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Membrane proteins studied within whole cells via liquid phase electron microscopy

Speaker: Prof. Dr. Dr. h.c. Niels de Jonge,
Group Leader Innovative Electron Microscopy INM - Leibniz Institute for New Materials, Saarland University, Germany.

Highlights:

• How can you to encapsulate cells with graphene to observe membrane proteins' distribution in electron microscopes?

• Learn how some membrane receptor proteins can form clusters and be used for cancer diagnosis

• Get a outlook on how this new mode of microscopy may help exploring protein interactions and develop diagnostic methods

• Get answers to your questions, followed by an open LiveNano discussion forum

Abstract:

Liquid phase scanning transmission electron microscopy (STEM) is capable of studying cells in their native liquid environment at the single molecule level [1, 2]. The cells in liquid are placed in a microfluidic chamber enclosing the sample in the vacuum of the electron microscope, and are then imaged with STEM. It is not always necessary to enclose the cells in the microfluidic chamber. For many studies, it is sufficient to obtain information from the thin outer regions of the cells, and those can be imaged with high resolution using environmental scanning electron microscopy (ESEM) with STEM detector [3]. A third option is to cover a liquid specimen under a thin membrane of graphene providing the thinnest possible layer [4]. The obtained spatial resolution is typically limited by ration damage [5] but radiation damage mitigation by at least an order of magnitude is possible in liquid compared to samples in ice [6].

Employing the unique capabilities of liquid phase STEM to image proteins in intact cells in their native liquid environment at the nanoscale, we study the biophysical principles of how a cell organizes its functional membrane proteins in specific locations and configurations in order to regulate function. We selected two membrane proteins, the ORAI1 protein, forming store-operated calcium channels, and HER2, member of the receptor tyrosine kinase family of epidermal growth factor receptors (EGFRs). ORAI1 was found to organize in elongated supramolecular clusters [7], in addition to the known assembly in larger clusters upon activation of the channel. HER2 plays an important role in breast cancer aggressiveness and progression. Examination of SKBR3 breast cancer cells and data analysis based on calculating the pair correlation function from individual HER2 positions revealed remarkable differences its functional state between rare- and bulk cancer cells [3]. We discovered a small sub-populations of cancer cells with a different response to a prescription drug [8] indicating a possible relevance for studying the role of cancer cell heterogeneity in the development of drug resistance.

The full scale application of LP-EM for soft matter research still faces several challenges but strategies to to overcome them are emerging, so that time-resolved LP-EM of biomolecular processes is within reach [9].

References:

[1] N. de Jonge, and F. M. Ross, Nat. Nanotechnol. 6, 695 (2011).

[2] N. de Jonge, D. B. Peckys, G. J. Kremers, and D. W. Piston, Proc. Natl. Acad. Sci. 106, 2159 (2009).

[3] D. B. Peckys, U. Korf, and N. de Jonge, Sci. Adv. 1, e1500165 (2015).

[4] I. N. Dahmke et al., ACS Nano 11, 11108 (2017).

[5] N. de Jonge, L. Houben, R. E. Dunin-Borkowski, and F. M. Ross, Nat. Rev. Mater. 4, 61 (2019).

[6] S. Keskin, and N. de Jonge, Nano Lett. 18, 7435 (2018).

[7] D. B. Peckys, D. Gaa, D. Alansary, B. A. Niemeyer, and N. Jonge, International journal of molecular sciences 22, 799 (2021).

[8] D. B. Peckys, U. Korf, S. Wiemann, and N. de Jonge, Mol. Biol. Cell 28, 3193 (2017).

[9] H. Wu, H. Friedrich, J. P. Patterson, N. Sommerdijk, and N. de Jonge, Adv Mater, e2001582 (2020).

Speaker Bio:
Prof. Dr. Dr. h.c. Niels de Jonge is senior group leader at the INM – Leibniz Institute for New Materials, Germany (2012 - present), and Honorary Professor of Experimental Physics, Saarland University, Germany. He received his M. Sc. in Physics from the University of Amsterdam, Netherlands (1994), and a Ph.D. in Natural Sciences, specialization Biophysics, from the University of Freiburg, Germany (1999). He worked as senior scientist at Philips Electronics, Research Department, Netherlands, on carbon nanotube electron sources (2000-2005). He was strategic hire at Oak Ridge National Laboratory, USA (ORNL), where he pioneered liquid-phase STEM (2005-2010). He was Assistant Professor of Biophysics at Vanderbilt University School of Medicine, USA (2007-2011). His research program includes a range of research projects on liquid phase electron microscopy for biological samples and soft matter with a specific emphasis on studying membrane protein function in cancer cells.

