Article
Chemistry, Multidisciplinary
Qingqing Sheng, Hao Chen, Wenting Mao, Congcong Cui, Shunai Che, Lu Han
Summary: This study reports the synthesis of a porous silica scaffold with a single-diamond-surface structure, revealing its unique framework. The formation of this structure is believed to be induced by structural transition and energetic change due to fluctuations of Gaussian curvature.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Multidisciplinary Sciences
Michael L. Aubrey, Abraham Saldivar Valdes, Marina R. Filip, Bridget A. Connor, Kurt P. Lindquist, Jeffrey B. Neaton, Hemamala Karunadasa
Summary: Using organic molecules as directing groups, a variety of perovskite heterostructures are self-assembled in solution to form single crystals. This method allows precise stacking of different 2D structures, revealing exotic phenomena at their interfaces. The interleaving of inorganic structures found in these heterostructures can lead to new electronic transitions, demonstrating the potential for directed synthesis of complex semiconductors that self-assemble in water.
Review
Chemistry, Multidisciplinary
Haofei Zhao, Yuchen Zhu, Huanyu Ye, Yang He, Hao Li, Yifei Sun, Feng Yang, Rongming Wang
Summary: Nanocrystals play a crucial role in material sciences and industry. Designing nanocrystals with desired structures and properties is a major challenge that requires a deep understanding of atomic-scale dynamics. In situ transmission electron microscopy (TEM), especially environmental TEM, has provided valuable insights into nanocrystals. This comprehensive review highlights the progress in the understanding of nanocrystal dynamics, including nucleation and growth, structure evolution, and dynamics in reaction conditions.
ADVANCED MATERIALS
(2023)
Article
Multidisciplinary Sciences
Vida Jamali, Cory Hargus, Assaf Ben-Moshe, Amirali Aghazadeh, Hyun Dong Ha, Kranthi K. Mandadapu, A. Paul Alivisatos
Summary: The study experimentally investigated the motion of gold nanoparticles dispersed in water and found that the motion of the nanoparticles exhibited anomalous diffusive behavior modulated by the electron beam dose rate. The results suggest that the nanoparticle motion is governed by different diffusion behaviors at different dose rates, which can be explained by the presence of surface molecular species.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Nesrine Aissaoui, Josephine Lai-Kee-Him, Allan Mills, Nathalie Declerck, Zakia Morichaud, Konstantin Brodolin, Sonia Baconnais, Eric Le Cam, Jean Baptiste Charbonnier, Remy Sounier, Sebastien Granier, Virginie Ropars, Patrick Bron, Gaetan Bellot
Summary: Technological breakthroughs in electron microscopy have made it possible to study biological macromolecular complexes with novel challenges, such as sample preparation and heterogeneous macromolecular assemblies. In this study, a V-shaped DNA origami template was used to position proteins, demonstrating a new approach for characterizing mechanosensitive proteins and expanding the range of potential targets for single-particle EM investigation. Validation with RNAP protein showed compatibility with cryo-EM sample preparation.
Article
Multidisciplinary Sciences
Carolyn M. Highland, Aaron Tan, Clifton L. Ricana, John A. G. Briggs, Robert A. Dick
Summary: In this study, the authors used cryoelectron tomography and single particle analysis to reveal detailed structural information of the HIV-1 capsid lattice, including both hexamers and pentamers. They also discovered the critical role of inositol hexakisphosphate in pentamer formation and determined the structure of the capsid lattice bound to the antiretroviral drug GS-6207. The combination of lattice templating and single particle analysis proved to be a robust strategy for studying retroviral capsid structure and interactions with host proteins and antiviral compounds.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Physical
Jin-Hu Dou, Maxx Q. Arguilla, Yi Luo, Jian Li, Weizhe Zhang, Lei Sun, Jenna L. Mancuso, Luming Yang, Tianyang Chen, Lucas R. Parent, Grigorii Skorupskii, Nicole J. Libretto, Chenyue Sun, Min Chieh Yang, Phat Vinh Dip, Edward J. Brignole, Jeffrey T. Miller, Jing Kong, Christopher H. Hendon, Junliang Sun, Mircea Dinca
Summary: Researchers have successfully grown single crystals of 2D metal-organic frameworks up to 200 µm in size by balancing in-plane and out-of-plane interactions, revealing anisotropic transport and a clear correlation between conductivity and the nature of the metal cation in the sheets.
