Search for: All records

Cryo-electron microscopy (cryo-EM) has transformed structural biology by enabling near-atomic resolution of large macromolecular complexes without the need for crystallization. Here, we describe our laboratory's transition from X-ray crystallography to single-particle cryo-EM to investigate the ATPase family AAA+ domain-containing protein 2B (ATAD2B), a chromatin regulator implicated in epigenetic signaling. We outline the challenges encountered during protein expression, purification and sample preparation, including co-purification of the chaperonin GroEL, and the strategies employed to overcome these obstacles. Our workflow highlights critical steps in sample optimization, grid vitrification and data processing usingCryoSPARC,cisTEMandTopaz, as well as computational requirements for high-resolution reconstructions. We also discuss model-building, refinement and validation approaches, emphasizing best practices for new cryo-EM users. This work provides practical insights for structural biologists adopting cryo-EM, particularly for large, flexible protein complexes, and underscores the importance of integrated approaches combining biochemical, computational and imaging strategies. 

HIV-1 uses the microtubule cytoskeleton to reach the host cell nucleus during replication, yet the molecular basis for microtubule-dependent HIV-1 motility is poorly understood. Using in vitro reconstitution biochemistry and single-molecule imaging, we found that HIV-1 binds to the retrograde microtubule-associated motor, dynein, directly and not via a cargo adaptor, as has been previously suggested. The HIV-1 capsid lattice binds to accessory chains on dynein’s tail domain. Further, we demonstrate that multiple dynein motors tethered to rigid cargoes, such as HIV-1 capsids, display reduced motility, distinct from the behavior of multiple motors on membranous cargoes. Our results provide an updated model of HIV-1 trafficking wherein HIV-1 binds to dynein directly to “hijack” the dynein transport machinery for microtubule motility. 

Science gateways, also known as advanced web portals, virtual research environments, and more, have changed the face of research and scholarship over the last two decades. Scholars world-wide leverage science gateways for a wide variety of individual research endeavors spanning diverse scientific fields. Evaluating the value of a given gateway to its constituent community is critical in obtaining the financial and human resources to sustain gateway operations. Accordingly, those who run gateways must routinely measure and communicate impact. Just as gateways are varied, their success metrics vary as well. In this survey paper, a variety of different gateways briefly share their approaches. 

Science gateways, also known as advanced web portals, virtual research environments, and more, have changed the face of research and scholarship over the last two decades. Scholars world-wide leverage science gateways for a wide variety of individual research endeavors spanning diverse scientific fields. Evaluating the value of a given gateway to its constituent community is critical in obtaining the financial and human resources to sustain gateway operations. Accordingly, those who run gateways must routinely measure and communicate impact. Just as gateways are varied, their success metrics vary as well. In this survey paper, a variety of different gateways briefly share their approaches. 

Science gateways, also known as advanced web portals, virtual research environments, and more, have changed the face of research and scholarship over the last two decades. Scholars world-wide leverage science gateways for a wide variety of individual research endeavors spanning diverse scientific fields. Evaluating the value of a given gateway to its constituent community is critical in obtaining the financial and human resources to sustain gateway operations. Accordingly, those who run gateways must routinely measure and communicate impact. Just as gateways are varied, their success metrics vary as well. In this survey paper, a variety of different gateways briefly share their approaches. 

Scholars worldwide leverage science gateways/virtual research environments (VREs) for a wide variety of research and education endeavors spanning diverse scientific fields. Evaluating the value of a given science gateway/VRE to its constituent community is critical in obtaining the financial and human resources necessary to sustain operations and increase adoption in the user community. In this article, we feature a variety of exemplar science gateways/VREs and detail how they define impact in terms of, for example, their purpose, operation principles, and size of user base. Further, the exemplars recognize that their science gateways/VREs will continuously evolve with technological advancements and standards in cloud computing platforms, web service architectures, data management tools and cybersecurity. Correspondingly, we present a number of technology advances that could be incorporated in next‐generation science gateways/VREs to enhance their scope and scale of their operations for greater success/impact. The exemplars are selected from owners of science gateways in the Science Gateways Community Institute (SGCI) clientele in the United States, and from the owners of VREs in the International Virtual Research Environment Interest Group (VRE‐IG) of the Research Data Alliance. Thus, community‐driven best practices and technology advances are compiled from diverse expert groups with an international perspective to envisage futuristic science gateway/VRE innovations.