Publications | Gonen Lab

2025

Nicolas, William J.; Shiriaeva, Anna; Martynowycz, Michael W.; Grey, Angus C.; Ruma, Yasmeen N.; Donaldson, Paul J.; Gonen, Tamir
Structure of the lens MP20 mediated adhesive junction
In: Nat Commun, vol. 16, pp. 2977, 2025, ISSN: 2041-1723.

Lin, Jieye; Unge, Johan; Gonen, Tamir
MicroED Structures of Fluticasone Furoate and Fluticasone Propionate Provide New Insights into Their Function
In: Crystal Growth & Design, vol. 25, no. 5, pp. 1588–1596, 2025. ISSN: 1528-7483.

Lin, Jieye; Gallenito, Marc J.; Hattne, Johan; Gonen, Tamir
Ligand Screening and Discovery using Cocktail Soaking and Automated MicroED
In: bioRxiv, 2025.

Clabbers, Max T. B.; Hattne, Johan; Martynowycz, Michael W.; Gonen, Tamir
Energy filtering enables macromolecular MicroED data at sub-atomic resolution
In: Nat Commun, vol. 16, pp. 2247, 2025, ISSN: 2041-1723.

Lin, Jieye; Gallenito, Marc J.; Hattne, Johan; Gonen, Tamir
Ligand Screening and Discovery using Cocktail Soaking and Automated MicroED
In: bioRxiv, 2025.

2024

Janilkarn-Urena, Isis; Tse, Amanda; Lin, Jieye; Tafolla-Aguirre, Bliss; Idrissova, Alina; Zhang, Mindy; Skinner, Samantha G; Mostowfi, Nader; Kim, Jinah; Kalapatapu, Nikhila; Chang, Xinmin; Efthymiou, Christina; Williams, Christopher K; Magaki, Shino D; Vinters, Harry V; Gonen, Tamir; Ahmed, S Kaleem; Gukasyan, Hovhannes J; Davies, Daryl L; Seidler, Paul M
Improving the solubility of pseudo-hydrophobic chemicals through co-crystal formulation
In: vol. 4, no. 1, 2024, ISSN: 2752-6542.

Nicolas, William J.; Gillman, Cody; Weaver, Sara J.; Clabbers, Max T. B.; Shiriaeva, Anna; Her, Ampon Sae; Martynowycz, Michael W.; Gonen, Tamir
Comprehensive microcrystal electron diffraction sample preparation for cryo-EM
In: Nat Protoc, 2024, ISSN: 1750-2799.

Ruma, Yasmeen N.; Bu, Guanhong; Hattne, Johan; Gonen, Tamir
MicroED structure of the C11 cysteine protease clostripain
In: Journal of Structural Biology: X, vol. 10, pp. 100107, 2024, ISSN: 2590-1524.

Liu, Xiaoyu; Xia, Xian; Martynowycz, Michael W.; Gonen, Tamir; Zhou, Z. Hong
Molecular sociology of virus-induced cellular condensates supporting reovirus assembly and replication
In: Nat Commun, vol. 15, 2024, ISSN: 2041-1723.

Lin, Jieye; Unge, Johan; Gonen, Tamir
MicroED Structures of Fluticasone Furoate and Fluticasone Propionate Provide New Insights to Their Function
In: bioRxiv, 2024.

Lin, Jieye; Bu, Guanhong; Unge, Johan; Gonen, Tamir
An Updated Structure of Oxybutynin Hydrochloride
In: Advanced Science, 2024, ISSN: 2198-3844.

Clabbers, Max T. B.; Hattne, Johan; Martynowycz, Michael W.; Gonen, Tamir
Energy filtering enables macromolecular MicroED data at sub-atomic resolution
In: bioRxiv, 2024.

Lin, Jieye; Bu, Guanhong; Unge, Johan; Gonen, Tamir
Uncovering the Elusive Structures and Mechanisms of Prevalent Antidepressants
In: Advanced Therapeutics, 2024, ISSN: 2366-3987.

Lin, Jieye; Bu, Guanhong; Unge, Johan; Gonen, Tamir
An Updated Structure of Oxybutynin Hydrochloride
In: bioRxiv, 2024.

Gillman, Cody; Bu, Guanhong; Danelius, Emma; Hattne, Johan; Nannenga, Brent L.; Gonen, Tamir
Eliminating the missing cone challenge through innovative approaches
In: Journal of Structural Biology: X, vol. 9, pp. 100102, 2024, ISSN: 2590-1524.