Article
Engineering, Multidisciplinary
Songjie Li, Mengyuan He, Guanjie Hu, Yun Tian, Chengduo Wang, Ben Jing, Dehai Ping
Summary: This study discusses the coarsening process of second-phase particles in a solid-phase matrix, emphasizing the importance of considering the microstructural evolution of the corresponding matrix phase. Experimental observations reveal that the aggregation of fine carbide particles and the shrinkage of cementite layers are key driving forces behind the coarsening of cementite particles and the development of pearlite structure in carbon steels.
COMPOSITES PART B-ENGINEERING
(2022)
Article
Chemistry, Multidisciplinary
Junling Chen, Hongru Li, Qiang Wu, Tan Zhao, Haijiao Xu, Jiayin Sun, Feng Liang, Hongda Wang
Summary: P-glycoproteins (P-gps) over-expressed in cancer cells play a crucial role in multi-drug resistance. By using a specific inhibitor, tariquidar modified with TAMRA, the study revealed that P-gps can facilitate pumping efficiency by forming functional platforms through aggregation. The specific distribution patterns of P-gps might serve as potential biomarkers for tumor and drug therapy screening.
Article
Multidisciplinary Sciences
Joshua B. R. White, Daniel P. Maskell, Andrew Howe, Martin Harrow, Daniel K. Clare, C. Alistair Siebert, Emma L. Hesketh, Rebecca F. Thompson
Summary: Cryo-electron microscopy is a powerful technique for structure determination of macromolecular complexes through single particle analysis, involving vitrification, specimen screening, data collection, and image processing, with options for user modification and common troubleshooting. Variations on imaging protocols to assist users in efficient operation and imaging when physical access to the microscope is limited are being developed due to remote microscope operation becoming standard.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Chemistry, Multidisciplinary
Le Tracy Yu, Maria C. Hancu, Mark A. B. Kreutzberger, Amy Henrickson, Borries Demeler, Edward H. Egelman, Jeffrey D. Hartgerink
Summary: The folding of collagen is a complex process, involving the association of three peptides into a triple helical fold. The bundling of collagen triple helices is poorly understood, and to shed light on this process, the collagenous region of complement component 1q was examined. Synthetic peptides were prepared to study self-assembly, revealing that short peptides can assemble into specific octadecamers with the help of noncollagenous sequences. Cryo-electron microscopy showed that the octadecamers formed a hollow, crown-like structure. This research provides insight into the assembly mechanism of collagen and lays the foundation for designing higher order collagen mimetic peptide assemblies.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Andrew J. Lee, Masayuki Endo, Jamie K. Hobbs, A. Giles Davies, Christoph Walti
Summary: The study used DNA nanostructure-augmented high-speed AFM to directly observe the RecA-orchestrated alignment of homologous DNA strands, revealing transient sampling of micro-homology by RecA during the search for sequence alignment. These transient interactions are early steps in the search for sequence homology.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Meenakshi Sharma, Eva de Alba
Summary: This study investigates the association and dissociation rates of the AIM2-DNA complex at the single molecule level using optical traps and confocal fluorescence microscopy. The results reveal distinct mechanisms for the growth of AIM2 oligomers and show that the size of the oligomers can increase fourfold within seconds. Additionally, it is found that single AIM2 molecules do not diffuse/scan along the DNA, suggesting that oligomerization depends on stochastic encounters with DNA and/or DNA-bound AIM2.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Sarah M. Smith, Gabrielle Larocque, Katherine M. Wood, Kyle L. Morris, Alan M. Roseman, Richard B. Sessions, Stephen J. Royle, Corinne J. Smith
Summary: The interaction between Clathrin and the AP2 complex plays a crucial role in coated-pit assembly, with a beta 2 appendage able to bind in at least two positions in the clathrin cage. This multi-modal binding is shown to be a fundamental property of clathrin-AP2 interactions.
