichs, Craig Dobbins, Alexis Hand, Suna Cheng, Mila Lamb, Paul M. Levine, Sidney Chan, Rebecca Skotheim, Jorge Fallas, George Ueda, Joshua Lubner, Masaharu Somiya, Alena Khmelinskaia, Neil P. King, David Baker. Computational design of non-porous, pH-responsive antibody nanoparticles. Nat Struct Mol Biol 31, 1404–1412.
https://doi.org/10.1038/s41594-024-01288-5

2023

A Khmelinskaia^#, NP Bethel*, F Fatehi*, A Antanasijevic, AJ Borst, S-H Lai, JY(J) Wang, B Basu Mallik, MM Miranda, AM Watkins, C Ogohara, S Caldwell, M Wu, AJR Heck, D Veesler, AB Ward, D Baker, R Twarock, NP King^# (2023) Local structural flexibility drives oligomorphism in computationally designed polyhedral protein assemblies. bioRxiv doi: 10.1101/2023.10.18.562842

Beatrice Ramm*, Alena Khmelinskaia*, Henri G. Franquelim, Petra Schwille. Patterning DNA Origami on Membranes Through Protein Self-Organization. In: Jonoska, N., Winfree, E. (eds) Visions of DNA Nanotechnology at 40 for the Next 40 . Natural Computing Series. Springer, Singapore.
https://doi.org/10.1007/978-981-19-9891-1_22

Will Sheffler^∗, Erin C. Yang^∗, Quinton Dowling^∗, Yang Hsia^∗, Chelsea N. Fries, Jenna Stanislaw, Mark D. Langowski, Marisa Brandy, Alena Khmelinskaia, Neil P. King, David A. Baker. Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock. PLoS Comput Biol 19(5): e1010680.
https://doi.org/10.1371/journal.pcbi.1010680
Repository: https://github.com/willsheffler/rpxdock

Alena Khmelinskaia, Petra Schwille, Henri G. Franquelim. Binding and characterization of DNA origami nanostructures on lipid membranes. In: Valero, J. (eds) DNA and RNA Origami. Methods in Molecular Biology, vol 2639. Humana, New York, NY.
https://link.springer.com/protocol/10.1007/978-1-0716-3028-0_14

Bhoomika Basu Mallik^∗, Jenna Stanislaw^∗, Tharindu Madhusankha Alawathurage^∗, Alena Khmelinskaia. De novo design of polyhedral protein assemblies: before and after the AI revolution. ChemBioChem, doi: 10.1002/cbic.202300117
https://doi.org/10.1002/cbic.202300117

Jing Yang (John) Wang^∗, Alena Khmelinskaia^∗, William Sheffler, Marcos C. Miranda, Aleksandar Antanasijevic, Andrew J. Borst, Susana Vazquez Torres, Chelsea Shu, Yang Hsia, Una Natterdam, Daniel Ellis, Carl Walkey, Maggie Ahlrichs, Sidney Chan, Alex Kang, Hannah Nguyen, Claire Sydeman, Banumathi Sankaran, Mengyu Wu, Asim K. Bera, Lauren Carter, Brooke Fiala, Michael Murphy, David Baker, Andrew B. Ward, Neil P. King. Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proceedings of the National Academy of Sciences USA, 120 (11) e2214556120.
https://www.pnas.org/doi/10.1073/pnas.2214556120

2022

Erin C. Yang, Robby Divine, Christine S. Kang, Sidney Chan, Elijah Arenas, Zoe Subol, Peter Tinker, Hayden Manninen, Alicia Feichtenbiner, Talal Mustafa, Julia Hallowell, Isiac Orr, Hugh Haddox, Brian Koepnick, Jacob O'Connor, Ian C. Haydon, Karla-Luise Herpoldt, Kandise Van Wormer, Celine Abell, David Baker, Alena Khmelinskaia#, Neil P. King#. Increasing computational protein design literacy through cohort-based learning for undergraduate students. Journal of Chemical Education, 99(9):3177–3186.
https://pubs.acs.org/doi/abs/10.1021/acs.jchemed.2c00500

2021

Alena Khmelinskaia, Henri G. Franquelim, Renukka Yaadav, Petra Schwille, Eugene P. Petrov. Membrane-mediated self-organization of rod-like DNA origami particles on supported lipid bilayers. Advanced Materials Interfaces, 8:2101094.
https://onlinelibrary.wiley.com/doi/full/10.1002/admi.202101094

Alena Khmelinskaia, Adam Wargacki, Neil P. King. Structure-based design of novel polyhedral protein nanomaterials. Current Opinion in Microbiology, 61:51-57.
https://www.sciencedirect.com/science/article/pii/S1369527421000382