Nicolas, William J.; Shiriaeva, Anna; Martynowycz, Michael W.; Grey, Angus C; Ruma, Yasmeen; Donaldson, Paul J; Gonen, Tamir
Structure of the lens MP20 mediated adhesive junction
In: bioRxiv, 2024.

Unge, Johan; Lin, Jieye; Weaver, Sara J; Her, Ampon Sae; Gonen, Tamir
Compositional Analysis of Complex Mixtures using Automatic MicroED Data Collection
In: Advanced Science, 2024, ISSN: 2198-3844.

Xia, Xian; Sung, Po-Yu; Martynowycz, Michael W.; Gonen, Tamir; Roy, Polly; Zhou, Z. Hong
RNA genome packaging and capsid assembly of bluetongue virus visualized in host cells
In: Cell, 2024, ISSN: 0092-8674.

Bu, Guanhong; Danelius, Emma; Wieske, Lianne H. E.; Gonen, Tamir
Polymorphic Structure Determination of the Macrocyclic Drug Paritaprevir by MicroED
In: Advanced Biology, vol. 8, iss. 5, pp. 2300570, 2024, ISSN: 2701-0198.

Gillman, Cody; Bu, Guanhong; Danelius, Emma; Hattne, Johan; Nannenga, Brent; Gonen, Tamir
Eliminating the Missing Cone Challenge through Innovative Approaches
In: bioRxiv, 2024.

Ruma, Yasmeen N; Bu, Guanhong; Gonen, Tamir
MicroED structure of the C11 cysteine protease Clostripain
In: bioRxiv, 2024.

Lin, Jieye; Bu, Guanhong; Unge, Johan; Gonen, Tamir
Uncovering the Elusive Structures and Mechanisms of Prevalent Antidepressants
In: bioRxiv, 2024.

2023

Lin, Jieye; Unge, Johan; Gonen, Tamir
Unraveling the Structure of Meclizine Dihydrochloride with MicroED
In: Adv Sci (Weinh), pp. e2306435, 2023, ISSN: 2198-3844.

Walsh, Martin A; Nannenga, Brent L; Gonen, Tamir; Sexton, Patrick M; Wootten, Denise; Chiu, Wah; Sun, Fei; Carragher, Bridget; Potter, Clinton S; Agard, David; Burley, Stephen K
The next decade in structural biology
In: Structure, vol. 31, no. 11, pp. 1284–1288, 2023, ISSN: 1878-4186.

Danelius, Emma; Bu, Guanhong; Wieske, Lianne H E; Gonen, Tamir
MicroED as a Powerful Tool for Structure Determination of Macrocyclic Drug Compounds Directly from Their Powder Formulations
In: ACS Chem Biol, 2023, ISSN: 1554-8937.

Hattne, Johan; Clabbers, Max T. B.; Martynowycz, Michael W.; Gonen, Tamir
Electron counting with direct electron detectors in MicroED
In: Structure, 2023, ISSN: 0969-2126.

Lin, Jieye; Unge, Johan; Gonen, Tamir
Distinct Conformations of Mirabegron Determined by MicroED
In: Adv Sci (Weinh), pp. e2304476, 2023, ISSN: 2198-3844.

Bai, Xiao-Chen; Gonen, Tamir; Gronenborn, Angela M; Perrakis, Anastassis; Thorn, Andrea; Yang, Jianyi
Challenges and opportunities in macromolecular structure determination
In: Nat Rev Mol Cell Biol, 2023, ISSN: 1471-0080.

Bu, G; Danelius, E; Wieske, L. H; Gonen, T
Polymorphic Structure Determination of the Macrocyclic Drug Paritaprevir by MicroED
In: bioRxiv, 2023.

Lin, Jieye; Unge, Johan; Gonen, Tamir
Unraveling the Structure of Meclizine Dihydrochloride with MicroED
In: bioRxiv, 2023.

Hattne, Johan; Clabbers, Max T. B.; Martynowycz, Michael W.; Gonen, Tamir
Electron counting with direct electron detectors in MicroED
In: Structure, 2023, ISSN: 0969-2126.

Lin, Jieye; Unge, Johan; Gonen, Tamir
Distinct Conformations of Mirabegron Determined by MicroED
In: Adv Sci (Weinh), pp. e2304476, 2023, ISSN: 2198-3844.

Bu, G; Danelius, E; Wieske, L. H; Gonen, T
Polymorphic Structure Determination of the Macrocyclic Drug Paritaprevir by MicroED
In: bioRxiv, 2023.