Group website: http://www.dejonge.physik.uni-saarland.de

Speaker:
Utkur Mirsaidov, Departments of Physics and Biological Sciences, National University of Singapore

Highlights:

• Get new insights in critical processes for forming new materials and nanostructures:
  1) Nucleation, 2) Self-assembly, and 3) Chemical etching of nanomaterials

• See how pre nucleation condensates can form and influence nucleation and growth of nanocrystals, such as gold and Metal-Organic Frameworks (MOF)

• See unprecedented liquid phase imaging of semiconductor etch processes used in cleanroom nanofabrication.

Abstract:
Understanding how materials form at the nanoscale is fundamental for materials engineering and fabrication in many functional nanodevices. Nanostructures are often defined and formed through solution-based “bottom-up” processes such as growth and assembly of nanomaterials, or “top-down” processes such as nanoscale etching. Despite the technological importance of these processes, many details of these processes remain unknown. In order to understand the detailed nanoscale mechanisms of materials synthesis, it is important to track their evolution dynamics directly. Here, using time-resolved in situ liquid cell transmission electron microscopy (TEM) [1], I will address three critical processes for forming new materials and nanostructures: 1) Nucleation, 2) Self-assembly, and 3) Chemical etching of nanomaterials by capturing their previously unknown intermediate steps.

Specifically, I will show that noble metals such as gold or metal organic framework nanocrystals nucleate from an aqueous solution via a general three-step mechanism: 1) liquid-liquid phase separation of the precursor solution into solute-rich and solute-poor regions, 2) condensation of the solute-rich region into an amorphous cluster which then 3) matures into crystalline nucleus large enough to sustain stable growth of nanoparticles [2, 3].

Next, I will conclude by discussing the top-down approach to fabrication. I talk about our results on visualizing the dynamics of solution-based processes used in semiconductor manufacturing: chemical wet-etching of Si nanowires [4] and how nanoscale capillary forces can lead to pattern collapse [5, 6].

Our studies highlight the importance of direct visualization of nanoscale processes for the rational design of materials.

References:

[1] U. Mirsaidov, J. Patterson, H. Zheng, MRS Bulletin 45, p.704 (2020).
[2] N. Loh, S. Sen, M. Bosman, S. Tan, J. Zhong, C. Nijhuis, P. Král, P. Matsudaira, U. Mirsaidov, Nature Chem, 9, 77-82, (2017).
[3] X. Liu, S.-W. Chee, S. Raj, M Sawczyk, P. Kral, U. Mirsaidov, Proceedings of National Academy of Sciences U.S.A. 118(10), p.e2008880118 (2021).
[4] Z. Aabdin, X. Xu, S. Sen, U. Anand, P. Kral, F. Holsteyns, U. Mirsaidov, Nano Lett. 17, 2953-2958 (2017).
[5] N. Vrancken, T. Ghosh, U. Anand, Z. Aabdin, S. W. Chee, Zh. Baraissov, H. Terryn, S. DeGendt, Z. Tao, X. M. Xu, F. Holsteyns, U. Mirsaidov, J. Phys. Chem. Lett. 11, p.2751 (2020).
[6] U. Anand, T. Ghosh, Z. Aabdin, N. Vrancken, H. Yan, X. M. Xu, F. Holsteyns, U. Mirsaidov, ACS Applied Nano Materials 4, p2664 (2021).

Speaker Bio:
Utkur Mirsaidov is an Associate Professor in the Department of Physics and co-Director at the Centre for BioImaging Sciences at the National University of Singapore (NUS). He obtained his Ph.D. degrees in Physics from the University of Texas at Austin. Afterwards, he completed his postdoctoral training at the University of Illinois at Urbana-Champaign and NUS, before joining NUS as a faculty member in 2013. His research program focuses on understanding fundamental chemical and physical processes relevant for synthesis and application of nanomaterials, and the development of advanced electron microscopy techniques for materials application.

Group website: www.mirsaidov.org

Speaker: Jim De Yoreo

Chief Scientist for Materials Science, Physical and Computational Sciences, Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352

Affiliate Prof., Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195

Highlights:

• Get an overview of recent progress in understanding hierarchical nucleation pathways beyond those of classical nucleation theory

• See several examples of where classical nucleation theory is insufficient

• Understand how liquid phase electron microscopy can be used to study these effects

Abstract:
The emergence of order in materials systems ranging from simple salts to complex supramolecular arrays has long been viewed through the lens of classical nucleation theory in which monomeric building blocks assemble into ordered structures identical to that of the bulk through inherent thermal fluctuations that overcome a free energy barrier.1 However, recent observations have revealed a rich set of hierarchical pathways involving higher-order species ranging from multi-ion clusters to dense liquid droplets to transient amorphous or crystalline phases.2 Moreover, both intrinsic factors, such as supersaturation and temperature, and extrinsic factors, including added electrolytes and organics, lead to divergent pathways in a single system. Identifying these pathways and determining the thermodynamic and/or kinetic reasons why they occur is a difficult challenge due to the transient, nanoscopic nature of the intermediates. Due to its unique combination of spatial and temporal resolution, liquid phase TEM has provided new insights into crystallization processes.3 After setting the context for understanding hierarchical nucleation pathways, I will describe results of recent liquid phase TEM studies on iron4 and zinc5 oxides and on calcium carbonate6-8 aimed at understanding crystallization pathways, including the impact of additives that act either as surface-bound ligands or dopants. The results provide insights into crystallization via dense liquid and amorphous precursors, oriented attachment of nanocrystals, and mesocrystal formation via interface-driven secondary nucleation and attachment. More broadly, these results highlight the opportunity that liquid phase TEM provides for deciphering underlying mechanisms of crystallization.

