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Cryo-EM sample preparation

The chameleons are coming! Next generation sample preparation for Cryo-EM based on Spotiton

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Key development references:

Spotiton: A prototype for an integrated inkjet dispense and vitrification system for cryo-TEM
Tilak Jain, Patrick Sheehan, John Crum, Bridget Carragher, Clinton S.Potter

A new method for vitrifying samples for cryoEM
Ivan Razinkov,Venkata P. Dandey, Hui Wei Zhening Zhang, David Melnekoff, William J.Rice, Christoph Wigge, Clinton S.Potter, Bridget Carragher

Spotiton: New features and applications 
Venkata P. Dandey, Hui Weia Zhening Zhang, Yong Zi Tan, Priyamvada Acharya, Edward T. Eng, William J. Rice, Peter A.Kahn, Clinton S.Potter, Bridget Carragher

Optimizing “self-wicking” nanowire grids 
Hui Wei, Venkata P. Dandey, Zhening Zhang, Ashleigh Raczkowski, Willam J. Rice, Bridget Carragher, Clinton S.Potter

Spotiton success stories

Structure of the insulin receptor–insulin complex by single-particle cryo-EM analysis

Nature volume 556, pages 122–125 (05 April 2018). Giovanna Scapin, Venkata P. Dandey, Zhening Zhang, Winifred Prosise, Alan Hruza, Theresa Kelly, Todd Mayhood, Corey Strickland, Clinton S. Potter and Bridget Carragher

abstract overview:

The insulin receptor is a dimeric protein that has a crucial role in controlling glucose homeostasis, regulating lipid, protein and carbohydrate metabolism, and modulating brain neurotransmitter levels1,2. Insulin receptor dysfunction has been associated with many diseases, including diabetes, cancer and Alzheimer’s disease1,3,4. Here we report single-particle cryo-electron microscopy reconstructions of the 1:2 (4.3 Å) and 1:1 (7.4 Å) complexes of the insulin receptor ECD dimer with insulin. The structures confirm the binding interactions at S1 and define the full S2 binding site.

Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme

Zhening Zhang, Wenguang G Liang, Lucas J Bailey, Yong Zi Tan,Hui Wei,Andrew Wang, Mara Farcasanu, Virgil A Woods, Lauren A McCord, David Lee, Weifeng Shang, Rebecca Deprez-Poulain, Benoit Deprez, David R Liu, Akiko Koide, Shohei Koide, Anthony A Kossiakoff, Sheng Li, Bridget Carragher, Clinton S Potter, and Wei-Jen Tang

eLife. 2018; 7: e33572.

abstract overview:

Insulin degrading enzyme (IDE) plays key roles in degrading peptides vital in type two diabetes, Alzheimer's, inflammation, and other human diseases. However, the process through which IDE recognizes peptides that tend to form amyloid fibrils remained unsolved. We used cryoEM to understand both the apo- and insulin-bound dimeric IDE states, revealing that IDE displays a large opening between the homologous ~55 kDa N- and C-terminal halves to allow selective substrate capture based on size and charge complementarity ...our studies provide a mechanism for how IDE selectively degrades amyloidogenic peptides and offers structural insights for developing IDE-based therapies.

Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1

Nature Medicine volume 24, pages 857–867 (2018). Kai Xu, Priyamvada Acharya, Rui Kong, Cheng Cheng, Gwo-Yu Chuang, Kevin Liu, Mark K. Louder, Sijy O’Dell, Reda Rawi, Mallika Sastry, Chen-Hsiang Shen, Baoshan Zhang, Tongqing Zhou, Mangaiarkarasi Asokan, Robert T. Bailer, Michael Chambers, Xuejun Chen, Chang W. Choi, Venkata P. Dandey, Nicole A. Doria-Rose, Aliaksandr Druz, Edward T. Eng, S. Katie Farney, Kathryn E. Foulds, Hui Geng, Ivelin S. Georgiev, Jason Gorman, Kurt R. Hill, Alexander J. Jafari, Young D. Kwon, Yen-Ting Lai, Thomas Lemmin, Krisha McKee, Tiffany Y. Ohr, Li Ou, Dongjun Peng, Ariana P. Rowshan, Zizhang Sheng, John-Paul Todd, Yaroslav Tsybovsky, Elise G. Viox, Yiran Wang, Hui Wei, Yongping Yang, Amy F. Zhou, Rui Chen, Lu Yang, Diana G. Scorpio, Adrian B. McDermott, Lawrence Shapiro, Bridget Carragher, Clinton S. Potter, John R. Mascola and Peter D. Kwong

abstract overview:

A central goal of HIV-1 vaccine research is the elicitation of antibodies capable of neutralizing diverse primary isolates of HIV-1. Here we show that focusing the immune response to exposed N-terminal residues of the fusion peptide, a critical component of the viral entry machinery and the epitope of antibodies elicited by HIV-1 infection, through immunization with fusion peptide-coupled carriers and prefusion stabilized envelope trimers, induces cross-clade neutralizing responses. Crystal and cryoelectron microscopy structures of these antibodies revealed fusion peptide conformational diversity as a molecular explanation for the cross-clade neutralization. The N terminus of the HIV-1 fusion peptide is thus a promising target of vaccine efforts aimed at eliciting broadly neutralizing antibodies.

Routine Single Particle CryoEM Sample and Grid Characterization by Tomography

 Alex J. Noble, Venkata P. Dandey, Hui Wei, Julia Brasch, Jillian Chase, Priyamvada Acharya, Yong Zi Tan, Zhening Zhang, Laura Y. Kim, Giovanna Scapin, Micah Rapp, Edward T. Eng, William J. Rice, Anchi Cheng, Carl J. N egro, Lawrence Shapiro, Peter D. Kwong, David Jeruzalmi, Amédée des Georges, Clinton S. Potter, and Bridget Carragher

eLife 2018; 7: e34257

abstract overview:

In this study, we performed fiducial-less tomography on over 50 different cryoEM grid/sample preparations to determine the particle distribution within the ice and the overall geometry of the ice in grid holes. Surprisingly, by studying particles in holes in 3D from over 1000 tomograms, we have determined that the vast majority of particles (approximately 90%) are adsorbed to an air-water interface. The implications of this observation are wide-ranging, with potential ramifications regarding protein denaturation, conformational change, and preferred orientation.

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