Lin, Jieye; Unge, Johan; Gonen, Tamir
Unraveling the Structure of Meclizine Dihydrochloride with MicroED
In: bioRxiv, 2023.

Nannenga, Brent L.; Gonen, Tamir
The 2023 Structural Biology Summit at UCLA
In: Structure, vol. 31, pp. 1–2, 2023, ISSN: 0969-2126.

Haymaker, Alison; Bardin, Andrey A.; Gonen, Tamir; Martynowycz, Michael W.; Nannenga, Brent L.
Structure determination of a DNA crystal by MicroED
In: Structure, 2023, ISSN: 0969-2126.

Shiriaeva, Anna; Martynowycz, Michael W; Nicolas, William J; Cherezov, Vadim; Gonen, Tamir
MicroED structure of the human vasopressin 1B receptor
In: bioRxiv, 2023.

Gonen, Tamir
Reflections on two decades of MicroED development
In: RefleXions, no. 2, pp. 7–8, 2023.

Gillman, Cody; Nicolas, William J; Martynowycz, Michael W; Gonen, Tamir
Design and implementation of suspended drop crystallization
In: IUCrJ, vol. 10, iss. 4, 2023, ISSN: 2052-2525.

Hattne, Johan; Clabbers, Max T. B.; Martynowycz, Michael W.; Gonen, Tamir
Electron-counting in MicroED
In: bioRxiv, 2023.

Lin, Jieye; Unge, Johan; Gonen, Tamir
Distinct Conformations of Mirabegron Determined by MicroED
In: bioRxiv, 2023.

Unge, Johan; Lin, Jieye; Weaver, Sara J; Her, Ampon Sae; Gonen, Tamir
Autonomous MicroED data collection enables compositional analysis
In: ChemRxiv, 2023.

Nguyen, Chi; Lei, Hsiang-Ting; Lai, Louis Tung Faat; Gallenito, Marc J; Mu, Xuelang; Matthies, Doreen; Gonen, Tamir
Lipid flipping in the omega-3 fatty-acid transporter
In: Nat Commun, vol. 14, pp. 2571, 2023, ISSN: 2041-1723.

Gillman, Cody; Patel, Khushboo; Unge, Johan; Gonen, Tamir
The structure of the neurotoxin palytoxin determined by MicroED
In: bioRxiv, 2023.

Haymaker, Alison; Bardin, Andrey A; Gonen, Tamir; Martynowycz, Michael W; Nannenga, Brent L
Structure determination of a DNA crystal by MicroED
In: bioRxiv, 2023.

Gillman, Cody; Martynowycz, Michael; Nicolas, William Jules; Gonen, Tamir
Design and implementation of suspended drop crystallization
In: bioRxiv, 2023.

Danelius, Emma; Porter, Nicholas J.; Unge, Johan; Arnold, Frances H.; Gonen, Tamir
MicroED Structure of a Protoglobin Reactive Carbene Intermediate
In: J. Am. Chem. Soc., 2023, ISSN: 1520-5126.

Martynowycz, Michael W; Shiriaeva, Anna; Clabbers, Max T B; Nicolas, William J; Weaver, Sara J; Hattne, Johan; Gonen, Tamir
A robust approach for MicroED sample preparation of lipidic cubic phase embedded membrane protein crystals
In: Nat Commun, vol. 14, pp. 1086, 2023, ISSN: 2041-1723.

Danelius, Emma; Patel, Khushboo; Gonzalez, Brenda; Gonen, Tamir
MicroED in drug discovery
In: Curr Opin Struct Biol, vol. 79, pp. 102549, 2023, ISSN: 1879-033X.

2022

Clabbers, Max T. B.; Martynowycz, Michael W.; Hattne, Johan; Gonen, Tamir
Hydrogens and hydrogen-bond networks in macromolecular MicroED data
In: J Struct Biol X, vol. 6, pp. 100078, 2022.

Danelius, Emma; Porter, Nicholas J.; Unge, Johan; Arnold, Frances H.; Gonen, Tamir
MicroED structure of a protoglobin reactive carbene intermediate
In: bioRxiv, 2022.

Clabbers, Max T. B.; Martynowycz, Michael W.; Hattne, Johan; Nannenga, Brent L.; Gonen, Tamir
Electron-counting MicroED data with the K2 and K3 direct electron detectors
In: J Struct Biol, vol. 214, iss. 4, 2022.