References:

1. Kaschiev, D., J. Chem. Phys. 76, 5098-5102 (1982).

2. De Yoreo, J. J. et al. Crystallization by particle attachment in synthetic, biogenic, and geologic environments. Science 349, aaa6760 (2015).

3. Zhu, G. et al. “Self-similar Mesocrystals Form Via Interface-Driven Nucleation and Oriented Attachment” Nature 590, 416-422 (2021)

4. Liu, L. et al. Connecting energetics to dynamics in particle growth by oriented attachment using real-time observations. Nat. Commun. 11, 1045 (2020).

5. Nielsen, M. H., Aloni, S. & De Yoreo, J. J. In situ TEM imaging of CaCO3 nucleation reveals coexistence of direct and indirect pathways. Science 345, 1158-1162 (2014).

6. Liu, Z. et al. “In situ TEM reveals pseudomorphic amorphous-to-crystalline CaCO3¬ transformation induced by Mg2+” Proc. Nat’l Acad. Sci USA 117, 3397–3404 (2020).

7. B. Jin et al., The chemical and structural evolution of the dense liquid phase of calcium carbonate (In prep).

Speaker Bio:
Jim De Yoreo is a Battelle Fellow at Pacific Northwest National Laboratory, an Affiliate Professor of Materials Science and Engineering at the University of Washington, and the founding co-Director of the Northwest Institute for Materials Physics, Chemistry, and Technology. He received his Ph.D. in Physics from Cornell University in 1985 and was a Postdoctoral Research Fellow at Princeton University before beginning his independent research career. His research has spanned a wide range of materials-related disciplines, focusing recently on in situ AFM and TEM investigations aimed at discovering the ways that atoms, molecules and particles come together to form materials in geochemical, biological and synthetic environments.

Group website:

https://www.pnnl.gov/science/staff/staff_info.asp?staff_num=7906

Speaker:

Damien Alloyeau, CNRS researcher at the Materials and Quantum Phenomena Laboratory (University of Paris), France.

Abstract:

Liquid-Phase Transmission Electron Microscopy (LPTEM) has been major technological rupture for understanding the complex phenomena arising at the liquid/solid interfaces. The possibility to follow the dynamics of hard, soft and biological nanosized materials in liquid media of controlled composition and temperature has paved the way for new TEM-based researches in nanochemistry, biology and environmental sciences. Through several collaborative works, I will illustrate the interdisciplinary potential of LPTEM and the deeper mechanistic understanding that in situ TEM investigations can provide into the synthesis of nanostructures by chemical route,[1, 2] the structural dynamics of soft/bio materials in their native environment [3] and the mineralization of metals in biofilms. [4]

References:
[1] A. Khelfa et al. Studying the effects of temperature on the nucleation and growth of nanoparticles by liquid-cell transmission electron microscopy. JOVE Methods (2021).

[2] K. Aliyah et al. Real-Time in situ Observations Reveal a Double Role for Ascorbic Acid in the Anisotropic Growth of Silver on Gold. J. Phys. Chem. Lett. 11, 2830-2837 (2020).

[3] M. Piffoux et al. Monitoring the dynamics of cell-derived extracellular vesicles at the nanoscale by liquid-cell transmission electron microscopy. Nanoscale 10, 1234 (2018).

[4] T. Couasnon, et al. In situ monitoring of exopolymer-dependent Mn mineralization on bacterial surfaces. Science Advances 6, eaaz3125 (2020).

Speaker Bio:
Damien Alloyeau is a CNRS researcher at the University of Paris. Following his PhD on magnetic nanoalloys performed at the French Aerospace Lab (ONERA), he was hired as a postdoctoral fellow by the Lawrence Berkeley National Laboratory to develop phase-contrast imaging techniques at the National Center for Electron Microscopy. He joined the University of Paris in 2010 where he has run a national user facility for transmission electron microscopy. Since 2013, he has exploited liquid and gas phase TEM to investigate the dynamics of nanomaterials in their formation and application media. Since 2018, he has been the director of the CNRS network NANOPERANDO that brings together more than 250 scientists with the view to better understand the behavior of materials in real environment.

Group website:

https://www.mpq.univ-paris-diderot.fr/?-microscopie-electronique-avancee-&lang=en