Beatrice Ramm^∗, Andriy Goychuk^∗, Alena Khmelinskaia, Philipp Blumhardt, Hiromune Eto, Kristina A. Ganzinger, Erwin Frey, Petra Schwille. ATP driven diffusiophoresis: active cargo transport without motor proteins. Nature Physics, 17:850–858.
https://www.nature.com/articles/s41567-021-01213-3

2020

Alena Khmelinskaia^∗, Joaquim M. T. Marquês^∗, André E.P. Bastos, Catarina A. C. Antunes, Silvia Scolari, Gerson M. da S. Lobo, Rui Malhó, Andreas Herrmann, H. Susana Marinho, Rodrigo F. M. de Almeida.Liquid-ordered phase formation by mammalian and yeast sterols: a common feature with organizational differences. Frontiers in Cell and Developmental Biology, Special Issue on Functional Heterogeneities in Biomembranes, 8:337.
https://www.frontiersin.org/articles/10.3389/fcell.2020.00337/full

2019

Hiromune Eto, Naoki Soga, Henri G. Franquelim, Philipp Glock, Alena Khmelinskaia, Lei Kai, Michael Heymann, Hiroyuki Noji, Petra Schwille. Design of Sealable Custom-Shaped Cell Mimicries based on Self-Assembled Monolayers on CYTOP Polymer. ACS Applied Materials & Interfaces, 11(24):21372-21380.
https://pubs.acs.org/doi/10.1021/acsami.9b05073

2018

Weixiang Ye, Sirin Celiksoy, Arpad Jakab, Alena Khmelinskaia, Tamara Heermann, Ana Raso, Seraphine V. Wegner, Germán Rivas, Petra Schwille, Rubén Ahijado-Guzmán, Carsten Sönnichsen. Plasmonic nanosensors show the axial location of the MinDE protein waves. Journal of the American Chemical Society, 13(2): 996-1002.
https://pubs.acs.org/doi/abs/10.1021/jacs.8b07759

Susanne Kempter, Alena Khmelinskaia, Maximilian T. Strauss, Petra Schwille, Ralf Jungmann, Tim Liedl, Wooli Bae. Stop-and-go super-resolution imaging of membrane-assisted DNA origami lattice assembly. ACS Nano, 140(51): 17901-17906.
https://pubs.acs.org/doi/abs/10.1021/acsnano.8b04631

Alena Khmelinskaia, Jonas Mücksch, Eugene P. Petrov, Henri G. Franquelim, Petra Schwille. Control of membrane binding and diffusion of cholesteryl-modified DNA origami nanostructures by DNA spacers. Langmuir, 34(49): 14921-14931.
https://pubs.acs.org/doi/10.1021/acs.langmuir.8b01850

Alena Khmelinskaia^∗, Jonas Mücksch^∗, Franco Conci, Grzegorz Chwastek, Petra Schwille. FCS analysis of protein mobility on lipid monolayers. Biophysical Journal, 114 (10):2444–2454.
https://www.sciencedirect.com/science/article/pii/S0006349518302911?via%3Dihub

Henri G. Franquelim, Alena Khmelinskaia, Jean-Philippe J. Sobczak, Hendrik Dietz, Petra Schwille. Membrane sculping by curved DNA origami scaffolds. Nature Communications, 9 (1):811.
https://www.nature.com/articles/s41467-018-03198-9

2017

Sven Kenjiro Vogel^∗, Ferdinand Greiss^∗, Alena Khmelinskaia, Petra Schwille. Control of lipid domain organization by a biomimetic contractile actomyosin cortex. eLife, 6:e24350.
https://elifesciences.org/articles/24350

2016

Alena Khmelinskaia, Henri G. Franquelim, Eugene P. Petrov, Petra Schwille. Effect of anchor positioning on binding and diffusion of elongated 3D DNA nanostructures on lipid membranes. Journal of Physics D: Applied Physics, Special Issue on Molecular Movements in Biomembranes, 49:194001.
https://iopscience.iop.org/article/10.1088/0022-3727/49/19/194001

2014

Alena Khmelinskaia^∗, Maitane Ibarguren^∗, Rodrigo F. M. de Almeida, David J. López, Vanda A. Paixão, Hasna Ahayayauch, Félix M. Goñi, Pablo Escriba. Changes in membrane organization upon spontaneous insertion of 2-hydroxylated un- saturated fatty acids in the lipid bilayer. Langmuir, 30(18): 2117-2128.
https://pubs.acs.org/doi/10.1021/la403977f