Martynowycz, Michael W.; Shiriaeva, Anna; Clabbers, Max T. B.; Nicolas, William J.; Weaver, Sara J.; Hattne, Johan; Gonen, Tamir
A robust approach for MicroED sample preparation of lipidic cubic phase embedded membrane protein crystals
In: bioRxiv 2022, visited: 26.07.2022.

Clabbers, Max T. B.; Martynowycz, Michael W.; Hattne, Johan; Nannenga, Brent L.; Gonen, Tamir
Electron-counting MicroED data with the K2 and K3 direct electron detectors
In: bioRxiv, 2022.

Nguyen, Chi; Lei, Hsiang-Ting; Lai, Louis Tung Faat; Gallenito, Marc J.; Matthies, Doreen; Gonen, Tamir
Lipid flipping in the omega-3 fatty-acid transporter
In: bioRxiv 2022, visited: 01.06.2022.

Martynowycz, Michael W.; Gonen, Tamir
Unlocking the potential of microcrystal electron diffraction
In: Physics Today, vol. 75, iss. 6, pp. 38–42, 2022.

Martynowycz, Michael W; Clabbers, Max T B; Hattne, Johan; Gonen, Tamir
Ab initio phasing macromolecular structures using electron-counted MicroED data
In: Nat Methods, vol. 19, iss. 6, pp. 724–729, 2022, ISSN: 1548-7105.

Porter, Nicholas; Danelius, Emma; Gonen, Tamir; Arnold, Frances
Biocatalytic Carbene Transfer Using Diazirines
In: ChemRxiv, 2022.

Porter, Nicholas J; Danelius, Emma; Gonen, Tamir; Arnold, Frances H
Biocatalytic Carbene Transfer Using Diazirines
In: J Am Chem Soc, 2022, ISSN: 1520-5126.

Clabbers, Max T. B.; Martynowycz, Michael W.; Hattne, Johan; Gonen, Tamir
Hydrogens and hydrogen-bond networks in macromolecular MicroED data
In: bioRxiv, 2022.

Clabbers, Max T B; Shiriaeva, Anna; Gonen, Tamir
MicroED: conception, practice and future opportunities
In: IUCrJ, vol. 9, no. Pt 2, pp. 169–179, 2022, ISSN: 2052-2525.

Gallenito, Marc J; Gonen, Tamir
Studying membrane proteins with MicroED
In: Biochem Soc Trans, vol. 50, no. 1, pp. 231–239, 2022, ISSN: 1470-8752.

2021

Gonen, Tamir; Nannenga, Brent (Ed.)
cryoEM: Methods and Protocols
In: Springer US, 2021, ISBN: 978-1-0716-0965-1.

Martynowycz, Michael W; Clabbers, Max T B; Unge, Johan; Hattne, Johan; Gonen, Tamir
Benchmarking the ideal sample thickness in cryo-EM
In: Proc Natl Acad Sci U S A, vol. 118, no. 49, 2021, ISSN: 1091-6490.

Clark, Lisa J.; Bu, Guanhong; Nannenga, Brent L.; Gonen, Tamir
MicroED for the study of protein–ligand interactions and the potential for drug discovery
In: Nat Rev Chem, vol. 5, pp. 853–858, 2021.

Martynowycz, Michael W.; Clabbers, Max T. B.; Hattne, Johan; Gonen, Tamir
Ab initio phasing macromolecular structures using electron-counted MicroED data
In: bioRxiv, 2021.

Martynowycz, Michael W; Gonen, Tamir
Protocol for the use of focused ion-beam milling to prepare crystalline lamellae for microcrystal electron diffraction (MicroED)
In: STAR Protoc, vol. 2, no. 3, pp. 100686, 2021, ISSN: 2666-1667.

Martynowycz, Michael W.; Shiriaeva, Anna; Ge, Xuanrui; Hattne, Johan; Nannenga, Brent L.; Cherezov, Vadim; Gonen, Tamir
MicroED structure of the human adenosine receptor determined from a single nanocrystal in LCP
In: Proc Natl Acad Sci U S A, vol. 118, no. 36, pp. e2106041118, 2021.

Martynowycz, Michael W.; Clabbers, Max T. B.; Unge, Johan; Hattne, Johan; Gonen, Tamir
Benchmarking ideal sample thickness in cryo-EM using MicroED
bioRxiv, 2021.

Mu, Xuelang; Gillman, Cody; Nguyen, Chi; Gonen, Tamir
An Overview of Microcrystal Electron Diffraction (MicroED)
In: Annu Rev Biochem, vol. 90, pp. 431–450, 2021, ISSN: 1545-4509.

