Cryogenic electron microscopy (cryoEM) is a rapidly growing structural biology modality that has been successful in revealing molecular details of biological systems. However, unlike established biophysical and analytical techniques with calibration standards, cryoEM has lacked comprehensive biological test samples. We introduce a cryoEM calibration sample that is a mixture of compatible macromolecules that can be used not only for resolution optimization but also provides multiple reference points for evaluating instrument performance, data quality, and image processing workflows in a single experiment. This combined test specimen provides researchers a reference point for validating their cryoEM pipeline, benchmarking their methodologies, and testing new algorithms.
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http://dx.doi.org/10.1101/2024.08.05.606612 | DOI Listing |
bioRxiv
November 2024
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
Unlabelled: Chromatin organization is essential for DNA packaging and gene regulation in eukaryotic genomes. While significant progresses have been made, the exact atomistic arrangement of nucleosomes remains controversial. Using a well-calibrated residue-level coarse-grained model and advanced dynamics modeling techniques, particularly the non-Markovian dynamics model, we map the free energy landscape of tetra-nucleosome systems, identify both metastable conformations and intermediate states in folding pathways, and quantify the folding kinetics.
View Article and Find Full Text PDFActa Crystallogr F Struct Biol Commun
November 2024
Simons Electron Microscopy Center, New York Structural Biology Center, New York, New York, USA.
Cryogenic electron microscopy (cryoEM) is a rapidly growing structural biology modality that has been successful in revealing molecular details of biological systems. However, unlike established biophysical and analytical techniques with calibration standards, cryoEM has lacked comprehensive biological test samples. Here, a cryoEM calibration sample consisting of a mixture of compatible macromolecules is introduced that can not only be used for resolution optimization, but also provides multiple reference points for evaluating instrument performance, data quality and image-processing workflows in a single experiment.
View Article and Find Full Text PDFbioRxiv
August 2024
Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA.
Cryogenic electron microscopy (cryoEM) is a rapidly growing structural biology modality that has been successful in revealing molecular details of biological systems. However, unlike established biophysical and analytical techniques with calibration standards, cryoEM has lacked comprehensive biological test samples. We introduce a cryoEM calibration sample that is a mixture of compatible macromolecules that can be used not only for resolution optimization but also provides multiple reference points for evaluating instrument performance, data quality, and image processing workflows in a single experiment.
View Article and Find Full Text PDFStructure
September 2024
Frontiers Science Center for Nonlinear Expectations (Ministry of Education), Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China; Shanghai YueXin Life-science Infomation Technology Co. Ltd, Shanghai 200235, China. Electronic address:
Cryoelectron tomography (cryo-ET) has become an indispensable technology for visualizing in situ biological ultrastructures, where the tilt series alignment is the key step to obtain a high-resolution three-dimensional reconstruction. Specifically, with the advent of high-throughput cryo-ET data collection, there is an increasing demand for high-accuracy and fully automatic tilt series alignment, to enable efficient data processing. Here, we propose Markerauto2, a fast and robust fully automatic software that enables accurate fiducial marker-based tilt series alignment.
View Article and Find Full Text PDFChem Commun (Camb)
June 2024
DST Unit of Nanoscience (DST UNS) & Thematic Unit of Excellence (TUE), Department of Chemistry, Indian Institute of Technology Madras (IITM), Chennai 600036, India.
We report the first mass photometric characterization of nanoaggregates of atomically precise nanoclusters (NCs) in solution. The differently-sized nanoaggregates of silver-gold alloy NCs, [AgAu(DPPB)ClO] [ = 1-5 and DPPB = 1,4-bis(diphenylphosphino)butane], formed in solution, were examined by mass photometry (MP) with a protein calibration. In addition, we conducted MP studies of varying solvent composition to understand the structural evolution of nanoaggregates.
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