Article
Multidisciplinary Sciences
Alexander Muller, Gauthier J-P Deblonde, Peter Ercius, Steven E. Zeltmann, Rebecca J. Abergel, Andrew M. Minor
Summary: In this work, the authors utilize transmission electron microscopy to characterize highly-radioactive compounds of berkelium and californium, requiring only small amounts of the elements. They find that berkelium exhibits unexpectedly weak spin-orbit coupling, while californium follows a jj coupling scheme.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Steven Castellano, Derek P. Claxton, Emel Ficici, Tsukasa Kusakizako, Robyn Stix, Wenchang Zhou, Osamu Nureki, Hassane S. Mchaourab, Jose D. Faraldo-Gomez
Summary: The research reveals a common sodium-binding site in three prokaryotic MATE proteins, which shows selectivity against potassium ions and may play a significant role in the ion-coupled drug efflux mechanisms of these transporters.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Benjamin C. McIlwain, Amanda L. Erwin, Alexander R. Davis, B. Ben Koff, Louise Chang, Tatsiana Bylund, Gwo-Yu Chuang, Peter D. Kwong, Melanie D. Ohi, Yen-Ting Lai, Randy B. Stockbridge
Summary: The study identified a helical epitope from the MPER region of the HIV envelope protein that can be used as a docking site for antibody fragments, aiding in structural studies of small membrane proteins. This approach was shown to be effective in crystallization and electron microscopy of challenging membrane proteins.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Derek P. Claxton, Kevin L. Jagessar, Hassane S. Mchaourab
Summary: MATE transporters catalyze the active efflux of a broad range of compounds, including antimicrobials and chemotherapeutics, contributing to multidrug resistance. Structural biology studies have revealed unique mechanisms in energy transduction and substrate translocation in MATE transporters, defining the molecular determinants that shape the transport energy landscape.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Sarah M. Fantin, Kristine F. Parson, Pramod Yadav, Brock Juliano, Geoffrey C. Li, Charles R. Sanders, Melanie D. Ohi, Brandon T. Ruotolo
Summary: Peripheral myelin protein (PMP22) misfolding is identified as a key factor in various peripheral neuropathies. Mutant forms of PMP22 exhibit differences in stability and propensity to form homodimeric complexes compared to wild-type protein. The formation of PMP22 dimers from destabilized monomers is proposed as a key element in PMP22 mistrafficking, based on combined findings from native ion mobility-mass spectrometry and cellular data.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Cell Biology
Elaine C. Chen, Pavlo Gilchuk, Seth J. Zost, Naveenchandra Suryadevara, Emma S. Winkler, Carly R. Cabel, Elad Binshtein, Rita E. Chen, Rachel E. Sutton, Jessica Rodriguez, Samuel Day, Luke Myers, Andrew Trivette, Jazmean K. Williams, Edgar Davidson, Shuaizhi Li, Benjamin J. Doranz, Samuel K. Campos, Robert H. Carnahan, Curtis A. Thorne, Michael S. Diamond, James E. Crowe
Summary: Unrelated individuals can produce genetically similar clones of antibodies known as public clonotypes, which have been identified in responses to different infectious diseases and in healthy individuals. By studying memory B cells from convalescent survivors of SARS-CoV-2 infection and plasmablasts from vaccinated individuals, researchers have identified 29 public clonotypes with potential neutralizing abilities against the virus. These findings provide insight into the molecular mechanisms behind the efficacy of SARS-CoV-2 vaccines and reveal the immune pressures influencing the selection of common viral escape mutants.
Article
Biochemistry & Molecular Biology
Emily M. Overway, Karin J. Bosma, Derek P. Claxton, James K. Oeser, Kritika Singh, Lindsay B. Breidenbach, Hassane S. Mchaourab, Lea K. Davis, Richard M. O'Brien
Summary: This study investigated the impact of 22 non synonymous G6PC2 SNPs on G6PC2 protein expression and enzyme activity, finding that 16 SNPs significantly impaired G6PC2 protein expression while 4 SNPs affected G6PC2 enzyme activity. High-impact SNPs were associated with FBG, but no associations were found with other diseases or metabolites.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Derek P. Claxton, Emily M. Overway, James K. Oeser, Richard M. O'Brien, Hassane S. Mchaourab
Summary: Glucose-6-phosphatase catalytic subunit 1 (G6PC1) plays a crucial role in regulating blood glucose levels and its dysregulation is linked to diabetes and glycogen storage disease type 1a. However, limited understanding of G6PC1 structure and mechanism is due to challenges in expression and purification. In this study, researchers successfully analyzed the catalytically active G6PC1 using biophysical and biochemical tools, providing a foundation for future studies on the structural biology and role of G6PC1 in complex metabolic disorders.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Immunology
Natasha M. Kafai, Lauren E. Williamson, Elad Binshtein, Soila Sukupolvi-Petty, Christina L. Gardner, Jaclyn Liu, Samantha Mackin, Arthur S. Kim, Nurgun Kose, Robert H. Carnahan, Ana Jung, Lindsay Droit, Douglas S. Reed, Scott A. Handley, William B. Klimstra, James E. Crowe, Michael S. Diamond
Summary: This study reveals the functional and structural mechanisms of neutralizing antibodies against Venezuelan equine encephalitis virus, and suggests the possibility of targeting multiple antigenic sites for vaccine or antibody-based therapeutic development.