Lei, Hsiang-Ting; Mu, Xuelang; Hattne, Johan; Gonen, Tamir
A conformational change in the N Terminus of SLC38A9 signals mTORC1 activation
In: Structure, vol. 29, no. 5, pp. 426–432.e8, 2021.

Danelius, E; Gonen, T
Protein and Small Molecule Structure Determination by the Cryo-EM Method MicroED
In: Owens, Raymond J. (Ed.): vol. 2305, pp. 323–342, 2021.

Martynowycz, M W; Gonen, T
Studying Membrane Protein Structures by MicroED
In: Schmidt-Krey, Ingeborg; Gumbart, James C. (Ed.): vol. 2302, pp. 137–151, 2021.

Martynowycz, M W; Gonen, T
Microcrystal Electron Diffraction of Small Molecules
In: J Vis Exp, no. 169, 2021.

Halaby, Steve; Martynowycz, Michael W.; Zhu, Ziyue; Tretiak, Sergei; Zhugayevych, Andriy; Gonen, Tamir; and Martin Seifrid,
Microcrystal Electron Diffraction for Molecular Design of Functional Non-Fullerene Acceptor Structures
In: Chem. Mater., vol. 33, no. 3, pp. 966–977, 2021.

Martynowycz, Michael W.; Gonen, Tamir
Ligand Incorporation into Protein Microcrystals for MicroED by On-Grid Soaking
In: Structure, vol. 29, no. 1, pp. 88–95.e2, 2021.

2020

Martynowycz, M W; Khan, F; Hattne, J; Abramson, J; Gonen, T
MicroED structure of lipid-embedded mammalian mitochondrial voltage-dependent anion channel
In: Proc Natl Acad Sci U S A, vol. 117, no. 51, pp. 32380–32385, 2020.

Zhu, Lan; Bu, Guanhong; Jing, Liang; Shi, Dan; Lee, Ming-Yue; Gonen, Tamir; Liu, Wei; Nannenga, Brent L.
Structure Determination from Lipidic Cubic Phase Embedded Microcrystals by MicroED
In: Structure, vol. 28, no. 10, pp. 1149–1159.e4, 2020.

Nannenga, Brent L.; Gonen, Tamir
Microcrystal electron diffraction methodology and applications
In: MRS Bulletin, vol. 44, pp. 956–960, 2020.

Martynowycz, Michael W.; Khan, Farha; Hattne, Johan; Abramson, Jeff; Gonen, Tamir
MicroED structure of lipid-embedded mammalian mitochondrial voltage dependent anion channel
In: bioRxiv, 2020.

Danelius, E; Halaby, S; van der Donk, W A; Gonen, T
MicroED in natural product and small molecule research
In: Nat Prod Rep, vol. 38, no. 3, 2020.

Richards, Logan S.; Millán, Claudia; Miao, Jennifer; Martynowycz, Michael W.; Sawaya, Michael R.; Gonen, Tamir; Borges, Rafael J.; Usón, Isabel; Rodriguez, Jose A.
Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER
In: Acta Crystallogr D Biol Crystallogr., vol. 76, no. 8, pp. 703-712, 2020.

Nguyen, Chi; Gonen, Tamir
Beyond protein structure determination with MicroED
In: Curr. Opin. Struct. Biol., vol. 64, pp. 51–58, 2020.

Martynowycz, Michael W.; Gonen, Tamir
Efficient, high-throughput ligand incorporation into protein microcrystals by on-grid soaking
In: bioRxiv, 2020.

Martynowycz, M W; Hattne, J; Gonen, T
Experimental Phasing of MicroED Data Using Radiation Damage
In: Structure, vol. 28, no. 4, pp. 458–464, 2020.

Wolff, A M; Young, I D; Sierra, R G; Brewster, A S; Martynowycz, M W; Nango, E; Sugahara, M; Nakane, T; Ito, K; Aquila, A; Bhowmick, A; Biel, J T; Carbajo, S; Cohen, A E; Cortez, S; Gonzalez, A; Hino, T; Im, D; Koralek, J D; Kubo, M; Lazarou, T S; Nomura, T; Owada, S; Samelson, A J; Tanaka, T; Tanaka, R; Thompson, E M; van den Bedem, H; Woldeyes, R A; Yumoto, F; Zhao, W; Tono, K; Boutet, S; Iwata, S; Gonen, T; Sauter, N K; Fraser, J S; Thompson, M C
Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals
In: IUCrJ, vol. 7, no. Pt 2, pp. 306–323, 2020.

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