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Biology subjects

Cianfrocco, M. A.

Publications and source records attributed to Cianfrocco, M. A..

3 recordsLinked to original sources

Generative adversarial networks as a tool to recover structural information from cryo-electron microscopy data

Cryo-electron microscopy (cryo-EM) is a powerful structural biology technique capable of determining atomic-resolution structures of biological macromolecules. Despite this ability, the low signal-to-noise ratio of cryo-EM data continues to remain a hurdle for assessing raw cryo-EM micrographs and subsequent image analysis. To help address this problem, we have performed proof-of-principle studies with generative adversarial networks, a form of artificial intelligence, to denoise individual particles. This approach effectively recovers global structural information for both synthetic and real cryo-EM data, facilitating per-particle assessment from noisy raw images. Our results suggest that generative adversarial networks may be able to provide an approach to denoise raw cryo-EM images to facilitate particle selection and raw particle interpretation for single particle and tomography cryo-EM data.

biochemistry

An integrated, pipeline-based approach for cryo-EM structure determination and atomic model refinement in the cloud

Access to streamlined computational resources remains a significant bottleneck for new users of cryo-electron microscopy (cryo-EM). To address this, we have built upon our previous work (Cianfrocco & Leschziner 2015) to develop software tools that will submit cryo-EM analysis routines and atomic model building jobs directly to Amazon Web Services (AWS) from a local computer or laptop. These new software tools (\"cryoem-cloud-tools\") have incorporated optimal data movement, security, and cost-saving strategies, giving novice users access to complex cryo-EM data processing pipelines. Integrating these tools into the RELION processing pipeline and graphical user interface we determined a 2.2 [A] structure of {beta}-galactosidase in ~55 hours on AWS. We implemented a similar strategy to submit Rosetta atomic model building and refinement to AWS. These software tools dramatically reduce the barrier for entry of new users to cloud computing for cryo-EM and are freely available at cryoem-tools.cloud.

biochemistry

Lis1 has two opposing modes of regulating cytoplasmic dynein

Regulation is central to the functional versatility of cytoplasmic dynein, a motor involved in intracellular transport, cell division, and neurodevelopment. Previous work established that Lis1, a conserved and ubiquitous regulator of dynein, binds to its motor domain and induces a tight microtubule-binding state in dynein. The work we present here--a combination of biochemistry, single-molecule assays, cryo-electron microscopy and in vivo experiments--led to the surprising discovery that Lis1 has two opposing modes of regulating dynein, being capable of inducing both low and high affinity for the microtubule. We show that these opposing modes depend on the stoichiometry of Lis1 binding to dynein and that this stoichiometry is regulated by the nucleotide state of dyneins AAA3 domain. We present data on the in vitro and in vivo consequences of abolishing the novel Lis1-induced weak microtubule-binding state in dynein and propose a new model for the regulation of dynein by Lis1.

cell biology