JOURNAL OF EXPERIMENTAL MEDICINE
(2022)
Article
Microbiology
Clara T. Schoeder, Pavlo Gilchuk, Amandeep K. Sangha, Kaitlyn V. Ledwitch, Delphine C. Malherbe, Xuan Zhang, Elad Binshtein, Lauren E. Williamson, Cristina E. Martina, Jinhui Dong, Erica Armstrong, Rachel Sutton, Rachel Nargi, Jessica Rodriguez, Natalia Kuzmina, Brooke Fiala, Neil P. King, Alexander Bukreyev, James E. Crowe, Jens Meiler
Summary: This study presents the design and functional validation of an epitope-focused immunogen based on the HR2-MPER epitope of the ebolavirus. The results demonstrate the capabilities and challenges of computational epitope-focused vaccine design, and provide insights for the rational design of immunogens against ebolavirus.
Article
Multidisciplinary Sciences
Jason C. Porta, Bing Han, Alican Gulsevin, Jeong Min Chung, Yelena Peskova, Sarah Connolly, Hassane S. Mchaourab, Jens Meiler, Erkan Karakas, Anne K. Kenworthy, Melanie D. Ohi
Summary: This study reveals the structural characteristics of the human caveolin-1 complex using cryo-electron microscopy, providing new insights into its membrane remodeling activity and uncovering the roles of key regions of caveolin-1 in its function.
Article
Biochemistry & Molecular Biology
Melanie D. Ohi, Anne K. Kenworthy
Summary: Caveolins are a unique family of membrane proteins that form small cave-like structures on the surface of cells, regulating various cellular processes. The molecular basis for the assembly and regulation of these structures has long puzzled researchers, but recent advances have started to uncover the answers.
JOURNAL OF MEMBRANE BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Adrien Chauvier, Jason C. C. Porta, Indrajit Deb, Emily Ellinger, Katarina Meze, Aaron T. T. Frank, Melanie D. D. Ohi, Nils G. G. Walter
Summary: This study investigates the interaction between RNA polymerase and nascent transcripts during transcription. It is found that the transcription process of a preQ(1) riboswitch can be modulated by the RNA polymerase and the conformation of the nascent RNA. Ligand binding to the riboswitch leads to the release of RNA polymerase pause and the continuation of transcription. The mechanism by which riboswitch folding modulates pausing is revealed through cryo-electron microscopy reconstructions.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Nathaniel S. Chapman, Ruben J. G. Hulswit, Jonna L. B. Westover, Robert Stass, Guido C. Paesen, Elad Binshtein, Joseph X. Reidy, Taylor B. Engdahl, Laura S. Handal, Alejandra Flores, Brian B. Gowen, Thomas A. Bowden, James E. Crowe
Summary: This article describes a dual-mechanism human monoclonal antibody combination against RVFV that shows potent efficacy in a mouse model, highlighting its potential for future use in combating RVFV infection.
NATURE COMMUNICATIONS
(2023)
Meeting Abstract
Biophysics
Matt Sinclair, Jonathan Sheehan, Richard A. Stein, Derek P. Claxton, Emad Tajkhorshid
BIOPHYSICAL JOURNAL
(2023)
Article
Medicine, Research & Experimental
Naveenchandra Suryadevara, Andrea R. Shiakolas, Laura A. VanBlargan, Elad Binshtein, Rita E. Chen, James Brett Case, Kevin J. Kramer, Erica C. Armstrong, Luke Myers, Andrew Trivette, Christopher Gainza, Rachel S. Nargi, Christopher N. Selverian, Edgar Davidson, Benjamin J. Doranz, Summer M. Diaz, Laura S. Handal, Robert H. Carnahan, Michael S. Diamond, Ivelin S. Georgiev, James E. Crowe
Summary: This study identifies a rare human antibody, COV23434, that disrupts the integrity of the SARS-CoV-2 S protein and possesses a distinct class of functional activity. The findings suggest that the trimer interface region of the S protein may be a vulnerable site for the virus.
JOURNAL OF CLINICAL INVESTIGATION
(2022)